sbuild (Debian sbuild) 0.89.3+deb13u4 (28 December 2025) on mjolnir.einval.org +==============================================================================+ | rsem 1.3.3+dfsg-4 (amd64) Fri, 08 May 2026 21:41:37 +0000 | +==============================================================================+ Package: rsem Version: 1.3.3+dfsg-4 Source Version: 1.3.3+dfsg-4 Distribution: unstable Machine Architecture: arm64 Host Architecture: amd64 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any I: Unpacking /home/helmut/.cache/sbuild/unstable-arm64-sbuild.tar.zst to /tmp/tmp.sbuild.yWKT6Uw1zY... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Fri, 08 May 2026 21:41:54 +0000 | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian unstable InRelease [189 kB] Get:2 http://mirror.einval.org/debian unstable/main Sources [11.6 MB] Get:3 http://mirror.einval.org/debian unstable/main amd64 Packages [10.4 MB] Get:4 http://mirror.einval.org/debian unstable/main arm64 Packages [10.3 MB] Fetched 32.5 MB in 8s (4322 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bash libblkid1 libc-bin libc-dev-bin libc-gconv-modules-extra libc6 libc6-dev libmount1 libsmartcols1 libuuid1 linux-libc-dev login util-linux 13 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 9978 kB of archives. After this operation, 7168 B of additional disk space will be used. Get:1 http://mirror.einval.org/debian unstable/main arm64 bash arm64 5.3-3 [1503 kB] Get:2 http://mirror.einval.org/debian unstable/main arm64 libc-dev-bin arm64 2.42-16 [36.8 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 libc6-dev arm64 2.42-16 [1617 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libc-gconv-modules-extra arm64 2.42-16 [1131 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 libc6 arm64 2.42-16 [1386 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev all 7.0.4-1 [1959 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 libsmartcols1 arm64 2.42-6 [137 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 libuuid1 arm64 2.42-6 [32.3 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 libblkid1 arm64 2.42-6 [164 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libmount1 arm64 2.42-6 [199 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 util-linux arm64 2.42-6 [1176 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 libc-bin arm64 2.42-16 [530 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 login arm64 1:4.16.0-2+really2.42-6 [106 kB] Preconfiguring packages ... Fetched 9978 kB in 0s (69.9 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12125 files and directories currently installed.) Preparing to unpack .../archives/bash_5.3-3_arm64.deb ... Unpacking bash (5.3-3) over (5.3-2) ... Setting up bash (5.3-3) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 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Processing triggers for debianutils (5.23.2+b1) ... +------------------------------------------------------------------------------+ | Fetch source files Fri, 08 May 2026 21:42:17 +0000 | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'rsem' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/rsem.git Please use: git clone https://salsa.debian.org/med-team/rsem.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 35.9 MB of source archives. Get:1 http://mirror.einval.org/debian unstable/main rsem 1.3.3+dfsg-4 (dsc) [1760 B] Get:2 http://mirror.einval.org/debian unstable/main rsem 1.3.3+dfsg-4 (tar) [275 kB] Get:3 http://mirror.einval.org/debian unstable/main rsem 1.3.3+dfsg-4 (diff) [35.7 MB] Fetched 35.9 MB in 0s (76.5 MB/s) Download complete and in download only mode +------------------------------------------------------------------------------+ | Install package build dependencies Fri, 08 May 2026 21:42:19 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libncurses-dev, libboost-dev, python3:any, help2man, libhts-dev, bowtie | bowtie2, libc-dev, libstdc++-dev, build-essential:arm64, crossbuild-essential-amd64:arm64, apt-utils:arm64, libc-dev:amd64, libstdc++-dev:amd64 Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libncurses-dev, libboost-dev, python3:any, help2man, libhts-dev, bowtie, libc-dev, libstdc++-dev, build-essential:arm64, crossbuild-essential-amd64:arm64, apt-utils:arm64, libc-dev:amd64, libstdc++-dev:amd64 dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-yFO7zh/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/reproducible-path/resolver-yFO7zh/apt_archive ./ InRelease Get:2 copy:/build/reproducible-path/resolver-yFO7zh/apt_archive ./ Release [609 B] Ign:3 copy:/build/reproducible-path/resolver-yFO7zh/apt_archive ./ Release.gpg Get:4 copy:/build/reproducible-path/resolver-yFO7zh/apt_archive ./ Sources [846 B] Get:5 copy:/build/reproducible-path/resolver-yFO7zh/apt_archive ./ Packages [843 B] Fetched 2298 B in 0s (106 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 bowtie bsdextrautils comerr-dev:amd64 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dwz file g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-15-base:amd64 gcc-15-cross-base gcc-15-x86-64-linux-gnu gcc-15-x86-64-linux-gnu-base gcc-16-base:amd64 gcc-16-cross-base gcc-x86-64-linux-gnu gettext gettext-base groff-base help2man intltool-debian krb5-multidev:amd64 libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libboost-dev:amd64 libboost1.90-dev:amd64 libbrotli-dev:amd64 libbrotli1:amd64 libbz2-1.0:amd64 libbz2-dev:amd64 libc-gconv-modules-extra:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcom-err2:amd64 libcurl3t64-gnutls:amd64 libcurl4-gnutls-dev:amd64 libdb5.3t64:amd64 libdebhelper-perl libdeflate-dev:amd64 libdeflate0:amd64 libelf1t64 libevent-2.1-7t64:amd64 libexpat1 libffi8 libffi8:amd64 libfile-stripnondeterminism-perl libgcc-15-dev:amd64 libgcc-15-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgmp-dev:amd64 libgmp10:amd64 libgmpxx4ldbl:amd64 libgnutls-dane0t64:amd64 libgnutls28-dev:amd64 libgnutls30t64:amd64 libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libgssrpc4t64:amd64 libhogweed6t64:amd64 libhts-dev:amd64 libhts3t64:amd64 libhtscodecs2:amd64 libhwasan0:amd64 libhwasan0-amd64-cross libidn2-0:amd64 libidn2-dev:amd64 libitm1:amd64 libitm1-amd64-cross libk5crypto3:amd64 libkadm5clnt-mit12:amd64 libkadm5srv-mit12:amd64 libkdb5-10t64:amd64 libkeyutils1:amd64 libkrb5-3:amd64 libkrb5-dev:amd64 libkrb5support0:amd64 libldap-dev:amd64 libldap2:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross liblzma-dev:amd64 liblzma5:amd64 libmagic-mgc libmagic1t64 libncurses-dev:amd64 libncurses6:amd64 libncursesw6 libncursesw6:amd64 libnettle8t64:amd64 libnghttp2-14:amd64 libnghttp2-dev:amd64 libnghttp3-9:amd64 libnghttp3-dev:amd64 libngtcp2-16:amd64 libngtcp2-crypto-gnutls-dev:amd64 libngtcp2-crypto-gnutls8:amd64 libngtcp2-dev:amd64 libp11-kit-dev:amd64 libp11-kit0:amd64 libpipeline1 libpkgconf7 libpsl-dev:amd64 libpsl5t64:amd64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libquadmath0:amd64 libquadmath0-amd64-cross libreadline8t64 librtmp-dev:amd64 librtmp1:amd64 libsasl2-2:amd64 libsasl2-modules-db:amd64 libsqlite3-0 libssh2-1-dev:amd64 libssh2-1t64:amd64 libssl-dev:amd64 libssl3t64:amd64 libstdc++-15-dev:amd64 libstdc++-15-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libtasn1-6:amd64 libtasn1-6-dev:amd64 libtinfo6:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunbound8:amd64 libunistring5 libunistring5:amd64 libxml2-16 libzstd-dev:amd64 libzstd1:amd64 linux-libc-dev-amd64-cross m4 man-db media-types netbase nettle-dev:amd64 pkgconf:amd64 pkgconf-bin po-debconf python3 python3-minimal python3.13 python3.13-minimal readline-common sensible-utils tzdata zlib1g:amd64 zlib1g-dev:amd64 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc bowtie-examples doc-base:amd64 gcc-15-locales cpp-15-doc cpp-doc dh-make gcc-15-doc manpages-dev flex bison gdb-x86-64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff krb5-doc:amd64 libboost-doc:amd64 libboost1.90-doc:amd64 libboost-atomic1.90-dev:amd64 libboost-chrono1.90-dev:amd64 libboost-container1.90-dev:amd64 libboost-context1.90-dev:amd64 libboost-contract1.90-dev:amd64 libboost-coroutine1.90-dev:amd64 libboost-date-time1.90-dev:amd64 libboost-exception1.90-dev:amd64 libboost-fiber1.90-dev:amd64 libboost-filesystem1.90-dev:amd64 libboost-graph-parallel1.90-dev:amd64 libboost-graph1.90-dev:amd64 libboost-iostreams1.90-dev:amd64 libboost-json1.90-dev:amd64 libboost-locale1.90-dev:amd64 libboost-log1.90-dev:amd64 libboost-math1.90-dev:amd64 libboost-mpi-python1.90-dev:amd64 libboost-mpi1.90-dev:amd64 libboost-nowide1.90-dev:amd64 libboost-numpy1.90-dev:amd64 libboost-program-options1.90-dev:amd64 libboost-python1.90-dev:amd64 libboost-random1.90-dev:amd64 libboost-regex1.90-dev:amd64 libboost-serialization1.90-dev:amd64 libboost-stacktrace1.90-dev:amd64 libboost-test1.90-dev:amd64 libboost-thread1.90-dev:amd64 libboost-timer1.90-dev:amd64 