sbuild (Debian sbuild) 0.89.3+deb13u4 (28 December 2025) on mjolnir.einval.org +==============================================================================+ | rna-star 2.7.11b+dfsg-4 (amd64) Thu, 15 Oct 2026 19:11:25 +0000 | +==============================================================================+ Package: rna-star Version: 2.7.11b+dfsg-4 Source Version: 2.7.11b+dfsg-4 Distribution: unstable Machine Architecture: arm64 Host Architecture: amd64 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any I: Unpacking /home/helmut/.cache/sbuild/unstable-arm64-sbuild.tar.zst to /tmp/tmp.sbuild.z0hsblgtKs... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Thu, 15 Oct 2026 19:11:42 +0000 | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian unstable InRelease [193 kB] Get:2 http://mirror.einval.org/debian unstable/main Sources [12.0 MB] Get:3 http://mirror.einval.org/debian unstable/main arm64 Packages [10.7 MB] Get:4 http://mirror.einval.org/debian unstable/main amd64 Packages [10.8 MB] Fetched 33.7 MB in 8s (4366 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: linux-libc-dev 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2022 kB of archives. After this operation, 10.2 kB of additional disk space will be used. Get:1 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev all 7.2.10-1 [2022 kB] Fetched 2022 kB in 0s (47.2 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12175 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_7.2.10-1_all.deb ... Unpacking linux-libc-dev (7.2.10-1) over (7.2.9-1) ... Setting up linux-libc-dev (7.2.10-1) ... +------------------------------------------------------------------------------+ | Fetch source files Thu, 15 Oct 2026 19:12:01 +0000 | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'rna-star' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/rna-star.git Please use: git clone https://salsa.debian.org/med-team/rna-star.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 903 kB of source archives. Get:1 http://mirror.einval.org/debian unstable/main rna-star 2.7.11b+dfsg-4 (dsc) [2162 B] Get:2 http://mirror.einval.org/debian unstable/main rna-star 2.7.11b+dfsg-4 (tar) [521 kB] Get:3 http://mirror.einval.org/debian unstable/main rna-star 2.7.11b+dfsg-4 (diff) [380 kB] Fetched 903 kB in 0s (10.4 MB/s) Download complete and in download only mode +------------------------------------------------------------------------------+ | Install package build dependencies Thu, 15 Oct 2026 19:12:03 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), architecture-is-64-bit, architecture-is-little-endian, libhts-dev, xxd, zlib1g-dev, libsimde-dev, libc-dev, libstdc++-dev, build-essential:arm64, crossbuild-essential-amd64:arm64, apt-utils:arm64, libc-dev:amd64, libstdc++-dev:amd64 Filtered Build-Depends: debhelper-compat (= 13), architecture-is-64-bit, architecture-is-little-endian, libhts-dev, xxd, zlib1g-dev, libsimde-dev, libc-dev, libstdc++-dev, build-essential:arm64, crossbuild-essential-amd64:arm64, apt-utils:arm64, libc-dev:amd64, libstdc++-dev:amd64 dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-8advCY/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/reproducible-path/resolver-8advCY/apt_archive ./ InRelease Get:2 copy:/build/reproducible-path/resolver-8advCY/apt_archive ./ Release [609 B] Ign:3 copy:/build/reproducible-path/resolver-8advCY/apt_archive ./ Release.gpg Get:4 copy:/build/reproducible-path/resolver-8advCY/apt_archive ./ Sources [813 B] Get:5 copy:/build/reproducible-path/resolver-8advCY/apt_archive ./ Packages [856 B] Fetched 2278 B in 0s (102 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: architecture-properties:amd64 autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils comerr-dev:amd64 cpp-16-x86-64-linux-gnu cpp-x86-64-linux-gnu crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dwz file g++-16-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-16-base:amd64 gcc-16-cross-base gcc-16-x86-64-linux-gnu gcc-16-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base intltool-debian krb5-multidev:amd64 libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libbrotli-dev:amd64 libbrotli1:amd64 libbz2-1.0:amd64 libbz2-dev:amd64 libc-gconv-modules-extra:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcom-err2:amd64 libcurl4-gnutls:amd64 libcurl4-gnutls-dev:amd64 libdb5.3t64:amd64 libdebhelper-perl libdeflate-dev:amd64 libdeflate0:amd64 libelf1t64 libevent-2.1-7t64:amd64 libffi8:amd64 libfile-stripnondeterminism-perl libgcc-16-dev:amd64 libgcc-16-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgmp-dev:amd64 libgmp10:amd64 libgmpxx4ldbl:amd64 libgnutls-dane0t64:amd64 libgnutls28-dev:amd64 libgnutls30t64:amd64 libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libgssrpc4t64:amd64 libhogweed6t64:amd64 libhts-dev:amd64 libhts3t64:amd64 libhtscodecs2:amd64 libhwasan0:amd64 libhwasan0-amd64-cross libidn2-0:amd64 libidn2-dev:amd64 libitm1:amd64 libitm1-amd64-cross libk5crypto3:amd64 libkadm5clnt-mit12:amd64 libkadm5srv-mit12:amd64 libkdb5-10t64:amd64 libkeyutils1:amd64 libkrb5-3:amd64 libkrb5-dev:amd64 libkrb5support0:amd64 libldap-dev:amd64 libldap2:amd64 liblsan0:amd64 liblsan0-amd64-cross liblzma-dev:amd64 liblzma5:amd64 libmagic-mgc libmagic1t64 libnettle8t64:amd64 libnghttp2-14:amd64 libnghttp2-dev:amd64 libnghttp3-9:amd64 libnghttp3-dev:amd64 libngtcp2-16:amd64 libngtcp2-crypto-gnutls-dev:amd64 libngtcp2-crypto-gnutls8:amd64 libngtcp2-dev:amd64 libp11-kit-dev:amd64 libp11-kit0:amd64 libpipeline1 libpkgconf7 libpsl-dev:amd64 libpsl5t64:amd64 libquadmath0:amd64 libquadmath0-amd64-cross librtmp-dev:amd64 librtmp1:amd64 libsasl2-2:amd64 libsasl2-modules-db:amd64 libsimde-dev libssh2-1-dev:amd64 libssh2-1t64:amd64 libssl-dev:amd64 libssl3t64:amd64 libstdc++-16-dev:amd64 libstdc++-16-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libtasn1-6:amd64 libtasn1-6-dev:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunbound8:amd64 libunistring-dev:amd64 libunistring5 libunistring5:amd64 libxml2-16 libzstd-dev:amd64 libzstd1:amd64 linux-libc-dev-amd64-cross m4 man-db nettle-dev:amd64 pkgconf:amd64 pkgconf-bin po-debconf sensible-utils xxd zlib1g:amd64 zlib1g-dev:amd64 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc doc-base:amd64 gcc-16-locales cpp-16-doc cpp-doc dh-make gcc-16-doc manpages-dev flex bison gdb-x86-64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff krb5-doc:amd64 glibc-doc:amd64 libc-l10n:amd64 locales:amd64 libnss-nis:amd64 manpages-dev:amd64 libcurl4-doc:amd64 libidn-dev:amd64 gmp-doc:amd64 libgmp10-doc:amd64 libmpfr-dev:amd64 dns-root-data:amd64 gnutls-bin:amd64 gnutls-doc:amd64 krb5-user:amd64 liblzma-doc:amd64 libnghttp2-doc:amd64 p11-kit-doc:amd64 libssl-doc:amd64 libstdc++-16-doc:amd64 libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx python3:any python3-requests bzip2-doc:amd64 ca-certificates:amd64 libarchive-cpio-perl krb5-locales:amd64 libldap-common:amd64 publicsuffix:amd64 libsasl2-modules:amd64 libtasn1-doc:amd64 libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: architecture-properties:amd64 autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils comerr-dev:amd64 cpp-16-x86-64-linux-gnu cpp-x86-64-linux-gnu crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dwz file g++-16-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-16-base:amd64 gcc-16-cross-base gcc-16-x86-64-linux-gnu gcc-16-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base intltool-debian krb5-multidev:amd64 libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libbrotli-dev:amd64 libbrotli1:amd64 libbz2-1.0:amd64 libbz2-dev:amd64 libc-gconv-modules-extra:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcom-err2:amd64 libcurl4-gnutls:amd64 libcurl4-gnutls-dev:amd64 libdb5.3t64:amd64 libdebhelper-perl libdeflate-dev:amd64 libdeflate0:amd64 libelf1t64 libevent-2.1-7t64:amd64 libffi8:amd64 libfile-stripnondeterminism-perl libgcc-16-dev:amd64 libgcc-16-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgmp-dev:amd64 libgmp10:amd64 libgmpxx4ldbl:amd64 libgnutls-dane0t64:amd64 libgnutls28-dev:amd64 libgnutls30t64:amd64 libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libgssrpc4t64:amd64 libhogweed6t64:amd64 libhts-dev:amd64 libhts3t64:amd64 libhtscodecs2:amd64 libhwasan0:amd64 libhwasan0-amd64-cross libidn2-0:amd64 libidn2-dev:amd64 libitm1:amd64 libitm1-amd64-cross libk5crypto3:amd64 libkadm5clnt-mit12:amd64 libkadm5srv-mit12:amd64 libkdb5-10t64:amd64 libkeyutils1:amd64 libkrb5-3:amd64 libkrb5-dev:amd64 libkrb5support0:amd64 libldap-dev:amd64 libldap2:amd64 liblsan0:amd64 liblsan0-amd64-cross liblzma-dev:amd64 liblzma5:amd64 libmagic-mgc libmagic1t64 libnettle8t64:amd64 libnghttp2-14:amd64 libnghttp2-dev:amd64 libnghttp3-9:amd64 libnghttp3-dev:amd64 libngtcp2-16:amd64 libngtcp2-crypto-gnutls-dev:amd64 libngtcp2-crypto-gnutls8:amd64 libngtcp2-dev:amd64 libp11-kit-dev:amd64 libp11-kit0:amd64 libpipeline1 libpkgconf7 libpsl-dev:amd64 libpsl5t64:amd64 libquadmath0:amd64 libquadmath0-amd64-cross librtmp-dev:amd64 librtmp1:amd64 libsasl2-2:amd64 libsasl2-modules-db:amd64 libsimde-dev libssh2-1-dev:amd64 libssh2-1t64:amd64 libssl-dev:amd64 libssl3t64:amd64 libstdc++-16-dev:amd64 libstdc++-16-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libtasn1-6:amd64 libtasn1-6-dev:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunbound8:amd64 libunistring-dev:amd64 libunistring5 libunistring5:amd64 libxml2-16 libzstd-dev:amd64 libzstd1:amd64 linux-libc-dev-amd64-cross m4 man-db nettle-dev:amd64 pkgconf:amd64 pkgconf-bin po-debconf sbuild-build-depends-main-dummy:amd64 sensible-utils xxd zlib1g:amd64 zlib1g-dev:amd64 0 upgraded, 150 newly installed, 0 to remove and 0 not upgraded. Need to get 129 MB of archives. After this operation, 534 MB of additional disk space will be used. Get:1 copy:/build/reproducible-path/resolver-8advCY/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [948 B] Get:2 http://mirror.einval.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.47-4 [345 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.47-4 [104 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 file arm64 1:5.47-4 [43.2 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 gettext-base arm64 1.0-5 [328 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2+b2 [69.1 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 groff-base arm64 1.24.2-2 [1279 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 bsdextrautils arm64 2.42.4-1 [99.1 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-3 [47.2 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 man-db arm64 2.13.1-1+b1 [1455 kB] Get:12 http://mirror.einval.org/debian unstable/main amd64 architecture-properties amd64 0.2.6+b2 [2632 B] Get:13 http://mirror.einval.org/debian unstable/main arm64 m4 arm64 1.4.21-1 [323 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 autoconf all 2.73-2 [516 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 automake all 1:1.19-2 [891 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 autopoint all 1.0-5 [820 kB] Get:18 http://mirror.einval.org/debian unstable/main amd64 gcc-16-base amd64 16.2.0-3 [38.7 kB] Get:19 http://mirror.einval.org/debian unstable/main amd64 libgcc-s1 amd64 16.2.0-3 [74.0 kB] Get:20 http://mirror.einval.org/debian unstable/main amd64 libc-gconv-modules-extra amd64 2.43-7 [1103 kB] Get:21 http://mirror.einval.org/debian unstable/main amd64 libc6 amd64 2.43-7 [1866 kB] Get:22 http://mirror.einval.org/debian unstable/main amd64 libc6-dev amd64 2.43-7 [2069 kB] Get:23 http://mirror.einval.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1+b2 [19.5 kB] Get:24 http://mirror.einval.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.4-1+b2 [51.2 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 gcc-16-x86-64-linux-gnu-base arm64 16.2.0-3cross1 [38.9 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 cpp-16-x86-64-linux-gnu arm64 16.2.0-3cross1 [11.7 MB] Get:27 http://mirror.einval.org/debian unstable/main arm64 cpp-x86-64-linux-gnu arm64 4:16.1.0-3 [4472 B] Get:28 http://mirror.einval.org/debian unstable/main arm64 binutils-x86-64-linux-gnu arm64 2.47-6 [1530 kB] Get:29 http://mirror.einval.org/debian unstable/main arm64 gcc-16-cross-base all 16.2.0-3cross1 [34.4 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1-amd64-cross all 16.2.0-3cross1 [74.1 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libgomp1-amd64-cross all 16.2.0-3cross1 [146 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 libitm1-amd64-cross all 16.2.0-3cross1 [27.0 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 libatomic1-amd64-cross all 16.2.0-3cross1 [10.5 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 libasan8-amd64-cross all 16.2.0-3cross1 [2878 kB] Get:35 http://mirror.einval.org/debian unstable/main arm64 liblsan0-amd64-cross all 16.2.0-3cross1 [1279 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 libtsan2-amd64-cross all 16.2.0-3cross1 [2562 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 libc6-amd64-cross all 2.43-3cross8 [1630 kB] Get:38 http://mirror.einval.org/debian unstable/main arm64 libstdc++6-amd64-cross all 16.2.0-3cross1 [799 kB] Get:39 http://mirror.einval.org/debian unstable/main arm64 libubsan1-amd64-cross all 16.2.0-3cross1 [1135 kB] Get:40 http://mirror.einval.org/debian unstable/main arm64 libhwasan0-amd64-cross all 16.2.0-3cross1 [1576 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 libquadmath0-amd64-cross all 16.2.0-3cross1 [147 kB] Get:42 http://mirror.einval.org/debian unstable/main arm64 libgcc-16-dev-amd64-cross all 16.2.0-3cross1 [2765 kB] Get:43 http://mirror.einval.org/debian unstable/main arm64 gcc-16-x86-64-linux-gnu arm64 16.2.0-3cross1 [22.7 MB] Get:44 http://mirror.einval.org/debian unstable/main arm64 gcc-x86-64-linux-gnu arm64 4:16.1.0-3 [1448 B] Get:45 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev-amd64-cross all 7.2.10-1 [12.4 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 libc6-dev-amd64-cross all 2.43-3cross8 [2063 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 libstdc++-16-dev-amd64-cross all 16.2.0-3cross1 [2737 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 g++-16-x86-64-linux-gnu arm64 16.2.0-3cross1 [12.8 MB] Get:49 http://mirror.einval.org/debian unstable/main arm64 g++-x86-64-linux-gnu arm64 4:16.1.0-3 [1196 B] Get:50 http://mirror.einval.org/debian unstable/main arm64 crossbuild-essential-amd64 all 12.12 [3552 B] Get:51 http://mirror.einval.org/debian unstable/main arm64 libdebhelper-perl all 14.5 [77.7 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 libtool all 2.6.2-3 [552 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 dh-autoreconf all 23 [12.7 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.1-1 [17.1 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Get:57 http://mirror.einval.org/debian unstable/main arm64 libelf1t64 arm64 0.196-1 [57.9 kB] Get:58 http://mirror.einval.org/debian unstable/main arm64 dwz arm64 0.17-1 [100 kB] Get:59 http://mirror.einval.org/debian unstable/main arm64 libunistring5 arm64 1.4.2-1 [455 kB] Get:60 http://mirror.einval.org/debian unstable/main arm64 libxml2-16 arm64 2.15.4+dfsg-1 [602 kB] Get:61 http://mirror.einval.org/debian unstable/main arm64 gettext arm64 1.0-5 [2549 kB] Get:62 http://mirror.einval.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:63 http://mirror.einval.org/debian unstable/main arm64 po-debconf all 1.0.22 [216 kB] Get:64 http://mirror.einval.org/debian unstable/main arm64 debhelper all 14.5 [944 kB] Get:65 http://mirror.einval.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-3 [31.1 kB] Get:66 http://mirror.einval.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-3 [79.0 kB] Get:67 http://mirror.einval.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b2 [9348 B] Get:68 http://mirror.einval.org/debian unstable/main amd64 libzstd1 amd64 1.5.7+dfsg-4 [304 kB] Get:69 http://mirror.einval.org/debian unstable/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.2-3 [90.9 kB] Get:70 http://mirror.einval.org/debian unstable/main amd64 libssl3t64 amd64 3.6.5-1 [2621 kB] Get:71 http://mirror.einval.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-3 [335 kB] Get:72 http://mirror.einval.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-3 [137 kB] Get:73 http://mirror.einval.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.22.1-3 [58.3 kB] Get:74 http://mirror.einval.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.22.1-3 [40.3 kB] Get:75 http://mirror.einval.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.22.1-3 [41.3 kB] Get:76 http://mirror.einval.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.22.1-3 [54.1 kB] Get:77 http://mirror.einval.org/debian unstable/main amd64 krb5-multidev amd64 1.22.1-3 [125 kB] Get:78 http://mirror.einval.org/debian unstable/main amd64 libasan8 amd64 16.2.0-3 [2888 kB] Get:79 http://mirror.einval.org/debian unstable/main amd64 libatomic1 amd64 16.2.0-3 [10.4 kB] Get:80 http://mirror.einval.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-4+b1 [312 kB] Get:81 http://mirror.einval.org/debian unstable/main amd64 libbrotli-dev amd64 1.2.0-4+b1 [324 kB] Get:82 http://mirror.einval.org/debian unstable/main amd64 libbz2-1.0 amd64 1.0.8-6+b2 [39.9 kB] Get:83 http://mirror.einval.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6+b2 [33.6 kB] Get:84 http://mirror.einval.org/debian unstable/main amd64 libnghttp3-9 amd64 1.17.0-1 [68.1 kB] Get:85 http://mirror.einval.org/debian unstable/main amd64 libngtcp2-16 amd64 1.24.0-1 [145 kB] Get:86 http://mirror.einval.org/debian unstable/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5+b2 [560 kB] Get:87 http://mirror.einval.org/debian unstable/main amd64 libnettle8t64 amd64 3.10.2-1+b1 [305 kB] Get:88 http://mirror.einval.org/debian unstable/main amd64 libhogweed6t64 amd64 3.10.2-1+b1 [335 kB] Get:89 http://mirror.einval.org/debian unstable/main amd64 libunistring5 amd64 1.4.2-1 [480 kB] Get:90 http://mirror.einval.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-5 [109 kB] Get:91 http://mirror.einval.org/debian unstable/main amd64 libffi8 amd64 3.8.0-2 [32.5 kB] Get:92 http://mirror.einval.org/debian unstable/main amd64 libp11-kit0 amd64 0.26.5-1 [482 kB] Get:93 http://mirror.einval.org/debian unstable/main amd64 libtasn1-6 amd64 4.21.0-2+b1 [49.3 kB] Get:94 http://mirror.einval.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.13-1 [1546 kB] Get:95 http://mirror.einval.org/debian unstable/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-11+b1 [709 kB] Get:96 http://mirror.einval.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-11 [17.2 kB] Get:97 http://mirror.einval.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-11 [55.2 kB] Get:98 http://mirror.einval.org/debian unstable/main amd64 libldap2 amd64 2.6.14+dfsg-2 [200 kB] Get:99 http://mirror.einval.org/debian unstable/main amd64 libnghttp2-14 amd64 1.70.0-1 [92.7 kB] Get:100 http://mirror.einval.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.24.0-1 [23.9 kB] Get:101 http://mirror.einval.org/debian unstable/main amd64 libpsl5t64 amd64 0.23.3-1 [61.7 kB] Get:102 http://mirror.einval.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-6 [253 kB] Get:103 http://mirror.einval.org/debian unstable/main amd64 libcurl4-gnutls amd64 8.23.0-1 [463 kB] Get:104 http://mirror.einval.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.13-stable-1 [183 kB] Get:105 http://mirror.einval.org/debian unstable/main amd64 libunbound8 amd64 1.26.1-1 [664 kB] Get:106 http://mirror.einval.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.13-1 [496 kB] Get:107 http://mirror.einval.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-5 [102 kB] Get:108 http://mirror.einval.org/debian unstable/main amd64 libp11-kit-dev amd64 0.26.5-1 [226 kB] Get:109 http://mirror.einval.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.21.0-2+b1 [98.6 kB] Get:110 http://mirror.einval.org/debian unstable/main amd64 libstdc++6 amd64 16.2.0-3 [823 kB] Get:111 http://mirror.einval.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5+b2 [328 kB] Get:112 http://mirror.einval.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5+b2 [641 kB] Get:113 http://mirror.einval.org/debian unstable/main amd64 nettle-dev amd64 3.10.2-1+b1 [1321 kB] Get:114 http://mirror.einval.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.13-1 [1479 kB] Get:115 http://mirror.einval.org/debian unstable/main amd64 libkrb5-dev amd64 1.22.1-3 [14.0 kB] Get:116 http://mirror.einval.org/debian unstable/main amd64 libldap-dev amd64 2.6.14+dfsg-2 [321 kB] Get:117 http://mirror.einval.org/debian unstable/main arm64 libpkgconf7 arm64 2.5.1-4 [45.5 kB] Get:118 http://mirror.einval.org/debian unstable/main arm64 pkgconf-bin arm64 2.5.1-4 [35.1 kB] Get:119 http://mirror.einval.org/debian unstable/main amd64 pkgconf amd64 2.5.1-4 [33.6 kB] Get:120 http://mirror.einval.org/debian unstable/main amd64 libnghttp2-dev amd64 1.70.0-1 [131 kB] Get:121 http://mirror.einval.org/debian unstable/main amd64 libnghttp3-dev amd64 1.17.0-1 [96.3 kB] Get:122 http://mirror.einval.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.24.0-1 [24.0 kB] Get:123 http://mirror.einval.org/debian unstable/main amd64 libngtcp2-dev amd64 1.24.0-1 [204 kB] Get:124 http://mirror.einval.org/debian unstable/main amd64 libunistring-dev amd64 1.4.2-1 [651 kB] Get:125 http://mirror.einval.org/debian unstable/main amd64 libpsl-dev amd64 0.23.3-1 [30.1 kB] Get:126 http://mirror.einval.org/debian unstable/main amd64 librtmp1 amd64 2.6-1 [60.3 kB] Get:127 http://mirror.einval.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-3 [918 kB] Get:128 http://mirror.einval.org/debian unstable/main amd64 librtmp-dev amd64 2.6-1 [69.7 kB] Get:129 http://mirror.einval.org/debian unstable/main amd64 libssl-dev amd64 3.6.5-1 [3165 kB] Get:130 http://mirror.einval.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-6 [402 kB] Get:131 http://mirror.einval.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-4 [371 kB] Get:132 http://mirror.einval.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.23.0-1 [597 kB] Get:133 http://mirror.einval.org/debian unstable/main amd64 libdeflate0 amd64 1.25-1 [48.0 kB] Get:134 http://mirror.einval.org/debian unstable/main amd64 libdeflate-dev amd64 1.25-1 [56.7 kB] Get:135 http://mirror.einval.org/debian unstable/main amd64 libgomp1 amd64 16.2.0-3 [151 kB] Get:136 http://mirror.einval.org/debian unstable/main amd64 libitm1 amd64 16.2.0-3 [26.9 kB] Get:137 http://mirror.einval.org/debian unstable/main amd64 liblsan0 amd64 16.2.0-3 [1281 kB] Get:138 http://mirror.einval.org/debian unstable/main amd64 libtsan2 amd64 16.2.0-3 [2574 kB] Get:139 http://mirror.einval.org/debian unstable/main amd64 libubsan1 amd64 16.2.0-3 [1136 kB] Get:140 http://mirror.einval.org/debian unstable/main amd64 libhwasan0 amd64 16.2.0-3 [1580 kB] Get:141 http://mirror.einval.org/debian unstable/main amd64 libquadmath0 amd64 16.2.0-3 [148 kB] Get:142 http://mirror.einval.org/debian unstable/main amd64 libgcc-16-dev amd64 16.2.0-3 [2782 kB] Get:143 http://mirror.einval.