sbuild (Debian sbuild) 0.85.0 (04 January 2023) on mjolnir.einval.org +==============================================================================+ | rna-star 2.7.10b+dfsg-2 (amd64) Wed, 03 May 2023 19:22:03 +0000 | +==============================================================================+ Package: rna-star Version: 2.7.10b+dfsg-2 Source Version: 2.7.10b+dfsg-2 Distribution: unstable Machine Architecture: arm64 Host Architecture: amd64 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Unpacking /home/helmut/.cache/sbuild/unstable-arm64-sbuild.tar.zst to /tmp/tmp.sbuild.64YIjQMiC8... I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<>' I: NOTICE: Log filtering will replace 'build/rna-star-ZZnl9e/resolver-drCN6l' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian unstable InRelease [188 kB] Get:2 http://mirror.einval.org/debian unstable/main Sources [10.1 MB] Get:3 http://mirror.einval.org/debian unstable/main amd64 Packages [9442 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 Packages [9297 kB] Fetched 29.0 MB in 8s (3785 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ 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 1000 kB of source archives. Get:1 http://mirror.einval.org/debian unstable/main rna-star 2.7.10b+dfsg-2 (dsc) [2158 B] Get:2 http://mirror.einval.org/debian unstable/main rna-star 2.7.10b+dfsg-2 (tar) [620 kB] Get:3 http://mirror.einval.org/debian unstable/main rna-star 2.7.10b+dfsg-2 (diff) [378 kB] Fetched 1000 kB in 0s (14.9 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/rna-star-ZZnl9e/rna-star-2.7.10b+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rna-star-ZZnl9e' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libhts-dev, xxd, zlib1g-dev, libsimde-dev, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64 Filtered Build-Depends: debhelper-compat (= 13), libhts-dev, xxd, zlib1g-dev, libsimde-dev, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64 dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [757 B] Get:5 copy:/<>/apt_archive ./ Packages [800 B] Fetched 2166 B in 0s (122 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: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cpp-12-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz fakeroot file g++-12-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-12-base:amd64 gcc-12-cross-base gcc-12-x86-64-linux-gnu gcc-12-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libbrotli1:amd64 libbz2-1.0:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcom-err2:amd64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:amd64 libcrypt1:amd64 libcurl3-gnutls:amd64 libcurl4-gnutls-dev:amd64 libdb5.3:amd64 libdebhelper-perl libdebian-dpkgcross-perl libdeflate-dev:amd64 libdeflate0:amd64 libelf1 libfakeroot libffi8:amd64 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-12-dev:amd64 libgcc-12-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgmp10:amd64 libgnutls30:amd64 libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libhogweed6:amd64 libhts-dev:amd64 libhts3:amd64 libhtscodecs2:amd64 libicu72 libidn2-0:amd64 libio-string-perl libitm1:amd64 libitm1-amd64-cross libk5crypto3:amd64 libkeyutils1:amd64 libkrb5-3:amd64 libkrb5support0:amd64 libldap-2.5-0:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross liblzma-dev:amd64 liblzma5:amd64 libmagic-mgc libmagic1 libnettle8:amd64 libnghttp2-14:amd64 libnsl-dev:amd64 libnsl2:amd64 libp11-kit0:amd64 libpipeline1 libpsl5:amd64 libquadmath0:amd64 libquadmath0-amd64-cross librtmp1:amd64 libsasl2-2:amd64 libsasl2-modules-db:amd64 libsimde-dev libssh2-1:amd64 libssl3:amd64 libstdc++-12-dev:amd64 libstdc++-12-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libsub-override-perl libtasn1-6:amd64 libtirpc-dev:amd64 libtirpc3:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunistring2:amd64 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl libzstd1:amd64 linux-libc-dev:amd64 linux-libc-dev-amd64-cross m4 man-db po-debconf sensible-utils ucf xxd zlib1g:amd64 zlib1g-dev:amd64 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-12-locales cpp-12-doc cpp-doc dh-make binutils-multiarch g++-12-multilib-x86-64-linux-gnu gcc-12-doc gcc-12-multilib-x86-64-linux-gnu manpages-dev flex bison gdb-x86-64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:amd64 libc-l10n:amd64 locales:amd64 libnss-nis:amd64 libnss-nisplus:amd64 manpages-dev:amd64 libcurl4-doc:amd64 libgnutls28-dev:amd64 libidn-dev:amd64 libkrb5-dev:amd64 libldap2-dev:amd64 librtmp-dev:amd64 libssh2-1-dev:amd64 pkg-config:amd64 gnutls-bin:amd64 krb5-doc:amd64 krb5-user:amd64 liblzma-doc:amd64 libstdc++-12-doc:amd64 libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx ca-certificates:amd64 libarchive-cpio-perl krb5-locales:amd64 libldap-common:amd64 publicsuffix:amd64 libsasl2-modules:amd64 libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cpp-12-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz fakeroot file g++-12-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-12-base:amd64 gcc-12-cross-base gcc-12-x86-64-linux-gnu gcc-12-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libbrotli1:amd64 libbz2-1.0:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcom-err2:amd64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:amd64 libcrypt1:amd64 libcurl3-gnutls:amd64 libcurl4-gnutls-dev:amd64 libdb5.3:amd64 libdebhelper-perl libdebian-dpkgcross-perl libdeflate-dev:amd64 libdeflate0:amd64 libelf1 libfakeroot libffi8:amd64 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-12-dev:amd64 libgcc-12-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgmp10:amd64 libgnutls30:amd64 libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libhogweed6:amd64 libhts-dev:amd64 libhts3:amd64 libhtscodecs2:amd64 libicu72 libidn2-0:amd64 libio-string-perl libitm1:amd64 libitm1-amd64-cross libk5crypto3:amd64 libkeyutils1:amd64 libkrb5-3:amd64 libkrb5support0:amd64 libldap-2.5-0:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross liblzma-dev:amd64 liblzma5:amd64 libmagic-mgc libmagic1 libnettle8:amd64 libnghttp2-14:amd64 libnsl-dev:amd64 libnsl2:amd64 libp11-kit0:amd64 libpipeline1 libpsl5:amd64 libquadmath0:amd64 libquadmath0-amd64-cross librtmp1:amd64 libsasl2-2:amd64 libsasl2-modules-db:amd64 libsimde-dev libssh2-1:amd64 libssl3:amd64 libstdc++-12-dev:amd64 libstdc++-12-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libsub-override-perl libtasn1-6:amd64 libtirpc-dev:amd64 libtirpc3:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunistring2:amd64 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl libzstd1:amd64 linux-libc-dev:amd64 linux-libc-dev-amd64-cross m4 man-db po-debconf sbuild-build-depends-main-dummy:amd64 sensible-utils ucf xxd zlib1g:amd64 zlib1g-dev:amd64 0 upgraded, 136 newly installed, 0 to remove and 0 not upgraded. Need to get 106 MB of archives. After this operation, 431 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [936 B] Get:2 http://mirror.einval.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-5 [15.1 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 file arm64 1:5.44-3 [42.5 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 gettext-base arm64 0.21-12 [159 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 m4 arm64 1.4.19-3 [276 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 autopoint all 0.21-12 [495 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 gcc-12-x86-64-linux-gnu-base arm64 12.2.0-14cross1 [37.7 kB] Get:20 http://mirror.einval.org/debian unstable/main arm64 cpp-12-x86-64-linux-gnu arm64 12.2.0-14cross1 [8764 kB] Get:21 http://mirror.einval.org/debian unstable/main arm64 cpp-x86-64-linux-gnu arm64 4:12.2.0-3 [3980 B] Get:22 http://mirror.einval.org/debian unstable/main arm64 cross-config all 2.6.20 [16.3 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 binutils-x86-64-linux-gnu arm64 2.40-2 [2368 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 gcc-12-cross-base all 12.2.0-14cross1 [33.2 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1-amd64-cross all 12.2.0-14cross1 [49.9 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 libgomp1-amd64-cross all 12.2.0-14cross1 [114 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 libitm1-amd64-cross all 12.2.0-14cross1 [25.5 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 libatomic1-amd64-cross all 12.2.0-14cross1 [9084 B] Get:29 http://mirror.einval.org/debian unstable/main arm64 libasan8-amd64-cross all 12.2.0-14cross1 [2194 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 liblsan0-amd64-cross all 12.2.0-14cross1 [968 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libtsan2-amd64-cross all 12.2.0-14cross1 [2197 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 libc6-amd64-cross all 2.36-8cross1 [1472 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 libstdc++6-amd64-cross all 12.2.0-14cross1 [570 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 libubsan1-amd64-cross all 12.2.0-14cross1 [882 kB] Get:35 http://mirror.einval.org/debian unstable/main arm64 libquadmath0-amd64-cross all 12.2.0-14cross1 [144 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 libgcc-12-dev-amd64-cross all 12.2.0-14cross1 [2437 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 gcc-12-x86-64-linux-gnu arm64 12.2.0-14cross1 [17.4 MB] Get:38 http://mirror.einval.org/debian unstable/main arm64 gcc-x86-64-linux-gnu arm64 4:12.2.0-3 [1472 B] Get:39 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev-amd64-cross all 6.1.4-1cross1 [1839 kB] Get:40 http://mirror.einval.org/debian unstable/main arm64 libc6-dev-amd64-cross all 2.36-8cross1 [1894 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 libstdc++-12-dev-amd64-cross all 12.2.0-14cross1 [2027 kB] Get:42 http://mirror.einval.org/debian unstable/main arm64 g++-12-x86-64-linux-gnu arm64 12.2.0-14cross1 [9602 kB] Get:43 http://mirror.einval.org/debian unstable/main arm64 g++-x86-64-linux-gnu arm64 4:12.2.0-3 [1176 B] Get:44 http://mirror.einval.org/debian unstable/main arm64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB] Get:45 http://mirror.einval.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-1+b1 [309 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 libyaml-perl all 1.30-2 [63.4 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB] Get:58 http://mirror.einval.org/debian unstable/main arm64 dpkg-cross all 2.6.20 [25.8 kB] Get:59 http://mirror.einval.org/debian unstable/main arm64 crossbuild-essential-amd64 all 12.9 [6708 B] Get:60 http://mirror.einval.org/debian unstable/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get:61 http://mirror.einval.org/debian unstable/main arm64 libtool all 2.4.7-5 [517 kB] Get:62 http://mirror.einval.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get:63 http://mirror.einval.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:64 http://mirror.einval.org/debian unstable/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get:65 http://mirror.einval.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get:66 http://mirror.einval.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get:67 http://mirror.einval.org/debian unstable/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get:68 http://mirror.einval.org/debian unstable/main arm64 dwz arm64 0.15-1 [101 kB] Get:69 http://mirror.einval.org/debian unstable/main arm64 gettext arm64 0.21-12 [1248 kB] Get:70 http://mirror.einval.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:71 http://mirror.einval.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get:72 http://mirror.einval.org/debian unstable/main arm64 debhelper all 13.11.4 [942 kB] Get:73 http://mirror.einval.org/debian unstable/main arm64 libfakeroot arm64 1.31-1.2 [27.9 kB] Get:74 http://mirror.einval.org/debian unstable/main arm64 fakeroot arm64 1.31-1.2 [66.4 kB] Get:75 http://mirror.einval.org/debian unstable/main amd64 gcc-12-base amd64 12.2.0-14 [37.5 kB] Get:76 http://mirror.einval.org/debian unstable/main amd64 libgcc-s1 amd64 12.2.0-14 [49.9 kB] Get:77 http://mirror.einval.org/debian unstable/main amd64 libc6 amd64 2.36-9 [2753 kB] Get:78 http://mirror.einval.org/debian unstable/main amd64 libasan8 amd64 12.2.0-14 [2195 kB] Get:79 http://mirror.einval.org/debian unstable/main amd64 libatomic1 amd64 12.2.0-14 [9328 B] Get:80 http://mirror.einval.org/debian unstable/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:81 http://mirror.einval.org/debian unstable/main amd64 libbz2-1.0 amd64 1.0.8-5+b1 [47.3 kB] Get:82 http://mirror.einval.org/debian unstable/main amd64 linux-libc-dev amd64 6.1.25-1 [1773 kB] Get:83 http://mirror.einval.org/debian unstable/main amd64 libcrypt1 amd64 1:4.4.33-2 [89.5 kB] Get:84 http://mirror.einval.org/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.33-2 [118 kB] Get:85 http://mirror.einval.org/debian unstable/main amd64 libcom-err2 amd64 1.47.0-2 [19.8 kB] Get:86 http://mirror.einval.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-1+b1 [32.5 kB] Get:87 http://mirror.einval.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-1+b1 [78.7 kB] Get:88 http://mirror.einval.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:89 http://mirror.einval.org/debian unstable/main amd64 libssl3 amd64 3.0.8-1 [2013 kB] Get:90 http://mirror.einval.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-1+b1 [332 kB] Get:91 http://mirror.einval.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-1+b1 [134 kB] Get:92 http://mirror.einval.org/debian unstable/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:93 http://mirror.einval.