libboost-type-erasure1.90-dev:amd64 libboost-url1.90-dev:amd64 libboost-wave1.90-dev:amd64 libboost1.90-tools-dev:amd64 libmpfrc++-dev:amd64 libntl-dev:amd64 glibc-doc:amd64 libc-l10n:amd64 locales:amd64 libnss-nis:amd64 libnss-nisplus:amd64 manpages-dev:amd64 libcurl4-doc:amd64 libidn-dev:amd64 gmp-doc:amd64 libgmp10-doc:amd64 libmpfr-dev:amd64 dns-root-data:amd64 gnutls-bin:amd64 gnutls-doc:amd64 krb5-user:amd64 liblzma-doc:amd64 ncurses-doc:amd64 libnghttp2-doc:amd64 p11-kit-doc:amd64 libssl-doc:amd64 libstdc++-15-doc:amd64 libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.13-venv python3.13-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx bzip2-doc:amd64 ca-certificates:amd64 libarchive-cpio-perl krb5-locales:amd64 libldap-common:amd64 libgpm2:amd64 libgpm2 publicsuffix:amd64 libsasl2-modules:amd64 libtasn1-doc:amd64 libltdl-dev libmail-sendmail-perl ca-certificates The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bowtie bsdextrautils comerr-dev:amd64 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dwz file g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-15-base:amd64 gcc-15-cross-base gcc-15-x86-64-linux-gnu gcc-15-x86-64-linux-gnu-base gcc-16-base:amd64 gcc-16-cross-base gcc-x86-64-linux-gnu gettext gettext-base groff-base help2man intltool-debian krb5-multidev:amd64 libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libboost-dev:amd64 libboost1.90-dev:amd64 libbrotli-dev:amd64 libbrotli1:amd64 libbz2-1.0:amd64 libbz2-dev:amd64 libc-gconv-modules-extra:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcom-err2:amd64 libcurl3t64-gnutls:amd64 libcurl4-gnutls-dev:amd64 libdb5.3t64:amd64 libdebhelper-perl libdeflate-dev:amd64 libdeflate0:amd64 libelf1t64 libevent-2.1-7t64:amd64 libexpat1 libffi8 libffi8:amd64 libfile-stripnondeterminism-perl libgcc-15-dev:amd64 libgcc-15-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgmp-dev:amd64 libgmp10:amd64 libgmpxx4ldbl:amd64 libgnutls-dane0t64:amd64 libgnutls28-dev:amd64 libgnutls30t64:amd64 libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libgssrpc4t64:amd64 libhogweed6t64:amd64 libhts-dev:amd64 libhts3t64:amd64 libhtscodecs2:amd64 libhwasan0:amd64 libhwasan0-amd64-cross libidn2-0:amd64 libidn2-dev:amd64 libitm1:amd64 libitm1-amd64-cross libk5crypto3:amd64 libkadm5clnt-mit12:amd64 libkadm5srv-mit12:amd64 libkdb5-10t64:amd64 libkeyutils1:amd64 libkrb5-3:amd64 libkrb5-dev:amd64 libkrb5support0:amd64 libldap-dev:amd64 libldap2:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross liblzma-dev:amd64 liblzma5:amd64 libmagic-mgc libmagic1t64 libncurses-dev:amd64 libncurses6:amd64 libncursesw6 libncursesw6:amd64 libnettle8t64:amd64 libnghttp2-14:amd64 libnghttp2-dev:amd64 libnghttp3-9:amd64 libnghttp3-dev:amd64 libngtcp2-16:amd64 libngtcp2-crypto-gnutls-dev:amd64 libngtcp2-crypto-gnutls8:amd64 libngtcp2-dev:amd64 libp11-kit-dev:amd64 libp11-kit0:amd64 libpipeline1 libpkgconf7 libpsl-dev:amd64 libpsl5t64:amd64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libquadmath0:amd64 libquadmath0-amd64-cross libreadline8t64 librtmp-dev:amd64 librtmp1:amd64 libsasl2-2:amd64 libsasl2-modules-db:amd64 libsqlite3-0 libssh2-1-dev:amd64 libssh2-1t64:amd64 libssl-dev:amd64 libssl3t64:amd64 libstdc++-15-dev:amd64 libstdc++-15-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libtasn1-6:amd64 libtasn1-6-dev:amd64 libtinfo6:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunbound8:amd64 libunistring5 libunistring5:amd64 libxml2-16 libzstd-dev:amd64 libzstd1:amd64 linux-libc-dev-amd64-cross m4 man-db media-types netbase nettle-dev:amd64 pkgconf:amd64 pkgconf-bin po-debconf python3 python3-minimal python3.13 python3.13-minimal readline-common sbuild-build-depends-main-dummy:amd64 sensible-utils tzdata zlib1g:amd64 zlib1g-dev:amd64 0 upgraded, 173 newly installed, 0 to remove and 0 not upgraded. Need to get 145 MB of archives. After this operation, 704 MB of additional disk space will be used. Get:1 copy:/build/reproducible-path/resolver-yFO7zh/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [948 B] Get:2 http://mirror.einval.org/debian unstable/main arm64 libexpat1 arm64 2.8.0-1 [102 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-9 [14.7 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.12-1 [860 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.12-1 [2070 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 python3-minimal arm64 3.13.9-3+b1 [25.4 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 media-types all 14.0.0 [30.8 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 tzdata all 2026b-1 [260 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libffi8 arm64 3.5.2-4 [22.2 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 libncursesw6 arm64 6.6+20251231-1+b1 [125 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 readline-common all 8.3-4 [74.8 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 libreadline8t64 arm64 8.3-4 [168 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 libsqlite3-0 arm64 3.46.1-9+b1 [851 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.12-1 [1908 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 python3.13 arm64 3.13.12-1 [776 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.9-3+b1 [8348 B] Get:18 http://mirror.einval.org/debian unstable/main arm64 python3 arm64 3.13.9-3+b1 [25.4 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get:20 http://mirror.einval.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5+b2 [337 kB] Get:21 http://mirror.einval.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5+b2 [102 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 file arm64 1:5.46-5+b2 [42.8 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 gettext-base arm64 0.23.2-2 [240 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2+b2 [69.1 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 groff-base arm64 1.24.1-1 [1270 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 bsdextrautils arm64 2.42-6 [97.9 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-3 [47.2 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 man-db arm64 2.13.1-1+b1 [1455 kB] Get:29 http://mirror.einval.org/debian unstable/main arm64 m4 arm64 1.4.21-1 [323 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 autoconf all 2.72-6 [494 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 automake all 1:1.18.1-4 [877 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 autopoint all 0.23.2-2 [770 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 bowtie arm64 1.3.1-3+b3 [1327 kB] Get:35 http://mirror.einval.org/debian unstable/main amd64 gcc-16-base amd64 16-20260425-1 [35.8 kB] Get:36 http://mirror.einval.org/debian unstable/main amd64 libgcc-s1 amd64 16-20260425-1 [74.0 kB] Get:37 http://mirror.einval.org/debian unstable/main amd64 libc-gconv-modules-extra amd64 2.42-16 [1098 kB] Get:38 http://mirror.einval.org/debian unstable/main amd64 libc6 amd64 2.42-16 [1789 kB] Get:39 http://mirror.einval.org/debian unstable/main amd64 libc6-dev amd64 2.42-16 [1996 kB] Get:40 http://mirror.einval.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1 [19.2 kB] Get:41 http://mirror.einval.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.4-1 [50.9 kB] Get:42 http://mirror.einval.org/debian unstable/main arm64 gcc-15-x86-64-linux-gnu-base arm64 15.2.0-17cross1 [37.0 kB] Get:43 http://mirror.einval.org/debian unstable/main arm64 cpp-15-x86-64-linux-gnu arm64 15.2.0-17cross1 [11.3 MB] Get:44 http://mirror.einval.org/debian unstable/main arm64 cpp-x86-64-linux-gnu arm64 4:15.2.0-5+b1 [4644 B] Get:45 http://mirror.einval.org/debian unstable/main arm64 binutils-x86-64-linux-gnu arm64 2.46-3 [1536 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 gcc-15-cross-base all 15.2.0-17cross1 [32.3 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 gcc-16-cross-base all 16-20260425-1cross1 [31.6 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1-amd64-cross all 16-20260425-1cross1 [74.0 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 libgomp1-amd64-cross all 16-20260425-1cross1 [146 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 libitm1-amd64-cross all 16-20260425-1cross1 [27.0 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 libatomic1-amd64-cross all 16-20260425-1cross1 [10.5 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 libasan8-amd64-cross all 16-20260425-1cross1 [2878 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 liblsan0-amd64-cross all 16-20260425-1cross1 [1279 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 libtsan2-amd64-cross all 16-20260425-1cross1 [2560 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libc6-amd64-cross all 2.42-12cross1 [1577 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 libstdc++6-amd64-cross all 16-20260425-1cross1 [801 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 libubsan1-amd64-cross all 16-20260425-1cross1 [1135 