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.7-1 [102 kB] Get:144 http://mirror.einval.org/debian unstable/main amd64 liblzma5 amd64 5.8.4-1 [354 kB] Get:145 http://mirror.einval.org/debian unstable/main amd64 libhts3t64 amd64 1.24-3 [506 kB] Get:146 http://mirror.einval.org/debian unstable/main amd64 liblzma-dev amd64 5.8.4-1 [391 kB] Get:147 http://mirror.einval.org/debian unstable/main amd64 libhts-dev amd64 1.24-3 [1918 kB] Get:148 http://mirror.einval.org/debian unstable/main arm64 libsimde-dev all 0.8.4~rc3-5 [500 kB] Get:149 http://mirror.einval.org/debian unstable/main amd64 libstdc++-16-dev amd64 16.2.0-3 [2755 kB] Get:150 http://mirror.einval.org/debian unstable/main arm64 xxd arm64 2:9.2.0858-1 [64.5 kB] Preconfiguring packages ... Fetched 129 MB in 2s (75.4 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 12175 files and directories currently installed.) Preparing to unpack .../000-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../001-libmagic-mgc_1%3a5.47-4_arm64.deb ... Unpacking libmagic-mgc (1:5.47-4) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../002-libmagic1t64_1%3a5.47-4_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.47-4) ... Selecting previously unselected package file. Preparing to unpack .../003-file_1%3a5.47-4_arm64.deb ... Unpacking file (1:5.47-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../004-gettext-base_1.0-5_arm64.deb ... Unpacking gettext-base (1.0-5) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../005-libuchardet0_0.0.8-2+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-2+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../006-groff-base_1.24.2-2_arm64.deb ... Unpacking groff-base (1.24.2-2) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../007-bsdextrautils_2.42.4-1_arm64.deb ... Unpacking bsdextrautils (2.42.4-1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../008-libpipeline1_1.5.8-3_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-3) ... Selecting previously unselected package man-db. Preparing to unpack .../009-man-db_2.13.1-1+b1_arm64.deb ... Unpacking man-db (2.13.1-1+b1) ... Selecting previously unselected package architecture-properties:amd64. Preparing to unpack .../010-architecture-properties_0.2.6+b2_amd64.deb ... Unpacking architecture-properties:amd64 (0.2.6+b2) ... Selecting previously unselected package m4. Preparing to unpack .../011-m4_1.4.21-1_arm64.deb ... Unpacking m4 (1.4.21-1) ... 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Preparing to unpack .../018-libc-gconv-modules-extra_2.43-7_amd64.deb ... Unpacking libc-gconv-modules-extra:amd64 (2.43-7) ... Selecting previously unselected package libc6:amd64. Preparing to unpack .../019-libc6_2.43-7_amd64.deb ... Unpacking libc6:amd64 (2.43-7) ... Selecting previously unselected package libc6-dev:amd64. Preparing to unpack .../020-libc6-dev_2.43-7_amd64.deb ... Unpacking libc6-dev:amd64 (2.43-7) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../021-libcom-err2_1.47.4-1+b2_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.4-1+b2) ... Selecting previously unselected package comerr-dev:amd64. Preparing to unpack .../022-comerr-dev_2.1-1.47.4-1+b2_amd64.deb ... Unpacking comerr-dev:amd64 (2.1-1.47.4-1+b2) ... Selecting previously unselected package gcc-16-x86-64-linux-gnu-base:arm64. Preparing to unpack .../023-gcc-16-x86-64-linux-gnu-base_16.2.0-3cross1_arm64.deb ... Unpacking gcc-16-x86-64-linux-gnu-base:arm64 (16.2.0-3cross1) ... Selecting previously unselected package cpp-16-x86-64-linux-gnu. Preparing to unpack .../024-cpp-16-x86-64-linux-gnu_16.2.0-3cross1_arm64.deb ... Unpacking cpp-16-x86-64-linux-gnu (16.2.0-3cross1) ... Selecting previously unselected package cpp-x86-64-linux-gnu. Preparing to unpack .../025-cpp-x86-64-linux-gnu_4%3a16.1.0-3_arm64.deb ... Unpacking cpp-x86-64-linux-gnu (4:16.1.0-3) ... Selecting previously unselected package binutils-x86-64-linux-gnu. Preparing to unpack .../026-binutils-x86-64-linux-gnu_2.47-6_arm64.deb ... Unpacking binutils-x86-64-linux-gnu (2.47-6) ... Selecting previously unselected package gcc-16-cross-base. Preparing to unpack .../027-gcc-16-cross-base_16.2.0-3cross1_all.deb ... Unpacking gcc-16-cross-base (16.2.0-3cross1) ... Selecting previously unselected package libgcc-s1-amd64-cross. Preparing to unpack .../028-libgcc-s1-amd64-cross_16.2.0-3cross1_all.deb ... Unpacking libgcc-s1-amd64-cross (16.2.0-3cross1) ... Selecting previously unselected package libgomp1-amd64-cross. Preparing to unpack .../029-libgomp1-amd64-cross_16.2.0-3cross1_all.deb ... Unpacking libgomp1-amd64-cross (16.2.0-3cross1) ... Selecting previously unselected package libitm1-amd64-cross. Preparing to unpack .../030-libitm1-amd64-cross_16.2.0-3cross1_all.deb ... Unpacking libitm1-amd64-cross (16.2.0-3cross1) ... Selecting previously unselected package libatomic1-amd64-cross. Preparing to unpack .../031-libatomic1-amd64-cross_16.2.0-3cross1_all.deb ... Unpacking libatomic1-amd64-cross (16.2.0-3cross1) ... Selecting previously unselected package libasan8-amd64-cross. Preparing to unpack .../032-libasan8-amd64-cross_16.2.0-3cross1_all.deb ... Unpacking libasan8-amd64-cross (16.2.0-3cross1) ... Selecting previously unselected package liblsan0-amd64-cross. Preparing to unpack .../033-liblsan0-amd64-cross_16.2.0-3cross1_all.deb ... Unpacking liblsan0-amd64-cross (16.2.0-3cross1) ... Selecting previously unselected package libtsan2-amd64-cross. Preparing to unpack .../034-libtsan2-amd64-cross_16.2.0-3cross1_all.deb ... Unpacking libtsan2-amd64-cross (16.2.0-3cross1) ... Selecting previously unselected package libc6-amd64-cross. Preparing to unpack .../035-libc6-amd64-cross_2.43-3cross8_all.deb ... Unpacking libc6-amd64-cross (2.43-3cross8) ... Selecting previously unselected package libstdc++6-amd64-cross. Preparing to unpack .../036-libstdc++6-amd64-cross_16.2.0-3cross1_all.deb ... Unpacking libstdc++6-amd64-cross (16.2.0-3cross1) ... Selecting previously unselected package libubsan1-amd64-cross. Preparing to unpack .../037-libubsan1-amd64-cross_16.2.0-3cross1_all.deb ... Unpacking libubsan1-amd64-cross (16.2.0-3cross1) ... Selecting previously unselected package libhwasan0-amd64-cross. Preparing to unpack .../038-libhwasan0-amd64-cross_16.2.0-3cross1_all.deb ... Unpacking libhwasan0-amd64-cross (16.2.0-3cross1) ... Selecting previously unselected package libquadmath0-amd64-cross. Preparing to unpack .../039-libquadmath0-amd64-cross_16.2.0-3cross1_all.deb ... Unpacking libquadmath0-amd64-cross (16.2.0-3cross1) ... Selecting previously unselected package libgcc-16-dev-amd64-cross. Preparing to unpack .../040-libgcc-16-dev-amd64-cross_16.2.0-3cross1_all.deb ... Unpacking libgcc-16-dev-amd64-cross (16.2.0-3cross1) ... Selecting previously unselected package gcc-16-x86-64-linux-gnu. Preparing to unpack .../041-gcc-16-x86-64-linux-gnu_16.2.0-3cross1_arm64.deb ... Unpacking gcc-16-x86-64-linux-gnu (16.2.0-3cross1) ... Selecting previously unselected package gcc-x86-64-linux-gnu. Preparing to unpack .../042-gcc-x86-64-linux-gnu_4%3a16.1.0-3_arm64.deb ... Unpacking gcc-x86-64-linux-gnu (4:16.1.0-3) ... Selecting previously unselected package linux-libc-dev-amd64-cross. Preparing to unpack .../043-linux-libc-dev-amd64-cross_7.2.10-1_all.deb ... Unpacking linux-libc-dev-amd64-cross (7.2.10-1) ... Selecting previously unselected package libc6-dev-amd64-cross. Preparing to unpack .../044-libc6-dev-amd64-cross_2.43-3cross8_all.deb ... Unpacking libc6-dev-amd64-cross (2.43-3cross8) ... Selecting previously unselected package libstdc++-16-dev-amd64-cross. Preparing to unpack .../045-libstdc++-16-dev-amd64-cross_16.2.0-3cross1_all.deb ... Unpacking libstdc++-16-dev-amd64-cross (16.2.0-3cross1) ... Selecting previously unselected package g++-16-x86-64-linux-gnu. Preparing to unpack .../046-g++-16-x86-64-linux-gnu_16.2.0-3cross1_arm64.deb ... Unpacking g++-16-x86-64-linux-gnu (16.2.0-3cross1) ... Selecting previously unselected package g++-x86-64-linux-gnu. Preparing to unpack .../047-g++-x86-64-linux-gnu_4%3a16.1.0-3_arm64.deb ... Unpacking g++-x86-64-linux-gnu (4:16.1.0-3) ... Selecting previously unselected package crossbuild-essential-amd64. Preparing to unpack .../048-crossbuild-essential-amd64_12.12_all.deb ... Unpacking crossbuild-essential-amd64 (12.12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../049-libdebhelper-perl_14.5_all.deb ... Unpacking libdebhelper-perl (14.5) ... Selecting previously unselected package libtool. Preparing to unpack .../050-libtool_2.6.2-3_all.deb ... Unpacking libtool (2.6.2-3) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../051-dh-autoreconf_23_all.deb ... Unpacking dh-autoreconf (23) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../052-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../053-libfile-stripnondeterminism-perl_1.15.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. 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Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:arm64 (0.0.8-2+b2) ... Setting up cpp-16-x86-64-linux-gnu (16.2.0-3cross1) ... Setting up libgcc-s1-amd64-cross (16.2.0-3cross1) ... Setting up binutils-x86-64-linux-gnu (2.47-6) ... Setting up libstdc++6-amd64-cross (16.2.0-3cross1) ... Setting up cpp-x86-64-linux-gnu (4:16.1.0-3) ... Setting up automake (1:1.19-2) ... update-alternatives: using /usr/bin/automake-1.19 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.1-1) ... Setting up gettext (1.0-5) ... Setting up libtool (2.6.2-3) ... Setting up libasan8-amd64-cross (16.2.0-3cross1) ... Setting up liblsan0-amd64-cross (16.2.0-3cross1) ... Setting up libc6-dev-amd64-cross (2.43-3cross8) ... Setting up libtsan2-amd64-cross (16.2.0-3cross1) ... Setting up libgomp1-amd64-cross (16.2.0-3cross1) ... Setting up pkgconf:amd64 (2.5.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (23) ... Setting up libhwasan0-amd64-cross (16.2.0-3cross1) ... Setting up libubsan1-amd64-cross (16.2.0-3cross1) ... Setting up libgcc-16-dev-amd64-cross (16.2.0-3cross1) ... Setting up dh-strip-nondeterminism (1.15.1-1) ... Setting up groff-base (1.24.2-2) ... Setting up libstdc++-16-dev-amd64-cross (16.2.0-3cross1) ... Setting up po-debconf (1.0.22) ... Setting up gcc-16-x86-64-linux-gnu (16.2.0-3cross1) ... Setting up man-db (2.13.1-1+b1) ... Not building database; man-db/auto-update is not 'true'. Setting up g++-16-x86-64-linux-gnu (16.2.0-3cross1) ... Setting up gcc-x86-64-linux-gnu (4:16.1.0-3) ... Setting up debhelper (14.5) ... Setting up g++-x86-64-linux-gnu (4:16.1.0-3) ... Setting up crossbuild-essential-amd64 (12.12) ... Setting up libgcc-s1:amd64 (16.2.0-3) ... Setting up libc6:amd64 (2.43-7) ... Setting up libnghttp3-9:amd64 (1.17.0-1) ... Setting up libnghttp3-dev:amd64 (1.17.0-1) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-11+b1) ... Setting up libffi8:amd64 (3.8.0-2) ... Setting up libhwasan0:amd64 (16.2.0-3) ... Setting up libasan8:amd64 (16.2.0-3) ... Setting up libtasn1-6:amd64 (4.21.0-2+b1) ... Setting up libc6-dev:amd64 (2.43-7) ... Setting up libngtcp2-16:amd64 (1.24.0-1) ... Setting up libtsan2:amd64 (16.2.0-3) ... Setting up libbz2-1.0:amd64 (1.0.8-6+b2) ... Setting up libtasn1-6-dev:amd64 (4.21.0-2+b1) ... Setting up libstdc++6:amd64 (16.2.0-3) ... Setting up liblsan0:amd64 (16.2.0-3) ... Setting up libitm1:amd64 (16.2.0-3) ... Setting up libbz2-dev:amd64 (1.0.8-6+b2) ... Setting up libhtscodecs2:amd64 (1.6.7-1) ... Setting up libzstd1:amd64 (1.5.7+dfsg-4) ... Setting up libkeyutils1:amd64 (1.6.3-6+b2) ... Setting up libzstd-dev:amd64 (1.5.7+dfsg-4) ... Setting up liblzma5:amd64 (5.8.4-1) ... Setting up libbrotli1:amd64 (1.2.0-4+b1) ... Setting up libnghttp2-14:amd64 (1.70.0-1) ... Setting up libdeflate0:amd64 (1.25-1) ... Setting up libevent-2.1-7t64:amd64 (2.1.13-stable-1) ... Setting up zlib1g:amd64 (1:1.3.dfsg+really1.3.2-3) ... Setting up libcom-err2:amd64 (1.47.4-1+b2) ... Setting up libngtcp2-dev:amd64 (1.24.0-1) ... Setting up libgomp1:amd64 (16.2.0-3) ... Setting up libkrb5support0:amd64 (1.22.1-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-11) ... Setting up libnettle8t64:amd64 (3.10.2-1+b1) ... Setting up libgmp10:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up libquadmath0:amd64 (16.2.0-3) ... Setting up libp11-kit0:amd64 (0.26.5-1) ... Setting up comerr-dev:amd64 (2.1-1.47.4-1+b2) ... Setting up libunistring5:amd64 (1.4.2-1) ... Setting up libatomic1:amd64 (16.2.0-3) ... Setting up libk5crypto3:amd64 (1.22.1-3) ... Setting up liblzma-dev:amd64 (5.8.4-1) ... Setting up libubsan1:amd64 (16.2.0-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.2-3) ... Setting up libhogweed6t64:amd64 (3.10.2-1+b1) ... Setting up libdeflate-dev:amd64 (1.25-1) ... Setting up libbrotli-dev:amd64 (1.2.0-4+b1) ... Setting up libp11-kit-dev:amd64 (0.26.5-1) ... Setting up libunistring-dev:amd64 (1.4.2-1) ... Setting up libnghttp2-dev:amd64 (1.70.0-1) ... Setting up libgcc-16-dev:amd64 (16.2.0-3) ... Setting up libssl3t64:amd64 (3.6.5-1) ... Setting up libidn2-0:amd64 (2.3.8-5) ... Setting up libunbound8:amd64 (1.26.1-1) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up libstdc++-16-dev:amd64 (16.2.0-3) ... Setting up libssl-dev:amd64 (3.6.5-1) ... Setting up libidn2-dev:amd64 (2.3.8-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-11) ... Setting up libkrb5-3:amd64 (1.22.1-3) ... Setting up libssh2-1t64:amd64 (1.11.1-6) ... Setting up libldap2:amd64 (2.6.14+dfsg-2) ... Setting up libgnutls30t64:amd64 (3.8.13-1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up nettle-dev:amd64 (3.10.2-1+b1) ... Setting up libpsl5t64:amd64 (0.23.3-1) ... Setting up libpsl-dev:amd64 (0.23.3-1) ... Setting up libgnutls-dane0t64:amd64 (3.8.13-1) ... Setting up librtmp1:amd64 (2.6-1) ... Setting up libldap-dev:amd64 (2.6.14+dfsg-2) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-3) ... Setting up libssh2-1-dev:amd64 (1.11.1-6) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.24.0-1) ... Setting up libgnutls28-dev:amd64 (3.8.13-1) ... Setting up libcurl4-gnutls:amd64 (8.23.0-1) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.24.0-1) ... Setting up libgssrpc4t64:amd64 (1.22.1-3) ... Setting up librtmp-dev:amd64 (2.6-1) ... Setting up libhts3t64:amd64 (1.24-3) ... Setting up libkadm5clnt-mit12:amd64 (1.22.1-3) ... Setting up libkdb5-10t64:amd64 (1.22.1-3) ... Setting up libkadm5srv-mit12:amd64 (1.22.1-3) ... Setting up krb5-multidev:amd64 (1.22.1-3) ... Setting up libkrb5-dev:amd64 (1.22.1-3) ... Setting up libcurl4-gnutls-dev:amd64 (8.23.0-1) ... Setting up libhts-dev:amd64 (1.24-3) ... Setting up sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ... Processing triggers for base-files (14.2) ... Processing triggers for libc-bin (2.43-7) ... +------------------------------------------------------------------------------+ | Check architectures Thu, 15 Oct 2026 19:13:03 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Thu, 15 Oct 2026 19:13:04 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.111+deb13-arm64 #1 SMP Debian 6.12.111-1 (2026-09-28) arm64 (aarch64) Toolchain package versions: binutils_2.47-6 dpkg-dev_1.23.11 g++-16_16.2.0-3 gcc-16_16.2.0-3 libc6-dev_2.43-7 libstdc++-16-dev_16.2.0-3 libstdc++-16-dev-amd64-cross_16.2.0-3cross1 libstdc++6_16.2.0-3 libstdc++6-amd64-cross_16.2.0-3cross1 linux-libc-dev_7.2.10-1 Package versions: apt_3.3.3 apt-utils_3.3.3 architecture-properties_0.2.6+b2 autoconf_2.73-2 automake_1:1.19-2 autopoint_1.0-5 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8+b1 bash_5.3-4 binutils_2.47-6 binutils-aarch64-linux-gnu_2.47-6 binutils-common_2.47-6 binutils-x86-64-linux-gnu_2.47-6 bsdextrautils_2.42.4-1 build-essential_12.12 bzip2_1.0.8-6+b2 comerr-dev_2.1-1.47.4-1+b2 coreutils_9.10-1 cpp_4:16.1.0-3 cpp-16_16.2.0-3 cpp-16-aarch64-linux-gnu_16.2.0-3 cpp-16-x86-64-linux-gnu_16.2.0-3cross1 cpp-aarch64-linux-gnu_4:16.1.0-3 cpp-x86-64-linux-gnu_4:16.1.0-3 crossbuild-essential-amd64_12.12 dash_0.5.12-12+b1 debconf_1.5.92 debhelper_14.5 debian-archive-keyring_2025.1 debianutils_5.24 dh-autoreconf_23 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1+b1 dpkg_1.23.11 dpkg-dev_1.23.11 dwz_0.17-1 file_1:5.47-4 findutils_4.11.0-3 g++_4:16.1.0-3 g++-16_16.2.0-3 g++-16-aarch64-linux-gnu_16.2.0-3 g++-16-x86-64-linux-gnu_16.2.0-3cross1 g++-aarch64-linux-gnu_4:16.1.0-3 g++-x86-64-linux-gnu_4:16.1.0-3 gcc_4:16.1.0-3 gcc-16_16.2.0-3 gcc-16-aarch64-linux-gnu_16.2.0-3 gcc-16-base_16.2.0-3 gcc-16-cross-base_16.2.0-3cross1 gcc-16-x86-64-linux-gnu_16.2.0-3cross1 gcc-16-x86-64-linux-gnu-base_16.2.0-3cross1 gcc-aarch64-linux-gnu_4:16.1.0-3 gcc-x86-64-linux-gnu_4:16.1.0-3 gettext_1.0-5 gettext-base_1.0-5 grep_3.12-1+b1 groff-base_1.24.2-2 gzip_1.14-1 hostname_3.25+b1 init-system-helpers_1.69+nmu3 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.22.1-3 libacl1_2.4.0-1 libapt-pkg7.0_3.3.3 libarchive-zip-perl_1.68-1 libasan8_16.2.0-3 libasan8-amd64-cross_16.2.0-3cross1 libatomic1_16.2.0-3 libatomic1-amd64-cross_16.2.0-3cross1 libattr1_1:2.6.0-1 libaudit-common_1:4.2.1-1 libaudit1_1:4.2.1-1 libbinutils_2.47-6 libblkid1_2.42.4-1 libbrotli-dev_1.2.0-4+b1 libbrotli1_1.2.0-4+b1 libbz2-1.0_1.0.8-6+b2 libbz2-dev_1.0.8-6+b2 libc-bin_2.43-7 libc-dev-bin_2.43-7 libc-gconv-modules-extra_2.43-7 libc6_2.43-7 libc6-amd64-cross_2.43-3cross8 libc6-dev_2.43-7 libc6-dev-amd64-cross_2.43-3cross8 libcap-ng0_0.9.6-1 libcc1-0_16.2.0-3 libcom-err2_1.47.4-1+b2 libcrypt1_1:4.5.2+20251210-1 libctf-nobfd0_2.47-6 libctf0_2.47-6 libcurl4-gnutls_8.23.0-1 libcurl4-gnutls-dev_8.23.0-1 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_14.5 libdeflate-dev_1.25-1 libdeflate0_1.25-1 libdpkg-perl_1.23.11 libelf1t64_0.196-1 libevent-2.1-7t64_2.1.13-stable-1 libffi8_3.8.0-2 libfile-stripnondeterminism-perl_1.15.1-1 libgcc-16-dev_16.2.0-3 libgcc-16-dev-amd64-cross_16.2.0-3cross1 libgcc-s1_16.2.0-3 libgcc-s1-amd64-cross_16.2.0-3cross1 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgmp-dev_2:6.3.0+dfsg-5+b2 libgmp10_2:6.3.0+dfsg-5+b2 libgmpxx4ldbl_2:6.3.0+dfsg-5+b2 libgnutls-dane0t64_3.8.13-1 libgnutls28-dev_3.8.13-1 libgnutls30t64_3.8.13-1 libgomp1_16.2.0-3 libgomp1-amd64-cross_16.2.0-3cross1 libgprofng0_2.47-6 libgssapi-krb5-2_1.22.1-3 libgssrpc4t64_1.22.1-3 libhogweed6t64_3.10.2-1+b1 libhts-dev_1.24-3 libhts3t64_1.24-3 libhtscodecs2_1.6.7-1 libhwasan0_16.2.0-3 libhwasan0-amd64-cross_16.2.0-3cross1 libidn2-0_2.3.8-5 libidn2-dev_2.3.8-5 libisl23_0.28-1 libitm1_16.2.0-3 libitm1-amd64-cross_16.2.0-3cross1 libjansson4_2.15.1-1 libk5crypto3_1.22.1-3 libkadm5clnt-mit12_1.22.1-3 libkadm5srv-mit12_1.22.1-3 libkdb5-10t64_1.22.1-3 libkeyutils1_1.6.3-6+b2 libkrb5-3_1.22.1-3 libkrb5-dev_1.22.1-3 libkrb5support0_1.22.1-3 libldap-dev_2.6.14+dfsg-2 libldap2_2.6.14+dfsg-2 liblsan0_16.2.0-3 liblsan0-amd64-cross_16.2.0-3cross1 liblz4-1_1.10.0-10 liblzma-dev_5.8.4-1 liblzma5_5.8.4-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.3.0-1 libmount1_2.42.4-1 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libnettle8t64_3.10.2-1+b1 libnghttp2-14_1.70.0-1 libnghttp2-dev_1.70.0-1 libnghttp3-9_1.17.0-1 libnghttp3-dev_1.17.0-1 libngtcp2-16_1.24.0-1 libngtcp2-crypto-gnutls-dev_1.24.0-1 libngtcp2-crypto-gnutls8_1.24.0-1 libngtcp2-dev_1.24.0-1 libp11-kit-dev_0.26.5-1 libp11-kit0_0.26.5-1 libpam-modules_1.7.0-8 libpam-modules-bin_1.7.0-8 libpam-runtime_1.7.0-8 libpam0g_1.7.0-8 libpcre2-8-0_10.48-3.1 libperl5.42_5.42.3-1 libpipeline1_1.5.8-3 libpkgconf7_2.5.1-4 libpsl-dev_0.23.3-1 libpsl5t64_0.23.3-1 libquadmath0_16.2.0-3 libquadmath0-amd64-cross_16.2.0-3cross1 librtmp-dev_2.6-1 librtmp1_2.6-1 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.1-1+b1 libselinux1_3.11-2.1 libsframe3_2.47-6 libsimde-dev_0.8.4~rc3-5 libsmartcols1_2.42.4-1 libssh2-1-dev_1.11.1-6 libssh2-1t64_1.11.1-6 libssl-dev_3.6.5-1 libssl3t64_3.6.5-1 libstdc++-16-dev_16.2.0-3 libstdc++-16-dev-amd64-cross_16.2.0-3cross1 libstdc++6_16.2.0-3 libstdc++6-amd64-cross_16.2.0-3cross1 libsystemd0_262-1 libtasn1-6_4.21.0-2+b1 libtasn1-6-dev_4.21.0-2+b1 libtinfo6_6.6+20260608-2 libtool_2.6.2-3 libtsan2_16.2.0-3 libtsan2-amd64-cross_16.2.0-3cross1 libubsan1_16.2.0-3 libubsan1-amd64-cross_16.2.0-3cross1 libuchardet0_0.0.8-2+b2 libudev1_262-1 libunbound8_1.26.1-1 libunistring-dev_1.4.2-1 libunistring5_1.4.2-1 libuuid1_2.42.4-1 libxml2-16_2.15.4+dfsg-1 libxxhash0_0.8.3-2+b2 libzstd-dev_1.5.7+dfsg-4 libzstd1_1.5.7+dfsg-4 linux-libc-dev_7.2.10-1 linux-libc-dev-amd64-cross_7.2.10-1 login_1:4.16.0-2+really2.42.4-1 login.defs_1:4.20.3-1 m4_1.4.21-1 make_4.4.1-3+b1 man-db_2.13.1-1+b1 mawk_1.3.4.20260302-2 ncurses-base_6.6+20260608-2 ncurses-bin_6.6+20260608-2 nettle-dev_3.10.2-1+b1 openssl-provider-legacy_3.6.5-1 patch_2.8-2+b1 perl_5.42.3-1 perl-base_5.42.3-1 perl-modules-5.42_5.42.3-1 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.5.0-1 sysvinit-utils_3.18-1 tar_1.35+dfsg-6 util-linux_2.42.4-1 xxd_2:9.2.0858-1 xz-utils_5.8.4-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Thu, 15 Oct 2026 19:13:04 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rna-star Binary: rna-star Architecture: any Version: 2.7.11b+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Sascha Steinbiss Homepage: https://github.com/alexdobin/STAR/ Standards-Version: 4.7.4 Vcs-Browser: https://salsa.debian.org/med-team/rna-star Vcs-Git: https://salsa.debian.org/med-team/rna-star.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), architecture-is-64-bit, architecture-is-little-endian, libhts-dev, xxd, zlib1g-dev, libsimde-dev Package-List: rna-star deb science optional arch=any Checksums-Sha1: afb7185ca0a5fb12a0997f2aa90081cd4dd33c03 520964 rna-star_2.7.11b+dfsg.orig.tar.xz 542aa8702c1c1c49dad5bb2fd445ce4e5d242df8 380176 rna-star_2.7.11b+dfsg-4.debian.tar.xz Checksums-Sha256: b06b9c0074fd7ab018edf7549582ee4ae29ed807aa8238811d888bf9ff73eaab 520964 rna-star_2.7.11b+dfsg.orig.tar.xz fe12934ab81aa7abb9c4ef219c8561ea2b97b2aca0d589004118c8e43006ba6c 380176 rna-star_2.7.11b+dfsg-4.debian.tar.xz Files: 003d1d688848cbc667285f514a8b62b5 520964 rna-star_2.7.11b+dfsg.orig.tar.xz 388eb079696a1016181236eca351dc08 380176 rna-star_2.7.11b+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAmqH8fIACgkQ6NN64vCf SHJJGw//blzxQygNQqZauN28ZUq6ztu2PfbruRS6xEUmmIaAYJmWFiUt3NbKLJW6 8PzfI2Y0bZOSCU+yZ0hnL71DO8kwlCp1zGzVARM2Vg1cUr2alnfde5aAhFhrQdbf lEekg1iSiWVaqWLfBjoawOyYqX4D9JyEYSzrUN2B7AIJkjAjUp5EdE4tBL6YE53c 9VQbumLxdZZ89W0LA0Dc9xiOFBfARh80toisLuNzWb3n3n32NU5K+5yrW46dx3UM GYTN58WYLNxTWtCZdkiA8LnRFr8wtwavrn4MNrHGNf1ADGnzWRxAdTILATw9lKay oLQEwztRLuJ2MINENa25sv/s8uun4CoCfcNW6ZCi+89iqZhJ4PJW98XzKIYsg2Dj yAiT2PjQr/mCmDH9BypEZbU21Fxu+ewWidmTQa6NJECj1GzAzJuCUyloDHvwDNpp rsjzk3k17JR0NyQ3J7HiDaA0jRzjwnlzSk/iMbJcf9/6DoAOo34Ev3PsekiXjTJG IGDdO4z4OEKAxirZum7SZ/HfkKPhzD1rZwoJU9KCLj2pjz6SPtufdJ6Cwl5kaEhI 9VQIhspt2UzSEf6lJ+F9RXMhL5t6PKRbXzh+C5N2KNqbED19LMr+B8KrcztWYAId tbkLqicWZCZf9Uh9O8MWvxOfihd6xfrDOoPGhmS5n+hD/fivheE= =bqja -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./rna-star_2.7.11b+dfsg-4.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./rna-star_2.7.11b+dfsg-4.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting rna-star in /build/reproducible-path/rna-star-2.7.11b+dfsg dpkg-source: info: unpacking rna-star_2.7.11b+dfsg.orig.tar.xz dpkg-source: info: unpacking rna-star_2.7.11b+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying donotuse_own_htslib.patch dpkg-source: info: applying mips_shm_noreserve.patch dpkg-source: warning: unexpected end of diff '/build/reproducible-path/rna-star-2.7.11b+dfsg/debian/patches/hurd_shm_noreserve.patch' dpkg-source: info: applying hurd_shm_noreserve.