Running as unit: rb-build-amd64_5-56371.service ==================================================================================== Tue Sep 16 14:51:01 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_5) on jenkins, called using "ionos11-amd64 ionos5-amd64" as arguments. Tue Sep 16 14:51:01 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-Vz4y0foR" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Sep 16 14:51:01 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Tue Sep 16 14:51:01 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-z7RGnV' Tue Sep 16 14:51:01 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Tue Sep 16 14:51:01 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-BvAyXh' ok, let's check if rsem is building anywhere yet… ok, rsem is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of rsem in forky on amd64 on jenkins now. 1st build will be done on ionos11-amd64.debian.net. 2nd build will be done on ionos5-amd64.debian.net. ============================================================================= Tue Sep 16 14:51:22 UTC 2025 I: starting to build rsem/forky/amd64 on jenkins on '2025-09-16 14:51' Tue Sep 16 14:51:22 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_5/56371/console.log 1758034282 amd64 forky rsem Tue Sep 16 14:51:22 UTC 2025 I: Downloading source for forky/rsem=1.3.3+dfsg-3 --2025-09-16 14:51:22-- http://deb.debian.org/debian/pool/main/r/rsem/rsem_1.3.3%2bdfsg-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2249 (2.2K) [text/prs.lines.tag] Saving to: ‘rsem_1.3.3+dfsg-3.dsc’ 0K .. 100% 227M=0s 2025-09-16 14:51:22 (227 MB/s) - ‘rsem_1.3.3+dfsg-3.dsc’ saved [2249/2249] --2025-09-16 14:51:22-- http://deb.debian.org/debian/pool/main/r/rsem/rsem_1.3.3%2bdfsg-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2249 (2.2K) [text/prs.lines.tag] Saving to: ‘rsem_1.3.3+dfsg-3.dsc’ 0K .. 100% 227M=0s 2025-09-16 14:51:22 (227 MB/s) - ‘rsem_1.3.3+dfsg-3.dsc’ saved [2249/2249] Tue Sep 16 14:51:22 UTC 2025 I: rsem_1.3.3+dfsg-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rsem Binary: rsem Architecture: any Version: 1.3.3+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille Homepage: https://deweylab.github.io/RSEM/ Standards-Version: 4.6.2 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 05cea0dbf74cb2855055322ee7ec48f022ac1a9a 35660968 rsem_1.3.3+dfsg-3.debian.tar.xz Checksums-Sha256: 43037765382f8942a03595eb12ee2ed68081f9f828cb2832388354a12ee00990 275380 rsem_1.3.3+dfsg.orig.tar.xz 957be6fa620d1a09db0e41fe6207d56ee60a8e938f5a594176c068d78e063204 35660968 rsem_1.3.3+dfsg-3.debian.tar.xz Files: 59bba49e9d7bba287320c5125d84e8bd 275380 rsem_1.3.3+dfsg.orig.tar.xz 4371920046ae5a0f654c8cae94a84c0c 35660968 rsem_1.3.3+dfsg-3.debian.tar.xz Dgit: 87fe4c33d81e96bb4704a476dde491ef3207ab24 debian archive/debian/1.3.3+dfsg-3 https://git.dgit.debian.org/rsem -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmWAQ20UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdokyQ//SNKe4BXEPLVFcAVF/7TrICkowWQ8 nzkIT5MS2BDq9HSbt3lb7XTbZ6g6gVQ5xLsBwgBLllWrcZPfipfuDrxSxku5gERB i9Fxyte8uqE97LX1AYiy4+Xbx/k8dOm97V3mwh6AVvV3zjP7OiUuhTR2xxTtV1A6 vv1YFYCph1kR91f2ZjzVr1NkKMGNxpe1UGQ002GNWgYVsp0Q36QfF5RJp8r18LWf bJn/j32atSIOO7IM28F8/x75OIBCgOPEDgAgEUWwl4S9lS+jxQCkXE5w9R+LAEl8 czo9H1iSAK9bAN+6SYQiL7pxkxUljaH8JhRoDJhKqDE3Df5mF51ATdwPzg7r7yam XFX5P9B5ViAd6CaOoWsF97M/FY1EnvL08ZxGILEgyliksi+1ye8UxT5T453yXwZm ajo2YBH/l0lm+/k861MMnssMcSkmeT5fTatn0g6RGUgdbMmjE5JnZxN5flJ+qNzC RobpHL4SLihWT7BDDogOSXMYnIByAMfrPiwSaG3do6/wa1+XfRMW5mzcA6Cyj+MY vFXjFL7i9FXJfYfyGNjSKOXrw3w2fw9QpP13QNkKawqoCfJ12EhrHni7oEqAg4J0 LNPU18sMMmki52BblJ4VN2rEimp0QxFGsZwBVvJvXqeUg0fdU0I97paVzcqFFMVT m+l1fDNky96/wR4= =j51B -----END PGP SIGNATURE----- Tue Sep 16 14:51:22 UTC 2025 I: Checking whether the package is not for us Tue Sep 16 14:51:22 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net. Tue Sep 16 14:51:22 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Tue Sep 16 14:51:22 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Tue Sep 16 14:51:22 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-9Xixlo' ==================================================================================== Tue Sep 16 14:51:23 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos11-amd64, called using "1 rsem forky /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv 1.3.3+dfsg-3" as arguments. Tue Sep 16 14:51:23 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-W0wLgC1N" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Sep 16 14:51:23 UTC 2025 I: Downloading source for forky/rsem=1.3.3+dfsg-3 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://deb.debian.org/debian forky/main rsem 1.3.3+dfsg-3 (dsc) [2249 B] Get:2 http://deb.debian.org/debian forky/main rsem 1.3.3+dfsg-3 (tar) [275 kB] Get:3 http://deb.debian.org/debian forky/main rsem 1.3.3+dfsg-3 (diff) [35.7 MB] Fetched 35.9 MB in 0s (83.6 MB/s) Download complete and in download only mode 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://deb.debian.org/debian forky/main rsem 1.3.3+dfsg-3 (dsc) [2249 B] Get:2 http://deb.debian.org/debian forky/main rsem 1.3.3+dfsg-3 (tar) [275 kB] Get:3 http://deb.debian.org/debian forky/main rsem 1.3.3+dfsg-3 (diff) [35.7 MB] Fetched 35.9 MB in 0s (83.6 MB/s) Download complete and in download only mode ============================================================================= Building rsem in forky on amd64 on ionos11-amd64 now. Date: Tue Sep 16 14:51:24 UTC 2025 Date UTC: Tue Sep 16 14:51:24 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 16 02:51:24 -12 2025 I: pbuilder-time-stamp: 1758034284 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [rsem_1.3.3+dfsg-3.dsc] I: copying [./rsem_1.3.3+dfsg.orig.tar.xz] I: copying [./rsem_1.3.3+dfsg-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./rsem_1.3.3+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting rsem in 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-3.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++11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3005475/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='013ecf1e04a346feaf2440c73bb01729' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3005475' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/pbuilderrc_R6G6 --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/b1 --logfile b1/build.log rsem_1.3.3+dfsg-3.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3005475/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libncurses-dev, libboost-dev, perl, python3:any, help2man, libhts-dev, hisat2, bowtie | bowtie2 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libncurses-dev; however: Package libncurses-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on python3:any. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on hisat2; however: Package hisat2 is not installed. pbuilder-satisfydepends-dummy depends on bowtie | bowtie2; however: Package bowtie is not installed. Package bowtie2 is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bowtie{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gcc-14-base{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} hisat2{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libboost-dev{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgcc-14-dev{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libidn2-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblocale-gettext-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libstdc++-14-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2-16{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bcftools bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix python3-hisat2 samtools wget 0 packages upgraded, 117 newly installed, 0 to remove and 0 not upgraded. Need to get 59.7 MB of archives. After unpacking 366 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 bowtie amd64 1.3.1-3 [1627 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 comerr-dev amd64 2.1-1.47.2-3+b3 [56.7 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 40 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 gcc-14-base amd64 14.3.0-7 [52.0 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 help2man amd64 1.49.3 [198 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 hisat2 amd64 2.2.1-5+b3 [3797 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 54 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 56 http://deb.debian.org/debian forky/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 libgcc-14-dev amd64 14.3.0-7 [2671 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 libstdc++-14-dev amd64 14.3.0-7 [2649 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 libboost1.83-dev amd64 1.83.0-4.2 [10.6 MB] Get: 64 http://deb.debian.org/debian forky/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 65 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 67 http://deb.debian.org/debian forky/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 69 http://deb.debian.org/debian forky/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get: 72 http://deb.debian.org/debian forky/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 73 http://deb.debian.org/debian forky/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 74 http://deb.debian.org/debian forky/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 75 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 libngtcp2-16 amd64 1.15.1-1 [140 kB] Get: 78 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-gnutls8 amd64 1.15.1-1 [20.9 kB] Get: 79 http://deb.debian.org/debian forky/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 80 http://deb.debian.org/debian forky/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 81 http://deb.debian.org/debian forky/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 82 http://deb.debian.org/debian forky/main amd64 libcurl3t64-gnutls amd64 8.15.0-1 [385 kB] Get: 83 http://deb.debian.org/debian forky/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 84 