kB] Get:58 http://mirror.einval.org/debian unstable/main arm64 libhwasan0-amd64-cross all 16-20260425-1cross1 [1576 kB] Get:59 http://mirror.einval.org/debian unstable/main arm64 libquadmath0-amd64-cross all 16-20260425-1cross1 [148 kB] Get:60 http://mirror.einval.org/debian unstable/main arm64 libgcc-15-dev-amd64-cross all 15.2.0-17cross1 [2704 kB] Get:61 http://mirror.einval.org/debian unstable/main arm64 gcc-15-x86-64-linux-gnu arm64 15.2.0-17cross1 [21.8 MB] Get:62 http://mirror.einval.org/debian unstable/main arm64 gcc-x86-64-linux-gnu arm64 4:15.2.0-5+b1 [1452 B] Get:63 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev-amd64-cross all 7.0.4-1 [12.5 kB] Get:64 http://mirror.einval.org/debian unstable/main arm64 libc6-dev-amd64-cross all 2.42-12cross1 [2010 kB] Get:65 http://mirror.einval.org/debian unstable/main arm64 libstdc++-15-dev-amd64-cross all 15.2.0-17cross1 [2737 kB] Get:66 http://mirror.einval.org/debian unstable/main arm64 g++-15-x86-64-linux-gnu arm64 15.2.0-17cross1 [12.3 MB] Get:67 http://mirror.einval.org/debian unstable/main arm64 g++-x86-64-linux-gnu arm64 4:15.2.0-5+b1 [1208 B] Get:68 http://mirror.einval.org/debian unstable/main arm64 crossbuild-essential-amd64 all 12.12 [3552 B] Get:69 http://mirror.einval.org/debian unstable/main arm64 libdebhelper-perl all 13.31 [75.7 kB] Get:70 http://mirror.einval.org/debian unstable/main arm64 libtool all 2.5.4-11 [539 kB] Get:71 http://mirror.einval.org/debian unstable/main arm64 dh-autoreconf all 22 [12.2 kB] Get:72 http://mirror.einval.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:73 http://mirror.einval.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get:74 http://mirror.einval.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get:75 http://mirror.einval.org/debian unstable/main arm64 libelf1t64 arm64 0.195-1 [57.5 kB] Get:76 http://mirror.einval.org/debian unstable/main arm64 dwz arm64 0.16-4 [99.2 kB] Get:77 http://mirror.einval.org/debian unstable/main arm64 libunistring5 arm64 1.4.2-1 [455 kB] Get:78 http://mirror.einval.org/debian unstable/main arm64 libxml2-16 arm64 2.15.2+dfsg-0.1 [592 kB] Get:79 http://mirror.einval.org/debian unstable/main arm64 gettext arm64 0.23.2-2 [1609 kB] Get:80 http://mirror.einval.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:81 http://mirror.einval.org/debian unstable/main arm64 po-debconf all 1.0.22 [216 kB] Get:82 http://mirror.einval.org/debian unstable/main arm64 debhelper all 13.31 [932 kB] Get:83 http://mirror.einval.org/debian unstable/main amd64 gcc-15-base amd64 15.2.0-17 [36.8 kB] Get:84 http://mirror.einval.org/debian unstable/main arm64 help2man arm64 1.49.3+b2 [198 kB] Get:85 http://mirror.einval.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-2+b1 [31.0 kB] Get:86 http://mirror.einval.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-2+b1 [78.9 kB] Get:87 http://mirror.einval.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b2 [9348 B] Get:88 http://mirror.einval.org/debian unstable/main amd64 libzstd1 amd64 1.5.7+dfsg-3+b2 [305 kB] Get:89 http://mirror.einval.org/debian unstable/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.2-3 [90.9 kB] Get:90 http://mirror.einval.org/debian unstable/main amd64 libssl3t64 amd64 3.6.2-1 [2482 kB] Get:91 http://mirror.einval.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-2+b1 [336 kB] Get:92 http://mirror.einval.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-2+b1 [137 kB] Get:93 http://mirror.einval.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.22.1-2+b1 [58.1 kB] Get:94 http://mirror.einval.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.22.1-2+b1 [40.2 kB] Get:95 http://mirror.einval.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.22.1-2+b1 [41.2 kB] Get:96 http://mirror.einval.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.22.1-2+b1 [54.0 kB] Get:97 http://mirror.einval.org/debian unstable/main amd64 krb5-multidev amd64 1.22.1-2+b1 [125 kB] Get:98 http://mirror.einval.org/debian unstable/main amd64 libasan8 amd64 16-20260425-1 [2888 kB] Get:99 http://mirror.einval.org/debian unstable/main amd64 libatomic1 amd64 16-20260425-1 [10.5 kB] Get:100 http://mirror.einval.org/debian unstable/main amd64 libgomp1 amd64 16-20260425-1 [151 kB] Get:101 http://mirror.einval.org/debian unstable/main amd64 libitm1 amd64 16-20260425-1 [27.0 kB] Get:102 http://mirror.einval.org/debian unstable/main amd64 liblsan0 amd64 16-20260425-1 [1280 kB] Get:103 http://mirror.einval.org/debian unstable/main amd64 libtsan2 amd64 16-20260425-1 [2572 kB] Get:104 http://mirror.einval.org/debian unstable/main amd64 libstdc++6 amd64 16-20260425-1 [824 kB] Get:105 http://mirror.einval.org/debian unstable/main amd64 libubsan1 amd64 16-20260425-1 [1136 kB] Get:106 http://mirror.einval.org/debian unstable/main amd64 libhwasan0 amd64 16-20260425-1 [1580 kB] Get:107 http://mirror.einval.org/debian unstable/main amd64 libquadmath0 amd64 16-20260425-1 [147 kB] Get:108 http://mirror.einval.org/debian unstable/main amd64 libgcc-15-dev amd64 15.2.0-17 [2718 kB] Get:109 http://mirror.einval.org/debian unstable/main amd64 libstdc++-15-dev amd64 15.2.0-17 [2780 kB] Get:110 http://mirror.einval.org/debian unstable/main amd64 libboost1.90-dev amd64 1.90.0-6 [11.3 MB] Get:111 http://mirror.einval.org/debian unstable/main amd64 libboost-dev amd64 1.90.0.2 [3064 B] Get:112 http://mirror.einval.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-3 [320 kB] Get:113 http://mirror.einval.org/debian unstable/main amd64 libbrotli-dev amd64 1.2.0-3 [324 kB] Get:114 http://mirror.einval.org/debian unstable/main amd64 libbz2-1.0 amd64 1.0.8-6+b2 [39.9 kB] Get:115 http://mirror.einval.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6+b2 [33.6 kB] Get:116 http://mirror.einval.org/debian unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB] Get:117 http://mirror.einval.org/debian unstable/main amd64 libngtcp2-16 amd64 1.22.1-1 [133 kB] Get:118 http://mirror.einval.org/debian unstable/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5+b2 [560 kB] Get:119 http://mirror.einval.org/debian unstable/main amd64 libnettle8t64 amd64 3.10.2-1+b1 [305 kB] Get:120 http://mirror.einval.org/debian unstable/main amd64 libhogweed6t64 amd64 3.10.2-1+b1 [335 kB] Get:121 http://mirror.einval.org/debian unstable/main amd64 libunistring5 amd64 1.4.2-1 [480 kB] Get:122 http://mirror.einval.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4+b2 [109 kB] Get:123 http://mirror.einval.org/debian unstable/main amd64 libffi8 amd64 3.5.2-4 [25.2 kB] Get:124 http://mirror.einval.org/debian unstable/main amd64 libp11-kit0 amd64 0.26.2-2 [470 kB] Get:125 http://mirror.einval.org/debian unstable/main amd64 libtasn1-6 amd64 4.21.0-2+b1 [49.3 kB] Get:126 http://mirror.einval.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.13-1 [1546 kB] Get:127 http://mirror.einval.org/debian unstable/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-11+b1 [709 kB] Get:128 http://mirror.einval.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-11 [17.2 kB] Get:129 http://mirror.einval.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-11 [55.2 kB] Get:130 http://mirror.einval.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1+b2 [188 kB] Get:131 http://mirror.einval.org/debian unstable/main amd64 libnghttp2-14 amd64 1.69.0-1 [89.0 kB] Get:132 http://mirror.einval.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.22.1-1 [20.8 kB] Get:133 http://mirror.einval.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.5-1 [59.9 kB] Get:134 http://mirror.einval.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-2 [244 kB] Get:135 http://mirror.einval.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.20.0-1 [403 kB] Get:136 http://mirror.einval.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b2 [184 kB] Get:137 http://mirror.einval.org/debian unstable/main amd64 libunbound8 amd64 1.25.0-1 [618 kB] Get:138 http://mirror.einval.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.13-1 [496 kB] Get:139 http://mirror.einval.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-4+b2 [102 kB] Get:140 http://mirror.einval.org/debian unstable/main amd64 libp11-kit-dev amd64 0.26.2-2 [223 kB] Get:141 http://mirror.einval.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.21.0-2+b1 [98.6 kB] Get:142 http://mirror.einval.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5+b2 [328 kB] Get:143 http://mirror.einval.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5+b2 [641 kB] Get:144 http://mirror.einval.org/debian unstable/main amd64 nettle-dev amd64 3.10.2-1+b1 [1321 kB] Get:145 http://mirror.einval.