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying mathRoutinesNotInScope.patch dpkg-source: info: applying do-not-enforce-avx2.patch dpkg-source: info: applying gcc-12.patch dpkg-source: info: applying packaged_simde dpkg-source: info: applying fix_typos.patch dpkg-source: info: applying cpp11.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.amd64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LC_ALL=C.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aamd64 -Pcross,nocheck -us -uc -B --jobs-try=1 dpkg-buildpackage: info: source package rna-star dpkg-buildpackage: info: source version 2.7.11b+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-architecture: warning: specified GNU system type x86_64-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=source debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' cd source; /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' dh_autoreconf_clean -O--sourcedirectory=source dh_clean -O--sourcedirectory=source debian/rules binary-arch dh binary-arch --sourcedirectory=source dh_update_autotools_config -a -O--sourcedirectory=source dh_autoreconf -a -O--sourcedirectory=source dh_auto_configure -a -O--sourcedirectory=source debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' mkdir --parents /build/reproducible-path/rna-star-2.7.11b+dfsg/debian/rna-star/usr/lib/rna-star/bin dh_auto_clean ; dh_auto_build -- SFX=-avx2 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-avx2 STARlong-avx2 && dh_auto_clean ; dh_auto_build -- SFX=-avx CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-avx STARlong-avx && dh_auto_clean ; dh_auto_build -- SFX=-sse4.1 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-sse4.1 STARlong-sse4.1 && dh_auto_clean ; dh_auto_build -- SFX=-ssse3 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-ssse3 STARlong-ssse3 && dh_auto_clean ; dh_auto_build -- SFX=-sse3 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-sse3 STARlong-sse3 && true cd source && make -j1 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j1 INSTALL="install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc SFX=-avx2 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-avx2 STARlong-avx2 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list x86_64-linux-gnu-g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list x86_64-linux-gnu-g++: warning: parametersDefault.xxd: linker input file unused because linking not done x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' systemFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' funPrimaryAlignMark.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_collapseUMI_Graph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_collapseUMIall.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersClip_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipMate_clip.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipCR4.cpp cd opal && \ x86_64-linux-gnu-g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 opal.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipMate_clipChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipMate_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_loadRawMatrix.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_emptyDrops_CR.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' soloInputFeatureUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_countSmartSeq.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_redistributeReadsByCB.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_quantTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_sumThreads.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_countVelocyto.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_countCBgeneUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_classifyAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_cellFiltering.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_statsOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' bamSortByCoordinate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersSolo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloRead_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadBarcode_getCBandUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloBarcode_extractBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadFeature_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadFeature_inputRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Solo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_outputResults.cpp SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool, std::string)’: SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of ‘char* getcwd(char*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_processRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_addBAMtags.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_convertGenomeCigar.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' twoPassRunPass1.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' samHeaders.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_genomeLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_genomeOutLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph_swScoreSpliced.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph_swTraceBack.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph_findSuperTr.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjAlignSplit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' GTF.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' GTF_transcriptGeneSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' GTF_superTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SuperTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputAlignments.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' STAR.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:225:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 225 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:230:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 230 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SharedMemory.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' PackedArray.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SuffixArrayFuns.cpp SuffixArrayFuns.cpp: In function ‘long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)’: SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 18 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function ‘long long unsigned int compareSeqToGenome1(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, long long unsigned int, int&)’: SuffixArrayFuns.cpp:234:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 234 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function ‘long long unsigned int funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, int&)’: SuffixArrayFuns.cpp:359:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 359 | register uint saind=0; | ^~~~~ SuffixArrayFuns.cpp:362:26: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register uint128 g1=*( (uint128*) (gSeq+SAstr) ); | ^~ SuffixArrayFuns.cpp:365:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 365 | register char g2=(char) g1; | ^~ SuffixArrayFuns.cpp:379:26: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 379 | register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) ); | ^~ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters_samAttributes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' InOutStreams.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SequenceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Stats.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_alignScore.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_generateCigarP.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Chain.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_variationAdjust.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Variation.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_waspMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_storeAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_stitchPieces.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_multMapSelect.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_mapOneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' readLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlignChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlignChunk_processChunks.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlignChunk_mapChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' OutSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' outputSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' blocksOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ThreadControl.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sysRemoveDir.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_maxMappableLength2strands.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' binarySearch2.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputTranscriptSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputTranscriptSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_assignAlignToWindow.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_oneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_stitchWindowSeeds.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_peOverlapMergeMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_mappedFilter.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersChimeric_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetectionOld.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericDetection_chimericDetectionMult.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' stitchWindowAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' extendAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' stitchAlignToTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericAlign_chimericJunctionOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericAlign_chimericBAMoutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericAlign_chimericStitching.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_genomeGenerate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' genomeParametersWrite.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' genomeScanFastaFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' genomeSAindex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_insertSequences.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' insertSeqSA.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' funCompareUintAndSuffixes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' funCompareUintAndSuffixesMemcmp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' TimeFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ErrorWarning.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' streamFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' stringSubstituteAll.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_quantAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_geneFullAlignOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_quantTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Quantifications.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_geneCountsAddAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbLoadFromFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbLoadFromStream.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbPrepare.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbBuildIndex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbInsertJunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' mapThreadsSpawn.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters_readFilesInit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters_readSAMheader.cpp Parameters_readSAMheader.cpp: In member function ‘void Parameters::readSAMheader(std::string, std::vector >)’: Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' bam_cat.c cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ bam_cat.c: In function ‘int bam_cat(int, char* const*, const bam_hdr_t*, const char*)’: bam_cat.c:80:25: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' serviceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMoutput.cpp BAMoutput.cpp: In member function ‘void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)’: BAMoutput.cpp:59:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function ‘void BAMoutput::unsortedFlush()’: BAMoutput.cpp:72:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMfunctions.cpp BAMfunctions.cpp: In function ‘void outBAMwriteHeader(BGZF*, const std::string&, const std::vector >&, const std::vector&)’: BAMfunctions.cpp:78:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 78 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ BAMfunctions.cpp:80:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:81:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | bgzf_write(fp,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:83:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 83 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:88:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 88 | bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 89 | bgzf_write(fp,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:91:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 91 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_alignBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMbinSortByCoordinate.cpp BAMbinSortByCoordinate.cpp: In function ‘void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)’: BAMbinSortByCoordinate.cpp:73:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 73 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 76 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' signalFromBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' bamRemoveDuplicates.cpp bamRemoveDuplicates.cpp: In function ‘void bamRemoveDuplicates(std::string, std::string, Parameters&)’: bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 269 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMbinSortUnmapped.cpp BAMbinSortUnmapped.cpp: In function ‘void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)’: BAMbinSortUnmapped.cpp:62:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 62 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:80:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ x86_64-linux-gnu-g++ -o STAR-avx2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-g++ -o STARlong-avx2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j1 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j1 INSTALL="install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc SFX=-avx CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-avx STARlong-avx make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list x86_64-linux-gnu-g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list x86_64-linux-gnu-g++: warning: parametersDefault.xxd: linker input file unused because linking not done x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' systemFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' funPrimaryAlignMark.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_collapseUMI_Graph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_collapseUMIall.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersClip_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipMate_clip.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipCR4.cpp cd opal && \ x86_64-linux-gnu-g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx opal.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipMate_clipChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipMate_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_loadRawMatrix.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_emptyDrops_CR.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' soloInputFeatureUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_countSmartSeq.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_redistributeReadsByCB.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_quantTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_sumThreads.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_countVelocyto.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_countCBgeneUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_classifyAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_cellFiltering.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_statsOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' bamSortByCoordinate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersSolo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloRead_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadBarcode_getCBandUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloBarcode_extractBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadFeature_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadFeature_inputRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Solo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_outputResults.cpp SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool, std::string)’: SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of ‘char* getcwd(char*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_processRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_addBAMtags.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_convertGenomeCigar.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' twoPassRunPass1.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' samHeaders.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_genomeLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_genomeOutLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph_swScoreSpliced.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph_swTraceBack.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph_findSuperTr.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjAlignSplit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' GTF.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' GTF_transcriptGeneSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' GTF_superTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SuperTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputAlignments.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' STAR.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:225:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 225 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:230:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 230 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SharedMemory.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' PackedArray.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SuffixArrayFuns.cpp SuffixArrayFuns.cpp: In function ‘long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)’: SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 18 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function ‘long long unsigned int compareSeqToGenome1(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, long long unsigned int, int&)’: SuffixArrayFuns.cpp:234:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 234 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function ‘long long unsigned int funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, int&)’: SuffixArrayFuns.cpp:359:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 359 | register uint saind=0; | ^~~~~ SuffixArrayFuns.cpp:362:26: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register uint128 g1=*( (uint128*) (gSeq+SAstr) ); | ^~ SuffixArrayFuns.cpp:365:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 365 | register char g2=(char) g1; | ^~ SuffixArrayFuns.cpp:379:26: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 379 | register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) ); | ^~ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters_samAttributes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' InOutStreams.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SequenceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Stats.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_alignScore.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_generateCigarP.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Chain.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_variationAdjust.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Variation.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_waspMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_storeAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_stitchPieces.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_multMapSelect.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_mapOneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' readLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlignChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlignChunk_processChunks.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlignChunk_mapChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' OutSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' outputSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' blocksOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ThreadControl.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sysRemoveDir.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_maxMappableLength2strands.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' binarySearch2.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputTranscriptSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputTranscriptSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_assignAlignToWindow.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_oneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_stitchWindowSeeds.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_peOverlapMergeMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_mappedFilter.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersChimeric_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetectionOld.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericDetection_chimericDetectionMult.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' stitchWindowAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' extendAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' stitchAlignToTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericAlign_chimericJunctionOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericAlign_chimericBAMoutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericAlign_chimericStitching.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_genomeGenerate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' genomeParametersWrite.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' genomeScanFastaFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' genomeSAindex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_insertSequences.