http://deb.debian.org/debian forky/main amd64 libunbound8 amd64 1.23.1-1 [606 kB] Get: 85 http://deb.debian.org/debian forky/main amd64 libgnutls-dane0t64 amd64 3.8.9-3 [455 kB] Get: 86 http://deb.debian.org/debian forky/main amd64 libgnutls-openssl27t64 amd64 3.8.9-3 [455 kB] Get: 87 http://deb.debian.org/debian forky/main amd64 libidn2-dev amd64 2.3.8-4 [103 kB] Get: 88 http://deb.debian.org/debian forky/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 89 http://deb.debian.org/debian forky/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 90 http://deb.debian.org/debian forky/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5 [330 kB] Get: 91 http://deb.debian.org/debian forky/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5 [658 kB] Get: 92 http://deb.debian.org/debian forky/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 93 http://deb.debian.org/debian forky/main amd64 libgnutls28-dev amd64 3.8.9-3 [1406 kB] Get: 94 http://deb.debian.org/debian forky/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get: 95 http://deb.debian.org/debian forky/main amd64 libldap-dev amd64 2.6.10+dfsg-1 [312 kB] Get: 96 http://deb.debian.org/debian forky/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 97 http://deb.debian.org/debian forky/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 98 http://deb.debian.org/debian forky/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 99 http://deb.debian.org/debian forky/main amd64 libnghttp2-dev amd64 1.64.0-1.1+b1 [117 kB] Get: 100 http://deb.debian.org/debian forky/main amd64 libnghttp3-dev amd64 1.11.0-1 [101 kB] Get: 101 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.15.1-1 [26.1 kB] Get: 102 http://deb.debian.org/debian forky/main amd64 libngtcp2-dev amd64 1.15.1-1 [196 kB] Get: 103 http://deb.debian.org/debian forky/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 104 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 105 http://deb.debian.org/debian forky/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-3 [67.9 kB] Get: 106 http://deb.debian.org/debian forky/main amd64 libssl-dev amd64 3.5.2-1 [2957 kB] Get: 107 http://deb.debian.org/debian forky/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 108 http://deb.debian.org/debian forky/main amd64 libzstd-dev amd64 1.5.7+dfsg-1.1 [389 kB] Get: 109 http://deb.debian.org/debian forky/main amd64 libcurl4-gnutls-dev amd64 8.15.0-1 [504 kB] Get: 110 http://deb.debian.org/debian forky/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 111 http://deb.debian.org/debian forky/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get: 112 http://deb.debian.org/debian forky/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 113 http://deb.debian.org/debian forky/main amd64 libhts3t64 amd64 1.22.1+ds2-1 [499 kB] Get: 114 http://deb.debian.org/debian forky/main amd64 liblzma-dev amd64 5.8.1-1.1 [357 kB] Get: 115 http://deb.debian.org/debian forky/main amd64 libhts-dev amd64 1.22.1+ds2-1 [1807 kB] Get: 116 http://deb.debian.org/debian forky/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get: 117 http://deb.debian.org/debian forky/main amd64 libncurses-dev amd64 6.5+20250216-2 [353 kB] Fetched 59.7 MB in 15s (4026 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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 ... 19917 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_amd64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:amd64 (3.13.7-1) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.7-1) ... Selecting previously unselected package python3-minimal. (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 ... 20266 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. (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 ... 21281 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../003-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../006-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../007-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../008-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../009-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../010-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../011-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../012-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../013-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../014-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../015-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package bowtie. Preparing to unpack .../016-bowtie_1.3.1-3_amd64.deb ... Unpacking bowtie (1.3.1-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../017-libcom-err2_1.47.2-3+b3_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b3) ... Selecting previously unselected package comerr-dev:amd64. Preparing to unpack .../018-comerr-dev_2.1-1.47.2-3+b3_amd64.deb ... Unpacking comerr-dev:amd64 (2.1-1.47.2-3+b3) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../019-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../020-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../021-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../022-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../023-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../024-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../025-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../026-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../027-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../028-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../029-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../030-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../031-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../032-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Selecting previously unselected package gcc-14-base:amd64. Preparing to unpack .../033-gcc-14-base_14.3.0-7_amd64.deb ... Unpacking gcc-14-base:amd64 (14.3.0-7) ... Selecting previously unselected package help2man. Preparing to unpack .../034-help2man_1.49.3_amd64.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package hisat2. Preparing to unpack .../035-hisat2_2.2.1-5+b3_amd64.deb ... Unpacking hisat2 (2.2.1-5+b3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../036-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../037-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../038-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../039-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../040-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package libgssrpc4t64:amd64. Preparing to unpack .../041-libgssrpc4t64_1.21.3-5_amd64.deb ... Unpacking libgssrpc4t64:amd64 (1.21.3-5) ... Selecting previously unselected package libkadm5clnt-mit12:amd64. Preparing to unpack .../042-libkadm5clnt-mit12_1.21.3-5_amd64.deb ... Unpacking libkadm5clnt-mit12:amd64 (1.21.3-5) ... Selecting previously unselected package libkdb5-10t64:amd64. Preparing to unpack .../043-libkdb5-10t64_1.21.3-5_amd64.deb ... Unpacking libkdb5-10t64:amd64 (1.21.3-5) ... 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Setting up libgcc-14-dev:amd64 (14.3.0-7) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up libdeflate-dev:amd64 (1.23-2) ... Setting up libstdc++-14-dev:amd64 (14.3.0-7) ... Setting up readline-common (8.3-3) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up libboost1.83-dev:amd64 (1.83.0-4.2) ... Setting up libncurses-dev:amd64 (6.5+20250216-2) ... Setting up gettext (0.23.1-2+b1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libtool (2.5.4-5) ... Setting up libidn2-0:amd64 (2.3.8-4) ... Setting up libngtcp2-dev:amd64 (1.15.1-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libidn2-dev:amd64 (2.3.8-4) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libpython3.13-stdlib:amd64 (3.13.7-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up libgnutls30t64:amd64 (3.8.9-3) ... Setting up libgnutls-openssl27t64:amd64 (3.8.9-3) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1+b1) ... Setting up python3.13 (3.13.7-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.7-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.9-3) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up hisat2 (2.2.1-5+b3) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.15.1-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libgnutls28-dev:amd64 (3.8.9-3) ... Setting up bowtie (1.3.1-3) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up libcurl3t64-gnutls:amd64 (8.15.0-1) ... Setting up debhelper (13.26) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.15.1-1) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up libcurl4-gnutls-dev:amd64 (8.15.0-1) ... Setting up libhts-dev:amd64 (1.22.1+ds2-1) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/rsem-1.3.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rsem_1.3.3+dfsg-3_source.changes dpkg-buildpackage: info: source package rsem dpkg-buildpackage: info: source version 1.3.3+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j40 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 dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure 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 -j40 "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=debian/tmp make[2]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg' 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o extractRef.o extractRef.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o synthesisRef.o synthesisRef.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o preRef.o preRef.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o buildReadIndex.o buildReadIndex.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o simulation.o simulation.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -c -o parseIt.o parseIt.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o EM.o EM.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o SamHeader.o SamHeader.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o tbam2gbam.o tbam2gbam.