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:94 http://mirror.einval.org/debian unstable/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [191 kB] Get:95 http://mirror.einval.org/debian unstable/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:96 http://mirror.einval.org/debian unstable/main amd64 libc6-dev amd64 2.36-9 [1898 kB] Get:97 http://mirror.einval.org/debian unstable/main amd64 libgmp10 amd64 2:6.2.1+dfsg1-1.1 [563 kB] Get:98 http://mirror.einval.org/debian unstable/main amd64 libnettle8 amd64 3.8.1-2 [288 kB] Get:99 http://mirror.einval.org/debian unstable/main amd64 libhogweed6 amd64 3.8.1-2 [328 kB] Get:100 http://mirror.einval.org/debian unstable/main amd64 libunistring2 amd64 1.0-2 [437 kB] Get:101 http://mirror.einval.org/debian unstable/main amd64 libidn2-0 amd64 2.3.3-1+b1 [124 kB] Get:102 http://mirror.einval.org/debian unstable/main amd64 libffi8 amd64 3.4.4-1 [22.9 kB] Get:103 http://mirror.einval.org/debian unstable/main amd64 libp11-kit0 amd64 0.24.1-2 [345 kB] Get:104 http://mirror.einval.org/debian unstable/main amd64 libtasn1-6 amd64 4.19.0-2 [56.6 kB] Get:105 http://mirror.einval.org/debian unstable/main amd64 libgnutls30 amd64 3.7.9-2 [1403 kB] Get:106 http://mirror.einval.org/debian unstable/main amd64 libdb5.3 amd64 5.3.28+dfsg2-1 [697 kB] Get:107 http://mirror.einval.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-11 [20.1 kB] Get:108 http://mirror.einval.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg-11 [59.5 kB] Get:109 http://mirror.einval.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:110 http://mirror.einval.org/debian unstable/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get:111 http://mirror.einval.org/debian unstable/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:112 http://mirror.einval.org/debian unstable/main amd64 zlib1g amd64 1:1.2.13.dfsg-1 [86.7 kB] Get:113 http://mirror.einval.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:114 http://mirror.einval.org/debian unstable/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:115 http://mirror.einval.org/debian unstable/main amd64 libzstd1 amd64 1.5.4+dfsg2-5 [290 kB] Get:116 http://mirror.einval.org/debian unstable/main amd64 libcurl3-gnutls amd64 7.88.1-9 [381 kB] Get:117 http://mirror.einval.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 7.88.1-9 [481 kB] Get:118 http://mirror.einval.org/debian unstable/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:119 http://mirror.einval.org/debian unstable/main amd64 libdeflate-dev amd64 1.14-1 [53.3 kB] Get:120 http://mirror.einval.org/debian unstable/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:121 http://mirror.einval.org/debian unstable/main amd64 libitm1 amd64 12.2.0-14 [26.1 kB] Get:122 http://mirror.einval.org/debian unstable/main amd64 liblsan0 amd64 12.2.0-14 [969 kB] Get:123 http://mirror.einval.org/debian unstable/main amd64 libtsan2 amd64 12.2.0-14 [2196 kB] Get:124 http://mirror.einval.org/debian unstable/main amd64 libstdc++6 amd64 12.2.0-14 [614 kB] Get:125 http://mirror.einval.org/debian unstable/main amd64 libubsan1 amd64 12.2.0-14 [883 kB] Get:126 http://mirror.einval.org/debian unstable/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:127 http://mirror.einval.org/debian unstable/main amd64 libgcc-12-dev amd64 12.2.0-14 [2437 kB] Get:128 http://mirror.einval.org/debian unstable/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get:129 http://mirror.einval.org/debian unstable/main amd64 liblzma5 amd64 5.4.1-0.2 [205 kB] Get:130 http://mirror.einval.org/debian unstable/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get:131 http://mirror.einval.org/debian unstable/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB] Get:132 http://mirror.einval.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get:133 http://mirror.einval.org/debian unstable/main amd64 libhts-dev amd64 1.16+ds-3 [1601 kB] Get:134 http://mirror.einval.org/debian unstable/main arm64 libsimde-dev all 0.7.4~rc2-2 [377 kB] Get:135 http://mirror.einval.org/debian unstable/main amd64 libstdc++-12-dev amd64 12.2.0-14 [2046 kB] Get:136 http://mirror.einval.org/debian unstable/main arm64 xxd arm64 2:9.0.1378-1 [83.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 106 MB in 1s (81.3 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 10360 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-5_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../003-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... 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Unpacking libgcc-s1-amd64-cross (12.2.0-14cross1) ... Selecting previously unselected package libgomp1-amd64-cross. Preparing to unpack .../024-libgomp1-amd64-cross_12.2.0-14cross1_all.deb ... Unpacking libgomp1-amd64-cross (12.2.0-14cross1) ... Selecting previously unselected package libitm1-amd64-cross. Preparing to unpack .../025-libitm1-amd64-cross_12.2.0-14cross1_all.deb ... Unpacking libitm1-amd64-cross (12.2.0-14cross1) ... Selecting previously unselected package libatomic1-amd64-cross. Preparing to unpack .../026-libatomic1-amd64-cross_12.2.0-14cross1_all.deb ... Unpacking libatomic1-amd64-cross (12.2.0-14cross1) ... Selecting previously unselected package libasan8-amd64-cross. Preparing to unpack .../027-libasan8-amd64-cross_12.2.0-14cross1_all.deb ... Unpacking libasan8-amd64-cross (12.2.0-14cross1) ... Selecting previously unselected package liblsan0-amd64-cross. Preparing to unpack .../028-liblsan0-amd64-cross_12.2.0-14cross1_all.deb ... 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Unpacking dwz (0.15-1) ... Selecting previously unselected package gettext. Preparing to unpack .../067-gettext_0.21-12_arm64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../068-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../069-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../070-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libfakeroot:arm64. Preparing to unpack .../071-libfakeroot_1.31-1.2_arm64.deb ... Unpacking libfakeroot:arm64 (1.31-1.2) ... Selecting previously unselected package fakeroot. Preparing to unpack .../072-fakeroot_1.31-1.2_arm64.deb ... Unpacking fakeroot (1.31-1.2) ... 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Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... 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 libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+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... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up gcc-12-x86-64-linux-gnu (12.2.0-14cross1) ... Setting up gcc-x86-64-linux-gnu (4:12.2.0-3) ... Setting up debhelper (13.11.4) ... Setting up libxml-simple-perl (2.25-2) ... 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Setting up libssl3:amd64 (3.0.8-1) ... Setting up libnghttp2-14:amd64 (1.52.0-1) ... Setting up libunistring2:amd64 (1.0-2) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up zlib1g:amd64 (1:1.2.13.dfsg-1) ... Setting up libcrypt1:amd64 (1:4.4.33-2) ... Setting up libidn2-0:amd64 (2.3.3-1+b1) ... Setting up libcom-err2:amd64 (1.47.0-2) ... Setting up libgomp1:amd64 (12.2.0-14) ... Setting up libkrb5support0:amd64 (1.20.1-1+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-11) ... Setting up libnettle8:amd64 (3.8.1-2) ... Setting up libgmp10:amd64 (2:6.2.1+dfsg1-1.1) ... Setting up libquadmath0:amd64 (12.2.0-14) ... Setting up libp11-kit0:amd64 (0.24.1-2) ... Setting up libatomic1:amd64 (12.2.0-14) ... Setting up libk5crypto3:amd64 (1.20.1-1+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-11) ... Setting up liblzma-dev:amd64 (5.4.1-0.2) ... Setting up libubsan1:amd64 (12.2.0-14) ... Setting up libcrypt-dev:amd64 (1:4.4.33-2) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up libkrb5-3:amd64 (1.20.1-1+b1) ... Setting up libdeflate-dev:amd64 (1.14-1) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libhogweed6:amd64 (3.8.1-2) ... Setting up libgnutls30:amd64 (3.7.9-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libgcc-12-dev:amd64 (12.2.0-14) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-1+b1) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libtirpc-dev:amd64 (1.3.3+ds-1) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libcurl3-gnutls:amd64 (7.88.1-9) ... Setting up libcurl4-gnutls-dev:amd64 (7.88.1-9) ... Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up libc6-dev:amd64 (2.36-9) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libstdc++-12-dev:amd64 (12.2.0-14) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up libhts-dev:amd64 (1.16+ds-3) ... 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Processing triggers for libc-bin (2.36-9) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64 arm64 ppc64el mips64el) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-7-arm64 #1 SMP Debian 6.1.20-1 (2023-03-19) arm64 (aarch64) Toolchain package versions: binutils_2.40-2 dpkg-dev_1.21.21 g++-12_12.2.0-14 gcc-12_12.2.0-14 libc6-dev_2.36-9 libstdc++-12-dev_12.2.0-14 libstdc++-12-dev-amd64-cross_12.2.0-14cross1 libstdc++6_12.2.0-14 libstdc++6-amd64-cross_12.2.0-14cross1 linux-libc-dev_6.1.25-1 Package versions: apt_2.6.0 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-12 autotools-dev_20220109.1 base-files_12.4 base-passwd_3.6.1 bash_5.2.15-2+b2 binutils_2.40-2 binutils-aarch64-linux-gnu_2.40-2 binutils-common_2.40-2 binutils-x86-64-linux-gnu_2.40-2 bsdextrautils_2.38.1-5+b1 bsdutils_1:2.38.1-5+b1 build-essential_12.9 bzip2_1.0.8-5+b1 coreutils_9.1-1 cpp_4:12.2.0-3 cpp-12_12.2.0-14 cpp-12-x86-64-linux-gnu_12.2.0-14cross1 cpp-x86-64-linux-gnu_4:12.2.0-3 cross-config_2.6.20 crossbuild-essential-amd64_12.9 dash_0.5.12-2 debconf_1.5.82 debhelper_13.11.4 debian-archive-keyring_2023.3 debianutils_5.7-0.4 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dpkg_1.21.21 dpkg-cross_2.6.20 dpkg-dev_1.21.21 dwz_0.15-1 fakeroot_1.31-1.2 file_1:5.44-3 findutils_4.9.0-4 g++_4:12.2.0-3 g++-12_12.2.0-14 g++-12-x86-64-linux-gnu_12.2.0-14cross1 g++-x86-64-linux-gnu_4:12.2.0-3 gcc_4:12.2.0-3 gcc-12_12.2.0-14 gcc-12-base_12.2.0-14 gcc-12-cross-base_12.2.0-14cross1 gcc-12-x86-64-linux-gnu_12.2.0-14cross1 gcc-12-x86-64-linux-gnu-base_12.2.0-14cross1 gcc-x86-64-linux-gnu_4:12.2.0-3 gettext_0.21-12 gettext-base_0.21-12 gpgv_2.2.40-1.1 grep_3.8-5 groff-base_1.22.4-10 gzip_1.12-1 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapt-pkg6.0_2.6.0 libarchive-zip-perl_1.68-1 libasan8_12.2.0-14 libasan8-amd64-cross_12.2.0-14cross1 libatomic1_12.2.0-14 libatomic1-amd64-cross_12.2.0-14cross1 libattr1_1:2.5.1-4 libaudit-common_1:3.0.9-1 libaudit1_1:3.0.9-1 libbinutils_2.40-2 libblkid1_2.38.1-5+b1 libbrotli1_1.0.9-2+b6 libbz2-1.0_1.0.8-5+b1 libc-bin_2.36-9 libc-dev-bin_2.36-9 libc6_2.36-9 libc6-amd64-cross_2.36-8cross1 libc6-dev_2.36-9 libc6-dev-amd64-cross_2.36-8cross1 libcap-ng0_0.8.3-1+b3 libcap2_1:2.66-3 libcc1-0_12.2.0-14 libcom-err2_1.47.0-2 libconfig-auto-perl_0.44-2 libconfig-inifiles-perl_3.000003-2 libcrypt-dev_1:4.4.33-2 libcrypt1_1:4.4.33-2 libctf-nobfd0_2.40-2 libctf0_2.40-2 libcurl3-gnutls_7.88.1-9 libcurl4-gnutls-dev_7.88.1-9 libdb5.3_5.3.28+dfsg2-1 libdebconfclient0_0.269 libdebhelper-perl_13.11.4 libdebian-dpkgcross-perl_2.6.20 libdeflate-dev_1.14-1 libdeflate0_1.14-1 libdpkg-perl_1.21.21 libelf1_0.188-2.1 libfakeroot_1.31-1.2 libffi8_3.4.4-1 libfile-find-rule-perl_0.34-3 libfile-homedir-perl_1.006-2 libfile-stripnondeterminism-perl_1.13.1-1 libfile-which-perl_1.27-2 libgcc-12-dev_12.2.0-14 libgcc-12-dev-amd64-cross_12.2.0-14cross1 libgcc-s1_12.2.0-14 libgcc-s1-amd64-cross_12.2.0-14cross1 libgcrypt20_1.10.1-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.9-2 libgomp1_12.2.0-14 libgomp1-amd64-cross_12.2.0-14cross1 libgpg-error0_1.46-1 libgprofng0_2.40-2 libgssapi-krb5-2_1.20.1-1+b1 libhogweed6_3.8.1-2 libhts-dev_1.16+ds-3 libhts3_1.16+ds-3 libhtscodecs2_1.3.0-4 libhwasan0_12.2.0-14 libicu72_72.1-3 libidn2-0_2.3.3-1+b1 libio-string-perl_1.08-4 libisl23_0.25-1 libitm1_12.2.0-14 libitm1-amd64-cross_12.2.0-14cross1 libjansson4_2.14-2 libk5crypto3_1.20.1-1+b1 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-1+b1 libkrb5support0_1.20.1-1+b1 libldap-2.5-0_2.5.13+dfsg-5 liblocale-gettext-perl_1.07-5 liblsan0_12.2.0-14 liblsan0-amd64-cross_12.2.0-14cross1 liblz4-1_1.9.4-1 liblzma-dev_5.4.1-0.2 liblzma5_5.4.1-0.2 libmagic-mgc_1:5.44-3 libmagic1_1:5.44-3 libmd0_1.0.4-2 libmount1_2.38.1-5+b1 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libnettle8_3.8.1-2 libnghttp2-14_1.52.0-1 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnumber-compare-perl_0.03-3 libp11-kit0_0.24.1-2 libpam-modules_1.5.2-6 libpam-modules-bin_1.5.2-6 libpam-runtime_1.5.2-6 libpam0g_1.5.2-6 libpcre2-8-0_10.42-1 libperl5.36_5.36.0-7 libpipeline1_1.5.7-1 libpsl5_0.21.2-1 libquadmath0_12.2.0-14 libquadmath0-amd64-cross_12.2.0-14cross1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-11 libsasl2-modules-db_2.1.28+dfsg-11 libseccomp2_2.5.4-1+b3 libselinux1_3.4-1+b5 libsimde-dev_0.7.4~rc2-2 libsmartcols1_2.38.1-5+b1 libssh2-1_1.10.0-3+b1 libssl3_3.0.8-1 libstdc++-12-dev_12.2.0-14 libstdc++-12-dev-amd64-cross_12.2.0-14cross1 libstdc++6_12.2.0-14 libstdc++6-amd64-cross_12.2.0-14cross1 libsub-override-perl_0.09-4 libsystemd0_252.6-1 libtasn1-6_4.19.0-2 libtext-glob-perl_0.11-3 libtinfo6_6.4-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libtsan2_12.2.0-14 libtsan2-amd64-cross_12.2.0-14cross1 libubsan1_12.2.0-14 libubsan1-amd64-cross_12.2.0-14cross1 libuchardet0_0.0.7-1 libudev1_252.6-1 libunistring2_1.0-2 libuuid1_2.38.1-5+b1 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b1 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-2 libxml2_2.9.14+dfsg-1.2 libxxhash0_0.8.1-1 libyaml-perl_1.30-2 libzstd1_1.5.4+dfsg2-5 linux-libc-dev_6.1.25-1 linux-libc-dev-amd64-cross_6.1.4-1cross1 login_1:4.13+dfsg1-1+b1 m4_1.4.19-3 make_4.3-4.1 man-db_2.11.2-2 mawk_1.3.4.20200120-3.1 ncurses-base_6.4-2 ncurses-bin_6.4-2 patch_2.7.6-7 perl_5.36.0-7 perl-base_5.36.0-7 perl-modules-5.36_5.36.0-7 po-debconf_1.0.21+nmu1 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.17+nmu1 sysvinit-utils_3.06-4 tar_1.34+dfsg-1.2 ucf_3.0043+nmu1 usrmerge_35 util-linux_2.38.1-5+b1 util-linux-extra_2.38.1-5+b1 xxd_2:9.0.1378-1 xz-utils_5.4.1-0.2 zlib1g_1:1.2.13.dfsg-1 zlib1g-dev_1:1.2.13.