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.13-1 [1479 kB] Get:146 http://mirror.einval.org/debian unstable/main amd64 libkrb5-dev amd64 1.22.1-2+b1 [14.0 kB] Get:147 http://mirror.einval.org/debian unstable/main amd64 libldap-dev amd64 2.6.10+dfsg-1+b2 [305 kB] Get:148 http://mirror.einval.org/debian unstable/main arm64 libpkgconf7 arm64 2.5.1-4 [45.5 kB] Get:149 http://mirror.einval.org/debian unstable/main arm64 pkgconf-bin arm64 2.5.1-4 [35.1 kB] Get:150 http://mirror.einval.org/debian unstable/main amd64 pkgconf amd64 2.5.1-4 [33.6 kB] Get:151 http://mirror.einval.org/debian unstable/main amd64 libnghttp2-dev amd64 1.69.0-1 [128 kB] Get:152 http://mirror.einval.org/debian unstable/main amd64 libnghttp3-dev amd64 1.15.0-1 [94.5 kB] Get:153 http://mirror.einval.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.22.1-1 [20.9 kB] Get:154 http://mirror.einval.org/debian unstable/main amd64 libngtcp2-dev amd64 1.22.1-1 [192 kB] Get:155 http://mirror.einval.org/debian unstable/main amd64 libpsl-dev amd64 0.21.5-1 [80.5 kB] Get:156 http://mirror.einval.org/debian unstable/main amd64 librtmp1 amd64 2.6-1 [60.3 kB] Get:157 http://mirror.einval.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-3 [918 kB] Get:158 http://mirror.einval.org/debian unstable/main amd64 librtmp-dev amd64 2.6-1 [69.7 kB] Get:159 http://mirror.einval.org/debian unstable/main amd64 libssl-dev amd64 3.6.2-1 [3019 kB] Get:160 http://mirror.einval.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-2 [393 kB] Get:161 http://mirror.einval.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-3+b2 [372 kB] Get:162 http://mirror.einval.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.20.0-1 [528 kB] Get:163 http://mirror.einval.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2+b2 [48.3 kB] Get:164 http://mirror.einval.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-2+b2 [56.9 kB] Get:165 http://mirror.einval.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.6-1 [101 kB] Get:166 http://mirror.einval.org/debian unstable/main amd64 liblzma5 amd64 5.8.3-1 [332 kB] Get:167 http://mirror.einval.org/debian unstable/main amd64 libhts3t64 amd64 1.22.1+ds2-1+b2 [475 kB] Get:168 http://mirror.einval.org/debian unstable/main amd64 liblzma-dev amd64 5.8.3-1 [369 kB] Get:169 http://mirror.einval.org/debian unstable/main amd64 libhts-dev amd64 1.22.1+ds2-1+b2 [1784 kB] Get:170 http://mirror.einval.org/debian unstable/main amd64 libtinfo6 amd64 6.6+20251231-1+b1 [350 kB] Get:171 http://mirror.einval.org/debian unstable/main amd64 libncurses6 amd64 6.6+20251231-1+b1 [107 kB] Get:172 http://mirror.einval.org/debian unstable/main amd64 libncursesw6 amd64 6.6+20251231-1+b1 [136 kB] Get:173 http://mirror.einval.org/debian unstable/main amd64 libncurses-dev amd64 6.6+20251231-1+b1 [356 kB] Preconfiguring packages ... Fetched 145 MB in 2s (82.5 MB/s) Selecting previously unselected package libexpat1:arm64. (Reading database ... 12126 files and directories currently installed.) Preparing to unpack .../libexpat1_2.8.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.8.0-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.07-9_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-9) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.12-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.12-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.12-1_arm64.deb ... Unpacking python3.13-minimal (3.13.12-1) ... Setting up libpython3.13-minimal:arm64 (3.13.12-1) ... Setting up libexpat1:arm64 (2.8.0-1) ... Setting up python3.13-minimal (3.13.12-1) ... Selecting previously unselected package python3-minimal. 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Unpacking sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ... Setting up libc-gconv-modules-extra:amd64 (2.42-16) ... Setting up media-types (14.0.0) ... Setting up libpipeline1:arm64 (1.5.8-3) ... Setting up linux-libc-dev-amd64-cross (7.0.4-1) ... Setting up bsdextrautils (2.42-6) ... Setting up libmagic-mgc (1:5.46-5+b2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:arm64 (2.15.2+dfsg-0.1) ... Setting up libdebhelper-perl (13.31) ... Setting up libsqlite3-0:arm64 (3.46.1-9+b1) ... Setting up libpkgconf7:arm64 (2.5.1-4) ... Setting up libmagic1t64:arm64 (1:5.46-5+b2) ... Setting up gettext-base (0.23.2-2) ... Setting up m4 (1.4.21-1) ... Setting up gcc-15-x86-64-linux-gnu-base:arm64 (15.2.0-17cross1) ... Setting up gcc-16-base:amd64 (16-20260425-1) ... Setting up file (1:5.46-5+b2) ... Setting up cpp-15-x86-64-linux-gnu (15.2.0-17cross1) ... Setting up gcc-16-cross-base (16-20260425-1cross1) ... Setting up libelf1t64:arm64 (0.195-1) ... Setting up tzdata (2026b-1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri May 8 21:43:29 UTC 2026. Universal Time is now: Fri May 8 21:43:29 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libitm1-amd64-cross (16-20260425-1cross1) ... Setting up autotools-dev (20240727.1+nmu1) ... Setting up libatomic1-amd64-cross (16-20260425-1cross1) ... Setting up libunistring5:arm64 (1.4.2-1) ... Setting up libquadmath0-amd64-cross (16-20260425-1cross1) ... Setting up autopoint (0.23.2-2) ... Setting up libc6-amd64-cross (2.42-12cross1) ... Setting up pkgconf-bin (2.5.1-4) ... Setting up libncursesw6:arm64 (6.6+20251231-1+b1) ... Setting up autoconf (2.72-6) ... Setting up libffi8:arm64 (3.5.2-4) ... Setting up dwz (0.16-4) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:arm64 (0.0.8-2+b2) ... Setting up netbase (6.5) ... Setting up gcc-15-cross-base (15.2.0-17cross1) ... Setting up libgcc-s1-amd64-cross (16-20260425-1cross1) ... 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Setting up dh-autoreconf (22) ... Setting up libhwasan0-amd64-cross (16-20260425-1cross1) ... Setting up libubsan1-amd64-cross (16-20260425-1cross1) ... Setting up libreadline8t64:arm64 (8.3-4) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.24.1-1) ... Setting up libpython3.13-stdlib:arm64 (3.13.12-1) ... Setting up libpython3-stdlib:arm64 (3.13.9-3+b1) ... Setting up python3.13 (3.13.12-1) ... Setting up po-debconf (1.0.22) ... Setting up python3 (3.13.9-3+b1) ... Setting up man-db (2.13.1-1+b1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgcc-15-dev-amd64-cross (15.2.0-17cross1) ... Setting up libstdc++-15-dev-amd64-cross (15.2.0-17cross1) ... Setting up bowtie (1.3.1-3+b3) ... Setting up debhelper (13.31) ... Setting up gcc-15-x86-64-linux-gnu (15.2.0-17cross1) ... Setting up g++-15-x86-64-linux-gnu (15.2.0-17cross1) ... Setting up gcc-x86-64-linux-gnu (4:15.2.0-5+b1) ... Setting up g++-x86-64-linux-gnu (4:15.2.0-5+b1) ... Setting up crossbuild-essential-amd64 (12.12) ... Setting up libgcc-s1:amd64 (16-20260425-1) ... Setting up libc6:amd64 (2.42-16) ... Setting up libnghttp3-9:amd64 (1.15.0-1) ... Setting up libnghttp3-dev:amd64 (1.15.0-1) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-11+b1) ... Setting up libffi8:amd64 (3.5.2-4) ... Setting up libhwasan0:amd64 (16-20260425-1) ... Setting up libasan8:amd64 (16-20260425-1) ... Setting up libtasn1-6:amd64 (4.21.0-2+b1) ... Setting up libc6-dev:amd64 (2.42-16) ... Setting up libngtcp2-16:amd64 (1.22.1-1) ... Setting up libtsan2:amd64 (16-20260425-1) ... Setting up libbz2-1.0:amd64 (1.0.8-6+b2) ... Setting up libtasn1-6-dev:amd64 (4.21.0-2+b1) ... Setting up libstdc++6:amd64 (16-20260425-1) ... Setting up liblsan0:amd64 (16-20260425-1) ... Setting up libitm1:amd64 (16-20260425-1) ... Setting up libtinfo6:amd64 (6.6+20251231-1+b1) ... Setting up libbz2-dev:amd64 (1.0.8-6+b2) ... Setting up libhtscodecs2:amd64 (1.6.6-1) ... Setting up libzstd1:amd64 (1.5.7+dfsg-3+b2) ... Setting up libkeyutils1:amd64 (1.6.3-6+b2) ... Setting up libzstd-dev:amd64 (1.5.7+dfsg-3+b2) ... Setting up liblzma5:amd64 (5.8.3-1) ... Setting up libbrotli1:amd64 (1.2.0-3) ... Setting up libnghttp2-14:amd64 (1.69.0-1) ... Setting up libdeflate0:amd64 (1.23-2+b2) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b2) ... Setting up zlib1g:amd64 (1:1.3.dfsg+really1.3.2-3) ... Setting up libcom-err2:amd64 (1.47.4-1) ... Setting up libngtcp2-dev:amd64 (1.22.1-1) ... Setting up libgomp1:amd64 (16-20260425-1) ... Setting up libkrb5support0:amd64 (1.22.1-2+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-11) ... Setting up libnettle8t64:amd64 (3.10.2-1+b1) ... Setting up libgmp10:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up libncurses6:amd64 (6.6+20251231-1+b1) ... Setting up libquadmath0:amd64 (16-20260425-1) ... Setting up libp11-kit0:amd64 (0.26.2-2) ... Setting up comerr-dev:amd64 (2.1-1.47.4-1) ... Setting up libunistring5:amd64 (1.4.2-1) ... Setting up libatomic1:amd64 (16-20260425-1) ... Setting up libncursesw6:amd64 (6.6+20251231-1+b1) ... Setting up libk5crypto3:amd64 (1.22.1-2+b1) ... Setting up liblzma-dev:amd64 (5.8.3-1) ... Setting up libubsan1:amd64 (16-20260425-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.2-3) ... Setting up libhogweed6t64:amd64 (3.10.2-1+b1) ... Setting up libdeflate-dev:amd64 (1.23-2+b2) ... Setting up libbrotli-dev:amd64 (1.2.0-3) ... Setting up libp11-kit-dev:amd64 (0.26.2-2) ... Setting up libnghttp2-dev:amd64 (1.69.0-1) ... Setting up libncurses-dev:amd64 (6.6+20251231-1+b1) ... Setting