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2wig.o bam2wig.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o wiggle.o wiggle.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2readdepth.o bam2readdepth.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o getUnique.o getUnique.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o samValidator.o samValidator.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o scanForPairedEndReads.o scanForPairedEndReads.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o Gibbs.o Gibbs.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o calcCI.o calcCI.cpp In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from simulation.cpp:22: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from calcCI.cpp:16: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from Gibbs.cpp:15: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from EM.cpp:28: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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} g++ -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o 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); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ 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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ 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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o 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; | ^~~~~~~~ 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); | ~~~~~~^~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-get-unique getUnique.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2wig bam2wig.o wiggle.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2readdepth bam2readdepth.o wiggle.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-sam-validator samValidator.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-scan-for-paired-end-reads scanForPairedEndReads.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-tbam2gbam tbam2gbam.o SamHeader.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-parse-alignments parseIt.o -lhts -lz 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/include/stdio.h:970, from /usr/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-synthesis-reference-transcripts synthesisRef.o g++ -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o 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/include/stdio.h:970, from /usr/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 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/include/stdio.h:970, from /usr/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ 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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 = PairedEndQModel]': calcCI.cpp:183:36: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 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/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 10006 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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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:183:36: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 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/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 10006 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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ 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/include/stdio.h:970, from /usr/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ 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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-simulate-reads simulation.o g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-gibbs Gibbs.o -lhts g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-calculate-credibility-intervals calcCI.o -lhts 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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-em EM.o SamHeader.o -lhts -lz 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 ./rsem-simulate-reads --no-info --version-string="1.3.3+dfsg" \ --name 'Simulate RNA-Seq data ("reads") for a given model and a RSEM reference transcript collection.' > \ debian/rsem-simulate-reads.1 make[1]: Leaving directory '/build/reproducible-path/rsem-1.3.3+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg' dh_auto_install -- BOOST=/usr/include prefix="/usr" make -j40 install DESTDIR=/build/reproducible-path/rsem-1.3.3\+dfsg/debian/rsem AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=/usr make[2]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg' install --strip-program=true -p rsem-extract-reference-transcripts /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-extract-reference-transcripts ; install --strip-program=true -p rsem-synthesis-reference-transcripts /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-synthesis-reference-transcripts ; install --strip-program=true -p rsem-preref /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-preref ; install --strip-program=true -p rsem-build-read-index /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-build-read-index ; install --strip-program=true -p rsem-simulate-reads /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-simulate-reads ; install --strip-program=true -p rsem-parse-alignments /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-parse-alignments ; install --strip-program=true -p rsem-run-em /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-run-em ; install --strip-program=true -p rsem-tbam2gbam /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-tbam2gbam ; install --strip-program=true -p rsem-bam2wig /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-bam2wig ; install --strip-program=true -p rsem-bam2readdepth /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-bam2readdepth ; install --strip-program=true -p rsem-get-unique /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-get-unique ; install --strip-program=true -p rsem-sam-validator /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-sam-validator ; install --strip-program=true -p rsem-scan-for-paired-end-reads /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-scan-for-paired-end-reads ; install --strip-program=true -p rsem-run-gibbs /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-run-gibbs ; install --strip-program=true -p rsem-calculate-credibility-intervals /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-calculate-credibility-intervals ; install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -p rsem-prepare-reference /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-prepare-reference ; install --strip-program=true -p rsem-calculate-expression /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-calculate-expression ; install --strip-program=true -p rsem-refseq-extract-primary-assembly /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-refseq-extract-primary-assembly ; install --strip-program=true -p rsem-gff3-to-gtf /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-gff3-to-gtf ; install --strip-program=true -p rsem-plot-model /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-plot-model ; install --strip-program=true -p rsem-plot-transcript-wiggles /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-plot-transcript-wiggles ; install --strip-program=true -p rsem-gen-transcript-plots /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-gen-transcript-plots ; install --strip-program=true -p rsem-generate-data-matrix /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-generate-data-matrix ; install --strip-program=true -p extract-transcript-to-gene-map-from-trinity /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/extract-transcript-to-gene-map-from-trinity ; install --strip-program=true -p convert-sam-for-rsem /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/convert-sam-for-rsem ; install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -p -m 644 rsem_perl_utils.pm /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem_perl_utils.pm install: WARNING: ignoring --strip-program option as -s option was not specified make[2]: Leaving directory '/build/reproducible-path/rsem-1.3.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/rsem-1.3.3+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/reproducible-path/rsem-1.3.3+dfsg' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'rsem-dbgsym' in '../rsem-dbgsym_1.3.3+dfsg-3_amd64.deb'. dpkg-deb: building package 'rsem' in '../rsem_1.3.3+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../rsem_1.3.3+dfsg-3_amd64.buildinfo dpkg-genchanges --build=binary -O../rsem_1.3.3+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3005475 and its subdirectories I: Current time: Tue Sep 16 02:57:14 -12 2025 I: pbuilder-time-stamp: 1758034634 Tue Sep 16 14:57:14 UTC 2025 I: Signing ./b1/rsem_1.3.3+dfsg-3_amd64.buildinfo as rsem_1.3.3+dfsg-3_amd64.buildinfo.asc Tue Sep 16 14:57:14 UTC 2025 I: Signed ./b1/rsem_1.3.3+dfsg-3_amd64.buildinfo as ./b1/rsem_1.3.3+dfsg-3_amd64.buildinfo.asc Tue Sep 16 14:57:14 UTC 2025 - build #1 for rsem/forky/amd64 on ionos11-amd64 done. Starting cleanup. All cleanup done. Tue Sep 16 14:57:14 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-W0wLgC1N, removing. /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 16 14:57 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 16 14:51 b2 -rw------- 1 jenkins jenkins 3350 Sep 16 14:51 rbuildlog.WYwYGnm -rw-rw-r-- 1 jenkins jenkins 2249 Dec 18 2023 rsem_1.3.3+dfsg-3.dsc /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/b1: total 76232 -rw-r--r-- 1 jenkins jenkins 143628 Sep 16 14:57 build.log -rw-r--r-- 1 jenkins jenkins 6016696 Sep 16 14:57 rsem-dbgsym_1.3.3+dfsg-3_amd64.deb -rw-r--r-- 1 jenkins jenkins 35660968 Sep 16 14:57 rsem_1.3.3+dfsg-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2249 Sep 16 14:57 rsem_1.3.3+dfsg-3.dsc -rw-r--r-- 1 jenkins jenkins 7627 Sep 16 14:57 rsem_1.3.3+dfsg-3_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 8509 Sep 16 14:57 rsem_1.3.3+dfsg-3_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1842 Sep 16 14:57 rsem_1.3.3+dfsg-3_amd64.changes -rw-r--r-- 1 jenkins jenkins 36196372 Sep 16 14:57 rsem_1.3.3+dfsg-3_amd64.deb -rw-r--r-- 1 jenkins jenkins 1721 Sep 16 14:57 rsem_1.3.3+dfsg-3_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/b2: total 0 Tue Sep 16 14:57:15 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 16 02:51:24 -12 2025 I: pbuilder-time-stamp: 1758034284 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [rsem_1.3.3+dfsg-3.dsc] I: copying [./rsem_1.3.3+dfsg.orig.tar.xz] I: copying [./rsem_1.3.3+dfsg-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./rsem_1.3.3+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting rsem in 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-3.