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rna-star Binary: rna-star Architecture: amd64 arm64 ppc64el mips64el Version: 2.7.10b+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Sascha Steinbiss , Homepage: https://github.com/alexdobin/STAR/ Standards-Version: 4.6.2 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), libhts-dev, xxd, zlib1g-dev, libsimde-dev Package-List: rna-star deb science optional arch=amd64,arm64,ppc64el,mips64el Checksums-Sha1: 38cedf2bdb3420d87f32466578913d4312d50d41 619528 rna-star_2.7.10b+dfsg.orig.tar.xz 253f000719fb12c4e037d3066c85d024c32ac2b6 378136 rna-star_2.7.10b+dfsg-2.debian.tar.xz Checksums-Sha256: 77b61638b3eda7f429364b1f1ff8fc806d95ee55a3c5992c25b29a641c9a83c4 619528 rna-star_2.7.10b+dfsg.orig.tar.xz 62fb8dac5feb22cbcab53c12e57dac4a4f6763171f67d0c8c3b3ee12ff1645d3 378136 rna-star_2.7.10b+dfsg-2.debian.tar.xz Files: 20e0f5ac4f2da8d32502a153fbdd2815 619528 rna-star_2.7.10b+dfsg.orig.tar.xz 806af201cdfd2517402e3db64006d400 378136 rna-star_2.7.10b+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmPNSjAACgkQPCZ2P2xn 5uLkKBAAmzwtNuFiuRbG2ACCTOdOI0ELa9HAZ7lsIzg+1stnlzXHpja1Y9Qm34kA OaG8dKXq4fecVkPXnD+1ff4cxx9w0c+HbfRcBVPAVfGBo2Y1xscttQARoq/3WNcf Lxfr41n7HOXjNySNAWcY+SLlYbGPsg9W5oMAPsHY90avp7Z9t+JgMn6rqsaWqxpf 7PJ5lWS4G460yZVV+B1U0vc2oeFQS42TTgsHESa5WHeihSi9UWV7M3thfCtmDjgy 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info: applying donotuse_own_htslib.patch dpkg-source: info: applying mips_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 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=/var/lib/sbuild LANG=en_GB.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aamd64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package rna-star dpkg-buildpackage: info: source version 2.7.10b+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe 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 '/<>' cd source && /usr/bin/make clean make[2]: Entering directory '/<>/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/<>/source' make[1]: Leaving directory '/<>' 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 '/<>' mkdir --parents /<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-sse3 STARlong-sse3 && true cd source && make -j1 clean make[2]: Entering directory '/<>/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-avx2 STARlong-avx2 make[2]: Entering directory '/<>/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 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 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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' systemFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMI_Graph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMIall.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersClip_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clip.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 opal.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clipChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_loadRawMatrix.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_emptyDrops_CR.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' soloInputFeatureUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countSmartSeq.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_redistributeReadsByCB.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_quantTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_sumThreads.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countVelocyto.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countCBgeneUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_classifyAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_cellFiltering.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_statsOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamSortByCoordinate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersSolo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode_getCBandUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode_extractBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_inputRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Solo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_processRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_addBAMtags.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_convertGenomeCigar.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' twoPassRunPass1.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' samHeaders.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swScoreSpliced.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swTraceBack.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_findSuperTr.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjAlignSplit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_transcriptGeneSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_superTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SuperTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputAlignments.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' STAR.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:190:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:194:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 194 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SharedMemory.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' PackedArray.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_samAttributes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' InOutStreams.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_alignScore.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_generateCigarP.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Chain.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_variationAdjust.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Variation.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_waspMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_storeAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchPieces.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_multMapSelect.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' readLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_processChunks.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_mapChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' OutSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' outputSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' blocksOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ThreadControl.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sysRemoveDir.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_maxMappableLength2strands.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' binarySearch2.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_assignAlignToWindow.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_oneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchWindowSeeds.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_peOverlapMergeMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mappedFilter.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersChimeric_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOld.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection_chimericDetectionMult.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchWindowAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' extendAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchAlignToTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericJunctionOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericBAMoutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericStitching.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeGenerate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeParametersWrite.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeScanFastaFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeSAindex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_insertSequences.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' insertSeqSA.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixesMemcmp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' TimeFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ErrorWarning.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' streamFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stringSubstituteAll.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_quantAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_quantTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Quantifications.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneCountsAddAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromStream.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbPrepare.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbBuildIndex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbInsertJunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' mapThreadsSpawn.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readFilesInit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bam_cat.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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' serviceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_alignBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' signalFromBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 systemFunctions.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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 systemFunctions.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 '/<>/source' cd source && make -j1 clean make[2]: Entering directory '/<>/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-avx STARlong-avx make[2]: Entering directory '/<>/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 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 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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' systemFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMI_Graph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMIall.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersClip_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clip.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx opal.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clipChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_loadRawMatrix.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_emptyDrops_CR.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' soloInputFeatureUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countSmartSeq.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_redistributeReadsByCB.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_quantTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_sumThreads.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countVelocyto.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countCBgeneUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_classifyAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_cellFiltering.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_statsOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamSortByCoordinate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersSolo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode_getCBandUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode_extractBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_inputRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Solo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_processRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_addBAMtags.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_convertGenomeCigar.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' twoPassRunPass1.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' samHeaders.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swScoreSpliced.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swTraceBack.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_findSuperTr.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjAlignSplit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_transcriptGeneSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_superTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SuperTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputAlignments.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' STAR.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:190:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:194:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 194 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SharedMemory.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' PackedArray.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_samAttributes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' InOutStreams.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_alignScore.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_generateCigarP.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Chain.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_variationAdjust.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Variation.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_waspMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_storeAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchPieces.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_multMapSelect.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' readLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_processChunks.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_mapChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' OutSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' outputSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' blocksOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ThreadControl.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sysRemoveDir.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_maxMappableLength2strands.