up libgcc-15-dev:amd64 (15.2.0-17) ... Setting up libssl3t64:amd64 (3.6.2-1) ... Setting up libidn2-0:amd64 (2.3.8-4+b2) ... Setting up libunbound8:amd64 (1.25.0-1) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up libstdc++-15-dev:amd64 (15.2.0-17) ... Setting up libssl-dev:amd64 (3.6.2-1) ... Setting up libidn2-dev:amd64 (2.3.8-4+b2) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-11) ... Setting up libboost1.90-dev:amd64 (1.90.0-6) ... Setting up libkrb5-3:amd64 (1.22.1-2+b1) ... Setting up libboost-dev:amd64 (1.90.0.2) ... Setting up libssh2-1t64:amd64 (1.11.1-2) ... Setting up libldap2:amd64 (2.6.10+dfsg-1+b2) ... Setting up libgnutls30t64:amd64 (3.8.13-1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up nettle-dev:amd64 (3.10.2-1+b1) ... Setting up libpsl5t64:amd64 (0.21.5-1) ... Setting up libpsl-dev:amd64 (0.21.5-1) ... Setting up libgnutls-dane0t64:amd64 (3.8.13-1) ... Setting up librtmp1:amd64 (2.6-1) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1+b2) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-2+b1) ... Setting up libssh2-1-dev:amd64 (1.11.1-2) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.22.1-1) ... Setting up libgnutls28-dev:amd64 (3.8.13-1) ... Setting up libcurl3t64-gnutls:amd64 (8.20.0-1) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.22.1-1) ... Setting up libgssrpc4t64:amd64 (1.22.1-2+b1) ... Setting up librtmp-dev:amd64 (2.6-1) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1+b2) ... Setting up libkadm5clnt-mit12:amd64 (1.22.1-2+b1) ... Setting up libkdb5-10t64:amd64 (1.22.1-2+b1) ... Setting up libkadm5srv-mit12:amd64 (1.22.1-2+b1) ... Setting up krb5-multidev:amd64 (1.22.1-2+b1) ... Setting up libkrb5-dev:amd64 (1.22.1-2+b1) ... Setting up libcurl4-gnutls-dev:amd64 (8.20.0-1) ... Setting up libhts-dev:amd64 (1.22.1+ds2-1+b2) ... Setting up sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ... Processing triggers for base-files (14) ... Processing triggers for libc-bin (2.42-16) ... +------------------------------------------------------------------------------+ | Check architectures Fri, 08 May 2026 21:43:35 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Fri, 08 May 2026 21:43:36 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.85+deb13-arm64 #1 SMP Debian 6.12.85-1 (2026-04-30) arm64 (aarch64) Toolchain package versions: binutils_2.46-3 dpkg-dev_1.23.7 g++-15_15.2.0-17 gcc-15_15.2.0-17 libc6-dev_2.42-16 libstdc++-15-dev_15.2.0-17 libstdc++-15-dev-amd64-cross_15.2.0-17cross1 libstdc++6_16-20260425-1 libstdc++6-amd64-cross_16-20260425-1cross1 linux-libc-dev_7.0.4-1 Package versions: apt_3.3.0 apt-utils_3.3.0 autoconf_2.72-6 automake_1:1.18.1-4 autopoint_0.23.2-2 autotools-dev_20240727.1+nmu1 base-files_14 base-passwd_3.6.8+b1 bash_5.3-3 binutils_2.46-3 binutils-aarch64-linux-gnu_2.46-3 binutils-common_2.46-3 binutils-x86-64-linux-gnu_2.46-3 bowtie_1.3.1-3+b3 bsdextrautils_2.42-6 build-essential_12.12 bzip2_1.0.8-6+b2 comerr-dev_2.1-1.47.4-1 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.2.0-17 cpp-15-aarch64-linux-gnu_15.2.0-17 cpp-15-x86-64-linux-gnu_15.2.0-17cross1 cpp-aarch64-linux-gnu_4:15.2.0-5+b1 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 crossbuild-essential-amd64_12.12 dash_0.5.12-12+b1 debconf_1.5.92 debhelper_13.31 debian-archive-keyring_2025.1 debianutils_5.23.2+b1 dh-autoreconf_22 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1+b1 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 file_1:5.46-5+b2 findutils_4.10.0-4 g++_4:15.2.0-5+b1 g++-15_15.2.0-17 g++-15-aarch64-linux-gnu_15.2.0-17 g++-15-x86-64-linux-gnu_15.2.0-17cross1 g++-aarch64-linux-gnu_4:15.2.0-5+b1 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.2.0-17 gcc-15-aarch64-linux-gnu_15.2.0-17 gcc-15-base_15.2.0-17 gcc-15-cross-base_15.2.0-17cross1 gcc-15-x86-64-linux-gnu_15.2.0-17cross1 gcc-15-x86-64-linux-gnu-base_15.2.0-17cross1 gcc-16-base_16-20260425-1 gcc-16-cross-base_16-20260425-1cross1 gcc-aarch64-linux-gnu_4:15.2.0-5+b1 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gettext_0.23.2-2 gettext-base_0.23.2-2 grep_3.12-1+b1 groff-base_1.24.1-1 gzip_1.13-1+b1 help2man_1.49.3+b2 hostname_3.25+b1 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.22.1-2+b1 libacl1_2.3.2-3 libapt-pkg7.0_3.3.0 libarchive-zip-perl_1.68-1 libasan8_16-20260425-1 libasan8-amd64-cross_16-20260425-1cross1 libatomic1_16-20260425-1 libatomic1-amd64-cross_16-20260425-1cross1 libattr1_1:2.5.2-4 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46-3 libblkid1_2.42-6 libboost-dev_1.90.0.2 libboost1.90-dev_1.90.0-6 libbrotli-dev_1.2.0-3 libbrotli1_1.2.0-3 libbz2-1.0_1.0.8-6+b2 libbz2-dev_1.0.8-6+b2 libc-bin_2.42-16 libc-dev-bin_2.42-16 libc-gconv-modules-extra_2.42-16 libc6_2.42-16 libc6-amd64-cross_2.42-12cross1 libc6-dev_2.42-16 libc6-dev-amd64-cross_2.42-12cross1 libcap-ng0_0.9.3-1 libcc1-0_16-20260425-1 libcom-err2_1.47.4-1 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46-3 libctf0_2.46-3 libcurl3t64-gnutls_8.20.0-1 libcurl4-gnutls-dev_8.20.0-1 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.282+b3 libdebhelper-perl_13.31 libdeflate-dev_1.23-2+b2 libdeflate0_1.23-2+b2 libdpkg-perl_1.23.7 libelf1t64_0.195-1 libevent-2.1-7t64_2.1.12-stable-10+b2 libexpat1_2.8.0-1 libffi8_3.5.2-4 libfile-stripnondeterminism-perl_1.15.0-1 libgcc-15-dev_15.2.0-17 libgcc-15-dev-amd64-cross_15.2.0-17cross1 libgcc-s1_16-20260425-1 libgcc-s1-amd64-cross_16-20260425-1cross1 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgmp-dev_2:6.3.0+dfsg-5+b2 libgmp10_2:6.3.0+dfsg-5+b2 libgmpxx4ldbl_2:6.3.0+dfsg-5+b2 libgnutls-dane0t64_3.8.13-1 libgnutls28-dev_3.8.13-1 libgnutls30t64_3.8.13-1 libgomp1_16-20260425-1 libgomp1-amd64-cross_16-20260425-1cross1 libgprofng0_2.46-3 libgssapi-krb5-2_1.22.1-2+b1 libgssrpc4t64_1.22.1-2+b1 libhogweed6t64_3.10.2-1+b1 libhts-dev_1.22.1+ds2-1+b2 libhts3t64_1.22.1+ds2-1+b2 libhtscodecs2_1.6.6-1 libhwasan0_16-20260425-1 libhwasan0-amd64-cross_16-20260425-1cross1 libidn2-0_2.3.8-4+b2 libidn2-dev_2.3.8-4+b2 libisl23_0.27-2 libitm1_16-20260425-1 libitm1-amd64-cross_16-20260425-1cross1 libjansson4_2.14-2+b4 libk5crypto3_1.22.1-2+b1 libkadm5clnt-mit12_1.22.1-2+b1 libkadm5srv-mit12_1.22.1-2+b1 libkdb5-10t64_1.22.1-2+b1 libkeyutils1_1.6.3-6+b2 libkrb5-3_1.22.1-2+b1 libkrb5-dev_1.22.1-2+b1 libkrb5support0_1.22.1-2+b1 libldap-dev_2.6.10+dfsg-1+b2 libldap2_2.6.10+dfsg-1+b2 liblocale-gettext-perl_1.07-9 liblsan0_16-20260425-1 liblsan0-amd64-cross_16-20260425-1cross1 liblz4-1_1.10.0-10 liblzma-dev_5.8.3-1 liblzma5_5.8.3-1 libmagic-mgc_1:5.46-5+b2 libmagic1t64_1:5.46-5+b2 libmd0_1.1.0-2+b2 libmount1_2.42-6 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libncurses-dev_6.6+20251231-1+b1 libncurses6_6.6+20251231-1+b1 libncursesw6_6.6+20251231-1+b1 libnettle8t64_3.10.2-1+b1 libnghttp2-14_1.69.0-1 libnghttp2-dev_1.69.0-1 libnghttp3-9_1.15.0-1 libnghttp3-dev_1.15.0-1 libngtcp2-16_1.22.1-1 libngtcp2-crypto-gnutls-dev_1.22.1-1 libngtcp2-crypto-gnutls8_1.22.1-1 libngtcp2-dev_1.22.1-1 libp11-kit-dev_0.26.2-2 libp11-kit0_0.26.2-2 libpam-modules_1.7.0-5+b2 libpam-modules-bin_1.7.0-5+b2 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5+b2 libpcre2-8-0_10.46-1+b2 libperl5.40_5.40.1-7+b1 libpipeline1_1.5.8-3 libpkgconf7_2.5.1-4 libpsl-dev_0.21.5-1 libpsl5t64_0.21.5-1 libpython3-stdlib_3.13.9-3+b1 libpython3.13-minimal_3.13.12-1 libpython3.13-stdlib_3.13.12-1 libquadmath0_16-20260425-1 libquadmath0-amd64-cross_16-20260425-1cross1 libreadline8t64_8.3-4 librtmp-dev_2.6-1 librtmp1_2.6-1 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.0-2+b1 libselinux1_3.10-1 libsframe3_2.46-3 libsmartcols1_2.42-6 libsqlite3-0_3.46.1-9+b1 libssh2-1-dev_1.11.1-2 libssh2-1t64_1.11.1-2 libssl-dev_3.6.2-1 libssl3t64_3.6.2-1 libstdc++-15-dev_15.2.0-17 libstdc++-15-dev-amd64-cross_15.2.0-17cross1 libstdc++6_16-20260425-1 libstdc++6-amd64-cross_16-20260425-1cross1 libsystemd0_260.1-1 libtasn1-6_4.21.0-2+b1 libtasn1-6-dev_4.21.0-2+b1 libtinfo6_6.6+20251231-1+b1 libtool_2.5.4-11 libtsan2_16-20260425-1 libtsan2-amd64-cross_16-20260425-1cross1 libubsan1_16-20260425-1 libubsan1-amd64-cross_16-20260425-1cross1 libuchardet0_0.0.8-2+b2 libudev1_260.1-1 libunbound8_1.25.0-1 libunistring5_1.4.2-1 libuuid1_2.42-6 libxml2-16_2.15.2+dfsg-0.1 libxxhash0_0.8.3-2+b2 libzstd-dev_1.5.7+dfsg-3+b2 libzstd1_1.5.7+dfsg-3+b2 linux-libc-dev_7.0.4-1 linux-libc-dev-amd64-cross_7.0.4-1 login_1:4.16.0-2+really2.42-6 login.defs_1:4.19.3-2 m4_1.4.21-1 make_4.4.1-3+b1 man-db_2.13.1-1+b1 mawk_1.3.4.20260302-1 media-types_14.0.0 ncurses-base_6.6+20251231-1 ncurses-bin_6.6+20251231-1+b1 netbase_6.5 nettle-dev_3.10.2-1+b1 openssl-provider-legacy_3.6.2-1 patch_2.8-2+b1 perl_5.40.1-7+b1 perl-base_5.40.1-7+b1 perl-modules-5.40_5.40.1-7 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 python3_3.13.9-3+b1 python3-minimal_3.13.9-3+b1 python3.13_3.13.12-1 python3.13-minimal_3.13.12-1 readline-common_8.3-4 rpcsvc-proto_1.4.3-1+b2 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.3.0-5+b1 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 tzdata_2026b-1 util-linux_2.42-6 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Fri, 08 May 2026 21:43:36 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rsem Binary: rsem Architecture: any Version: 1.3.3+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille Homepage: https://deweylab.github.io/RSEM/ Standards-Version: 4.7.3 Vcs-Browser: https://salsa.debian.org/med-team/rsem Vcs-Git: https://salsa.debian.org/med-team/rsem.