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++11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3005475/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='013ecf1e04a346feaf2440c73bb01729' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3005475' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/pbuilderrc_R6G6 --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/b1 --logfile b1/build.log rsem_1.3.3+dfsg-3.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3005475/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libncurses-dev, libboost-dev, perl, python3:any, help2man, libhts-dev, hisat2, bowtie | bowtie2 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libncurses-dev; however: Package libncurses-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on python3:any. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on hisat2; however: Package hisat2 is not installed. pbuilder-satisfydepends-dummy depends on bowtie | bowtie2; however: Package bowtie is not installed. Package bowtie2 is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bowtie{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gcc-14-base{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} hisat2{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libboost-dev{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgcc-14-dev{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libidn2-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblocale-gettext-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libstdc++-14-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2-16{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bcftools bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix python3-hisat2 samtools wget 0 packages upgraded, 117 newly installed, 0 to remove and 0 not upgraded. Need to get 59.7 MB of archives. After unpacking 366 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 bowtie amd64 1.3.1-3 [1627 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 comerr-dev amd64 2.1-1.47.2-3+b3 [56.7 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 40 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 gcc-14-base amd64 14.3.0-7 [52.0 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 help2man amd64 1.49.3 [198 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 hisat2 amd64 2.2.1-5+b3 [3797 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 54 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 56 http://deb.debian.org/debian forky/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 libgcc-14-dev amd64 14.3.0-7 [2671 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 libstdc++-14-dev amd64 14.3.0-7 [2649 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 libboost1.83-dev amd64 1.83.0-4.2 [10.6 MB] Get: 64 http://deb.debian.org/debian forky/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 65 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 67 http://deb.debian.org/debian forky/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 69 http://deb.debian.org/debian forky/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get: 72 http://deb.debian.org/debian forky/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 73 http://deb.debian.org/debian forky/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 74 http://deb.debian.org/debian forky/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 75 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 libngtcp2-16 amd64 1.15.1-1 [140 kB] Get: 78 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-gnutls8 amd64 1.15.1-1 [20.9 kB] Get: 79 http://deb.debian.org/debian forky/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 80 http://deb.debian.org/debian forky/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 81 http://deb.debian.org/debian forky/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 82 http://deb.debian.org/debian forky/main amd64 libcurl3t64-gnutls amd64 8.15.0-1 [385 kB] Get: 83 http://deb.debian.org/debian forky/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 84 http://deb.debian.org/debian forky/main amd64 libunbound8 amd64 1.23.1-1 [606 kB] Get: 85 http://deb.debian.org/debian forky/main amd64 libgnutls-dane0t64 amd64 3.8.9-3 [455 kB] Get: 86 http://deb.debian.org/debian forky/main amd64 libgnutls-openssl27t64 amd64 3.8.9-3 [455 kB] Get: 87 http://deb.debian.org/debian forky/main amd64 libidn2-dev amd64 2.3.8-4 [103 kB] Get: 88 http://deb.debian.org/debian forky/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 89 http://deb.debian.org/debian forky/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 90 http://deb.debian.org/debian forky/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5 [330 kB] Get: 91 http://deb.debian.org/debian forky/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5 [658 kB] Get: 92 http://deb.debian.org/debian forky/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 93 http://deb.debian.org/debian forky/main amd64 libgnutls28-dev amd64 3.8.9-3 [1406 kB] Get: 94 http://deb.debian.org/debian forky/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get: 95 http://deb.debian.org/debian forky/main amd64 libldap-dev amd64 2.6.10+dfsg-1 [312 kB] Get: 96 http://deb.debian.org/debian forky/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 97 http://deb.debian.org/debian forky/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 98 http://deb.debian.org/debian forky/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 99 http://deb.debian.org/debian forky/main amd64 libnghttp2-dev amd64 1.64.0-1.1+b1 [117 kB] Get: 100 http://deb.debian.org/debian forky/main amd64 libnghttp3-dev amd64 1.11.0-1 [101 kB] Get: 101 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.15.1-1 [26.1 kB] Get: 102 http://deb.debian.org/debian forky/main amd64 libngtcp2-dev amd64 1.15.1-1 [196 kB] Get: 103 http://deb.debian.org/debian forky/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 104 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 105 http://deb.debian.org/debian forky/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-3 [67.9 kB] Get: 106 http://deb.debian.org/debian forky/main amd64 libssl-dev amd64 3.5.2-1 [2957 kB] Get: 107 http://deb.debian.org/debian forky/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 108 http://deb.debian.org/debian forky/main amd64 libzstd-dev amd64 1.5.7+dfsg-1.1 [389 kB] Get: 109 http://deb.debian.org/debian forky/main amd64 libcurl4-gnutls-dev amd64 8.15.0-1 [504 kB] Get: 110 http://deb.debian.org/debian forky/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 111 http://deb.debian.org/debian forky/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get: 112 http://deb.debian.org/debian forky/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 113 http://deb.debian.org/debian forky/main amd64 libhts3t64 amd64 1.22.1+ds2-1 [499 kB] Get: 114 http://deb.debian.org/debian forky/main amd64 liblzma-dev amd64 5.8.1-1.1 [357 kB] Get: 115 http://deb.debian.org/debian forky/main amd64 libhts-dev amd64 1.22.1+ds2-1 [1807 kB] Get: 116 http://deb.debian.org/debian forky/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get: 117 http://deb.debian.org/debian forky/main amd64 libncurses-dev amd64 6.5+20250216-2 [353 kB] Fetched 59.7 MB in 15s (4026 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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 ... 19917 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_amd64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:amd64 (3.13.7-1) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.7-1) ... Selecting previously unselected package python3-minimal. (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 ... 20266 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/rsem-1.3.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rsem_1.3.3+dfsg-3_source.changes dpkg-buildpackage: info: source package rsem dpkg-buildpackage: info: source version 1.3.3+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j40 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 dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure 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 -j40 "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=debian/tmp make[2]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg' 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o extractRef.o extractRef.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o synthesisRef.o synthesisRef.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o preRef.o preRef.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o buildReadIndex.o buildReadIndex.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o simulation.o simulation.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -c -o parseIt.o parseIt.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o EM.o EM.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o SamHeader.o SamHeader.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o tbam2gbam.o tbam2gbam.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2wig.o bam2wig.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o wiggle.o wiggle.