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' insertSeqSA.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' funCompareUintAndSuffixes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' funCompareUintAndSuffixesMemcmp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' TimeFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ErrorWarning.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' streamFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' stringSubstituteAll.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_quantAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_geneFullAlignOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_quantTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Quantifications.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_geneCountsAddAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbLoadFromFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbLoadFromStream.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbPrepare.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbBuildIndex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbInsertJunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' mapThreadsSpawn.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters_readFilesInit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters_readSAMheader.cpp Parameters_readSAMheader.cpp: In member function ‘void Parameters::readSAMheader(std::string, std::vector >)’: Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' bam_cat.c cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ bam_cat.c: In function ‘int bam_cat(int, char* const*, const bam_hdr_t*, const char*)’: bam_cat.c:80:25: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' serviceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMoutput.cpp BAMoutput.cpp: In member function ‘void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)’: BAMoutput.cpp:59:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function ‘void BAMoutput::unsortedFlush()’: BAMoutput.cpp:72:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMfunctions.cpp BAMfunctions.cpp: In function ‘void outBAMwriteHeader(BGZF*, const std::string&, const std::vector >&, const std::vector&)’: BAMfunctions.cpp:78:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 78 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ BAMfunctions.cpp:80:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:81:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | bgzf_write(fp,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:83:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 83 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:88:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 88 | bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 89 | bgzf_write(fp,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:91:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 91 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_alignBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMbinSortByCoordinate.cpp BAMbinSortByCoordinate.cpp: In function ‘void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)’: BAMbinSortByCoordinate.cpp:73:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 73 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 76 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' signalFromBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' bamRemoveDuplicates.cpp bamRemoveDuplicates.cpp: In function ‘void bamRemoveDuplicates(std::string, std::string, Parameters&)’: bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 269 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMbinSortUnmapped.cpp BAMbinSortUnmapped.cpp: In function ‘void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)’: BAMbinSortUnmapped.cpp:62:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 62 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:80:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ x86_64-linux-gnu-g++ -o STAR-avx -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-g++ -o STARlong-avx -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j1 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j1 INSTALL="install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc SFX=-sse4.1 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-sse4.1 STARlong-sse4.1 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list x86_64-linux-gnu-g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list x86_64-linux-gnu-g++: warning: parametersDefault.xxd: linker input file unused because linking not done x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' systemFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' funPrimaryAlignMark.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_collapseUMI_Graph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_collapseUMIall.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersClip_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipMate_clip.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipCR4.cpp cd opal && \ x86_64-linux-gnu-g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 opal.cpp opal.cpp: In static member function ‘static __mxxxi SimdSW::add(const __mxxxi&, const __mxxxi&)’: opal.cpp:103:67: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 103 | static inline __mxxxi add(const __mxxxi& a, const __mxxxi& b) { return _mmxxx_adds_epi8(a, b); } | ^ In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:303:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 303 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipMate_clipChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipMate_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_loadRawMatrix.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_emptyDrops_CR.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' soloInputFeatureUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_countSmartSeq.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_redistributeReadsByCB.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_quantTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_sumThreads.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_countVelocyto.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_countCBgeneUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_classifyAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_cellFiltering.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_statsOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' bamSortByCoordinate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersSolo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloRead_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadBarcode_getCBandUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloBarcode_extractBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadFeature_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadFeature_inputRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Solo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_outputResults.cpp SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool, std::string)’: SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of ‘char* getcwd(char*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_processRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_addBAMtags.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_convertGenomeCigar.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' twoPassRunPass1.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' samHeaders.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_genomeLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_genomeOutLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph_swScoreSpliced.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph_swTraceBack.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph_findSuperTr.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjAlignSplit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' GTF.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' GTF_transcriptGeneSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' GTF_superTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SuperTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputAlignments.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' STAR.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:225:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 225 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:230:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 230 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SharedMemory.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' PackedArray.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SuffixArrayFuns.cpp SuffixArrayFuns.cpp: In function ‘long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)’: SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 18 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function ‘long long unsigned int compareSeqToGenome1(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, long long unsigned int, int&)’: SuffixArrayFuns.cpp:234:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 234 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function ‘long long unsigned int funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, int&)’: SuffixArrayFuns.cpp:359:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 359 | register uint saind=0; | ^~~~~ SuffixArrayFuns.cpp:362:26: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register uint128 g1=*( (uint128*) (gSeq+SAstr) ); | ^~ SuffixArrayFuns.cpp:365:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 365 | register char g2=(char) g1; | ^~ SuffixArrayFuns.cpp:379:26: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 379 | register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) ); | ^~ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters_samAttributes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' InOutStreams.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SequenceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Stats.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_alignScore.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_generateCigarP.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Chain.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_variationAdjust.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Variation.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_waspMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_storeAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_stitchPieces.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_multMapSelect.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_mapOneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' readLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlignChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlignChunk_processChunks.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlignChunk_mapChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' OutSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' outputSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' blocksOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ThreadControl.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sysRemoveDir.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_maxMappableLength2strands.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' binarySearch2.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputTranscriptSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputTranscriptSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_assignAlignToWindow.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_oneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_stitchWindowSeeds.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_peOverlapMergeMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_mappedFilter.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersChimeric_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetectionOld.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericDetection_chimericDetectionMult.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' stitchWindowAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' extendAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' stitchAlignToTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericAlign_chimericJunctionOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericAlign_chimericBAMoutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericAlign_chimericStitching.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_genomeGenerate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' genomeParametersWrite.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' genomeScanFastaFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' genomeSAindex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_insertSequences.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' insertSeqSA.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' funCompareUintAndSuffixes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' funCompareUintAndSuffixesMemcmp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' TimeFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ErrorWarning.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' streamFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' stringSubstituteAll.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_quantAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_geneFullAlignOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_quantTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Quantifications.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_geneCountsAddAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbLoadFromFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbLoadFromStream.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbPrepare.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbBuildIndex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbInsertJunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' mapThreadsSpawn.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters_readFilesInit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters_readSAMheader.cpp Parameters_readSAMheader.cpp: In member function ‘void Parameters::readSAMheader(std::string, std::vector >)’: Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' bam_cat.c cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ bam_cat.c: In function ‘int bam_cat(int, char* const*, const bam_hdr_t*, const char*)’: bam_cat.c:80:25: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' serviceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMoutput.cpp BAMoutput.cpp: In member function ‘void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)’: BAMoutput.cpp:59:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function ‘void BAMoutput::unsortedFlush()’: BAMoutput.cpp:72:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMfunctions.cpp BAMfunctions.cpp: In function ‘void outBAMwriteHeader(BGZF*, const std::string&, const std::vector >&, const std::vector&)’: BAMfunctions.cpp:78:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 78 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ BAMfunctions.cpp:80:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:81:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | bgzf_write(fp,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:83:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 83 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:88:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 88 | bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 89 | bgzf_write(fp,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:91:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 91 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_alignBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMbinSortByCoordinate.cpp BAMbinSortByCoordinate.cpp: In function ‘void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)’: BAMbinSortByCoordinate.cpp:73:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 73 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 76 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' signalFromBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' bamRemoveDuplicates.cpp bamRemoveDuplicates.cpp: In function ‘void bamRemoveDuplicates(std::string, std::string, Parameters&)’: bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 269 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMbinSortUnmapped.cpp BAMbinSortUnmapped.cpp: In function ‘void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)’: BAMbinSortUnmapped.cpp:62:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 62 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:80:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ x86_64-linux-gnu-g++ -o STAR-sse4.1 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-g++ -o STARlong-sse4.1 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j1 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j1 INSTALL="install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc SFX=-ssse3 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-ssse3 STARlong-ssse3 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list x86_64-linux-gnu-g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list x86_64-linux-gnu-g++: warning: parametersDefault.xxd: linker input file unused because linking not done x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' systemFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' funPrimaryAlignMark.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_collapseUMI_Graph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_collapseUMIall.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersClip_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipMate_clip.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipCR4.cpp cd opal && \ x86_64-linux-gnu-g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 opal.cpp opal.cpp: In static member function ‘static __mxxxi SimdSW::add(const __mxxxi&, const __mxxxi&)’: opal.cpp:103:67: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 103 | static inline __mxxxi add(const __mxxxi& a, const __mxxxi& b) { return _mmxxx_adds_epi8(a, b); } | ^ In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:303:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 303 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipMate_clipChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipMate_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_loadRawMatrix.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_emptyDrops_CR.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' soloInputFeatureUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_countSmartSeq.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_redistributeReadsByCB.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_quantTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_sumThreads.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_countVelocyto.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_countCBgeneUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_classifyAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_cellFiltering.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_statsOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' bamSortByCoordinate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersSolo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloRead_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadBarcode_getCBandUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloBarcode_extractBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadFeature_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadFeature_inputRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Solo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_outputResults.cpp SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool, std::string)’: SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of ‘char* getcwd(char*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_processRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_addBAMtags.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_convertGenomeCigar.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' twoPassRunPass1.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' samHeaders.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_genomeLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_genomeOutLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph_swScoreSpliced.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph_swTraceBack.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph_findSuperTr.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjAlignSplit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' GTF.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' GTF_transcriptGeneSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' GTF_superTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SuperTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputAlignments.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' STAR.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:225:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 225 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:230:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 230 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SharedMemory.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' PackedArray.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SuffixArrayFuns.cpp SuffixArrayFuns.cpp: In function ‘long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)’: SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 18 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function ‘long long unsigned int compareSeqToGenome1(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, long long unsigned int, int&)’: SuffixArrayFuns.cpp:234:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 234 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function ‘long long unsigned int funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, int&)’: SuffixArrayFuns.cpp:359:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 359 | register uint saind=0; | ^~~~~ SuffixArrayFuns.cpp:362:26: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register uint128 g1=*( (uint128*) (gSeq+SAstr) ); | ^~ SuffixArrayFuns.cpp:365:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 365 | register char g2=(char) g1; | ^~ SuffixArrayFuns.cpp:379:26: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 379 | register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) ); | ^~ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters_samAttributes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' InOutStreams.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SequenceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Stats.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_alignScore.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_generateCigarP.