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' binarySearch2.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_assignAlignToWindow.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_oneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchWindowSeeds.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_peOverlapMergeMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mappedFilter.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersChimeric_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOld.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection_chimericDetectionMult.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchWindowAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' extendAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchAlignToTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericJunctionOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericBAMoutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericStitching.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeGenerate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeParametersWrite.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeScanFastaFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeSAindex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_insertSequences.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' insertSeqSA.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixesMemcmp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' TimeFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ErrorWarning.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' streamFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stringSubstituteAll.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_quantAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_quantTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Quantifications.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneCountsAddAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromStream.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbPrepare.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbBuildIndex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbInsertJunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' mapThreadsSpawn.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readFilesInit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bam_cat.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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' serviceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_alignBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' signalFromBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx systemFunctions.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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx systemFunctions.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 '/<>/source' cd source && make -j1 clean make[2]: Entering directory '/<>/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-sse4.1 STARlong-sse4.1 make[2]: Entering directory '/<>/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 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 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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' systemFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMI_Graph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMIall.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersClip_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clip.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 opal.cpp In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | 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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clipChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_loadRawMatrix.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_emptyDrops_CR.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' soloInputFeatureUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countSmartSeq.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_redistributeReadsByCB.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_quantTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_sumThreads.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countVelocyto.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countCBgeneUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_classifyAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_cellFiltering.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_statsOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamSortByCoordinate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersSolo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode_getCBandUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode_extractBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_inputRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Solo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_processRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_addBAMtags.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_convertGenomeCigar.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' twoPassRunPass1.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' samHeaders.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swScoreSpliced.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swTraceBack.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_findSuperTr.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjAlignSplit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_transcriptGeneSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_superTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SuperTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputAlignments.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' STAR.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:190:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:194:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 194 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SharedMemory.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' PackedArray.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_samAttributes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' InOutStreams.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_alignScore.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_generateCigarP.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Chain.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_variationAdjust.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Variation.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_waspMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_storeAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchPieces.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_multMapSelect.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' readLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_processChunks.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_mapChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' OutSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' outputSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' blocksOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ThreadControl.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sysRemoveDir.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_maxMappableLength2strands.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' binarySearch2.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_assignAlignToWindow.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_oneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchWindowSeeds.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_peOverlapMergeMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mappedFilter.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersChimeric_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOld.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection_chimericDetectionMult.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchWindowAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' extendAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchAlignToTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericJunctionOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericBAMoutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericStitching.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeGenerate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeParametersWrite.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeScanFastaFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeSAindex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_insertSequences.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' insertSeqSA.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixesMemcmp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' TimeFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ErrorWarning.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' streamFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stringSubstituteAll.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_quantAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_quantTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Quantifications.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneCountsAddAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromStream.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbPrepare.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbBuildIndex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbInsertJunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' mapThreadsSpawn.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readFilesInit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bam_cat.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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' serviceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_alignBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' signalFromBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 systemFunctions.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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 systemFunctions.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 '/<>/source' cd source && make -j1 clean make[2]: Entering directory '/<>/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-ssse3 STARlong-ssse3 make[2]: Entering directory '/<>/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 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 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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' systemFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMI_Graph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMIall.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersClip_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clip.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 opal.cpp In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | 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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clipChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_loadRawMatrix.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_emptyDrops_CR.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' soloInputFeatureUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countSmartSeq.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_redistributeReadsByCB.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_quantTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_sumThreads.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countVelocyto.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countCBgeneUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_classifyAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_cellFiltering.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_statsOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamSortByCoordinate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersSolo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode_getCBandUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode_extractBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_inputRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Solo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_processRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_addBAMtags.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_convertGenomeCigar.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' twoPassRunPass1.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' samHeaders.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swScoreSpliced.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swTraceBack.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_findSuperTr.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjAlignSplit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_transcriptGeneSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_superTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SuperTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputAlignments.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' STAR.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:190:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:194:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 194 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SharedMemory.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' PackedArray.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_samAttributes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' InOutStreams.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_alignScore.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_generateCigarP.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Chain.