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2readdepth.o bam2readdepth.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o getUnique.o getUnique.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o samValidator.o samValidator.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o scanForPairedEndReads.o scanForPairedEndReads.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o Gibbs.o Gibbs.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o calcCI.o calcCI.cpp In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from simulation.cpp:22: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from calcCI.cpp:16: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from Gibbs.cpp:15: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from EM.cpp:28: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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} g++ -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o 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); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ 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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ 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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o 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; | ^~~~~~~~ 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); | ~~~~~~^~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-get-unique getUnique.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2wig bam2wig.o wiggle.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2readdepth bam2readdepth.o wiggle.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-sam-validator samValidator.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-scan-for-paired-end-reads scanForPairedEndReads.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-tbam2gbam tbam2gbam.o SamHeader.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-parse-alignments parseIt.o -lhts -lz 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/include/stdio.h:970, from /usr/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-synthesis-reference-transcripts synthesisRef.o g++ -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o 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/include/stdio.h:970, from /usr/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 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/include/stdio.h:970, from /usr/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ 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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 = PairedEndQModel]': calcCI.cpp:183:36: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 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/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 10006 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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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:183:36: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 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/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 10006 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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ 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/include/stdio.h:970, from /usr/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ 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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-simulate-reads simulation.o g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-gibbs Gibbs.o -lhts g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-calculate-credibility-intervals calcCI.o -lhts 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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-em EM.o SamHeader.o -lhts -lz 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 ./rsem-simulate-reads --no-info --version-string="1.3.3+dfsg" \ --name 'Simulate RNA-Seq data ("reads") for a given model and a RSEM reference transcript collection.' > \ debian/rsem-simulate-reads.1 make[1]: Leaving directory '/build/reproducible-path/rsem-1.3.3+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg' dh_auto_install -- BOOST=/usr/include prefix="/usr" make -j40 install DESTDIR=/build/reproducible-path/rsem-1.3.3\+dfsg/debian/rsem AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=/usr make[2]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg' install --strip-program=true -p rsem-extract-reference-transcripts /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-extract-reference-transcripts ; install --strip-program=true -p rsem-synthesis-reference-transcripts /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-synthesis-reference-transcripts ; install --strip-program=true -p rsem-preref /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-preref ; install --strip-program=true -p rsem-build-read-index /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-build-read-index ; install --strip-program=true -p rsem-simulate-reads /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-simulate-reads ; install --strip-program=true -p rsem-parse-alignments /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-parse-alignments ; install --strip-program=true -p rsem-run-em /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-run-em ; install --strip-program=true -p rsem-tbam2gbam /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-tbam2gbam ; install --strip-program=true -p rsem-bam2wig /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-bam2wig ; install --strip-program=true -p rsem-bam2readdepth /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-bam2readdepth ; install --strip-program=true -p rsem-get-unique /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-get-unique ; install --strip-program=true -p rsem-sam-validator /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-sam-validator ; install --strip-program=true -p rsem-scan-for-paired-end-reads /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-scan-for-paired-end-reads ; install --strip-program=true -p rsem-run-gibbs /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-run-gibbs ; install --strip-program=true -p rsem-calculate-credibility-intervals /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-calculate-credibility-intervals ; install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -p rsem-prepare-reference /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-prepare-reference ; install --strip-program=true -p rsem-calculate-expression /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-calculate-expression ; install --strip-program=true -p rsem-refseq-extract-primary-assembly /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-refseq-extract-primary-assembly ; install --strip-program=true -p rsem-gff3-to-gtf /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-gff3-to-gtf ; install --strip-program=true -p rsem-plot-model /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-plot-model ; install --strip-program=true -p rsem-plot-transcript-wiggles /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-plot-transcript-wiggles ; install --strip-program=true -p rsem-gen-transcript-plots /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-gen-transcript-plots ; install --strip-program=true -p rsem-generate-data-matrix /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-generate-data-matrix ; install --strip-program=true -p extract-transcript-to-gene-map-from-trinity /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/extract-transcript-to-gene-map-from-trinity ; install --strip-program=true -p convert-sam-for-rsem /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/convert-sam-for-rsem ; install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -p -m 644 rsem_perl_utils.pm /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem_perl_utils.pm install: WARNING: ignoring --strip-program option as -s option was not specified make[2]: Leaving directory '/build/reproducible-path/rsem-1.3.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/rsem-1.3.3+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/reproducible-path/rsem-1.3.3+dfsg' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'rsem-dbgsym' in '../rsem-dbgsym_1.3.3+dfsg-3_amd64.deb'. dpkg-deb: building package 'rsem' in '../rsem_1.3.3+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../rsem_1.3.3+dfsg-3_amd64.buildinfo dpkg-genchanges --build=binary -O../rsem_1.3.3+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3005475 and its subdirectories I: Current time: Tue Sep 16 02:57:14 -12 2025 I: pbuilder-time-stamp: 1758034634 Tue Sep 16 14:57:15 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Tue Sep 16 14:57:15 UTC 2025 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Tue Sep 16 14:57:15 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Tue Sep 16 14:57:15 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-mFaosz' ==================================================================================== Mon Oct 19 21:20:16 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos5-amd64, called using "2 rsem forky /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv 1.3.3+dfsg-3" as arguments. Mon Oct 19 21:20:16 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-tKRs84k1" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Oct 19 21:20:16 UTC 2026 I: Downloading source for forky/rsem=1.3.3+dfsg-3 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://deb.debian.org/debian forky/main rsem 1.3.3+dfsg-3 (dsc) [2249 B] Get:2 http://deb.debian.org/debian forky/main rsem 1.3.3+dfsg-3 (tar) [275 kB] Get:3 http://deb.debian.org/debian forky/main rsem 1.3.3+dfsg-3 (diff) [35.7 MB] Fetched 35.9 MB in 0s (75.9 MB/s) Download complete and in download only mode 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://deb.debian.org/debian forky/main rsem 1.3.3+dfsg-3 (dsc) [2249 B] Get:2 http://deb.debian.org/debian forky/main rsem 1.3.3+dfsg-3 (tar) [275 kB] Get:3 http://deb.debian.org/debian forky/main rsem 1.3.3+dfsg-3 (diff) [35.7 MB] Fetched 35.9 MB in 0s (75.9 MB/s) Download complete and in download only mode ============================================================================= Re-Building rsem in forky on amd64 on ionos5-amd64 now. Date: Mon Oct 19 21:20:17 UTC 2026 Date UTC: Mon Oct 19 21:20:17 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/pbuilderrc_gMHG + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' rsem = debian-installer -o rsem = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' rsem = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/pbuilderrc_gMHG --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/b2 --logfile b2/build.log rsem_1.3.3+dfsg-3.