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Chain.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_variationAdjust.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Variation.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_waspMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_storeAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_stitchPieces.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_multMapSelect.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_mapOneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' readLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlignChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlignChunk_processChunks.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlignChunk_mapChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' OutSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' outputSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' blocksOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ThreadControl.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sysRemoveDir.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_maxMappableLength2strands.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' binarySearch2.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputTranscriptSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputTranscriptSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_assignAlignToWindow.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_oneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_stitchWindowSeeds.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_peOverlapMergeMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_mappedFilter.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersChimeric_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetectionOld.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericDetection_chimericDetectionMult.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' stitchWindowAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' extendAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' stitchAlignToTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericAlign_chimericJunctionOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericAlign_chimericBAMoutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericAlign_chimericStitching.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_genomeGenerate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' genomeParametersWrite.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' genomeScanFastaFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' genomeSAindex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_insertSequences.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' insertSeqSA.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' funCompareUintAndSuffixes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' funCompareUintAndSuffixesMemcmp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' TimeFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ErrorWarning.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' streamFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' stringSubstituteAll.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_quantAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_geneFullAlignOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_quantTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Quantifications.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_geneCountsAddAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbLoadFromFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbLoadFromStream.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbPrepare.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbBuildIndex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbInsertJunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' mapThreadsSpawn.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters_readFilesInit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters_readSAMheader.cpp Parameters_readSAMheader.cpp: In member function ‘void Parameters::readSAMheader(std::string, std::vector >)’: Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' bam_cat.c cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ bam_cat.c: In function ‘int bam_cat(int, char* const*, const bam_hdr_t*, const char*)’: bam_cat.c:80:25: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' serviceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMoutput.cpp BAMoutput.cpp: In member function ‘void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)’: BAMoutput.cpp:59:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function ‘void BAMoutput::unsortedFlush()’: BAMoutput.cpp:72:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMfunctions.cpp BAMfunctions.cpp: In function ‘void outBAMwriteHeader(BGZF*, const std::string&, const std::vector >&, const std::vector&)’: BAMfunctions.cpp:78:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 78 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ BAMfunctions.cpp:80:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:81:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | bgzf_write(fp,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:83:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 83 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:88:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 88 | bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 89 | bgzf_write(fp,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:91:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 91 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_alignBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMbinSortByCoordinate.cpp BAMbinSortByCoordinate.cpp: In function ‘void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)’: BAMbinSortByCoordinate.cpp:73:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 73 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 76 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' signalFromBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' bamRemoveDuplicates.cpp bamRemoveDuplicates.cpp: In function ‘void bamRemoveDuplicates(std::string, std::string, Parameters&)’: bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 269 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMbinSortUnmapped.cpp BAMbinSortUnmapped.cpp: In function ‘void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)’: BAMbinSortUnmapped.cpp:62:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 62 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:80:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ x86_64-linux-gnu-g++ -o STAR-ssse3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-g++ -o STARlong-ssse3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j1 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j1 INSTALL="install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc SFX=-sse3 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-sse3 STARlong-sse3 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list x86_64-linux-gnu-g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list x86_64-linux-gnu-g++: warning: parametersDefault.xxd: linker input file unused because linking not done x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' systemFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' funPrimaryAlignMark.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_collapseUMI_Graph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_collapseUMIall.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersClip_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipMate_clip.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipCR4.cpp cd opal && \ x86_64-linux-gnu-g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 opal.cpp opal.cpp: In static member function ‘static __mxxxi SimdSW::add(const __mxxxi&, const __mxxxi&)’: opal.cpp:103:67: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 103 | static inline __mxxxi add(const __mxxxi& a, const __mxxxi& b) { return _mmxxx_adds_epi8(a, b); } | ^ In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:303:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 303 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipMate_clipChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipMate_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_loadRawMatrix.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_emptyDrops_CR.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' soloInputFeatureUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_countSmartSeq.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_redistributeReadsByCB.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_quantTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_sumThreads.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_countVelocyto.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_countCBgeneUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_classifyAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_cellFiltering.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_statsOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' bamSortByCoordinate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersSolo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloRead_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadBarcode_getCBandUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloBarcode_extractBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadFeature_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadFeature_inputRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Solo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_outputResults.cpp SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool, std::string)’: SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of ‘char* getcwd(char*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_processRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_addBAMtags.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_convertGenomeCigar.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' twoPassRunPass1.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' samHeaders.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_genomeLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_genomeOutLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph_swScoreSpliced.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph_swTraceBack.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph_findSuperTr.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjAlignSplit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' GTF.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' GTF_transcriptGeneSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' GTF_superTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SuperTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputAlignments.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' STAR.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:225:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 225 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:230:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 230 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SharedMemory.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' PackedArray.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SuffixArrayFuns.cpp SuffixArrayFuns.cpp: In function ‘long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)’: SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 18 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function ‘long long unsigned int compareSeqToGenome1(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, long long unsigned int, int&)’: SuffixArrayFuns.cpp:234:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 234 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function ‘long long unsigned int funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, int&)’: SuffixArrayFuns.cpp:359:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 359 | register uint saind=0; | ^~~~~ SuffixArrayFuns.cpp:362:26: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register uint128 g1=*( (uint128*) (gSeq+SAstr) ); | ^~ SuffixArrayFuns.cpp:365:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 365 | register char g2=(char) g1; | ^~ SuffixArrayFuns.cpp:379:26: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 379 | register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) ); | ^~ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters_samAttributes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' InOutStreams.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SequenceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Stats.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_alignScore.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_generateCigarP.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Chain.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_variationAdjust.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Variation.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_waspMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_storeAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_stitchPieces.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_multMapSelect.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_mapOneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' readLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlignChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlignChunk_processChunks.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlignChunk_mapChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' OutSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' outputSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' blocksOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ThreadControl.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sysRemoveDir.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_maxMappableLength2strands.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' binarySearch2.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputTranscriptSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputTranscriptSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_assignAlignToWindow.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_oneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_stitchWindowSeeds.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_peOverlapMergeMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_mappedFilter.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersChimeric_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetectionOld.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericDetection_chimericDetectionMult.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' stitchWindowAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' extendAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' stitchAlignToTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericAlign_chimericJunctionOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericAlign_chimericBAMoutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericAlign_chimericStitching.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_genomeGenerate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' genomeParametersWrite.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' genomeScanFastaFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' genomeSAindex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_insertSequences.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' insertSeqSA.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' funCompareUintAndSuffixes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' funCompareUintAndSuffixesMemcmp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' TimeFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ErrorWarning.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' streamFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' stringSubstituteAll.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_quantAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_geneFullAlignOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_quantTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Quantifications.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_geneCountsAddAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbLoadFromFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbLoadFromStream.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbPrepare.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbBuildIndex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbInsertJunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' mapThreadsSpawn.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters_readFilesInit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters_readSAMheader.cpp Parameters_readSAMheader.cpp: In member function ‘void Parameters::readSAMheader(std::string, std::vector >)’: Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' bam_cat.c cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ bam_cat.c: In function ‘int bam_cat(int, char* const*, const bam_hdr_t*, const char*)’: bam_cat.c:80:25: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' serviceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMoutput.cpp BAMoutput.cpp: In member function ‘void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)’: BAMoutput.cpp:59:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function ‘void BAMoutput::unsortedFlush()’: BAMoutput.cpp:72:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMfunctions.cpp BAMfunctions.cpp: In function ‘void outBAMwriteHeader(BGZF*, const std::string&, const std::vector >&, const std::vector&)’: BAMfunctions.cpp:78:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 78 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ BAMfunctions.cpp:80:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:81:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | bgzf_write(fp,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:83:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 83 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:88:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 88 | bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 89 | bgzf_write(fp,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:91:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 91 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_alignBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMbinSortByCoordinate.cpp BAMbinSortByCoordinate.cpp: In function ‘void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)’: BAMbinSortByCoordinate.cpp:73:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 73 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 76 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' signalFromBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' bamRemoveDuplicates.cpp bamRemoveDuplicates.cpp: In function ‘void bamRemoveDuplicates(std::string, std::string, Parameters&)’: bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 269 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMbinSortUnmapped.cpp BAMbinSortUnmapped.cpp: In function ‘void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)’: BAMbinSortUnmapped.cpp:62:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 62 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:80:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ x86_64-linux-gnu-g++ -o STAR-sse3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-g++ -o STARlong-sse3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' dh_auto_clean ; dh_auto_build -- SFX=-plain CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-plain STARlong-plain cd source && make -j1 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j1 INSTALL="install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc SFX=-plain CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-plain STARlong-plain make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list x86_64-linux-gnu-g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list x86_64-linux-gnu-g++: warning: parametersDefault.xxd: linker input file unused because linking not done x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' systemFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' funPrimaryAlignMark.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_collapseUMI_Graph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_collapseUMIall.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersClip_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipMate_clip.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipCR4.cpp cd opal && \ x86_64-linux-gnu-g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 opal.cpp opal.cpp: In static member function ‘static __mxxxi SimdSW::add(const __mxxxi&, const __mxxxi&)’: opal.cpp:103:67: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 103 | static inline __mxxxi add(const __mxxxi& a, const __mxxxi& b) { return _mmxxx_adds_epi8(a, b); } | ^ In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:303:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 303 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipMate_clipChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ClipMate_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_loadRawMatrix.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_emptyDrops_CR.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' soloInputFeatureUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_countSmartSeq.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_redistributeReadsByCB.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_quantTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_sumThreads.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_countVelocyto.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_countCBgeneUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_classifyAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_cellFiltering.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_statsOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' bamSortByCoordinate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersSolo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloRead_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadBarcode_getCBandUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloBarcode_extractBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadFeature_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloReadFeature_inputRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Solo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_outputResults.cpp SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool, std::string)’: SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of ‘char* getcwd(char*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_processRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SoloFeature_addBAMtags.