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_variationAdjust.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Variation.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_waspMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_storeAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchPieces.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_multMapSelect.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' readLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_processChunks.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_mapChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' OutSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' outputSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' blocksOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ThreadControl.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sysRemoveDir.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_maxMappableLength2strands.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' binarySearch2.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_assignAlignToWindow.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_oneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchWindowSeeds.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_peOverlapMergeMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mappedFilter.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersChimeric_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOld.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection_chimericDetectionMult.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchWindowAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' extendAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchAlignToTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericJunctionOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericBAMoutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericStitching.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeGenerate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeParametersWrite.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeScanFastaFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeSAindex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_insertSequences.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' insertSeqSA.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixesMemcmp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' TimeFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ErrorWarning.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' streamFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stringSubstituteAll.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_quantAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_quantTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Quantifications.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneCountsAddAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromStream.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbPrepare.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbBuildIndex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbInsertJunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' mapThreadsSpawn.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readFilesInit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bam_cat.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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' serviceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_alignBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' signalFromBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 systemFunctions.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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 systemFunctions.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 '/<>/source' cd source && make -j1 clean make[2]: Entering directory '/<>/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-sse3 STARlong-sse3 make[2]: Entering directory '/<>/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 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 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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' systemFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMI_Graph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_collapseUMIall.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersClip_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clip.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 opal.cpp In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | 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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_clipChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ClipMate_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_loadRawMatrix.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_emptyDrops_CR.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' soloInputFeatureUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countSmartSeq.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_redistributeReadsByCB.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_quantTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_sumThreads.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countVelocyto.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countCBgeneUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_classifyAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_cellFiltering.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_statsOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamSortByCoordinate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersSolo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloRead_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadBarcode_getCBandUMI.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloBarcode_extractBarcode.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_record.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloReadFeature_inputRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Solo.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_processRecords.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_addBAMtags.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_convertGenomeCigar.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' twoPassRunPass1.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' samHeaders.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_transformGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swScoreSpliced.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swTraceBack.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_findSuperTr.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjAlignSplit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_transcriptGeneSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_superTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SuperTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputAlignments.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' STAR.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:190:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:194:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 194 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SharedMemory.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' PackedArray.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_samAttributes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' InOutStreams.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_alignScore.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_generateCigarP.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Chain.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_variationAdjust.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Variation.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_waspMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_storeAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchPieces.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_multMapSelect.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' readLoad.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_processChunks.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlignChunk_mapChunk.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' OutSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' outputSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' blocksOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ThreadControl.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sysRemoveDir.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_maxMappableLength2strands.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' binarySearch2.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptSJ.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_assignAlignToWindow.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_oneRead.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_stitchWindowSeeds.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_peOverlapMergeMap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mappedFilter.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersChimeric_initialize.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOld.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericDetection_chimericDetectionMult.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchWindowAligns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' extendAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stitchAlignToTranscript.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericJunctionOutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericBAMoutput.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ChimericAlign_chimericStitching.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeGenerate.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeParametersWrite.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeScanFastaFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' genomeSAindex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_insertSequences.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' insertSeqSA.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixes.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' funCompareUintAndSuffixesMemcmp.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' TimeFunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ErrorWarning.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' streamFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' stringSubstituteAll.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_quantAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_quantTranscriptome.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Quantifications.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneCountsAddAlign.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromFiles.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbLoadFromStream.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbPrepare.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbBuildIndex.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjdbInsertJunctions.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' mapThreadsSpawn.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readFilesInit.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bam_cat.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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' serviceFuns.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_alignBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' signalFromBAM.cpp x86_64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 systemFunctions.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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 systemFunctions.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 '/<>/source' dh_auto_clean ; dh_auto_build -- SFX=-plain CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 '/<>/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CCFLAGS=-flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 '/<>/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 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 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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 opal.cpp In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | 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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' STAR.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:190:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:194:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 194 | 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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bam_cat.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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 systemFunctions.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 24 LTRANS jobs lto-wrapper: note: see the ‘-flto’ option documentation for more information In function ‘searchDatabase_’, inlined from ‘searchDatabase’ at opal/opal.cpp:1013:21, inlined from ‘opalSearchDatabase’ at opal/opal.cpp:1465:46, inlined from ‘opalAlign’ at ClipCR4.cpp:77:23, inlined from ‘clipChunk’ at ClipMate_clipChunk.cpp:41:23, inlined from ‘mapChunk’ at ReadAlignChunk_mapChunk.cpp:10:39: 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 | ^ In function ‘opalSearchDatabase’, inlined from ‘opalAlign’ at ClipCR4.cpp:77:23, inlined from ‘clipChunk’ at ClipMate_clipChunk.cpp:41:23, inlined from ‘mapChunk’ at ReadAlignChunk_mapChunk.cpp:10:39: opal/opal.cpp:1450:35: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1450 | bool *skip = new bool[dbLength]; | ^ /usr/x86_64-linux-gnu/include/c++/12/new: In member function ‘mapChunk’: /usr/x86_64-linux-gnu/include/c++/12/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘assign’, inlined from ‘_M_set_length’ at /usr/x86_64-linux-gnu/include/c++/12/bits/basic_string.h:268:21, inlined from ‘__ct ’ at /usr/x86_64-linux-gnu/include/c++/12/bits/basic_string.h:520:15, inlined from ‘signalFromBAM’ at signalFromBAM.cpp:44:43: /usr/x86_64-linux-gnu/include/c++/12/bits/char_traits.h:354:14: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 354 | __c1 = __c2; | ^ signalFromBAM.cpp: In function ‘signalFromBAM’: signalFromBAM.cpp:44:43: note: at offset 152 into destination object of size [72, 136] allocated by ‘operator new []’ 44 | string* sigOutFileName=new string[sigN]; | ^ 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="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILE_FOR_LONG_READS' -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 systemFunctions.