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Oct 20 11:20:17 +14 2026 I: pbuilder-time-stamp: 1792444817 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [rsem_1.3.3+dfsg-3.dsc] I: copying [./rsem_1.3.3+dfsg.orig.tar.xz] I: copying [./rsem_1.3.3+dfsg-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./rsem_1.3.3+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting rsem in 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-3.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++11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/757674/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Oct 19 21:20 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/757674/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/757674/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=forky EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=0621a12eaff24b398ee9f1b8612294b3 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=757674 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/pbuilderrc_gMHG --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/b2 --logfile b2/build.log rsem_1.3.3+dfsg-3.dsc' SUDO_GID=110 SUDO_HOME=/var/lib/jenkins SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/757674/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libncurses-dev, libboost-dev, perl, python3:any, help2man, libhts-dev, hisat2, bowtie | bowtie2 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libncurses-dev; however: Package libncurses-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on python3:any. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on hisat2; however: Package hisat2 is not installed. pbuilder-satisfydepends-dummy depends on bowtie | bowtie2; however: Package bowtie is not installed. Package bowtie2 is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bowtie{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gcc-14-base{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} hisat2{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libboost-dev{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgcc-14-dev{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libidn2-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblocale-gettext-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libstdc++-14-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2-16{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bcftools bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix python3-hisat2 samtools wget 0 packages upgraded, 117 newly installed, 0 to remove and 0 not upgraded. Need to get 59.7 MB of archives. After unpacking 366 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 bowtie amd64 1.3.1-3 [1627 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 comerr-dev amd64 2.1-1.47.2-3+b3 [56.7 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 40 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 gcc-14-base amd64 14.3.0-7 [52.0 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 help2man amd64 1.49.3 [198 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 hisat2 amd64 2.2.1-5+b3 [3797 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 54 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 56 http://deb.debian.org/debian forky/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 libgcc-14-dev amd64 14.3.0-7 [2671 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 libstdc++-14-dev amd64 14.3.0-7 [2649 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 libboost1.83-dev amd64 1.83.0-4.2 [10.6 MB] Get: 64 http://deb.debian.org/debian forky/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 65 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 67 http://deb.debian.org/debian forky/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 69 http://deb.debian.org/debian forky/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get: 72 http://deb.debian.org/debian forky/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 73 http://deb.debian.org/debian forky/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 74 http://deb.debian.org/debian forky/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 75 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 libngtcp2-16 amd64 1.15.1-1 [140 kB] Get: 78 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-gnutls8 amd64 1.15.1-1 [20.9 kB] Get: 79 http://deb.debian.org/debian forky/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 80 http://deb.debian.org/debian forky/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 81 http://deb.debian.org/debian forky/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 82 http://deb.debian.org/debian forky/main amd64 libcurl3t64-gnutls amd64 8.15.0-1 [385 kB] Get: 83 http://deb.debian.org/debian forky/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 84 http://deb.debian.org/debian forky/main amd64 libunbound8 amd64 1.23.1-1 [606 kB] Get: 85 http://deb.debian.org/debian forky/main amd64 libgnutls-dane0t64 amd64 3.8.9-3 [455 kB] Get: 86 http://deb.debian.org/debian forky/main amd64 libgnutls-openssl27t64 amd64 3.8.9-3 [455 kB] Get: 87 http://deb.debian.org/debian forky/main amd64 libidn2-dev amd64 2.3.8-4 [103 kB] Get: 88 http://deb.debian.org/debian forky/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 89 http://deb.debian.org/debian forky/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 90 http://deb.debian.org/debian forky/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5 [330 kB] Get: 91 http://deb.debian.org/debian forky/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5 [658 kB] Get: 92 http://deb.debian.org/debian forky/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 93 http://deb.debian.org/debian forky/main amd64 libgnutls28-dev amd64 3.8.9-3 [1406 kB] Get: 94 http://deb.debian.org/debian forky/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get: 95 http://deb.debian.org/debian forky/main amd64 libldap-dev amd64 2.6.10+dfsg-1 [312 kB] Get: 96 http://deb.debian.org/debian forky/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 97 http://deb.debian.org/debian forky/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 98 http://deb.debian.org/debian forky/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 99 http://deb.debian.org/debian forky/main amd64 libnghttp2-dev amd64 1.64.0-1.1+b1 [117 kB] Get: 100 http://deb.debian.org/debian forky/main amd64 libnghttp3-dev amd64 1.11.0-1 [101 kB] Get: 101 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.15.1-1 [26.1 kB] Get: 102 http://deb.debian.org/debian forky/main amd64 libngtcp2-dev amd64 1.15.1-1 [196 kB] Get: 103 http://deb.debian.org/debian forky/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 104 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 105 http://deb.debian.org/debian forky/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-3 [67.9 kB] Get: 106 http://deb.debian.org/debian forky/main amd64 libssl-dev amd64 3.5.2-1 [2957 kB] Get: 107 http://deb.debian.org/debian forky/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 108 http://deb.debian.org/debian forky/main amd64 libzstd-dev amd64 1.5.7+dfsg-1.1 [389 kB] Get: 109 http://deb.debian.org/debian forky/main amd64 libcurl4-gnutls-dev amd64 8.15.0-1 [504 kB] Get: 110 http://deb.debian.org/debian forky/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 111 http://deb.debian.org/debian forky/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get: 112 http://deb.debian.org/debian forky/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 113 http://deb.debian.org/debian forky/main amd64 libhts3t64 amd64 1.22.1+ds2-1 [499 kB] Get: 114 http://deb.debian.org/debian forky/main amd64 liblzma-dev amd64 5.8.1-1.1 [357 kB] Get: 115 http://deb.debian.org/debian forky/main amd64 libhts-dev amd64 1.22.1+ds2-1 [1807 kB] Get: 116 http://deb.debian.org/debian forky/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get: 117 http://deb.debian.org/debian forky/main amd64 libncurses-dev amd64 6.5+20250216-2 [353 kB] Fetched 59.7 MB in 7s (8642 kB/s) Preconfiguring packages 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up python3 (3.13.7-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.9-3) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up hisat2 (2.2.1-5+b3) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.15.1-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libgnutls28-dev:amd64 (3.8.9-3) ... Setting up bowtie (1.3.1-3) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up libcurl3t64-gnutls:amd64 (8.15.0-1) ... Setting up debhelper (13.26) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.15.1-1) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up libcurl4-gnutls-dev:amd64 (8.15.0-1) ... Setting up libhts-dev:amd64 (1.22.1+ds2-1) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/757674/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for forky I: user script /srv/workspace/pbuilder/757674/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/rsem-1.3.