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev, libncurses-dev, libboost-dev, perl , python3:any, help2man, libhts-dev, hisat2 , bowtie | bowtie2 Package-List: rsem deb science optional arch=any Checksums-Sha1: 5565e925e1efe216153215392b623d655ab513bf 275380 rsem_1.3.3+dfsg.orig.tar.xz 58ffaeac24185972b2e90830a6f29a2720ed27cb 35661072 rsem_1.3.3+dfsg-4.debian.tar.xz Checksums-Sha256: 43037765382f8942a03595eb12ee2ed68081f9f828cb2832388354a12ee00990 275380 rsem_1.3.3+dfsg.orig.tar.xz b665d5d10223825ae1e421e8d27eaeb6231a5ca2d24d8547287721ed1dc67420 35661072 rsem_1.3.3+dfsg-4.debian.tar.xz Files: 59bba49e9d7bba287320c5125d84e8bd 275380 rsem_1.3.3+dfsg.orig.tar.xz d082549f96dd7714d8aad81c203fb05f 35661072 rsem_1.3.3+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEE1Uw7+v+wQt44LaXXQc5/C58bizIFAmnFwIwACgkQQc5/C58b izLCpAf9HEtVW2dKO4fxxyJLJnX6zZh2SkLJnPcp2K4BBapLNvy32yn2kTaQZb8l ZfWVCacZ9CbYXfXkmzhBjO7TiH39MrLENHKOxjuEXvbM0taoP6SXtrERP8BnCajb 6W05Bj51a+SQYulCt4ICvFEksHEq+4tLMejM45eIOBUU0APdsVLAV4XvDzSBIW6B snRcgJifKDPD8fGIF7SmuvsN5g0fDSl7YLp8igXDedzki3Mx7OyIMnWWoxPewmDC kTaF8xzBu/gdhUEZn1HJWUzUgzX8N02se3SaMQLTgI8QDxVr/C49cwnz8/HEKon7 j//1XZqmE+BM+ZI9MnT29ZTF1FaZpA== =da2r -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./rsem_1.3.3+dfsg-4.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./rsem_1.3.3+dfsg-4.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting rsem in /build/reproducible-path/rsem-1.3.3+dfsg dpkg-source: info: unpacking rsem_1.3.3+dfsg.orig.tar.xz dpkg-source: info: unpacking rsem_1.3.3+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening dpkg-source: info: applying use_debian_packaged_samtools.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying stdgnu++14.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.amd64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LC_ALL=C.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aamd64 -Pcross,nocheck -us -uc -B --jobs-try=1 dpkg-buildpackage: info: source package rsem dpkg-buildpackage: info: source version 1.3.3+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Santiago Vila 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 dh_auto_clean make -j1 clean make[1]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg' rm -f *.o *~ rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-build-read-index rsem-simulate-reads rsem-parse-alignments rsem-run-em rsem-tbam2gbam rsem-bam2wig rsem-bam2readdepth rsem-get-unique rsem-sam-validator rsem-scan-for-paired-end-reads rsem-run-gibbs rsem-calculate-credibility-intervals cd EBSeq && make clean make[2]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg/EBSeq' rm -rf EBSeq rsem-for-ebseq-calculate-clustering-info blockmodeling gplots gtools gdata caTools bitops KernSmooth BiocInstaller *~ make[2]: Leaving directory '/build/reproducible-path/rsem-1.3.3+dfsg/EBSeq' cd pRSEM && make clean make[2]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg/pRSEM' rm -fr bigWigSummary RLib filterSam2Bed *.pyc make[2]: Leaving directory '/build/reproducible-path/rsem-1.3.3+dfsg/pRSEM' make[1]: Leaving directory '/build/reproducible-path/rsem-1.3.3+dfsg' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg' dh_auto_build -- BOOST=/usr/include prefix=debian/tmp 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 BOOST=/usr/include prefix=debian/tmp make[2]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg' x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++14 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o extractRef.o extractRef.cpp x86_64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++14 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o synthesisRef.o synthesisRef.cpp x86_64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-synthesis-reference-transcripts synthesisRef.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++14 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o preRef.o preRef.cpp x86_64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++14 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o buildReadIndex.o buildReadIndex.cpp x86_64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++14 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o simulation.o simulation.cpp In file included from simulation.cpp:13: utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/x86_64-linux-gnu/include/stdio.h:970, from /usr/x86_64-linux-gnu/include/c++/15/cstdio:47, from simulation.cpp:3: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleModel::estimateFromReads(const char*)’ at SingleModel.h:284:20: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleQModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleQModel::estimateFromReads(const char*)’ at SingleQModel.h:294:20: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-simulate-reads simulation.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++14 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -c -o parseIt.o parseIt.cpp In file included from SamParser.h:13, from parseIt.cpp:27: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ x86_64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-parse-alignments parseIt.o -lhts -lz x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++14 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o EM.o EM.cpp In file included from BamWriter.h:14, from EM.cpp:45: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ BamWriter.h: In constructor ‘BamWriter::BamWriter(const char*, const char*, const char*, Transcripts&, int)’: BamWriter.h:70:16: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 70 | sam_hdr_write(out, out_header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ BamWriter.h: In member function ‘void BamWriter::work(HitWrapper)’: BamWriter.h:101:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 101 | sam_write1(out, out_header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BamWriter.h: In member function ‘void BamWriter::work(HitWrapper)’: BamWriter.h:136:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 136 | sam_write1(out, out_header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BamWriter.h:137:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 137 | sam_write1(out, out_header, b2); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘int main(int, char**)’: EM.cpp:635:31: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 635 | system(command); | ~~~~~~^~~~~~~~~ In file included from EM.cpp:47: WriteResults.h: In function ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’: WriteResults.h:138:28: warning: ‘.grp’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 138 | sprintf(groupF, "%s.grp", refName); | ^~~~ In file included from /usr/x86_64-linux-gnu/include/stdio.h:970, from /usr/x86_64-linux-gnu/include/c++/15/cstdio:47, from EM.cpp:3: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’ at WriteResults.h:138:9: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ WriteResults.h: In function ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’: WriteResults.h:225:28: warning: ‘.iso_res’ directive writing 8 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 225 | sprintf(outF, "%s.iso_res", imdName); | ^~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’ at WriteResults.h:225:11: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 9 and 10013 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ WriteResults.h: In function ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’: WriteResults.h:259:28: warning: ‘.allele_res’ directive writing 11 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 259 | sprintf(outF, "%s.allele_res", imdName); | ^~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’ at WriteResults.h:259:11: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 12 and 10016 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ WriteResults.h: In function ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’: WriteResults.h:290:28: warning: ‘.iso_res’ directive writing 8 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 290 | sprintf(outF, "%s.iso_res", imdName); | ^~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’ at WriteResults.h:290:11: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 9 and 10013 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ WriteResults.h: In function ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’: WriteResults.h:316:26: warning: ‘.gene_res’ directive writing 9 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 316 | sprintf(outF, "%s.gene_res", imdName); | ^~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’ at WriteResults.h:316:9: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 10 and 10014 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:127:26: warning: ‘.dat’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:127:9: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:435:45: warning: ‘.ofg’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 435 | sprintf(out_for_gibbs_F, "%s.ofg", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:435:10: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:484:28: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:484:9: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResults(ModelType&, double*) [with ModelType = SingleQModel]’ at EM.cpp:282:10, inlined from ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:502:25: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:505:37: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:505:10: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:127:26: warning: ‘.dat’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:127:9: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:435:45: warning: ‘.ofg’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 435 | sprintf(out_for_gibbs_F, "%s.ofg", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:435:10: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:484:28: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:484:9: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResults(ModelType&, double*) [with ModelType = PairedEndQModel]’ at EM.cpp:282:10, inlined from ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:502:25: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:505:37: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:505:10: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:127:26: warning: ‘.dat’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:127:9: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:435:45: warning: ‘.ofg’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 435 | sprintf(out_for_gibbs_F, "%s.ofg", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:435:10: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:484:28: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:484:9: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResults(ModelType&, double*) [with ModelType = SingleModel]’ at EM.cpp:282:10, inlined from ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:502:25: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:505:37: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:505:10: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:127:26: warning: ‘.dat’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:127:9: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:435:45: warning: ‘.ofg’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 435 | sprintf(out_for_gibbs_F, "%s.ofg", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:435:10: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:484:28: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:484:9: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResults(ModelType&, double*) [with ModelType = PairedEndModel]’ at EM.cpp:282:10, inlined from ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:502:25: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:505:37: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:505:10: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘int main(int, char**)’: EM.cpp:633:49: warning: ‘%s’ directive writing up to 10004 bytes into a region of size 1001 [-Wformat-overflow=] 633 | sprintf(command, "cp %s %s", inpSamF, outBamF); | ^~ ~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int main(int, char**)’ at EM.cpp:633:11: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 10009) into a destination of size 1005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++14 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o SamHeader.o SamHeader.cpp x86_64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-em EM.o SamHeader.o -lhts -lz x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++14 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o tbam2gbam.o tbam2gbam.cpp In file included from BamConverter.h:12, from tbam2gbam.cpp:8: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ BamConverter.h: In constructor ‘BamConverter::BamConverter(const char*, const char*, const char*, Transcripts&, int, const std::string&)’: BamConverter.h:70:22: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 70 | sam_hdr_write(out, out_header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ BamConverter.h: In member function ‘void BamConverter::process()’: BamConverter.h:137:29: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 137 | sam_write1(out, out_header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BamConverter.h:138:43: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | if (isPaired) sam_write1(out, out_header, b2); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ BamConverter.h: In member function ‘void BamConverter::writeCollapsedLines()’: BamConverter.h:208:35: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 208 | sam_write1(out, out_header, tmp_b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ BamConverter.h:212:43: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 212 | sam_write1(out, out_header, tmp_b2); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-tbam2gbam tbam2gbam.o SamHeader.o -lhts -lz x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++14 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2wig.o bam2wig.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++14 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o wiggle.o wiggle.cpp In file included from wiggle.cpp:8: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ x86_64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2wig bam2wig.o wiggle.o -lhts -lz x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++14 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2readdepth.o bam2readdepth.cpp x86_64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2readdepth bam2readdepth.o wiggle.o -lhts -lz x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++14 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o getUnique.o getUnique.cpp In file included from getUnique.cpp:10: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ getUnique.cpp: In function ‘void output()’: getUnique.cpp:29:59: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | for (size_t i = 0; i < arr.size(); ++i) sam_write1(out, header, arr[i]); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ getUnique.cpp: In function ‘int main(int, char**)’: getUnique.cpp:45:22: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | sam_hdr_write(out, header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ x86_64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-get-unique getUnique.o -lhts -lz x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++14 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o samValidator.o samValidator.cpp In file included from samValidator.cpp:11: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ samValidator.cpp: In function ‘bool check_read(bam1_t*, bam_hdr_t*)’: samValidator.cpp:28:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 28 | for (int i = 0; i < b->core.n_cigar; ++i) { | ~~^~~~~~~~~~~~~~~~~ samValidator.cpp:53:38: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=] 53 | printf(" aligns to [%d, %d) of transcript %s, which exceeds the transcript's boundary [0, %d)!\n", | ~^ | | | int | %ld 54 | b->core.pos, bam_endpos(b), header->target_name[b->core.tid], header->target_len[b->core.tid]); | ~~~~~~~~~~~ | | | hts_pos_t {aka long int} samValidator.cpp:53:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=] 53 | printf(" aligns to [%d, %d) of transcript %s, which exceeds the transcript's boundary [0, %d)!\n", | ~^ | | | int | %ld 54 | b->core.pos, bam_endpos(b), header->target_name[b->core.tid], header->target_len[b->core.tid]); | ~~~~~~~~~~~~~ | | | hts_pos_t {aka long int} samValidator.cpp: In function ‘int main(int, char**)’: samValidator.cpp:145:82: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=] 145 | printf("\nPaired-end read %s aligns to [%d, %d) of transcript %s, which exceeds the transcript's boundary [0, %d)!\n", | ~^ | | | int | %ld 146 | bam_get_qname(b), tb->core.pos, tb->core.pos + abs(tb->core.isize), header->target_name[tb->core.tid], header->target_len[tb->core.tid]); | ~~~~~~~~~~~~ | | | hts_pos_t {aka long int} samValidator.cpp:145:86: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=] 145 | printf("\nPaired-end read %s aligns to [%d, %d) of transcript %s, which exceeds the transcript's boundary [0, %d)!