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:210:14: warning: type of ‘calcCIGAR’ does not match original declaration [-Wlto-type-mismatch] 210 | 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 24 LTRANS jobs lto-wrapper: note: see the ‘-flto’ option documentation for more information In function ‘searchDatabase_’, inlined from ‘searchDatabase’ at opal/opal.cpp:1013:21, inlined from ‘opalSearchDatabase’ at opal/opal.cpp:1465:46, inlined from ‘opalAlign’ at ClipCR4.cpp:77:23, inlined from ‘clipChunk’ at ClipMate_clipChunk.cpp:41:23, inlined from ‘mapChunk’ at ReadAlignChunk_mapChunk.cpp:10:39: 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 | ^ In function ‘opalSearchDatabase’, inlined from ‘opalAlign’ at ClipCR4.cpp:77:23, inlined from ‘clipChunk’ at ClipMate_clipChunk.cpp:41:23, inlined from ‘mapChunk’ at ReadAlignChunk_mapChunk.cpp:10:39: opal/opal.cpp:1450:35: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1450 | bool *skip = new bool[dbLength]; | ^ /usr/x86_64-linux-gnu/include/c++/12/new: In member function ‘mapChunk’: /usr/x86_64-linux-gnu/include/c++/12/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘assign’, inlined from ‘_M_set_length’ at /usr/x86_64-linux-gnu/include/c++/12/bits/basic_string.h:268:21, inlined from ‘__ct ’ at /usr/x86_64-linux-gnu/include/c++/12/bits/basic_string.h:520:15, inlined from ‘signalFromBAM’ at signalFromBAM.cpp:44:43: /usr/x86_64-linux-gnu/include/c++/12/bits/char_traits.h:354:14: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 354 | __c1 = __c2; | ^ signalFromBAM.cpp: In function ‘signalFromBAM’: signalFromBAM.cpp:44:43: note: at offset 152 into destination object of size [72, 136] allocated by ‘operator new []’ 44 | string* sigOutFileName=new string[sigN]; | ^ 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 '/<>/source' cp source/STAR-plain source/STARlong-plain /<>/debian/rna-star/usr/lib/rna-star/bin/ make[1]: Leaving directory '/<>' 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 '/<>' mkdir --parents /<>/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 /<>/debian/rna-star/usr/bin && for prog in STAR STARlong ; do ln -s \ ../lib/rna-star/simd-dispatch ${prog} ; done make[1]: Leaving directory '/<>' 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 '/<>' dh_compress --exclude=.pdf make[1]: Leaving directory '/<>' 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 '/<>' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.4~rc2-2), " make[1]: Leaving directory '/<>' dh_md5sums -a -O--sourcedirectory=source dh_builddeb -a -O--sourcedirectory=source dpkg-deb: building package 'rna-star' in '../rna-star_2.7.10b+dfsg-2_amd64.deb'. dpkg-deb: building package 'rna-star-dbgsym' in '../rna-star-dbgsym_2.7.10b+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=any -O../rna-star_2.7.10b+dfsg-2_amd64.buildinfo dpkg-genchanges --build=any -O../rna-star_2.7.10b+dfsg-2_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 2023-05-03T21:46:40Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ rna-star_2.7.10b+dfsg-2_amd64.changes: -------------------------------------- Format: 1.8 Date: Sun, 22 Jan 2023 15:33:29 +0100 Source: rna-star Binary: rna-star rna-star-dbgsym Built-For-Profiles: cross nocheck Architecture: amd64 Version: 2.7.10b+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: rna-star - ultrafast universal RNA-seq aligner Changes: rna-star (2.7.10b+dfsg-2) unstable; urgency=medium . * Team upload. * debian/patches/packaged_simde: Use packaged SIMDe header, not the code-copy. * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: 444496bb71c118ff3eab04b4cfd45a800cece8a4 78080192 rna-star-dbgsym_2.7.10b+dfsg-2_amd64.deb e4711217c5f4b306d38c70e83267002c2fa055a7 5927 rna-star_2.7.10b+dfsg-2_amd64.buildinfo 92a3c8708aa68ce7d4ed72da50156464675f61b7 3445032 rna-star_2.7.10b+dfsg-2_amd64.deb Checksums-Sha256: e4625f6af62d41c6ed5a1976e4019351c274c4a3fd888f86cd3c78e35e5cef91 78080192 rna-star-dbgsym_2.7.10b+dfsg-2_amd64.deb 7b489f080fb260ac5c115531054b67f54997ae132da07ffd13d0c14a9fc40ce4 5927 rna-star_2.7.10b+dfsg-2_amd64.buildinfo 0014fbe9d62dbc9175d7ccfaebb7eaecb140422bb9af6a5b261f2e117ad123a3 3445032 rna-star_2.7.10b+dfsg-2_amd64.deb Files: c759eb183357644021a4e6fd7aa5a955 78080192 debug optional rna-star-dbgsym_2.7.10b+dfsg-2_amd64.deb c0b4b4f903a399e53aae8dbee99495a4 5927 science optional rna-star_2.7.10b+dfsg-2_amd64.buildinfo 05fec30cb5cf467117b8539c8beb0407 3445032 science optional rna-star_2.7.10b+dfsg-2_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: rna-star Binary: rna-star rna-star-dbgsym Architecture: amd64 Version: 2.7.10b+dfsg-2 Checksums-Md5: c759eb183357644021a4e6fd7aa5a955 78080192 rna-star-dbgsym_2.7.10b+dfsg-2_amd64.deb 05fec30cb5cf467117b8539c8beb0407 3445032 rna-star_2.7.10b+dfsg-2_amd64.deb Checksums-Sha1: 444496bb71c118ff3eab04b4cfd45a800cece8a4 78080192 rna-star-dbgsym_2.7.10b+dfsg-2_amd64.deb 92a3c8708aa68ce7d4ed72da50156464675f61b7 3445032 rna-star_2.7.10b+dfsg-2_amd64.deb Checksums-Sha256: e4625f6af62d41c6ed5a1976e4019351c274c4a3fd888f86cd3c78e35e5cef91 78080192 rna-star-dbgsym_2.7.10b+dfsg-2_amd64.deb 0014fbe9d62dbc9175d7ccfaebb7eaecb140422bb9af6a5b261f2e117ad123a3 3445032 rna-star_2.7.10b+dfsg-2_amd64.deb Build-Origin: Debian Build-Architecture: arm64 Build-Date: Wed, 03 May 2023 21:46:36 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-12), autotools-dev (= 20220109.1), base-files (= 12.4), base-passwd (= 3.6.1), bash (= 5.2.15-2+b2), binutils (= 2.40-2), binutils-aarch64-linux-gnu (= 2.40-2), binutils-common (= 2.40-2), bsdextrautils (= 2.38.1-5+b1), bsdutils (= 1:2.38.1-5+b1), build-essential (= 12.9), bzip2 (= 1.0.8-5+b1), coreutils (= 9.1-1), cpp (= 4:12.2.0-3), cpp-12 (= 12.2.0-14), dash (= 0.5.12-2), debconf (= 1.5.82), debhelper (= 13.11.4), debianutils (= 5.7-0.4), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.8-4), dpkg (= 1.21.21), dpkg-dev (= 1.21.21), dwz (= 0.15-1), file (= 1:5.44-3), findutils (= 4.9.0-4), g++ (= 4:12.2.0-3), g++-12 (= 12.2.0-14), gcc (= 4:12.2.0-3), gcc-12 (= 12.2.0-14), gcc-12-base (= 12.2.0-14), gettext (= 0.21-12), gettext-base (= 0.21-12), grep (= 3.8-5), groff-base (= 1.22.4-10), gzip (= 1.12-1), hostname (= 3.23+nmu1), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 12.2.0-14), libatomic1 (= 12.2.0-14), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.0.9-1), libaudit1 (= 1:3.0.9-1), libbinutils (= 2.40-2), libblkid1 (= 2.38.1-5+b1), libbrotli1 (= 1.0.9-2+b6), libbz2-1.0 (= 1.0.8-5+b1), libc-bin (= 2.36-9), libc-dev-bin (= 2.36-9), libc6 (= 2.36-9), libc6-dev (= 2.36-9), libcap-ng0 (= 0.8.3-1+b3), libcap2 (= 1:2.66-3), libcc1-0 (= 12.2.0-14), libcom-err2 (= 1.47.0-2), libcrypt-dev (= 1:4.4.33-2), libcrypt1 (= 1:4.4.33-2), libctf-nobfd0 (= 2.40-2), libctf0 (= 2.40-2), libcurl3-gnutls (= 7.88.1-9), libcurl4-gnutls-dev (= 7.88.1-9), libdb5.3 (= 5.3.28+dfsg2-1), libdebconfclient0 (= 0.269), libdebhelper-perl (= 13.11.4), libdeflate-dev (= 1.14-1), libdeflate0 (= 1.14-1), libdpkg-perl (= 1.21.21), libelf1 (= 0.188-2.1), libffi8 (= 3.4.4-1), libfile-find-rule-perl (= 0.34-3), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-12-dev (= 12.2.0-14), libgcc-s1 (= 12.2.0-14), libgcrypt20 (= 1.10.1-3), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgmp10 (= 2:6.2.1+dfsg1-1.1), libgnutls30 (= 3.7.9-2), libgomp1 (= 12.2.0-14), libgpg-error0 (= 1.46-1), libgprofng0 (= 2.40-2), libgssapi-krb5-2 (= 1.20.1-1+b1), libhogweed6 (= 3.8.1-2), libhts-dev (= 1.16+ds-3), libhts3 (= 1.16+ds-3), libhtscodecs2 (= 1.3.0-4), libicu72 (= 72.1-3), libidn2-0 (= 2.3.3-1+b1), libisl23 (= 0.25-1), libitm1 (= 12.2.0-14), libjansson4 (= 2.14-2), libk5crypto3 (= 1.20.1-1+b1), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-1+b1), libkrb5support0 (= 1.20.1-1+b1), libldap-2.5-0 (= 2.5.13+dfsg-5), liblsan0 (= 12.2.0-14), liblz4-1 (= 1.9.4-1), liblzma-dev (= 5.4.1-0.2), liblzma5 (= 5.4.1-0.2), libmagic-mgc (= 1:5.44-3), libmagic1 (= 1:5.44-3), libmd0 (= 1.0.4-2), libmount1 (= 2.38.1-5+b1), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.0-1), libnettle8 (= 3.8.1-2), libnghttp2-14 (= 1.52.0-1), libnsl-dev (= 1.3.0-2), libnsl2 (= 1.3.0-2), libnumber-compare-perl (= 0.03-3), libp11-kit0 (= 0.24.1-2), libpam-modules (= 1.5.2-6), libpam-modules-bin (= 1.5.2-6), libpam-runtime (= 1.5.2-6), libpam0g (= 1.5.2-6), libpcre2-8-0 (= 10.42-1), libperl5.36 (= 5.36.0-7), libpipeline1 (= 1.5.7-1), libpsl5 (= 0.21.2-1), libquadmath0 (= 12.2.0-14), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2), libsasl2-2 (= 2.1.28+dfsg-11), libsasl2-modules-db (= 2.1.28+dfsg-11), libseccomp2 (= 2.5.4-1+b3), libselinux1 (= 3.4-1+b5), libsimde-dev (= 0.7.4~rc2-2), libsmartcols1 (= 2.38.1-5+b1), libssh2-1 (= 1.10.0-3+b1), libssl3 (= 3.0.8-1), libstdc++-12-dev (= 12.2.0-14), libstdc++6 (= 12.2.0-14), libsub-override-perl (= 0.09-4), libsystemd0 (= 252.6-1), libtasn1-6 (= 4.19.0-2), libtext-glob-perl (= 0.11-3), libtinfo6 (= 6.4-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-5), libtsan2 (= 12.2.0-14), libubsan1 (= 12.2.0-14), libuchardet0 (= 0.0.7-1), libudev1 (= 252.6-1), libunistring2 (= 1.0-2), libuuid1 (= 2.38.1-5+b1), libxml2 (= 2.9.14+dfsg-1.2), libzstd1 (= 1.5.4+dfsg2-5), linux-libc-dev (= 6.1.25-1), login (= 1:4.13+dfsg1-1+b1), m4 (= 1.4.19-3), make (= 4.3-4.1), man-db (= 2.11.2-2), mawk (= 1.3.4.20200120-3.1), ncurses-base (= 6.4-2), ncurses-bin (= 6.4-2), patch (= 2.7.6-7), perl (= 5.36.0-7), perl-base (= 5.36.0-7), perl-modules-5.36 (= 5.36.0-7), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-1), sensible-utils (= 0.0.17+nmu1), sysvinit-utils (= 3.06-4), tar (= 1.34+dfsg-1.2), usrmerge (= 35), util-linux (= 2.38.1-5+b1), util-linux-extra (= 2.38.1-5+b1), xxd (= 2:9.0.1378-1), xz-utils (= 5.4.1-0.2), zlib1g (= 1:1.2.13.dfsg-1), zlib1g-dev (= 1:1.2.13.dfsg-1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_GB.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1674398009" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ rna-star-dbgsym_2.7.10b+dfsg-2_amd64.deb ---------------------------------------- new Debian package, version 2.0. size 78080192 bytes: control archive=908 bytes. 636 bytes, 12 lines control 827 bytes, 8 lines md5sums Package: rna-star-dbgsym Source: rna-star Version: 2.7.10b+dfsg-2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 78454 Depends: rna-star (= 2.7.10b+dfsg-2) Section: debug Priority: optional Description: debug symbols for rna-star Build-Ids: 64566d95ef8d8aeb477c05c5da463d78635533d4 6668609c24b5accd8acadd576e8e3fc1ceb82688 90d779157494c9aa90e9460fffd3f313d325bad1 9fdea4a07d0e1b9da0f6177e270a6d46c9ca0673 d7d4281226de7dfa353298ff34e36037573afc22 e273544202f19a030eb8f4c92f1b19264ded21af f8e45fca605bd8d609760a923057d7bab92c872e drwxr-xr-x root/root 0 2023-01-22 14:33 ./ drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/ drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/lib/ drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/lib/debug/ drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/lib/debug/.build-id/64/ -rw-r--r-- root/root 11149008 2023-01-22 14:33 ./usr/lib/debug/.build-id/64/566d95ef8d8aeb477c05c5da463d78635533d4.debug drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/lib/debug/.build-id/66/ -rw-r--r-- root/root 11163904 2023-01-22 14:33 ./usr/lib/debug/.build-id/66/68609c24b5accd8acadd576e8e3fc1ceb82688.debug drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/lib/debug/.build-id/90/ -rw-r--r-- root/root 6557096 2023-01-22 14:33 ./usr/lib/debug/.build-id/90/d779157494c9aa90e9460fffd3f313d325bad1.debug drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/lib/debug/.build-id/9f/ -rw-r--r-- root/root 6556136 2023-01-22 14:33 ./usr/lib/debug/.build-id/9f/dea4a07d0e1b9da0f6177e270a6d46c9ca0673.debug drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/lib/debug/.build-id/d7/ -rw-r--r-- root/root 11251816 2023-01-22 14:33 ./usr/lib/debug/.build-id/d7/d4281226de7dfa353298ff34e36037573afc22.debug drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/lib/debug/.build-id/e2/ -rw-r--r-- root/root 11165952 2023-01-22 14:33 ./usr/lib/debug/.build-id/e2/73544202f19a030eb8f4c92f1b19264ded21af.debug drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/lib/debug/.build-id/f8/ -rw-r--r-- root/root 11232640 2023-01-22 14:33 ./usr/lib/debug/.build-id/f8/e45fca605bd8d609760a923057d7bab92c872e.debug drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 11236528 2023-01-22 14:33 ./usr/lib/debug/.dwz/x86_64-linux-gnu/rna-star.debug drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/share/ drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/share/doc/ lrwxrwxrwx root/root 0 2023-01-22 14:33 ./usr/share/doc/rna-star-dbgsym -> rna-star rna-star_2.7.10b+dfsg-2_amd64.deb --------------------------------- new Debian package, version 2.0. size 3445032 bytes: control archive=1644 bytes. 