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_convertGenomeCigar.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' twoPassRunPass1.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' samHeaders.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_genomeLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_genomeOutLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph_swScoreSpliced.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph_swTraceBack.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SpliceGraph_findSuperTr.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjAlignSplit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' GTF.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' GTF_transcriptGeneSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' GTF_superTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SuperTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputAlignments.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' STAR.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:225:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 225 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:230:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 230 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SharedMemory.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' PackedArray.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SuffixArrayFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters_samAttributes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' InOutStreams.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' SequenceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Stats.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_alignScore.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_generateCigarP.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Chain.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcript_variationAdjust.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Variation.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_waspMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_storeAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_stitchPieces.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_multMapSelect.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_mapOneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' readLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlignChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlignChunk_processChunks.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlignChunk_mapChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' OutSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' outputSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' blocksOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ThreadControl.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sysRemoveDir.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_maxMappableLength2strands.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' binarySearch2.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputTranscriptSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputTranscriptSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_assignAlignToWindow.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_oneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_stitchWindowSeeds.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_peOverlapMergeMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_mappedFilter.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ParametersChimeric_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetectionOld.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericDetection_chimericDetectionMult.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' stitchWindowAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' extendAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' stitchAlignToTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericAlign_chimericJunctionOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericAlign_chimericBAMoutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ChimericAlign_chimericStitching.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_genomeGenerate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' genomeParametersWrite.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' genomeScanFastaFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' genomeSAindex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Genome_insertSequences.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' insertSeqSA.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' funCompareUintAndSuffixes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' funCompareUintAndSuffixesMemcmp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' TimeFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ErrorWarning.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' streamFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' stringSubstituteAll.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_quantAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_geneFullAlignOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_quantTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Quantifications.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Transcriptome_geneCountsAddAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbLoadFromFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbLoadFromStream.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbPrepare.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbBuildIndex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' sjdbInsertJunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' mapThreadsSpawn.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters_readFilesInit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' Parameters_readSAMheader.cpp Parameters_readSAMheader.cpp: In member function ‘void Parameters::readSAMheader(std::string, std::vector >)’: Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' bam_cat.c cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ bam_cat.c: In function ‘int bam_cat(int, char* const*, const bam_hdr_t*, const char*)’: bam_cat.c:80:25: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' serviceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMoutput.cpp BAMoutput.cpp: In member function ‘void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)’: BAMoutput.cpp:59:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function ‘void BAMoutput::unsortedFlush()’: BAMoutput.cpp:72:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMfunctions.cpp BAMfunctions.cpp: In function ‘void outBAMwriteHeader(BGZF*, const std::string&, const std::vector >&, const std::vector&)’: BAMfunctions.cpp:78:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 78 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ BAMfunctions.cpp:80:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:81:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | bgzf_write(fp,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:83:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 83 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:88:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 88 | bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 89 | bgzf_write(fp,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:91:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 91 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' ReadAlign_alignBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMbinSortByCoordinate.cpp BAMbinSortByCoordinate.cpp: In function ‘void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)’: BAMbinSortByCoordinate.cpp:73:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 73 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 76 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' signalFromBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' bamRemoveDuplicates.cpp bamRemoveDuplicates.cpp: In function ‘void bamRemoveDuplicates(std::string, std::string, Parameters&)’: bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 269 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' BAMbinSortUnmapped.cpp BAMbinSortUnmapped.cpp: In function ‘void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)’: BAMbinSortUnmapped.cpp:62:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 62 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:80:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ x86_64-linux-gnu-g++ -o STAR-plain -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now In function ‘min’: lto1: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] lto-wrapper: warning: using serial compilation of 22 LTRANS jobs lto-wrapper: note: see the ‘-flto’ option documentation for more information opal/opal.cpp: In function ‘min’: opal/opal.cpp:756:29: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 756 | minF = SIMD::min(minF, F); // For overflow detection | ^ x86_64-linux-gnu-g++ -o STARlong-plain -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2026-08-21T05:16:37+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILE_FOR_LONG_READS' -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now Transcript.h:10:7: warning: type ‘struct Transcript’ violates the C++ One Definition Rule [-Wodr] 10 | class Transcript { | ^ Transcript.h:10:7: note: a different type is defined in another translation unit 10 | class Transcript { | ^ Transcript.h:12:10: note: the first difference of corresponding definitions is field ‘exons’ 12 | uint exons[MAX_N_EXONS][EX_SIZE]; //coordinates of all exons: r-start, g-start, length | ^ Transcript.h:12:10: note: a field of same name but different type is defined in another translation unit 12 | uint exons[MAX_N_EXONS][EX_SIZE]; //coordinates of all exons: r-start, g-start, length | ^ Transcript.h:10:7: note: array types have different bounds 10 | class Transcript { | ^ ReadAlign.h:22:7: warning: type ‘struct ReadAlign’ violates the C++ One Definition Rule [-Wodr] 22 | class ReadAlign { | ^ ReadAlign.h:22:7: note: a different type is defined in another translation unit 22 | class ReadAlign { | ^ ReadAlign.h:57:20: note: the first difference of corresponding definitions is field ‘trA’ 57 | Transcript trA, trA1, *trInit; //transcript, best tr, next best tr, initialized tr | ^ ReadAlign.h:57:20: note: a field of same name but different type is defined in another translation unit 57 | Transcript trA, trA1, *trInit; //transcript, best tr, next best tr, initialized tr | ^ Transcript.h:10:7: note: type ‘struct Transcript’ itself violates the C++ One Definition Rule 10 | class Transcript { | ^ ReadAlign.h:214:14: warning: type of ‘calcCIGAR’ does not match original declaration [-Wlto-type-mismatch] 214 | void calcCIGAR(Transcript const &trOut, uint nMates, uint iExMate, uint leftMate); | ^ ReadAlign_calcCIGAR.cpp:3:6: note: ‘calcCIGAR’ was previously declared here 3 | void ReadAlign::calcCIGAR(Transcript const &trOut, uint nMates, uint iExMate, uint leftMate) { | ^ In function ‘min’: lto1: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] lto-wrapper: warning: using serial compilation of 22 LTRANS jobs lto-wrapper: note: see the ‘-flto’ option documentation for more information opal/opal.cpp: In function ‘min’: opal/opal.cpp:756:29: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 756 | minF = SIMD::min(minF, F); // For overflow detection | ^ make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cp source/STAR-plain source/STARlong-plain /build/reproducible-path/rna-star-2.7.11b+dfsg/debian/rna-star/usr/lib/rna-star/bin/ make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--sourcedirectory=source dh_prep -a -O--sourcedirectory=source debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' mkdir --parents /build/reproducible-path/rna-star-2.7.11b+dfsg/debian/rna-star/usr/bin dh_install source/STAR-avx2 source/STARlong-avx2 /usr/lib/rna-star/bin && dh_install source/STAR-avx source/STARlong-avx /usr/lib/rna-star/bin && dh_install source/STAR-sse4.1 source/STARlong-sse4.1 /usr/lib/rna-star/bin && dh_install source/STAR-ssse3 source/STARlong-ssse3 /usr/lib/rna-star/bin && dh_install source/STAR-sse3 source/STARlong-sse3 /usr/lib/rna-star/bin && dh_install source/STAR-plain source/STARlong-plain /usr/lib/rna-star/bin && true dh_install debian/bin/simd-dispatch /usr/lib/rna-star/ set -e && cd /build/reproducible-path/rna-star-2.7.11b+dfsg/debian/rna-star/usr/bin && for prog in STAR STARlong ; do ln -s \ ../lib/rna-star/simd-dispatch ${prog} ; done make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' dh_installdocs -a -O--sourcedirectory=source dh_installchangelogs -a -O--sourcedirectory=source dh_installman -a -O--sourcedirectory=source dh_installsystemduser -a -O--sourcedirectory=source dh_perl -a -O--sourcedirectory=source dh_link -a -O--sourcedirectory=source dh_strip_nondeterminism -a -O--sourcedirectory=source debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' dh_fixperms -a -O--sourcedirectory=source dh_missing -a -O--sourcedirectory=source dh_dwz -a -O--sourcedirectory=source dh_strip -a -O--sourcedirectory=source dh_makeshlibs -a -O--sourcedirectory=source dh_shlibdeps -a -O--sourcedirectory=source dh_installdeb -a -O--sourcedirectory=source debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.4~rc3-5), " make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' dh_md5sums -a -O--sourcedirectory=source dh_builddeb -a -O--sourcedirectory=source dpkg-deb: building package 'rna-star' in '../rna-star_2.7.11b+dfsg-4_amd64.deb'. dpkg-deb: building package 'rna-star-dbgsym' in '../rna-star-dbgsym_2.7.11b+dfsg-4_amd64.deb'. dpkg-genbuildinfo --build=any -O../rna-star_2.7.11b+dfsg-4_amd64.buildinfo dpkg-genchanges --build=any -O../rna-star_2.7.11b+dfsg-4_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2026-10-15T21:51:03Z +------------------------------------------------------------------------------+ | Finished Timed Build Commands Thu, 15 Oct 2026 21:51:03 +0000 | +------------------------------------------------------------------------------+ rm -Rf /build/reproducible-path/rna-star-2.7.11b+dfsg/ ------------------------------------------------------ I: Finished running 'rm -Rf /build/reproducible-path/rna-star-2.7.11b+dfsg/'. Finished processing commands. -------------------------------------------------------------------------------- Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Thu, 15 Oct 2026 21:51:04 +0000 | +------------------------------------------------------------------------------+ rna-star_2.7.11b+dfsg-4_amd64.changes: -------------------------------------- Format: 1.8 Date: Fri, 21 Aug 2026 07:16:37 +0200 Source: rna-star Binary: rna-star rna-star-dbgsym Built-For-Profiles: cross nocheck Architecture: amd64 Version: 2.7.11b+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: rna-star - ultrafast universal RNA-seq aligner Changes: rna-star (2.7.11b+dfsg-4) unstable; urgency=medium . * Fix FTBFS on Hurd. Checksums-Sha1: 503ba9edc6a2a10ee63dcfa976fe7c7c2edd00f0 78331076 rna-star-dbgsym_2.7.11b+dfsg-4_amd64.deb 69ec5bf20be3ce77209ce6d22e18a4080a6018b5 6828 rna-star_2.7.11b+dfsg-4_amd64.buildinfo ba645bfe889d4dce9f796356468c2fd20da84126 4200408 rna-star_2.7.11b+dfsg-4_amd64.deb Checksums-Sha256: 2bc220a718bd7bf71a2187161a773af59a035b83cd2d9eccdc03ae94fd0848a1 78331076 rna-star-dbgsym_2.7.11b+dfsg-4_amd64.deb 8026fe91ff08a5637b80e9e784339c92537976eaf4ecb17c510f7b5fb6a3cd39 6828 rna-star_2.7.11b+dfsg-4_amd64.buildinfo 94ef69c1e7ca10b6bef3406ef5df51398eac5bee6dc8ccbb0bda8b3cdc2a2944 4200408 rna-star_2.7.11b+dfsg-4_amd64.deb Files: c91b0e6192eed398fec8ad5e81e018f8 78331076 debug optional rna-star-dbgsym_2.7.11b+dfsg-4_amd64.deb e319f9e386ae160977ca00a528d0cf6f 6828 science optional rna-star_2.7.11b+dfsg-4_amd64.buildinfo fe9f93c2ab292c80762fcfaf44f7d2a5 4200408 science optional rna-star_2.7.11b+dfsg-4_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Thu, 15 Oct 2026 21:51:06 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: rna-star Binary: rna-star rna-star-dbgsym Architecture: amd64 Version: 2.7.11b+dfsg-4 Checksums-Md5: c91b0e6192eed398fec8ad5e81e018f8 78331076 rna-star-dbgsym_2.7.11b+dfsg-4_amd64.deb fe9f93c2ab292c80762fcfaf44f7d2a5 4200408 rna-star_2.7.11b+dfsg-4_amd64.deb Checksums-Sha1: 503ba9edc6a2a10ee63dcfa976fe7c7c2edd00f0 78331076 rna-star-dbgsym_2.7.11b+dfsg-4_amd64.deb ba645bfe889d4dce9f796356468c2fd20da84126 4200408 rna-star_2.7.11b+dfsg-4_amd64.deb Checksums-Sha256: 2bc220a718bd7bf71a2187161a773af59a035b83cd2d9eccdc03ae94fd0848a1 78331076 rna-star-dbgsym_2.7.11b+dfsg-4_amd64.deb 94ef69c1e7ca10b6bef3406ef5df51398eac5bee6dc8ccbb0bda8b3cdc2a2944 4200408 rna-star_2.7.11b+dfsg-4_amd64.deb Build-Origin: Debian Build-Architecture: arm64 Build-Date: Thu, 15 Oct 2026 21:51:00 +0000 Build-Path: /build/reproducible-path/rna-star-2.7.11b+dfsg Installed-Build-Depends: architecture-properties (= 0.2.6+b2), autoconf (= 2.73-2), automake (= 1:1.19-2), autopoint (= 1.0-5), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8+b1), bash (= 5.3-4), binutils (= 2.47-6), binutils-aarch64-linux-gnu (= 2.47-6), binutils-common (= 2.47-6), bsdextrautils (= 2.42.4-1), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), comerr-dev (= 2.1-1.47.4-1+b2), coreutils (= 9.10-1), cpp (= 4:16.1.0-3), cpp-16 (= 16.2.0-3), cpp-16-aarch64-linux-gnu (= 16.2.0-3), cpp-aarch64-linux-gnu (= 4:16.1.0-3), dash (= 0.5.12-12+b1), debconf (= 1.5.92), debhelper (= 14.5), debianutils (= 5.24), dh-autoreconf (= 23), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1+b1), dpkg (= 1.23.11), dpkg-dev (= 1.23.11), dwz (= 0.17-1), file (= 1:5.47-4), findutils (= 4.11.0-3), g++ (= 4:16.1.0-3), g++-16 (= 16.2.0-3), g++-16-aarch64-linux-gnu (= 16.2.0-3), g++-aarch64-linux-gnu (= 4:16.1.0-3), gcc (= 4:16.1.0-3), gcc-16 (= 16.2.0-3), gcc-16-aarch64-linux-gnu (= 16.2.0-3), gcc-16-base (= 16.2.0-3), gcc-aarch64-linux-gnu (= 4:16.1.0-3), gettext (= 1.0-5), gettext-base (= 1.0-5), grep (= 3.12-1+b1), groff-base (= 1.24.2-2), gzip (= 1.14-1), hostname (= 3.25+b1), init-system-helpers (= 1.69+nmu3), intltool-debian (= 0.35.0+20060710.6), krb5-multidev (= 1.22.1-3), libacl1 (= 2.4.0-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 16.2.0-3), libatomic1 (= 16.2.0-3), libattr1 (= 1:2.6.0-1), libaudit-common (= 1:4.2.1-1), libaudit1 (= 1:4.2.1-1), libbinutils (= 2.47-6), libblkid1 (= 2.42.4-1), libbrotli-dev (= 1.2.0-4+b1), libbrotli1 (= 1.2.0-4+b1), libbz2-1.0 (= 1.0.8-6+b2), libbz2-dev (= 1.0.8-6+b2), libc-bin (= 2.43-7), libc-dev-bin (= 2.43-7), libc-gconv-modules-extra (= 2.43-7), libc6 (= 2.43-7), libc6-dev (= 2.43-7), libcap-ng0 (= 0.9.6-1), libcc1-0 (= 16.2.0-3), libcom-err2 (= 1.47.4-1+b2), libcrypt1 (= 1:4.5.2+20251210-1), libctf-nobfd0 (= 2.47-6), libctf0 (= 2.47-6), libcurl4-gnutls (= 8.23.0-1), libcurl4-gnutls-dev (= 8.23.0-1), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.5), libdeflate-dev (= 1.25-1), libdeflate0 (= 1.25-1), libdpkg-perl (= 1.23.11), libelf1t64 (= 0.196-1), libevent-2.1-7t64 (= 2.1.13-stable-1), libffi8 (= 3.8.0-2), libfile-stripnondeterminism-perl (= 1.15.1-1), libgcc-16-dev (= 16.2.0-3), libgcc-s1 (= 16.2.0-3), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgmp-dev (= 2:6.3.0+dfsg-5+b2), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgmpxx4ldbl (= 2:6.3.0+dfsg-5+b2), libgnutls-dane0t64 (= 3.8.13-1), libgnutls28-dev (= 3.8.13-1), libgnutls30t64 (= 3.8.13-1), libgomp1 (= 16.2.0-3), libgprofng0 (= 2.47-6), libgssapi-krb5-2 (= 1.22.1-3), libgssrpc4t64 (= 1.22.1-3), libhogweed6t64 (= 3.10.2-1+b1), libhts-dev (= 1.24-3), libhts3t64 (= 1.24-3), libhtscodecs2 (= 1.6.7-1), libhwasan0 (= 16.2.0-3), libidn2-0 (= 2.3.8-5), libidn2-dev (= 2.3.8-5), libisl23 (= 0.28-1), libitm1 (= 16.2.0-3), libjansson4 (= 2.15.1-1), libk5crypto3 (= 1.22.1-3), libkadm5clnt-mit12 (= 1.22.1-3), libkadm5srv-mit12 (= 1.22.1-3), libkdb5-10t64 (= 1.22.1-3), libkeyutils1 (= 1.6.3-6+b2), libkrb5-3 (= 1.22.1-3), libkrb5-dev (= 1.22.1-3), libkrb5support0 (= 1.22.1-3), libldap-dev (= 2.6.14+dfsg-2), libldap2 (= 2.6.14+dfsg-2), liblsan0 (= 16.2.0-3), liblzma-dev (= 5.8.4-1), liblzma5 (= 5.8.4-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.3.0-1), libmount1 (= 2.42.4-1), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libnettle8t64 (= 3.10.2-1+b1), libnghttp2-14 (= 1.70.0-1), libnghttp2-dev (= 1.70.0-1), libnghttp3-9 (= 1.17.0-1), libnghttp3-dev (= 1.17.0-1), libngtcp2-16 (= 1.24.0-1), libngtcp2-crypto-gnutls-dev (= 1.24.0-1), libngtcp2-crypto-gnutls8 (= 1.24.0-1), libngtcp2-dev (= 1.24.0-1), libp11-kit-dev (= 0.26.5-1), libp11-kit0 (= 0.26.5-1), libpam-modules (= 1.7.0-8), libpam-modules-bin (= 1.7.0-8), libpam-runtime (= 1.7.0-8), libpam0g (= 1.7.0-8), libpcre2-8-0 (= 10.48-3.1), libperl5.42 (= 5.42.3-1), libpipeline1 (= 1.5.8-3), libpkgconf7 (= 2.5.1-4), libpsl-dev (= 0.23.3-1), libpsl5t64 (= 0.23.3-1), libquadmath0 (= 16.2.0-3), librtmp-dev (= 2.6-1), librtmp1 (= 2.6-1), libsasl2-2 (= 2.1.28+dfsg1-11), libsasl2-modules-db (= 2.1.28+dfsg1-11), libseccomp2 (= 2.6.1-1+b1), libselinux1 (= 3.11-2.1), libsframe3 (= 2.47-6), libsimde-dev (= 0.8.4~rc3-5), libsmartcols1 (= 2.42.4-1), libssh2-1-dev (= 1.11.1-6), libssh2-1t64 (= 1.11.1-6), libssl-dev (= 3.6.5-1), libssl3t64 (= 3.6.5-1), libstdc++-16-dev (= 16.2.0-3), libstdc++6 (= 16.2.0-3), libsystemd0 (= 262-1), libtasn1-6 (= 4.21.0-2+b1), libtasn1-6-dev (= 4.21.0-2+b1), libtinfo6 (= 6.6+20260608-2), libtool (= 2.6.2-3), libtsan2 (= 16.2.0-3), libubsan1 (= 16.2.0-3), libuchardet0 (= 0.0.8-2+b2), libudev1 (= 262-1), libunbound8 (= 1.26.1-1), libunistring-dev (= 1.4.2-1), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.4-1), libxml2-16 (= 2.15.4+dfsg-1), libzstd-dev (= 1.5.7+dfsg-4), libzstd1 (= 1.5.7+dfsg-4), linux-libc-dev (= 7.2.10-1), m4 (= 1.4.21-1), make (= 4.4.1-3+b1), man-db (= 2.13.1-1+b1), mawk (= 1.3.4.20260302-2), ncurses-base (= 6.6+20260608-2), ncurses-bin (= 6.6+20260608-2), nettle-dev (= 3.10.2-1+b1), openssl-provider-legacy (= 3.6.5-1), patch (= 2.8-2+b1), perl (= 5.42.3-1), perl-base (= 5.42.3-1), perl-modules-5.42 (= 5.42.3-1), pkgconf (= 2.5.1-4), pkgconf-bin (= 2.5.1-4), po-debconf (= 1.0.22), sed (= 4.9-3), sensible-utils (= 0.0.26), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-6), util-linux (= 2.42.4-1), xxd (= 2:9.2.0858-1), xz-utils (= 5.8.4-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" SOURCE_DATE_EPOCH="1787289397" +------------------------------------------------------------------------------+ | Package contents Thu, 15 Oct 2026 21:51:06 +0000 | +------------------------------------------------------------------------------+ rna-star-dbgsym_2.7.11b+dfsg-4_amd64.deb ---------------------------------------- new Debian package, version 2.0. size 78331076 bytes: control archive=912 bytes. 