\n", | ~^ | | | int | %ld 146 | bam_get_qname(b), tb->core.pos, tb->core.pos + abs(tb->core.isize), header->target_name[tb->core.tid], header->target_len[tb->core.tid]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hts_pos_t {aka long int} samValidator.cpp:176:83: warning: ‘creadlen2’ may be used uninitialized [-Wmaybe-uninitialized] 176 | isValid = (creadlen == readlen && (!ispaired || creadlen2 == readlen2)); | ~~~~~~~~~~^~~~~~~~~~~ samValidator.cpp:78:36: note: ‘creadlen2’ was declared here 78 | int creadlen = 0, readlen, creadlen2, readlen2; | ^~~~~~~~~ samValidator.cpp:176:83: warning: ‘readlen2’ may be used uninitialized [-Wmaybe-uninitialized] 176 | isValid = (creadlen == readlen && (!ispaired || creadlen2 == readlen2)); | ~~~~~~~~~~^~~~~~~~~~~ samValidator.cpp:78:47: note: ‘readlen2’ was declared here 78 | int creadlen = 0, readlen, creadlen2, readlen2; | ^~~~~~~~ x86_64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-sam-validator samValidator.o -lhts -lz x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++14 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o scanForPairedEndReads.o scanForPairedEndReads.cpp In file included from scanForPairedEndReads.cpp:11: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ scanForPairedEndReads.cpp: In function ‘int main(int, char**)’: scanForPairedEndReads.cpp:66:22: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | sam_hdr_write(out, header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ scanForPairedEndReads.cpp:94:72: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 94 | for (size_t i = 0; i < arr_both.size(); i++) { sam_write1(out, header, arr_both[i]); bam_destroy1(arr_both[i]); } | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:100:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | sam_write1(out, header, arr_partial_1.back()); bam_destroy1(arr_partial_1.back()); arr_partial_1.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:101:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 101 | sam_write1(out, header, arr_partial_2.back()); bam_destroy1(arr_partial_2.back()); arr_partial_2.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:104:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 104 | sam_write1(out, header, arr_partial_1.back()); bam_destroy1(arr_partial_1.back()); arr_partial_1.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:105:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 105 | sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:108:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 108 | sam_write1(out, header, arr_partial_2.back()); bam_destroy1(arr_partial_2.back()); arr_partial_2.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:109:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 109 | sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:114:25: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 114 | sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:118:23: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 118 | sam_write1(out, header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:120:25: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 120 | sam_write1(out, header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-scan-for-paired-end-reads scanForPairedEndReads.o -lhts -lz x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++14 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o Gibbs.o Gibbs.cpp Gibbs.cpp: In function ‘void init()’: Gibbs.cpp:214:26: warning: ‘.countvectors’ directive writing 13 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 214 | sprintf(cvsF, "%s.countvectors", imdName); | ^~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/stdio.h:970, from /usr/x86_64-linux-gnu/include/c++/15/cstdio:47, from Gibbs.cpp:1: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init()’ at Gibbs.cpp:214:9: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 14 and 10018 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ Gibbs.cpp: In function ‘void init()’: Gibbs.cpp:225:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 225 | sprintf(outF, "%s%d", cvsF, i); | ^~ Gibbs.cpp:225:31: note: directive argument in the range [0, 2147483646] 225 | sprintf(outF, "%s%d", cvsF, i); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init()’ at Gibbs.cpp:225:10: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from Gibbs.cpp:10: utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleModel::estimateFromReads(const char*)’ at SingleModel.h:284:20: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleQModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleQModel::estimateFromReads(const char*)’ at SingleQModel.h:294:20: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-gibbs Gibbs.o -lhts x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++14 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o calcCI.o calcCI.cpp In file included from calcCI.cpp:11: utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/x86_64-linux-gnu/include/stdio.h:970, from /usr/x86_64-linux-gnu/include/c++/15/cstdio:47, from calcCI.cpp:2: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndQModel]’: calcCI.cpp:183:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~ calcCI.cpp:183:31: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndQModel]’ at calcCI.cpp:183:10: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndModel]’: calcCI.cpp:183:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~ calcCI.cpp:183:31: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndModel]’ at calcCI.cpp:183:10: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleQModel]’: calcCI.cpp:183:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~ calcCI.cpp:183:31: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleQModel]’ at calcCI.cpp:183:10: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleModel]’: calcCI.cpp:183:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~ calcCI.cpp:183:31: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleModel]’ at calcCI.cpp:183:10: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleModel::estimateFromReads(const char*)’ at SingleModel.h:284:20: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleQModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleQModel::estimateFromReads(const char*)’ at SingleQModel.h:294:20: /usr/x86_64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-calculate-credibility-intervals calcCI.o -lhts make[2]: Leaving directory '/build/reproducible-path/rsem-1.3.3+dfsg' for prog in convert-sam-for-rsem rsem-calculate-expression \ rsem-control-fdr rsem-generate-ngvector \ rsem-plot-transcript-wiggles rsem-prepare-reference \ rsem-run-ebseq; do pod2man ${prog} debian/${prog}.1; done help2man ./rsem-gff3-to-gtf --no-info --version-string="1.3.3+dfsg" \ --name 'Convert GFF3 files to GTF files.' > \ debian/rsem-gff3-to-gtf.1 help2man ./rsem-bam2wig --no-info --version-string="1.3.3+dfsg" \ --name 'Convert BAM files to wiggle files.' > \ debian/rsem-bam2wig.1 help2man: can't get `--help' info from ./rsem-bam2wig Try `--no-discard-stderr' if option outputs to stderr make[1]: *** [debian/rules:16: override_dh_auto_build] Error 126 make[1]: Leaving directory '/build/reproducible-path/rsem-1.3.3+dfsg' make: *** [debian/rules:10: binary-arch] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess failed with exit status 2 -------------------------------------------------------------------------------- Build finished at 2026-05-08T21:50:14Z +------------------------------------------------------------------------------+ | Finished Timed Build Commands Fri, 08 May 2026 21:50:14 +0000 | +------------------------------------------------------------------------------+ rm -Rf /build/reproducible-path/rsem-1.3.3+dfsg/ ------------------------------------------------ I: Finished running 'rm -Rf /build/reproducible-path/rsem-1.3.3+dfsg/'. Finished processing commands. -------------------------------------------------------------------------------- Finished -------- +------------------------------------------------------------------------------+ | Cleanup Fri, 08 May 2026 21:50:14 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died with exit 2) +------------------------------------------------------------------------------+ | Summary Fri, 08 May 2026 21:50:19 +0000 | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Build-Space: n/a Build-Time: 392 Distribution: unstable Fail-Stage: build Foreign Architectures: amd64 Host Architecture: amd64 Install-Time: 76 Job: rsem_1.3.3+dfsg-4 Machine Architecture: arm64 Package: rsem Package-Time: 517 Source-Version: 1.3.3+dfsg-4 Space: n/a Status: attempted Version: 1.3.3+dfsg-4 -------------------------------------------------------------------------------- Finished at 2026-05-08T21:50:14Z Build needed 00:08:37, no disk space