1408 bytes, 25 lines control 1509 bytes, 22 lines md5sums Package: rna-star Version: 2.7.10b+dfsg-2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 21812 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.3.1), libgomp1 (>= 6), libhts3 (>= 1.10), libstdc++6 (>= 11) Built-Using: simde (= 0.7.4~rc2-2) 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 2023-01-22 14:33 ./ drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/ drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/bin/ lrwxrwxrwx root/root 0 2023-01-22 14:33 ./usr/bin/STAR -> ../lib/rna-star/simd-dispatch lrwxrwxrwx root/root 0 2023-01-22 14:33 ./usr/bin/STARlong -> ../lib/rna-star/simd-dispatch drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/lib/ drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/lib/rna-star/ drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/lib/rna-star/bin/ -rwxr-xr-x root/root 1957872 2023-01-22 14:33 ./usr/lib/rna-star/bin/STAR-avx -rwxr-xr-x root/root 1957872 2023-01-22 14:33 ./usr/lib/rna-star/bin/STAR-avx2 -rwxr-xr-x root/root 1359824 2023-01-22 14:33 ./usr/lib/rna-star/bin/STAR-plain -rwxr-xr-x root/root 1921008 2023-01-22 14:33 ./usr/lib/rna-star/bin/STAR-sse3 -rwxr-xr-x root/root 1900528 2023-01-22 14:33 ./usr/lib/rna-star/bin/STAR-sse4.1 -rwxr-xr-x root/root 1925104 2023-01-22 14:33 ./usr/lib/rna-star/bin/STAR-ssse3 -rwxr-xr-x root/root 1957872 2023-01-22 14:33 ./usr/lib/rna-star/bin/STARlong-avx -rwxr-xr-x root/root 1957872 2023-01-22 14:33 ./usr/lib/rna-star/bin/STARlong-avx2 -rwxr-xr-x root/root 1359824 2023-01-22 14:33 ./usr/lib/rna-star/bin/STARlong-plain -rwxr-xr-x root/root 1921008 2023-01-22 14:33 ./usr/lib/rna-star/bin/STARlong-sse3 -rwxr-xr-x root/root 1900528 2023-01-22 14:33 ./usr/lib/rna-star/bin/STARlong-sse4.1 -rwxr-xr-x root/root 1925104 2023-01-22 14:33 ./usr/lib/rna-star/bin/STARlong-ssse3 -rwxr-xr-x root/root 380 2021-03-01 19:12 ./usr/lib/rna-star/simd-dispatch drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/share/ drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/share/doc-base/ -rw-r--r-- root/root 1179 2019-12-17 15:00 ./usr/share/doc-base/rna-star.rna-star drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/share/doc/rna-star/ -rw-r--r-- root/root 220 2019-12-17 15:00 ./usr/share/doc/rna-star/README.Debian -rw-r--r-- root/root 3547 2022-11-01 14:50 ./usr/share/doc/rna-star/README.md -rw-r--r-- root/root 7407 2022-11-01 14:50 ./usr/share/doc/rna-star/RELEASEnotes.md.gz -rw-r--r-- root/root 237134 2022-11-01 14:50 ./usr/share/doc/rna-star/STARmanual.pdf -rw-r--r-- root/root 2048 2023-01-22 14:33 ./usr/share/doc/rna-star/changelog.Debian.gz -rw-r--r-- root/root 14643 2022-11-01 14:50 ./usr/share/doc/rna-star/changelog.gz -rw-r--r-- root/root 2606 2023-01-22 14:33 ./usr/share/doc/rna-star/copyright drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/share/man/ drwxr-xr-x root/root 0 2023-01-22 14:33 ./usr/share/man/man1/ -rw-r--r-- root/root 824 2023-01-22 14:33 ./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 '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [615 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [1339 B] Get:5 copy:/<>/apt_archive ./ Packages [1418 B] Fetched 3372 B in 0s (169 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: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl 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 libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl 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 libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-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 libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 libregexp-ipv6-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 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 libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-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 libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common t1utils unzip Suggested packages: isoquery libxml-parser-perl libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl readline-doc zip Recommended packages: gnupg libcgi-fast-perl libhtml-format-perl liblist-someutils-xs-perl libfreezethaw-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl libxstring-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl The following NEW packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl 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 libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl 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 libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-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 libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 libregexp-ipv6-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 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 libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-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 libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common sbuild-build-depends-lintian-dummy:amd64 t1utils unzip 0 upgraded, 127 newly installed, 0 to remove and 0 not upgraded. Need to get 13.5 MB of archives. After this operation, 53.2 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [844 B] Get:2 http://mirror.einval.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 openssl arm64 3.0.8-1 [1373 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 ca-certificates all 20230311 [153 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 diffstat arm64 1.65-1 [31.2 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 libassuan0 arm64 2.5.5-5 [45.9 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 gpgconf arm64 2.2.40-1.1 [557 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libsqlite3-0 arm64 3.40.1-2 [786 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 gpg arm64 2.2.40-1.1 [903 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 iso-codes all 4.15.0-1 [2906 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 libaliased-perl all 0.34-3 [13.5 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 libapt-pkg-perl arm64 0.1.40+b2 [66.1 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 libb-hooks-op-check-perl arm64 0.22-2+b1 [10.4 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 libdevel-callchecker-perl arm64 0.008-2 [15.9 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 libparams-classify-perl arm64 0.015-2+b1 [22.9 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:20 http://mirror.einval.org/debian unstable/main arm64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:21 http://mirror.einval.org/debian unstable/main arm64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:23 http://mirror.einval.org/debian unstable/main arm64 libvariable-magic-perl arm64 0.63-1+b1 [42.8 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 libb-hooks-endofscope-perl all 0.26-1 [19.6 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 libberkeleydb-perl arm64 0.64-2+b1 [121 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get:29 http://mirror.einval.org/debian unstable/main arm64 liburi-perl all 5.17-1 [90.4 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.81-1 [98.6 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libcgi-pm-perl all 4.55-1 [220 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:33 http://mirror.einval.org/debian unstable/main arm64 libclass-method-modifiers-perl all 2.14-1 [18.1 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b1 [35.3 kB] Get:35 http://mirror.einval.org/debian unstable/main arm64 libclone-perl arm64 0.46-1 [13.5 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 libconfig-tiny-perl all 2.28-2 [16.4 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 libparams-util-perl arm64 1.102-2+b1 [24.2 kB] Get:38 http://mirror.einval.org/debian unstable/main arm64 libsub-install-perl all 0.929-1 [10.5 kB] Get:39 http://mirror.einval.org/debian unstable/main arm64 libdata-optlist-perl all 0.113-1 [10.6 kB] Get:40 http://mirror.einval.org/debian unstable/main arm64 libsub-exporter-perl all 0.989-1 [50.5 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 libconst-fast-perl all 0.014-2 [8792 B] Get:42 http://mirror.einval.org/debian unstable/main arm64 libcpanel-json-xs-perl arm64 4.35-1 [128 kB] Get:43 http://mirror.einval.org/debian unstable/main arm64 libdevel-stacktrace-perl all 2.0400-2 [26.8 kB] Get:44 http://mirror.einval.org/debian unstable/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get:45 http://mirror.einval.org/debian unstable/main arm64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 libdata-dpath-perl all 0.58-2 [43.6 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libdata-messagepack-perl arm64 1.02-1+b1 [34.0 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 libnet-domain-tld-perl all 1.75-3 [31.9 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 libnet-netmask-perl all 2.0002-2 [28.6 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 libnetaddr-ip-perl arm64 4.079+dfsg-2+b1 [98.8 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-ip-perl all 0.31-1 [20.6 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-uri-perl all 0.07-2 [11.2 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 libdevel-size-perl arm64 0.83-2+b1 [24.2 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 libemail-address-xs-perl arm64 1.05-1+b1 [28.3 kB] Get:58 http://mirror.einval.org/debian unstable/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:59 http://mirror.einval.org/debian unstable/main arm64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:60 http://mirror.einval.org/debian unstable/main arm64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:61 http://mirror.einval.org/debian unstable/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:62 http://mirror.einval.org/debian unstable/main arm64 libhttp-date-perl all 6.05-2 [10.5 kB] Get:63 http://mirror.einval.org/debian unstable/main arm64 libfile-listing-perl all 6.15-1 [12.6 kB] Get:64 http://mirror.einval.org/debian unstable/main arm64 libfont-ttf-perl all 1.06-2 [318 kB] Get:65 http://mirror.einval.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get:66 http://mirror.einval.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:67 http://mirror.einval.org/debian unstable/main arm64 libhttp-message-perl all 6.44-1 [81.7 kB] Get:68 http://mirror.einval.org/debian unstable/main arm64 libhtml-form-perl all 6.11-1 [33.1 kB] Get:69 http://mirror.einval.org/debian unstable/main arm64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:70 http://mirror.einval.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get:71 http://mirror.einval.org/debian unstable/main arm64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get:72 http://mirror.einval.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:73 http://mirror.einval.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b1 [7924 B] Get:74 http://mirror.einval.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.92-2+b1 [308 kB] Get:75 http://mirror.einval.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.081-2 [219 kB] Get:76 http://mirror.einval.org/debian unstable/main arm64 libnet-http-perl all 6.22-1 [25.3 kB] Get:77 http://mirror.einval.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get:78 http://mirror.einval.org/debian unstable/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:79 http://mirror.einval.org/debian unstable/main arm64 libwww-perl all 6.68-1 [186 kB] Get:80 http://mirror.einval.org/debian unstable/main arm64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:81 http://mirror.einval.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:82 http://mirror.einval.org/debian unstable/main arm64 libio-interactive-perl all 1.023-2 [11.0 kB] Get:83 http://mirror.einval.org/debian unstable/main arm64 libipc-run3-perl all 0.048-3 [33.2 kB] Get:84 http://mirror.einval.org/debian unstable/main arm64 libjson-maybexs-perl all 1.004004-1 [13.3 kB] Get:85 http://mirror.einval.org/debian unstable/main arm64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:86 http://mirror.einval.org/debian unstable/main arm64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:87 http://mirror.einval.org/debian unstable/main arm64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:88 http://mirror.einval.org/debian unstable/main arm64 liblz1 arm64 1.13-5 [38.9 kB] Get:89 http://mirror.einval.org/debian unstable/main arm64 liblzo2-2 arm64 2.10-2 [51.8 kB] Get:90 http://mirror.einval.org/debian unstable/main arm64 libmarkdown2 arm64 2.2.7-2 [34.1 kB] Get:91 http://mirror.einval.org/debian unstable/main arm64 libmldbm-perl all 2.05-4 [16.8 kB] Get:92 http://mirror.einval.org/debian unstable/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:93 http://mirror.einval.org/debian unstable/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get:94 http://mirror.einval.