636 bytes, 12 lines control 827 bytes, 8 lines md5sums Package: rna-star-dbgsym Source: rna-star Version: 2.7.11b+dfsg-4 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 79804 Depends: rna-star (= 2.7.11b+dfsg-4) Section: debug Priority: optional Description: debug symbols for rna-star Build-Ids: 2ccef8ae56f7a3d785eb58ce5d4054e570d5cdb9 3032930d047a2cafa57bed4aa26e7d1f9fcaefec 7633f537b8c4deb98fa121209a2ab86e84fd6bb4 78c5a1dc39f9ad53657f2dad32e685de88339f09 8f5aa2dba29960eed973258b965514ad9a70b6d2 9898536d5aee01a73781323d78c9f350fbbf7ef1 cd33c2893e8557b59eb450f20117996f102b723e drwxr-xr-x root/root 0 2026-08-21 05:16 ./ drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/ drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/lib/ drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/lib/debug/.build-id/2c/ -rw-r--r-- root/root 11368728 2026-08-21 05:16 ./usr/lib/debug/.build-id/2c/cef8ae56f7a3d785eb58ce5d4054e570d5cdb9.debug drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/lib/debug/.build-id/30/ -rw-r--r-- root/root 11273232 2026-08-21 05:16 ./usr/lib/debug/.build-id/30/32930d047a2cafa57bed4aa26e7d1f9fcaefec.debug drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/lib/debug/.build-id/76/ -rw-r--r-- root/root 11328472 2026-08-21 05:16 ./usr/lib/debug/.build-id/76/33f537b8c4deb98fa121209a2ab86e84fd6bb4.debug drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/lib/debug/.build-id/78/ -rw-r--r-- root/root 11267592 2026-08-21 05:16 ./usr/lib/debug/.build-id/78/c5a1dc39f9ad53657f2dad32e685de88339f09.debug drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/lib/debug/.build-id/8f/ -rw-r--r-- root/root 6677864 2026-08-21 05:16 ./usr/lib/debug/.build-id/8f/5aa2dba29960eed973258b965514ad9a70b6d2.debug drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/lib/debug/.build-id/98/ -rw-r--r-- root/root 6673648 2026-08-21 05:16 ./usr/lib/debug/.build-id/98/98536d5aee01a73781323d78c9f350fbbf7ef1.debug drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/lib/debug/.build-id/cd/ -rw-r--r-- root/root 11299784 2026-08-21 05:16 ./usr/lib/debug/.build-id/cd/33c2893e8557b59eb450f20117996f102b723e.debug drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 11807248 2026-08-21 05:16 ./usr/lib/debug/.dwz/x86_64-linux-gnu/rna-star.debug drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/share/ drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-08-21 05:16 ./usr/share/doc/rna-star-dbgsym -> rna-star rna-star_2.7.11b+dfsg-4_amd64.deb --------------------------------- new Debian package, version 2.0. size 4200408 bytes: control archive=1644 bytes. 1411 bytes, 25 lines control 1509 bytes, 22 lines md5sums Package: rna-star Version: 2.7.11b+dfsg-4 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 24265 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.3.1), libgomp1 (>= 6), libhts3t64 (>= 1.17), libstdc++6 (>= 14) Built-Using: simde (= 0.8.4~rc3-5) Section: science Priority: optional Homepage: https://github.com/alexdobin/STAR/ Description: ultrafast universal RNA-seq aligner Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, the authors experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. drwxr-xr-x root/root 0 2026-08-21 05:16 ./ drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/ drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/bin/ lrwxrwxrwx root/root 0 2026-08-21 05:16 ./usr/bin/STAR -> ../lib/rna-star/simd-dispatch lrwxrwxrwx root/root 0 2026-08-21 05:16 ./usr/bin/STARlong -> ../lib/rna-star/simd-dispatch drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/lib/ drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/lib/rna-star/ drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/lib/rna-star/bin/ -rwxr-xr-x root/root 2269928 2026-08-21 05:16 ./usr/lib/rna-star/bin/STAR-avx -rwxr-xr-x root/root 2253544 2026-08-21 05:16 ./usr/lib/rna-star/bin/STAR-avx2 -rwxr-xr-x root/root 1434312 2026-08-21 05:16 ./usr/lib/rna-star/bin/STAR-plain -rwxr-xr-x root/root 2085608 2026-08-21 05:16 ./usr/lib/rna-star/bin/STAR-sse3 -rwxr-xr-x root/root 2142952 2026-08-21 05:16 ./usr/lib/rna-star/bin/STAR-sse4.1 -rwxr-xr-x root/root 2089704 2026-08-21 05:16 ./usr/lib/rna-star/bin/STAR-ssse3 -rwxr-xr-x root/root 2269928 2026-08-21 05:16 ./usr/lib/rna-star/bin/STARlong-avx -rwxr-xr-x root/root 2253544 2026-08-21 05:16 ./usr/lib/rna-star/bin/STARlong-avx2 -rwxr-xr-x root/root 1434312 2026-08-21 05:16 ./usr/lib/rna-star/bin/STARlong-plain -rwxr-xr-x root/root 2085608 2026-08-21 05:16 ./usr/lib/rna-star/bin/STARlong-sse3 -rwxr-xr-x root/root 2142952 2026-08-21 05:16 ./usr/lib/rna-star/bin/STARlong-sse4.1 -rwxr-xr-x root/root 2089704 2026-08-21 05:16 ./usr/lib/rna-star/bin/STARlong-ssse3 -rwxr-xr-x root/root 380 2024-05-04 14:07 ./usr/lib/rna-star/simd-dispatch drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/share/ drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/share/doc-base/ -rw-r--r-- root/root 1179 2024-05-04 14:07 ./usr/share/doc-base/rna-star.rna-star drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/share/doc/rna-star/ -rw-r--r-- root/root 220 2024-05-04 14:07 ./usr/share/doc/rna-star/README.Debian -rw-r--r-- root/root 3547 2024-01-25 21:55 ./usr/share/doc/rna-star/README.md -rw-r--r-- root/root 7407 2024-01-25 21:55 ./usr/share/doc/rna-star/RELEASEnotes.md.gz -rw-r--r-- root/root 239211 2024-01-25 21:55 ./usr/share/doc/rna-star/STARmanual.pdf -rw-r--r-- root/root 765 2026-08-21 05:16 ./usr/share/doc/rna-star/changelog.Debian.gz -rw-r--r-- root/root 15091 2024-01-25 21:55 ./usr/share/doc/rna-star/changelog.gz -rw-r--r-- root/root 2600 2026-08-19 11:14 ./usr/share/doc/rna-star/copyright drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/share/man/ drwxr-xr-x root/root 0 2026-08-21 05:16 ./usr/share/man/man1/ -rw-r--r-- root/root 824 2026-08-21 05:16 ./usr/share/man/man1/STAR.1.gz lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:arm64 Filtered Build-Depends: lintian:arm64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/build/reproducible-path/resolver-8advCY/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/build/reproducible-path/resolver-8advCY/apt_archive ./ InRelease Get:2 copy:/build/reproducible-path/resolver-8advCY/apt_archive ./ Release [615 B] Ign:3 copy:/build/reproducible-path/resolver-8advCY/apt_archive ./ Release.gpg Get:4 copy:/build/reproducible-path/resolver-8advCY/apt_archive ./ Sources [1395 B] Get:5 copy:/build/reproducible-path/resolver-8advCY/apt_archive ./ Packages [1474 B] Fetched 3484 B in 0s (145 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: appstream ca-certificates diffstat distro-info-data gpg gpgconf iso-codes libaliased-perl libappstream5 libapt-pkg-perl libassuan9 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libbrotli1 libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libcom-err2 libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libcurl4-gnutls libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdistro-info-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libffi8 libfile-basedir-perl libfile-find-rule-perl libfile-libmagic-perl libfile-listing-perl libfile-sharedir-perl libfont-ttf-perl libfyaml0 libgcrypt20 libglib2.0-0t64 libgnutls30t64 libgpg-error0 libgssapi-krb5-2 libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libidn2-0 libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libio-string-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libksba8 libldap2 liblist-compare-perl liblist-someutils-perl liblist-someutils-xs-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libncursesw6 libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnpth0t64 libnumber-compare-perl libp11-kit0 libpackage-stash-perl libparams-classify-perl libparams-someutil-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libproc2-1 libpsl5t64 libreadline8t64 libregexp-wildcards-perl librole-tiny-perl libsasl2-2 libsasl2-modules-db libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libssh2-1t64 libstemmer0d libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libtasn1-6 libterm-readkey-perl libtext-charwidth-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-wrapi18n-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxmlb2 libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip procps readline-common shared-mime-info t1utils ucf unzip Suggested packages: apt-config-icons isoquery libxml-parser-perl rng-tools low-memory-monitor gnutls-bin krb5-doc krb5-user libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libmime-base32-perl libregexp-ipv6-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl python3 readline-doc zip Recommended packages: gnupg libcgi-fast-perl libglib2.0-data xdg-user-dirs libgpg-error-l10n libhtml-format-perl libio-compress-brotli-perl krb5-locales libldap-common libfreezethaw-perl libgpm2 libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl publicsuffix libsasl2-modules libxstring-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl libxml-sax-expat-perl psmisc linux-sysctl-defaults The following NEW packages will be installed: appstream ca-certificates diffstat distro-info-data gpg gpgconf iso-codes libaliased-perl libappstream5 libapt-pkg-perl libassuan9 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libbrotli1 libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libcom-err2 libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libcurl4-gnutls libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdistro-info-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libffi8 libfile-basedir-perl libfile-find-rule-perl libfile-libmagic-perl libfile-listing-perl libfile-sharedir-perl libfont-ttf-perl libfyaml0 libgcrypt20 libglib2.0-0t64 libgnutls30t64 libgpg-error0 libgssapi-krb5-2 libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libidn2-0 libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libio-string-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libksba8 libldap2 liblist-compare-perl liblist-someutils-perl liblist-someutils-xs-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libncursesw6 libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnpth0t64 libnumber-compare-perl libp11-kit0 libpackage-stash-perl libparams-classify-perl libparams-someutil-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libproc2-1 libpsl5t64 libreadline8t64 libregexp-wildcards-perl librole-tiny-perl libsasl2-2 libsasl2-modules-db libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libssh2-1t64 libstemmer0d libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libtasn1-6 libterm-readkey-perl libtext-charwidth-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-wrapi18n-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxmlb2 libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip procps readline-common sbuild-build-depends-lintian-dummy:amd64 shared-mime-info t1utils ucf unzip 0 upgraded, 179 newly installed, 0 to remove and 0 not upgraded. Need to get 23.8 MB of archives. After this operation, 98.5 MB of additional disk space will be used. Get:1 copy:/build/reproducible-path/resolver-8advCY/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [832 B] Get:2 http://mirror.einval.org/debian unstable/main arm64 netbase all 6.6 [10.3 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 libncursesw6 arm64 6.6+20260608-2 [125 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libproc2-1 arm64 2:4.0.7-1 [66.2 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 procps arm64 2:4.0.7-1 [971 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 readline-common all 8.3-4 [74.8 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 openssl arm64 3.6.5-1 [1507 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 ca-certificates all 20260816 [134 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 libtext-charwidth-perl arm64 0.04-12+b1 [9412 B] Get:10 http://mirror.einval.org/debian unstable/main arm64 libtext-wrapi18n-perl all 0.06-11 [7788 B] Get:11 http://mirror.einval.org/debian unstable/main arm64 ucf all 3.0056 [47.1 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 libffi8 arm64 3.8.0-2 [25.9 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.90.1-2 [1439 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 shared-mime-info arm64 2.4-5+b4 [754 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 libnghttp3-9 arm64 1.17.0-1 [63.0 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 libngtcp2-16 arm64 1.24.0-1 [129 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 libbrotli1 arm64 1.2.0-4+b1 [293 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-5 [107 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 libp11-kit0 arm64 0.26.5-1 [440 kB] Get:20 http://mirror.einval.org/debian unstable/main arm64 libtasn1-6 arm64 4.21.0-2+b1 [46.9 kB] Get:21 http://mirror.einval.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.13-1 [1434 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 libkrb5support0 arm64 1.22.1-3 [30.2 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 libcom-err2 arm64 1.47.4-1+b2 [19.4 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 libk5crypto3 arm64 1.22.1-3 [74.7 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6+b2 [9444 B] Get:26 http://mirror.einval.org/debian unstable/main arm64 libkrb5-3 arm64 1.22.1-3 [314 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.22.1-3 [125 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-11 [17.1 kB] Get:29 http://mirror.einval.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-11 [52.4 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 libldap2 arm64 2.6.14+dfsg-2 [173 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libnghttp2-14 arm64 1.70.0-1 [87.9 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.24.0-1 [22.5 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 libpsl5t64 arm64 0.23.3-1 [61.0 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-6 [235 kB] Get:35 http://mirror.einval.org/debian unstable/main arm64 libcurl4-gnutls arm64 8.23.0-1 [394 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 libfyaml0 arm64 0.9.4-1 [245 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 libstemmer0d arm64 3.1.1-1 [132 kB] Get:38 http://mirror.einval.org/debian unstable/main arm64 libxmlb2 arm64 0.3.29-1 [58.5 kB] Get:39 http://mirror.einval.org/debian unstable/main arm64 libappstream5 arm64 1.2.1-1 [230 kB] Get:40 http://mirror.einval.org/debian unstable/main arm64 appstream arm64 1.2.1-1 [624 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 diffstat arm64 1.69-1 [32.5 kB] Get:42 http://mirror.einval.org/debian unstable/main arm64 distro-info-data all 2026.10.12-1 [6372 B] Get:43 http://mirror.einval.org/debian unstable/main arm64 libgpg-error0 arm64 1.61-5 [84.8 kB] Get:44 http://mirror.einval.org/debian unstable/main arm64 libassuan9 arm64 3.0.2-2+b2 [57.6 kB] Get:45 http://mirror.einval.org/debian unstable/main arm64 libgcrypt20 arm64 1.12.4-2 [804 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 libreadline8t64 arm64 8.3-4 [168 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 gpgconf arm64 2.4.9-8 [118 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libksba8 arm64 1.8.1-1 [127 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 libnpth0t64 arm64 1.8-4 [22.7 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 libsqlite3-0 arm64 3.53.4-2 [901 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 gpg arm64 2.4.9-8 [568 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 iso-codes all 4.20.1-1 [3319 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 libaliased-perl all 0.34-3 [13.5 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 libapt-pkg-perl arm64 0.1.43+b1 [64.6 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b5 [10.7 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 libdynaloader-functions-perl all 0.004-2 [12.2 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 libdevel-callchecker-perl arm64 0.009-3+b1 [15.8 kB] Get:58 http://mirror.einval.org/debian unstable/main arm64 libparams-classify-perl arm64 0.015-2+b7 [22.4 kB] Get:59 http://mirror.einval.org/debian unstable/main arm64 libmodule-runtime-perl all 0.018-1 [17.8 kB] Get:60 http://mirror.einval.org/debian unstable/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get:61 http://mirror.einval.org/debian unstable/main arm64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:62 http://mirror.einval.org/debian unstable/main arm64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:63 http://mirror.einval.org/debian unstable/main arm64 libvariable-magic-perl arm64 0.65-1 [44.1 kB] Get:64 http://mirror.einval.org/debian unstable/main arm64 libb-hooks-endofscope-perl all 0.28-2 [17.6 kB] Get:65 http://mirror.einval.org/debian unstable/main arm64 libberkeleydb-perl arm64 0.66-2+b2 [116 kB] Get:66 http://mirror.einval.org/debian unstable/main arm64 libcapture-tiny-perl all 0.50-1 [24.6 kB] Get:67 http://mirror.einval.org/debian unstable/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:68 http://mirror.einval.org/debian unstable/main arm64 liburi-perl all 5.37-1 [113 kB] Get:69 http://mirror.einval.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.83-2+b2 [96.7 kB] Get:70 http://mirror.einval.org/debian unstable/main arm64 libcgi-pm-perl all 4.72-1 [217 kB] Get:71 http://mirror.einval.org/debian unstable/main arm64 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get:72 http://mirror.einval.org/debian unstable/main arm64 libclass-inspector-perl all 1.36-3 [17.5 kB] Get:73 http://mirror.einval.org/debian unstable/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get:74 http://mirror.einval.org/debian unstable/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b8 [35.4 kB] Get:75 http://mirror.einval.org/debian unstable/main arm64 libclone-perl arm64 0.51-1 [23.2 kB] Get:76 http://mirror.einval.org/debian unstable/main arm64 libconfig-tiny-perl all 2.30-1 [18.9 kB] Get:77 http://mirror.einval.org/debian unstable/main arm64 libparams-someutil-perl arm64 1.12-1 [24.4 kB] Get:78 http://mirror.einval.org/debian unstable/main arm64 libsub-install-perl all 0.929-1 [10.5 kB] Get:79 http://mirror.einval.org/debian unstable/main arm64 libdata-optlist-perl all 0.115-1 [10.4 kB] Get:80 http://mirror.einval.org/debian unstable/main arm64 libsub-exporter-perl all 0.992-1 [49.3 kB] Get:81 http://mirror.einval.org/debian unstable/main arm64 libconst-fast-perl all 0.014-2 [8792 B] Get:82 http://mirror.einval.org/debian unstable/main arm64 libcpanel-json-xs-perl arm64 4.51-1 [137 kB] Get:83 http://mirror.einval.org/debian unstable/main arm64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get:84 http://mirror.einval.org/debian unstable/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get:85 http://mirror.einval.org/debian unstable/main arm64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:86 http://mirror.einval.org/debian unstable/main arm64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:87 http://mirror.einval.org/debian unstable/main arm64 libdata-dpath-perl all 0.60-1 [41.8 kB] Get:88 http://mirror.einval.org/debian unstable/main arm64 libdata-messagepack-perl arm64 1.02-3+b2 [30.9 kB] Get:89 http://mirror.einval.org/debian unstable/main arm64 libnet-domain-tld-perl all 1.75-4 [31.5 kB] Get:90 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-domain-perl all 0.15-1 [11.9 kB] Get:91 http://mirror.einval.org/debian unstable/main arm64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:92 http://mirror.einval.org/debian unstable/main arm64 libnet-netmask-perl all 2.0003-1 [28.5 kB] Get:93 http://mirror.einval.org/debian unstable/main arm64 libnetaddr-ip-perl arm64 4.079+dfsg-2+b7 [98.0 kB] Get:94 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-ip-perl all 0.31-1 [20.6 kB] Get:95 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-uri-perl all 0.07-3 [11.0 kB] Get:96 http://mirror.einval.org/debian unstable/main arm64 libdevel-size-perl arm64 0.87-1+b1 [24.0 kB] Get:97 http://mirror.einval.org/debian unstable/main arm64 libdistro-info-perl all 1.20 [5488 B] Get:98 http://mirror.einval.org/debian unstable/main arm64 libemail-address-xs-perl arm64 1.05-1+b6 [28.3 kB] Get:99 http://mirror.einval.org/debian unstable/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:100 http://mirror.einval.org/debian unstable/main arm64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:101 http://mirror.einval.org/debian unstable/main arm64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:102 http://mirror.einval.org/debian unstable/main arm64 libnumber-compare-perl all 0.03-3 [6332 B] Get:103 http://mirror.einval.org/debian unstable/main arm64 libtext-glob-perl all 0.11-3 [7676 B] Get:104 http://mirror.einval.org/debian unstable/main arm64 libfile-find-rule-perl all 0.35-1 [25.9 kB] Get:105 http://mirror.einval.org/debian unstable/main arm64 libfile-libmagic-perl arm64 1.23-2+b4 [31.2 kB] Get:106 http://mirror.einval.org/debian unstable/main arm64 libtimedate-perl all 2.3500-1 [64.2 kB] Get:107 http://mirror.einval.org/debian unstable/main arm64 libhttp-date-perl all 6.08-1 [12.1 kB] Get:108 http://mirror.einval.org/debian unstable/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:109 http://mirror.einval.org/debian unstable/main arm64 libfile-sharedir-perl all 1.118-3 [16.0 kB] Get:110 http://mirror.einval.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get:111 http://mirror.einval.org/debian unstable/main arm64 libfont-ttf-perl all 1.06-2 [318 kB] Get:112 http://mirror.einval.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get:113 http://mirror.einval.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:114 http://mirror.einval.org/debian unstable/main arm64 libhttp-message-perl all 7.04-1 [80.6 kB] Get:115 http://mirror.einval.org/debian unstable/main arm64 libhtml-form-perl all 6.13-1 [32.6 kB] Get:116 http://mirror.einval.org/debian unstable/main arm64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:117 http://mirror.einval.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get:118 http://mirror.einval.org/debian unstable/main arm64 libhttp-cookies-perl all 6.12-2 [19.2 kB] Get:119 http://mirror.einval.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:120 http://mirror.einval.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get:121 http://mirror.einval.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.96-2 [327 kB] Get:122 http://mirror.einval.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.099-1 [229 kB] Get:123 http://mirror.einval.org/debian unstable/main arm64 libnet-http-perl all 6.24-1 [23.2 kB] Get:124 http://mirror.einval.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.15-1 [10.7 kB] Get:125 http://mirror.einval.org/debian unstable/main arm64 libwww-robotrules-perl all 6.03-1 [15.8 kB] Get:126 http://mirror.einval.org/debian unstable/main arm64 libwww-perl all 6.83-1 [186 kB] Get:127 http://mirror.einval.org/debian unstable/main arm64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:128 http://mirror.einval.