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rsem_1.3.3+dfsg-3_source.changes dpkg-buildpackage: info: source package rsem dpkg-buildpackage: info: source version 1.3.3+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j42 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 dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure 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 -j42 "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=debian/tmp make[2]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg' 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o extractRef.o extractRef.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o synthesisRef.o synthesisRef.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o preRef.o preRef.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o buildReadIndex.o buildReadIndex.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o simulation.o simulation.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -c -o parseIt.o parseIt.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o EM.o EM.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o SamHeader.o SamHeader.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o tbam2gbam.o tbam2gbam.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2wig.o bam2wig.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o wiggle.o wiggle.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2readdepth.o bam2readdepth.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o getUnique.o getUnique.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o samValidator.o samValidator.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o scanForPairedEndReads.o scanForPairedEndReads.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o Gibbs.o Gibbs.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o calcCI.o calcCI.cpp In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from simulation.cpp:22: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from EM.cpp:28: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from Gibbs.cpp:15: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from calcCI.cpp:16: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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} 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ 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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o 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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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; | ^~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-get-unique getUnique.o -lhts -lz 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); | ~~~~~~^~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2wig bam2wig.o wiggle.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2readdepth bam2readdepth.o wiggle.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-sam-validator samValidator.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-scan-for-paired-end-reads scanForPairedEndReads.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-tbam2gbam tbam2gbam.o SamHeader.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-parse-alignments parseIt.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o 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/include/stdio.h:970, from /usr/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-synthesis-reference-transcripts synthesisRef.o 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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ 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/include/stdio.h:970, from /usr/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 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/include/stdio.h:970, from /usr/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ 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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 = PairedEndQModel]': calcCI.cpp:183:36: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 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/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 10006 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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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:183:36: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 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/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 10006 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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ 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/include/stdio.h:970, from /usr/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ 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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-simulate-reads simulation.o g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-gibbs Gibbs.o -lhts g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-calculate-credibility-intervals calcCI.o -lhts 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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-em EM.o SamHeader.o -lhts -lz 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 ./rsem-simulate-reads --no-info --version-string="1.3.3+dfsg" \ --name 'Simulate RNA-Seq data ("reads") for a given model and a RSEM reference transcript collection.' > \ debian/rsem-simulate-reads.1 make[1]: Leaving directory '/build/reproducible-path/rsem-1.3.3+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg' dh_auto_install -- BOOST=/usr/include prefix="/usr" make -j42 install DESTDIR=/build/reproducible-path/rsem-1.3.3\+dfsg/debian/rsem AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=/usr make[2]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg' install --strip-program=true -p rsem-extract-reference-transcripts /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-extract-reference-transcripts ; install --strip-program=true -p rsem-synthesis-reference-transcripts /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-synthesis-reference-transcripts ; install --strip-program=true -p rsem-preref /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-preref ; install --strip-program=true -p rsem-build-read-index /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-build-read-index ; install --strip-program=true -p rsem-simulate-reads /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-simulate-reads ; install --strip-program=true -p rsem-parse-alignments /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-parse-alignments ; install --strip-program=true -p rsem-run-em /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-run-em ; install --strip-program=true -p rsem-tbam2gbam /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-tbam2gbam ; install --strip-program=true -p rsem-bam2wig /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-bam2wig ; install --strip-program=true -p rsem-bam2readdepth /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-bam2readdepth ; install --strip-program=true -p rsem-get-unique /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-get-unique ; install --strip-program=true -p rsem-sam-validator /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-sam-validator ; install --strip-program=true -p rsem-scan-for-paired-end-reads /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-scan-for-paired-end-reads ; install --strip-program=true -p rsem-run-gibbs /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-run-gibbs ; install --strip-program=true -p rsem-calculate-credibility-intervals /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-calculate-credibility-intervals ; install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -p rsem-prepare-reference /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-prepare-reference ; install --strip-program=true -p rsem-calculate-expression /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-calculate-expression ; install --strip-program=true -p rsem-refseq-extract-primary-assembly /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-refseq-extract-primary-assembly ; install --strip-program=true -p rsem-gff3-to-gtf /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-gff3-to-gtf ; install --strip-program=true -p rsem-plot-model /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-plot-model ; install --strip-program=true -p rsem-plot-transcript-wiggles /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-plot-transcript-wiggles ; install --strip-program=true -p rsem-gen-transcript-plots /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-gen-transcript-plots ; install --strip-program=true -p rsem-generate-data-matrix /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-generate-data-matrix ; install --strip-program=true -p extract-transcript-to-gene-map-from-trinity /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/extract-transcript-to-gene-map-from-trinity ; install --strip-program=true -p convert-sam-for-rsem /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/convert-sam-for-rsem ; install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -p -m 644 rsem_perl_utils.pm /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem_perl_utils.pm install: WARNING: ignoring --strip-program option as -s option was not specified make[2]: Leaving directory '/build/reproducible-path/rsem-1.3.