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get:95 http://mirror.einval.org/debian unstable/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:96 http://mirror.einval.org/debian unstable/main arm64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:97 http://mirror.einval.org/debian unstable/main arm64 libmouse-perl arm64 2.5.10-1+b3 [167 kB] Get:98 http://mirror.einval.org/debian unstable/main arm64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:99 http://mirror.einval.org/debian unstable/main arm64 libsub-identify-perl arm64 0.14-3 [10.9 kB] Get:100 http://mirror.einval.org/debian unstable/main arm64 libsub-name-perl arm64 0.26-2+b1 [12.4 kB] Get:101 http://mirror.einval.org/debian unstable/main arm64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:102 http://mirror.einval.org/debian unstable/main arm64 libpath-tiny-perl all 0.144-1 [56.4 kB] Get:103 http://mirror.einval.org/debian unstable/main arm64 libperlio-gzip-perl arm64 0.20-1+b1 [17.1 kB] Get:104 http://mirror.einval.org/debian unstable/main arm64 libperlio-utf8-strict-perl arm64 0.010-1 [11.2 kB] Get:105 http://mirror.einval.org/debian unstable/main arm64 libproc-processtable-perl arm64 0.634-1+b2 [42.4 kB] Get:106 http://mirror.einval.org/debian unstable/main arm64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:107 http://mirror.einval.org/debian unstable/main arm64 libsereal-decoder-perl arm64 5.003+ds-1 [95.6 kB] Get:108 http://mirror.einval.org/debian unstable/main arm64 libsereal-encoder-perl arm64 5.003+ds-1 [97.1 kB] Get:109 http://mirror.einval.org/debian unstable/main arm64 libsort-versions-perl all 1.62-3 [8928 B] Get:110 http://mirror.einval.org/debian unstable/main arm64 libxs-parse-keyword-perl arm64 0.33-1 [57.0 kB] Get:111 http://mirror.einval.org/debian unstable/main arm64 libsyntax-keyword-try-perl arm64 0.28-1 [28.2 kB] Get:112 http://mirror.einval.org/debian unstable/main arm64 libterm-readkey-perl arm64 2.38-2+b1 [24.1 kB] Get:113 http://mirror.einval.org/debian unstable/main arm64 libtext-levenshteinxs-perl arm64 0.03-5+b1 [8396 B] Get:114 http://mirror.einval.org/debian unstable/main arm64 libtext-markdown-discount-perl arm64 0.16-1 [13.0 kB] Get:115 http://mirror.einval.org/debian unstable/main arm64 libtext-xslate-perl arm64 3.5.9-1+b2 [196 kB] Get:116 http://mirror.einval.org/debian unstable/main arm64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:117 http://mirror.einval.org/debian unstable/main arm64 libtime-moment-perl arm64 0.44-2+b1 [72.2 kB] Get:118 http://mirror.einval.org/debian unstable/main arm64 libunicode-utf8-perl arm64 0.62-2 [19.9 kB] Get:119 http://mirror.einval.org/debian unstable/main arm64 libwww-mechanize-perl all 2.16-1 [116 kB] Get:120 http://mirror.einval.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-1 [50.4 kB] Get:121 http://mirror.einval.org/debian unstable/main arm64 libyaml-libyaml-perl arm64 0.86+ds-1 [32.8 kB] Get:122 http://mirror.einval.org/debian unstable/main arm64 plzip arm64 1.10-5 [58.0 kB] Get:123 http://mirror.einval.org/debian unstable/main arm64 lzop arm64 1.04-2 [82.8 kB] Get:124 http://mirror.einval.org/debian unstable/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get:125 http://mirror.einval.org/debian unstable/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get:126 http://mirror.einval.org/debian unstable/main arm64 unzip arm64 6.0-28 [157 kB] Get:127 http://mirror.einval.org/debian unstable/main arm64 lintian all 2.116.3 [1130 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 13.5 MB in 0s (52.0 MB/s) Selecting previously unselected package netbase. (Reading database ... 17346 files and directories currently installed.) Preparing to unpack .../000-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package readline-common. Preparing to unpack .../001-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.0.8-1_arm64.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package diffstat. Preparing to unpack .../004-diffstat_1.65-1_arm64.deb ... Unpacking diffstat (1.65-1) ... Selecting previously unselected package libassuan0:arm64. Preparing to unpack .../005-libassuan0_2.5.5-5_arm64.deb ... Unpacking libassuan0:arm64 (2.5.5-5) ... Selecting previously unselected package libreadline8:arm64. 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Unpacking libapt-pkg-perl (0.1.40+b2) ... Selecting previously unselected package libb-hooks-op-check-perl:arm64. Preparing to unpack .../013-libb-hooks-op-check-perl_0.22-2+b1_arm64.deb ... Unpacking libb-hooks-op-check-perl:arm64 (0.22-2+b1) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../014-libdynaloader-functions-perl_0.003-3_all.deb ... Unpacking libdynaloader-functions-perl (0.003-3) ... Selecting previously unselected package libdevel-callchecker-perl:arm64. Preparing to unpack .../015-libdevel-callchecker-perl_0.008-2_arm64.deb ... Unpacking libdevel-callchecker-perl:arm64 (0.008-2) ... Selecting previously unselected package libparams-classify-perl:arm64. Preparing to unpack .../016-libparams-classify-perl_0.015-2+b1_arm64.deb ... Unpacking libparams-classify-perl:arm64 (0.015-2+b1) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../017-libmodule-runtime-perl_0.016-2_all.deb ... Unpacking libmodule-runtime-perl (0.016-2) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../018-libtry-tiny-perl_0.31-2_all.deb ... Unpacking libtry-tiny-perl (0.31-2) ... Selecting previously unselected package libmodule-implementation-perl. Preparing to unpack .../019-libmodule-implementation-perl_0.09-2_all.deb ... Unpacking libmodule-implementation-perl (0.09-2) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../020-libsub-exporter-progressive-perl_0.001013-3_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001013-3) ... Selecting previously unselected package libvariable-magic-perl. Preparing to unpack .../021-libvariable-magic-perl_0.63-1+b1_arm64.deb ... Unpacking libvariable-magic-perl (0.63-1+b1) ... Selecting previously unselected package libb-hooks-endofscope-perl. Preparing to unpack .../022-libb-hooks-endofscope-perl_0.26-1_all.deb ... Unpacking libb-hooks-endofscope-perl (0.26-1) ... Selecting previously unselected package libberkeleydb-perl:arm64. Preparing to unpack .../023-libberkeleydb-perl_0.64-2+b1_arm64.deb ... Unpacking libberkeleydb-perl:arm64 (0.64-2+b1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../024-libcapture-tiny-perl_0.48-2_all.deb ... Unpacking libcapture-tiny-perl (0.48-2) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../025-libhtml-tagset-perl_3.20-6_all.deb ... Unpacking libhtml-tagset-perl (3.20-6) ... Selecting previously unselected package libregexp-ipv6-perl. Preparing to unpack .../026-libregexp-ipv6-perl_0.03-3_all.deb ... Unpacking libregexp-ipv6-perl (0.03-3) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../027-liburi-perl_5.17-1_all.deb ... Unpacking liburi-perl (5.17-1) ... Selecting previously unselected package libhtml-parser-perl:arm64. Preparing to unpack .../028-libhtml-parser-perl_3.81-1_arm64.deb ... Unpacking libhtml-parser-perl:arm64 (3.81-1) ... Selecting previously unselected package libcgi-pm-perl. Preparing to unpack .../029-libcgi-pm-perl_4.55-1_all.deb ... Unpacking libcgi-pm-perl (4.55-1) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../030-libclass-data-inheritable-perl_0.08-3_all.deb ... Unpacking libclass-data-inheritable-perl (0.08-3) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../031-libclass-method-modifiers-perl_2.14-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.14-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../032-libclass-xsaccessor-perl_1.19-4+b1_arm64.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b1) ... Selecting previously unselected package libclone-perl:arm64. Preparing to unpack .../033-libclone-perl_0.46-1_arm64.deb ... Unpacking libclone-perl:arm64 (0.46-1) ... Selecting previously unselected package libconfig-tiny-perl. Preparing to unpack .../034-libconfig-tiny-perl_2.28-2_all.deb ... Unpacking libconfig-tiny-perl (2.28-2) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../035-libparams-util-perl_1.102-2+b1_arm64.deb ... Unpacking libparams-util-perl (1.102-2+b1) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../036-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 .../037-libdata-optlist-perl_0.113-1_all.deb ... Unpacking libdata-optlist-perl (0.113-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../038-libsub-exporter-perl_0.989-1_all.deb ... Unpacking libsub-exporter-perl (0.989-1) ... Selecting previously unselected package libconst-fast-perl. Preparing to unpack .../039-libconst-fast-perl_0.014-2_all.deb ... Unpacking libconst-fast-perl (0.014-2) ... Selecting previously unselected package libcpanel-json-xs-perl:arm64. Preparing to unpack .../040-libcpanel-json-xs-perl_4.35-1_arm64.deb ... Unpacking libcpanel-json-xs-perl:arm64 (4.35-1) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../041-libdevel-stacktrace-perl_2.0400-2_all.deb ... Unpacking libdevel-stacktrace-perl (2.0400-2) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../042-libexception-class-perl_1.45-1_all.deb ... Unpacking libexception-class-perl (1.45-1) ... Selecting previously unselected package libiterator-perl. Preparing to unpack .../043-libiterator-perl_0.03+ds1-2_all.deb ... Unpacking libiterator-perl (0.03+ds1-2) ... Selecting previously unselected package libiterator-util-perl. Preparing to unpack .../044-libiterator-util-perl_0.02+ds1-2_all.deb ... 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Setting up liblz1:arm64 (1.13-5) ... Setting up libberkeleydb-perl:arm64 (0.64-2+b1) ... Setting up plzip (1.10-5) ... 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 libunicode-utf8-perl (0.62-2) ... Setting up libmouse-perl (2.5.10-1+b3) ... Setting up libdata-messagepack-perl (1.02-1+b1) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libclass-method-modifiers-perl (2.14-1) ... Setting up liblist-compare-perl (0.55-2) ... Setting up libclone-perl:arm64 (0.46-1) ... Setting up libyaml-0-2:arm64 (0.2.5-1) ... Setting up libsub-identify-perl (0.14-3) ... Setting up libcpanel-json-xs-perl:arm64 (4.35-1) ... Setting up libhtml-tagset-perl (3.20-6) ... Setting up libdevel-size-perl (0.83-2+b1) ... Setting up unzip (6.0-28) ... Setting up libsqlite3-0:arm64 (3.40.1-2) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libyaml-libyaml-perl (0.86+ds-1) ... Setting up libio-interactive-perl (1.023-2) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up perl-openssl-defaults:arm64 (7+b1) ... Setting up libmldbm-perl (2.05-4) ... Setting up liblzo2-2:arm64 (2.10-2) ... Setting up libtime-moment-perl (0.44-2+b1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libassuan0:arm64 (2.5.5-5) ... Setting up libconfig-tiny-perl (2.28-2) ... Setting up libsereal-encoder-perl (5.003+ds-1) ... Setting up liblist-utilsby-perl (0.12-2) ... Setting up libnet-netmask-perl (2.0002-2) ... Setting up libsub-install-perl (0.929-1) ... Setting up patchutils (0.4.2-1) ... Setting up libjson-maybexs-perl (1.004004-1) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2+b1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libxs-parse-keyword-perl (0.33-1) ... Setting up libipc-system-simple-perl (1.30-2) ... Setting up libnet-domain-tld-perl (1.75-3) ... Setting up libperlio-utf8-strict-perl (0.010-1) ... Setting up t1utils (1.41-4) ... Setting up diffstat (1.65-1) ... Setting up libvariable-magic-perl (0.63-1+b1) ... Setting up libio-html-perl (1.004-3) ... Setting up libb-hooks-op-check-perl:arm64 (0.22-2+b1) ... Setting up libparams-util-perl (1.102-2+b1) ... Setting up libtime-duration-perl (1.21-2) ... Setting up libtext-xslate-perl:arm64 (3.5.9-1+b2) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libregexp-ipv6-perl (0.03-3) ... Setting up libsub-name-perl:arm64 (0.26-2+b1) ... Setting up libsyntax-keyword-try-perl (0.28-1) ... Setting up libdata-validate-domain-perl (0.10-1.1) ... Setting up libproc-processtable-perl:arm64 (0.634-1+b2) ... Setting up libpath-tiny-perl (0.144-1) ... Setting up lzop (1.04-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.048-3) ... Setting up libregexp-wildcards-perl (1.05-3) ... Setting up libaliased-perl (0.34-3) ... Setting up netbase (6.4) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libdevel-stacktrace-perl (2.0400-2) ... Setting up libclass-xsaccessor-perl (1.19-4+b1) ... Setting up libsort-versions-perl (1.62-3) ... Setting up libterm-readkey-perl (2.38-2+b1) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.0.8-1) ... Setting up libtext-levenshteinxs-perl (0.03-5+b1) ... Setting up libperlio-gzip-perl (0.20-1+b1) ... Setting up readline-common (8.2-1.3) ... Setting up libhtml-html5-entities-perl (0.004-3) ... Setting up libsereal-decoder-perl (5.003+ds-1) ... Setting up libmarkdown2:arm64 (2.2.7-2) ... Setting up liburi-perl (5.17-1) ... Setting up iso-codes (4.15.0-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up libdata-validate-ip-perl (0.31-1) ... Setting up libemail-address-xs-perl (1.05-1+b1) ... Setting up libnet-ssleay-perl:arm64 (1.92-2+b1) ... Setting up libhttp-date-perl (6.05-2) ... Setting up libfile-basedir-perl (0.09-2) ... Setting up libfile-listing-perl (6.15-1) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up libnet-http-perl (6.22-1) ... Setting up libtext-markdown-discount-perl (0.16-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:arm64 (0.008-2) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libdata-validate-uri-perl (0.07-2) ... Setting up libdata-optlist-perl (0.113-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl:arm64 (3.81-1) ... Setting up gpgconf (2.2.40-1.1) ... Setting up libio-socket-ssl-perl (2.081-2) ... Setting up gpg (2.2.40-1.1) ... Setting up libsub-exporter-perl (0.989-1) ... Setting up libhttp-message-perl (6.44-1) ... Setting up libhtml-form-perl (6.11-1) ... 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 (6.10-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:arm64 (0.015-2+b1) ... Setting up libcgi-pm-perl (4.55-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.58-2) ... 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 libmoox-aliases-perl (0.001006-2) ... Setting up libb-hooks-endofscope-perl (0.26-1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-perl (6.68-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.16-1) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up lintian (2.116.3) ... Setting up sbuild-build-depends-lintian-dummy:amd64 (0.invalid.0) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for ca-certificates (20230311) ... 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 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Build-Space: 1118248 Build-Time: 8591 Distribution: unstable Foreign Architectures: amd64 Host Architecture: amd64 Install-Time: 51 Job: rna-star_2.7.10b+dfsg-2 Lintian: pass Machine Architecture: arm64 Package: rna-star Package-Time: 8677 Source-Version: 2.7.10b+dfsg-2 Space: 1118248 Status: successful Version: 2.7.10b+dfsg-2 -------------------------------------------------------------------------------- Finished at 2023-05-03T21:46:40Z Build needed 02:24:37, 1118248k disk space