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:129 http://mirror.einval.org/debian unstable/main arm64 libio-interactive-perl all 1.027-1 [11.8 kB] Get:130 http://mirror.einval.org/debian unstable/main arm64 libipc-run3-perl all 0.049-1 [31.5 kB] Get:131 http://mirror.einval.org/debian unstable/main arm64 libjson-maybexs-perl all 1.004008-1 [12.9 kB] Get:132 http://mirror.einval.org/debian unstable/main arm64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:133 http://mirror.einval.org/debian unstable/main arm64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:134 http://mirror.einval.org/debian unstable/main arm64 liblist-someutils-xs-perl arm64 0.59-1+b1 [33.1 kB] Get:135 http://mirror.einval.org/debian unstable/main arm64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:136 http://mirror.einval.org/debian unstable/main arm64 liblz1 arm64 1.16-2 [38.5 kB] Get:137 http://mirror.einval.org/debian unstable/main arm64 liblzo2-2 arm64 2.10-3+b2 [50.7 kB] Get:138 http://mirror.einval.org/debian unstable/main arm64 libmarkdown2 arm64 2.2.7-2.1+b2 [33.8 kB] Get:139 http://mirror.einval.org/debian unstable/main arm64 libmldbm-perl all 2.05-4 [16.8 kB] Get:140 http://mirror.einval.org/debian unstable/main arm64 librole-tiny-perl all 2.002005-1 [19.5 kB] Get:141 http://mirror.einval.org/debian unstable/main arm64 libsub-quote-perl all 2.006009-1 [21.3 kB] Get:142 http://mirror.einval.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get:143 http://mirror.einval.org/debian unstable/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:144 http://mirror.einval.org/debian unstable/main arm64 libmoox-aliases-perl all 0.001006-3 [6996 B] Get:145 http://mirror.einval.org/debian unstable/main arm64 libmouse-perl arm64 2.6.2-1+b1 [141 kB] Get:146 http://mirror.einval.org/debian unstable/main arm64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:147 http://mirror.einval.org/debian unstable/main arm64 libsub-identify-perl arm64 0.14-4+b1 [11.3 kB] Get:148 http://mirror.einval.org/debian unstable/main arm64 libsub-name-perl arm64 0.28-1+b3 [12.4 kB] Get:149 http://mirror.einval.org/debian unstable/main arm64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:150 http://mirror.einval.org/debian unstable/main arm64 libpath-tiny-perl all 0.150-1 [56.4 kB] Get:151 http://mirror.einval.org/debian unstable/main arm64 libperlio-gzip-perl arm64 0.20-1+b6 [17.6 kB] Get:152 http://mirror.einval.org/debian unstable/main arm64 libperlio-utf8-strict-perl arm64 0.010-1+b5 [11.5 kB] Get:153 http://mirror.einval.org/debian unstable/main arm64 libproc-processtable-perl arm64 0.637-1+b4 [41.1 kB] Get:154 http://mirror.einval.org/debian unstable/main arm64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:155 http://mirror.einval.org/debian unstable/main arm64 libsereal-decoder-perl arm64 5.010+ds-1 [102 kB] Get:156 http://mirror.einval.org/debian unstable/main arm64 libsereal-encoder-perl arm64 5.010+ds-1 [104 kB] Get:157 http://mirror.einval.org/debian unstable/main arm64 libsort-versions-perl all 1.62-3 [8928 B] Get:158 http://mirror.einval.org/debian unstable/main arm64 libxs-parse-keyword-perl arm64 0.51-1 [64.5 kB] Get:159 http://mirror.einval.org/debian unstable/main arm64 libsyntax-keyword-try-perl arm64 0.31-1+b1 [27.0 kB] Get:160 http://mirror.einval.org/debian unstable/main arm64 libterm-readkey-perl arm64 2.38-2+b6 [24.5 kB] Get:161 http://mirror.einval.org/debian unstable/main arm64 libtext-levenshteinxs-perl arm64 0.03-5+b6 [8868 B] Get:162 http://mirror.einval.org/debian unstable/main arm64 libtext-markdown-discount-perl arm64 0.18-1+b2 [13.3 kB] Get:163 http://mirror.einval.org/debian unstable/main arm64 libtext-xslate-perl arm64 3.5.9-2+b3 [173 kB] Get:164 http://mirror.einval.org/debian unstable/main arm64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:165 http://mirror.einval.org/debian unstable/main arm64 libtime-moment-perl arm64 0.46-1+b1 [77.5 kB] Get:166 http://mirror.einval.org/debian unstable/main arm64 libunicode-utf8-perl arm64 0.75-1+b1 [27.8 kB] Get:167 http://mirror.einval.org/debian unstable/main arm64 libwww-mechanize-perl all 2.22-1 [117 kB] Get:168 http://mirror.einval.org/debian unstable/main arm64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:169 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:170 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-perl all 1.02+dfsg-5 [53.6 kB] Get:171 http://mirror.einval.org/debian unstable/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-8+b1 [299 kB] Get:172 http://mirror.einval.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-2+b1 [47.8 kB] Get:173 http://mirror.einval.org/debian unstable/main arm64 libyaml-libyaml-perl arm64 0.910.0+ds-1+b1 [44.9 kB] Get:174 http://mirror.einval.org/debian unstable/main arm64 plzip arm64 1.13-2 [64.5 kB] Get:175 http://mirror.einval.org/debian unstable/main arm64 lzop arm64 1.04-2+b2 [82.0 kB] Get:176 http://mirror.einval.org/debian unstable/main arm64 patchutils arm64 0.4.5-1 [81.0 kB] Get:177 http://mirror.einval.org/debian unstable/main arm64 t1utils arm64 1.41-4+b2 [57.5 kB] Get:178 http://mirror.einval.org/debian unstable/main arm64 unzip arm64 6.0-31 [163 kB] Get:179 http://mirror.einval.org/debian unstable/main arm64 lintian all 2.142.0 [1040 kB] Preconfiguring packages ... Fetched 23.8 MB in 1s (20.0 MB/s) Selecting previously unselected package netbase. (Reading database ... 20442 files and directories currently installed.) Preparing to unpack .../000-netbase_6.6_all.deb ... Unpacking netbase (6.6) ... Selecting previously unselected package libncursesw6:arm64. Preparing to unpack .../001-libncursesw6_6.6+20260608-2_arm64.deb ... Unpacking libncursesw6:arm64 (6.6+20260608-2) ... Selecting previously unselected package libproc2-1:arm64. Preparing to unpack .../002-libproc2-1_2%3a4.0.7-1_arm64.deb ... Unpacking libproc2-1:arm64 (2:4.0.7-1) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.7-1_arm64.deb ... Unpacking procps (2:4.0.7-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../004-readline-common_8.3-4_all.deb ... Unpacking readline-common (8.3-4) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.6.5-1_arm64.deb ... Unpacking openssl (3.6.5-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20260816_all.deb ... Unpacking ca-certificates (20260816) ... Selecting previously unselected package libtext-charwidth-perl:arm64. Preparing to unpack .../007-libtext-charwidth-perl_0.04-12+b1_arm64.deb ... Unpacking libtext-charwidth-perl:arm64 (0.04-12+b1) ... Selecting previously unselected package libtext-wrapi18n-perl. Preparing to unpack .../008-libtext-wrapi18n-perl_0.06-11_all.deb ... Unpacking libtext-wrapi18n-perl (0.06-11) ... Selecting previously unselected package ucf. Preparing to unpack .../009-ucf_3.0056_all.deb ... Moving old data out of the way Unpacking ucf (3.0056) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../010-libffi8_3.8.0-2_arm64.deb ... Unpacking libffi8:arm64 (3.8.0-2) ... Selecting previously unselected package libglib2.0-0t64:arm64. Preparing to unpack .../011-libglib2.0-0t64_2.90.1-2_arm64.deb ... Unpacking libglib2.0-0t64:arm64 (2.90.1-2) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../012-shared-mime-info_2.4-5+b4_arm64.deb ... Unpacking shared-mime-info (2.4-5+b4) ... Selecting previously unselected package libnghttp3-9:arm64. Preparing to unpack .../013-libnghttp3-9_1.17.0-1_arm64.deb ... Unpacking libnghttp3-9:arm64 (1.17.0-1) ... Selecting previously unselected package libngtcp2-16:arm64. Preparing to unpack .../014-libngtcp2-16_1.24.0-1_arm64.deb ... Unpacking libngtcp2-16:arm64 (1.24.0-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../015-libbrotli1_1.2.0-4+b1_arm64.deb ... Unpacking libbrotli1:arm64 (1.2.0-4+b1) ... Selecting previously unselected package libidn2-0:arm64. Preparing to unpack .../016-libidn2-0_2.3.8-5_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.8-5) ... Selecting previously unselected package libp11-kit0:arm64. 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Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../023-libkeyutils1_1.6.3-6+b2_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-6+b2) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../024-libkrb5-3_1.22.1-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.22.1-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../025-libgssapi-krb5-2_1.22.1-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.22.1-3) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../026-libsasl2-modules-db_2.1.28+dfsg1-11_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-11) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../027-libsasl2-2_2.1.28+dfsg1-11_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-11) ... Selecting previously unselected package libldap2:arm64. 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Selecting previously unselected package libfyaml0:arm64. Preparing to unpack .../034-libfyaml0_0.9.4-1_arm64.deb ... Unpacking libfyaml0:arm64 (0.9.4-1) ... Selecting previously unselected package libstemmer0d:arm64. Preparing to unpack .../035-libstemmer0d_3.1.1-1_arm64.deb ... Unpacking libstemmer0d:arm64 (3.1.1-1) ... Selecting previously unselected package libxmlb2:arm64. Preparing to unpack .../036-libxmlb2_0.3.29-1_arm64.deb ... Unpacking libxmlb2:arm64 (0.3.29-1) ... Selecting previously unselected package libappstream5:arm64. Preparing to unpack .../037-libappstream5_1.2.1-1_arm64.deb ... Unpacking libappstream5:arm64 (1.2.1-1) ... Selecting previously unselected package appstream. Preparing to unpack .../038-appstream_1.2.1-1_arm64.deb ... Unpacking appstream (1.2.1-1) ... Selecting previously unselected package diffstat. Preparing to unpack .../039-diffstat_1.69-1_arm64.deb ... Unpacking diffstat (1.69-1) ... Selecting previously unselected package distro-info-data. Preparing to unpack .../040-distro-info-data_2026.10.12-1_all.deb ... Unpacking distro-info-data (2026.10.12-1) ... Selecting previously unselected package libgpg-error0:arm64. Preparing to unpack .../041-libgpg-error0_1.61-5_arm64.deb ... Unpacking libgpg-error0:arm64 (1.61-5) ... Selecting previously unselected package libassuan9:arm64. Preparing to unpack .../042-libassuan9_3.0.2-2+b2_arm64.deb ... Unpacking libassuan9:arm64 (3.0.2-2+b2) ... Selecting previously unselected package libgcrypt20:arm64. Preparing to unpack .../043-libgcrypt20_1.12.4-2_arm64.deb ... Unpacking libgcrypt20:arm64 (1.12.4-2) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../044-libreadline8t64_8.3-4_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.3-4) ... Selecting previously unselected package gpgconf. Preparing to unpack .../045-gpgconf_2.4.9-8_arm64.deb ... Unpacking gpgconf (2.4.9-8) ... Selecting previously unselected package libksba8:arm64. Preparing to unpack .../046-libksba8_1.8.1-1_arm64.deb ... Unpacking libksba8:arm64 (1.8.1-1) ... Selecting previously unselected package libnpth0t64:arm64. 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Preparing to unpack .../053-libb-hooks-op-check-perl_0.22-3+b5_arm64.deb ... Unpacking libb-hooks-op-check-perl:arm64 (0.22-3+b5) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../054-libdynaloader-functions-perl_0.004-2_all.deb ... Unpacking libdynaloader-functions-perl (0.004-2) ... Selecting previously unselected package libdevel-callchecker-perl:arm64. Preparing to unpack .../055-libdevel-callchecker-perl_0.009-3+b1_arm64.deb ... Unpacking libdevel-callchecker-perl:arm64 (0.009-3+b1) ... Selecting previously unselected package libparams-classify-perl:arm64. Preparing to unpack .../056-libparams-classify-perl_0.015-2+b7_arm64.deb ... Unpacking libparams-classify-perl:arm64 (0.015-2+b7) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../057-libmodule-runtime-perl_0.018-1_all.deb ... Unpacking libmodule-runtime-perl (0.018-1) ... Selecting previously unselected package libtry-tiny-perl. 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Preparing to unpack .../063-libberkeleydb-perl_0.66-2+b2_arm64.deb ... Unpacking libberkeleydb-perl:arm64 (0.66-2+b2) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../064-libcapture-tiny-perl_0.50-1_all.deb ... Unpacking libcapture-tiny-perl (0.50-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../065-libhtml-tagset-perl_3.24-1_all.deb ... Unpacking libhtml-tagset-perl (3.24-1) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../066-liburi-perl_5.37-1_all.deb ... Unpacking liburi-perl (5.37-1) ... Selecting previously unselected package libhtml-parser-perl:arm64. Preparing to unpack .../067-libhtml-parser-perl_3.83-2+b2_arm64.deb ... Unpacking libhtml-parser-perl:arm64 (3.83-2+b2) ... Selecting previously unselected package libcgi-pm-perl. Preparing to unpack .../068-libcgi-pm-perl_4.72-1_all.deb ... Unpacking libcgi-pm-perl (4.72-1) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../069-libclass-data-inheritable-perl_0.10-1_all.deb ... Unpacking libclass-data-inheritable-perl (0.10-1) ... Selecting previously unselected package libclass-inspector-perl. Preparing to unpack .../070-libclass-inspector-perl_1.36-3_all.deb ... Unpacking libclass-inspector-perl (1.36-3) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../071-libclass-method-modifiers-perl_2.15-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.15-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../072-libclass-xsaccessor-perl_1.19-4+b8_arm64.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b8) ... Selecting previously unselected package libclone-perl:arm64. Preparing to unpack .../073-libclone-perl_0.51-1_arm64.deb ... Unpacking libclone-perl:arm64 (0.51-1) ... Selecting previously unselected package libconfig-tiny-perl. Preparing to unpack .../074-libconfig-tiny-perl_2.30-1_all.deb ... Unpacking libconfig-tiny-perl (2.30-1) ... Selecting previously unselected package libparams-someutil-perl. Preparing to unpack .../075-libparams-someutil-perl_1.12-1_arm64.deb ... Unpacking libparams-someutil-perl (1.12-1) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../076-libsub-install-perl_0.929-1_all.deb ... Unpacking libsub-install-perl (0.929-1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../077-libdata-optlist-perl_0.115-1_all.deb ... Unpacking libdata-optlist-perl (0.115-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../078-libsub-exporter-perl_0.992-1_all.deb ... Unpacking libsub-exporter-perl (0.992-1) ... Selecting previously unselected package libconst-fast-perl. 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Selecting previously unselected package sbuild-build-depends-lintian-dummy:amd64. Preparing to unpack .../178-sbuild-build-depends-lintian-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-lintian-dummy:amd64 (0.invalid.0) ... Setting up libapt-pkg-perl (0.1.43+b1) ... Setting up liblz1:arm64 (1.16-2) ... Setting up libberkeleydb-perl:arm64 (0.66-2+b2) ... Setting up plzip (1.13-2) ... update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode Setting up libtext-charwidth-perl:arm64 (0.04-12+b1) ... Setting up libnpth0t64:arm64 (1.8-4) ... Setting up libkeyutils1:arm64 (1.6.3-6+b2) ... Setting up libunicode-utf8-perl (0.75-1+b1) ... Setting up libmouse-perl:arm64 (2.6.2-1+b1) ... Setting up libgpg-error0:arm64 (1.61-5) ... Setting up libdata-messagepack-perl (1.02-3+b2) ... Setting up libclass-inspector-perl (1.36-3) ... Setting up libdynaloader-functions-perl (0.004-2) ... Setting up libtext-glob-perl (0.11-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up liblist-compare-perl (0.55-2) ... Setting up libclone-perl:arm64 (0.51-1) ... Setting up libyaml-0-2:arm64 (0.2.5-2+b1) ... Setting up libsub-identify-perl (0.14-4+b1) ... Setting up distro-info-data (2026.10.12-1) ... Setting up libcpanel-json-xs-perl:arm64 (4.51-1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdevel-size-perl (0.87-1+b1) ... Setting up unzip (6.0-31) ... Setting up libbrotli1:arm64 (1.2.0-4+b1) ... Setting up libsqlite3-0:arm64 (3.53.4-2) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libyaml-libyaml-perl (0.910.0+ds-1+b1) ... Setting up libio-interactive-perl (1.027-1) ... Setting up libtry-tiny-perl (0.32-1) ... Setting up libnghttp2-14:arm64 (1.70.0-1) ... Setting up perl-openssl-defaults:arm64 (7+b2) ... Setting up libmldbm-perl (2.05-4) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up libgcrypt20:arm64 (1.12.4-2) ... Setting up liblzo2-2:arm64 (2.10-3+b2) ... Setting up libtime-moment-perl (0.46-1+b1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libidn2-0:arm64 (2.3.8-5) ... Setting up libcom-err2:arm64 (1.47.4-1+b2) ... Setting up libparams-someutil-perl (1.12-1) ... Setting up libconfig-tiny-perl (2.30-1) ... Setting up libsereal-encoder-perl (5.010+ds-1) ... Setting up liblist-utilsby-perl (0.12-2) ... Setting up libtext-wrapi18n-perl (0.06-11) ... Setting up libnet-netmask-perl (2.0003-1) ... Setting up libsub-install-perl (0.929-1) ... Setting up libfyaml0:arm64 (0.9.4-1) ... Setting up libkrb5support0:arm64 (1.22.1-3) ... Setting up libnumber-compare-perl (0.03-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-11) ... Setting up patchutils (0.4.5-1) ... Setting up libjson-maybexs-perl (1.004008-1) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2+b7) ... Setting up libclass-data-inheritable-perl (0.10-1) ... Setting up libproc2-1:arm64 (2:4.0.7-1) ... Setting up libfile-find-rule-perl (0.35-1) ... Setting up libipc-system-simple-perl (1.30-2) ... Setting up libnet-domain-tld-perl (1.75-4) ... Setting up libperlio-utf8-strict-perl (0.010-1+b5) ... Setting up t1utils (1.41-4+b2) ... Setting up diffstat (1.69-1) ... Setting up libvariable-magic-perl (0.65-1) ... Setting up libio-html-perl (1.004-3) ... Setting up libdata-optlist-perl (0.115-1) ... Setting up libb-hooks-op-check-perl:arm64 (0.22-3+b5) ... Setting up libfile-libmagic-perl (1.23-2+b4) ... Setting up libncursesw6:arm64 (6.6+20260608-2) ... Setting up libk5crypto3:arm64 (1.22.1-3) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-11) ... Setting up libtime-duration-perl (1.21-2) ... Setting up libtext-xslate-perl:arm64 (3.5.9-2+b3) ... Setting up libnghttp3-9:arm64 (1.17.0-1) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libcapture-tiny-perl (0.50-1) ... Setting up libtimedate-perl (2.3500-1) ... Setting up libsub-name-perl:arm64 (0.28-1+b3) ... Setting up libffi8:arm64 (3.8.0-2) ... Setting up libdata-validate-domain-perl (0.15-1) ... Setting up libproc-processtable-perl:arm64 (0.637-1+b4) ... Setting up libpath-tiny-perl (0.150-1) ... Setting up lzop (1.04-2+b2) ... Setting up libassuan9:arm64 (3.0.2-2+b2) ... Setting up procps (2:4.0.7-1) ... Setting up librole-tiny-perl (2.002005-1) ... Setting up libtasn1-6:arm64 (4.21.0-2+b1) ... Setting up libipc-run3-perl (0.049-1) ... Setting up libregexp-wildcards-perl (1.05-3) ... Setting up libfile-sharedir-perl (1.118-3) ... Setting up libaliased-perl (0.34-3) ... Setting up netbase (6.6) ... Setting up libngtcp2-16:arm64 (1.24.0-1) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006009-1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b8) ... Setting up libkrb5-3:arm64 (1.22.1-3) ... Setting up libstemmer0d:arm64 (3.1.1-1) ... Setting up libsort-versions-perl (1.62-3) ... Setting up libssh2-1t64:arm64 (1.11.1-6) ... Setting up libterm-readkey-perl (2.38-2+b6) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.6.5-1) ... Setting up libtext-levenshteinxs-perl (0.03-5+b6) ... Setting up libperlio-gzip-perl (0.20-1+b6) ... Setting up readline-common (8.3-4) ... Setting up libhtml-html5-entities-perl (0.004-3) ... Setting up libsereal-decoder-perl (5.010+ds-1) ... Setting up libmarkdown2:arm64 (2.2.7-2.1+b2) ... Setting up libldap2:arm64 (2.6.14+dfsg-2) ... Setting up liburi-perl (5.37-1) ... Setting up iso-codes (4.20.1-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up libsub-exporter-perl (0.992-1) ... Setting up libdata-validate-ip-perl (0.31-1) ... Setting up libemail-address-xs-perl (1.05-1+b6) ... Setting up libnet-ssleay-perl:arm64 (1.96-2) ... Setting up libksba8:arm64 (1.8.1-1) ... Setting up libhttp-date-perl (6.08-1) ... Setting up libfile-basedir-perl (0.09-2) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libdistro-info-perl (1.20) ... Setting up libpsl5t64:arm64 (0.23.3-1) ... Setting up libnet-http-perl (6.24-1) ... Setting up libtext-markdown-discount-perl (0.18-1+b2) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:arm64 (0.009-3+b1) ... Setting up ca-certificates (20260816) ... Updating certificates in /etc/ssl/certs... 121 added, 0 removed; done. Setting up libglib2.0-0t64:arm64 (2.90.1-2) ... No schema files found: doing nothing. Setting up libdata-validate-uri-perl (0.07-3) ... Setting up libxs-parse-keyword-perl (0.51-1) ... Setting up shared-mime-info (2.4-5+b4) ... Setting up libp11-kit0:arm64 (0.26.5-1) ... Setting up libgssapi-krb5-2:arm64 (1.22.1-3) ... Setting up ucf (3.0056) ... Setting up libreadline8t64:arm64 (8.3-4) ... Setting up libwww-robotrules-perl (6.03-1) ... Setting up libsyntax-keyword-try-perl (0.31-1+b1) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libhtml-parser-perl:arm64 (3.83-2+b2) ... Setting up gpgconf (2.4.9-8) ... Setting up libio-socket-ssl-perl (2.099-1) ... Setting up gpg (2.4.9-8) ... Setting up libhttp-message-perl (7.04-1) ... Setting up libhtml-form-perl (6.13-1) ... Setting up libgnutls30t64:arm64 (3.8.13-1) ... Setting up libiterator-perl (0.03+ds1-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libiterator-util-perl (0.02+ds1-2) ... Setting up libhttp-cookies-perl (6.12-2) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libxmlb2:arm64 (0.3.29-1) ... Setting up libparams-classify-perl:arm64 (0.015-2+b7) ... Setting up libcgi-pm-perl (4.72-1) ... Setting up libxml-sax-perl (1.02+dfsg-5) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libmodule-runtime-perl (0.018-1) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-8+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Setting up libdata-dpath-perl (0.60-1) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.24.0-1) ... Setting up libcurl4-gnutls:arm64 (8.23.0-1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblist-someutils-perl (0.59-1) ... Setting up libappstream5:arm64 (1.2.1-1) ... Setting up liblist-someutils-xs-perl:arm64 (0.59-1+b1) ... Setting up appstream (1.2.1-1) ... ✔ Metadata cache was updated successfully. Setting up libmoox-aliases-perl (0.001006-3) ... Setting up libb-hooks-endofscope-perl (0.28-2) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up liblwp-protocol-https-perl (6.15-1) ... Setting up libwww-perl (6.83-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.22-1) ... Setting up lintian (2.142.0) ... Setting up sbuild-build-depends-lintian-dummy:amd64 (0.invalid.0) ... Processing triggers for libc-bin (2.43-7) ... Processing triggers for man-db (2.13.1-1+b1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for ca-certificates (20260816) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Running lintian... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build Thu, 15 Oct 2026 21:52:17 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Thu, 15 Oct 2026 21:52:17 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Thu, 15 Oct 2026 21:52:21 +0000 | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Build-Space: n/a Build-Time: 9474 Distribution: unstable Foreign Architectures: amd64 Host Architecture: amd64 Install-Time: 60 Job: rna-star_2.7.11b+dfsg-4 Lintian: pass Machine Architecture: arm64 Package: rna-star Package-Time: 9578 Source-Version: 2.7.11b+dfsg-4 Space: n/a Status: successful Version: 2.7.11b+dfsg-4 -------------------------------------------------------------------------------- Finished at 2026-10-15T21:51:03Z Build needed 02:39:38, no disk space