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/rsem-1.3.3+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/reproducible-path/rsem-1.3.3+dfsg' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'rsem' in '../rsem_1.3.3+dfsg-3_amd64.deb'. dpkg-deb: building package 'rsem-dbgsym' in '../rsem-dbgsym_1.3.3+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../rsem_1.3.3+dfsg-3_amd64.buildinfo dpkg-genchanges --build=binary -O../rsem_1.3.3+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/757674/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/757674/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/757674 and its subdirectories I: Current time: Tue Oct 20 11:22:02 +14 2026 I: pbuilder-time-stamp: 1792444922 + false + set +x Mon Oct 19 21:22:02 UTC 2026 I: Signing ./b2/rsem_1.3.3+dfsg-3_amd64.buildinfo as rsem_1.3.3+dfsg-3_amd64.buildinfo.asc Mon Oct 19 21:22:02 UTC 2026 I: Signed ./b2/rsem_1.3.3+dfsg-3_amd64.buildinfo as ./b2/rsem_1.3.3+dfsg-3_amd64.buildinfo.asc Mon Oct 19 21:22:02 UTC 2026 - build #2 for rsem/forky/amd64 on ionos5-amd64 done. Starting cleanup. All cleanup done. Mon Oct 19 21:22:02 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-tKRs84k1, removing. /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv: total 160 drwxrwxr-x 2 jenkins jenkins 4096 Sep 16 14:57 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 16 14:59 b2 -rw------- 1 jenkins jenkins 147265 Sep 16 14:57 rbuildlog.WYwYGnm -rw-rw-r-- 1 jenkins jenkins 2249 Dec 18 2023 rsem_1.3.3+dfsg-3.dsc /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/b1: total 76328 -rw-r--r-- 1 jenkins jenkins 143628 Sep 16 14:57 build.log -rw-r--r-- 1 jenkins jenkins 6016696 Sep 16 14:57 rsem-dbgsym_1.3.3+dfsg-3_amd64.deb -rw-r--r-- 1 jenkins jenkins 35660968 Sep 16 14:57 rsem_1.3.3+dfsg-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2249 Sep 16 14:57 rsem_1.3.3+dfsg-3.dsc -rw-r--r-- 1 jenkins jenkins 7627 Sep 16 14:57 rsem_1.3.3+dfsg-3_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 8509 Sep 16 14:57 rsem_1.3.3+dfsg-3_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1842 Sep 16 14:57 rsem_1.3.3+dfsg-3_amd64.changes -rw-r--r-- 1 jenkins jenkins 36196372 Sep 16 14:57 rsem_1.3.3+dfsg-3_amd64.deb -rw-r--r-- 1 jenkins jenkins 1721 Sep 16 14:57 rsem_1.3.3+dfsg-3_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/b2: total 76232 -rw-rw-r-- 1 jenkins jenkins 145543 Sep 16 14:59 build.log -rw-r--r-- 1 jenkins jenkins 6016696 Sep 16 14:59 rsem-dbgsym_1.3.3+dfsg-3_amd64.deb -rw-r--r-- 1 jenkins jenkins 35660968 Sep 16 14:59 rsem_1.3.3+dfsg-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2249 Sep 16 14:59 rsem_1.3.3+dfsg-3.dsc -rw-rw-r-- 1 jenkins jenkins 7627 Sep 16 14:59 rsem_1.3.3+dfsg-3_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 8509 Sep 16 14:59 rsem_1.3.3+dfsg-3_amd64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 1842 Sep 16 14:59 rsem_1.3.3+dfsg-3_amd64.changes -rw-r--r-- 1 jenkins jenkins 36196372 Sep 16 14:59 rsem_1.3.3+dfsg-3_amd64.deb -rw-rw-r-- 1 jenkins jenkins 1721 Sep 16 14:59 rsem_1.3.3+dfsg-3_source.changes Tue Sep 16 14:59:05 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Tue Sep 16 14:59:05 UTC 2025 I: rsem_1.3.3+dfsg-3_amd64.changes: Format: 1.8 Date: Mon, 18 Dec 2023 13:58:36 +0100 Source: rsem Binary: rsem rsem-dbgsym Architecture: amd64 Version: 1.3.3+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: rsem - RNA-Seq by Expectation-Maximization Closes: 1056010 Changes: rsem (1.3.3+dfsg-3) unstable; urgency=medium . * Team upload. . [ Andreas Tille ] * Fix salca-ci since i386 is explicitly excluded by Build-Depends: bowtie2 . [ Étienne Mollier ] * stdgnu++11.patch: new: fix ftbfs with boost1.83. boost1.83 looks to require building with gnu++11, but upstream codebase is still at gnu++98 for now, hence the nature of the patch. (Closes: #1056010) * d/control: declare compliance to standards version 4.6.2. * d/control: build depend on libncurses-dev. This replaces the obsolete libncurses5-dev. Checksums-Sha1: 4ede56150d903ab4aaae04b30f1bce98453c93cb 6016696 rsem-dbgsym_1.3.3+dfsg-3_amd64.deb 84cd349222657b33b132662f4491b6461c53006f 7627 rsem_1.3.3+dfsg-3_amd64.buildinfo 146478cd89202d79d80cc23e56e52d82d7ac4ad4 36196372 rsem_1.3.3+dfsg-3_amd64.deb Checksums-Sha256: bc94317e4f93926a41561b658a9749ef6c5233333762f3d7b2342dcff84ff79f 6016696 rsem-dbgsym_1.3.3+dfsg-3_amd64.deb c8cd1c61869e546a7ba74fd791139edf2055eb541561a74593e7eb71cc822867 7627 rsem_1.3.3+dfsg-3_amd64.buildinfo 8059a0885cb9d980202760fe404ae81200cb6ac394d2a6408d80a8ebeaae3e15 36196372 rsem_1.3.3+dfsg-3_amd64.deb Files: b96fed59ca527c1dafa0ade1c242c47a 6016696 debug optional rsem-dbgsym_1.3.3+dfsg-3_amd64.deb f3980d9867606912cf77b91c9ab76614 7627 science optional rsem_1.3.3+dfsg-3_amd64.buildinfo 8d993ff69d859bb8dcc1c6b39aca10fb 36196372 science optional rsem_1.3.3+dfsg-3_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/rsem_1.3.3+dfsg-3.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/rsem_1.3.3+dfsg-3.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/forky/amd64/rsem_1.3.3+dfsg-3.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/forky/amd64/rsem_1.3.3+dfsg-3.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/forky/amd64/rsem_1.3.3+dfsg-3_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/rsem_1.3.3+dfsg-3.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-09-16 14:57:14.856478946 +0000 +++ b2/build.log 2025-09-16 14:59:02.836611295 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Sep 16 02:51:24 -12 2025 -I: pbuilder-time-stamp: 1758034284 +I: Current time: Tue Oct 20 11:20:17 +14 2026 +I: pbuilder-time-stamp: 1792444817 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -27,53 +27,85 @@ dpkg-source: info: applying stdgnu++11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3005475/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/757674/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 19 21:20 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/757674/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/757674/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='013ecf1e04a346feaf2440c73bb01729' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3005475' - PS1='# ' - PS2='> ' + INVOCATION_ID=0621a12eaff24b398ee9f1b8612294b3 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=757674 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/pbuilderrc_R6G6 --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/b1 --logfile b1/build.log rsem_1.3.3+dfsg-3.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/pbuilderrc_gMHG --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/b2 --logfile b2/build.log rsem_1.3.3+dfsg-3.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3005475/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/757674/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -242,7 +274,7 @@ Get: 115 http://deb.debian.org/debian forky/main amd64 libhts-dev amd64 1.22.1+ds2-1 [1807 kB] Get: 116 http://deb.debian.org/debian forky/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get: 117 http://deb.debian.org/debian forky/main amd64 libncurses-dev amd64 6.5+20250216-2 [353 kB] -Fetched 59.7 MB in 15s (4026 kB/s) +Fetched 59.7 MB in 7s (8642 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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 ... 19917 files and directories currently installed.) @@ -632,8 +664,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Sep 16 14:56:19 UTC 2025. -Universal Time is now: Tue Sep 16 14:56:19 UTC 2025. +Local time is now: Mon Oct 19 21:21:14 UTC 2026. +Universal Time is now: Mon Oct 19 21:21:14 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -737,7 +769,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rsem-1.3.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rsem_1.3.3+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/757674/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/757674/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rsem-1.3.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rsem_1.3.3+dfsg-3_source.changes dpkg-buildpackage: info: source package rsem dpkg-buildpackage: info: source version 1.3.3+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -747,7 +783,7 @@ debian/rules clean dh clean dh_auto_clean - make -j40 clean + make -j42 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 @@ -768,7 +804,7 @@ 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 -j40 "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=debian/tmp + make -j42 "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=debian/tmp make[2]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg' 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o extractRef.o extractRef.cpp 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++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o synthesisRef.o synthesisRef.cpp @@ -803,7 +839,7 @@ from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, - from calcCI.cpp:16: + from EM.cpp:28: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ @@ -823,17 +859,17 @@ from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, - from EM.cpp:28: + from calcCI.cpp:16: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ -In file included from BamConverter.h:12, - from tbam2gbam.cpp:8: +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) { | ~~~~~~~~~~^~~~~~~~~~~ -In file included from getUnique.cpp:10: +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) { @@ -853,12 +889,6 @@ 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) { | ~~~~~~~~~~^~~~~~~~~~~ -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) { - | ~~~~~~~~~~^~~~~~~~~~~ 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) { @@ -904,7 +934,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hts_pos_t {aka long int} -g++ -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o +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) { + | ~~~~~~~~~~^~~~~~~~~~~ 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]); @@ -947,6 +982,7 @@ 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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ +g++ -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o 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); @@ -965,13 +1001,13 @@ 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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o 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) { | ~~~~~~~~~~^~~~~~~~~~~ -g++ -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o samValidator.cpp:176:83: warning: 'creadlen2' may be used uninitialized [-Wmaybe-uninitialized] 176 | isValid = (creadlen == readlen && (!ispaired || creadlen2 == readlen2)); | ~~~~~~~~~~^~~~~~~~~~~ @@ -984,6 +1020,7 @@ samValidator.cpp:78:47: note: 'readlen2' was declared here 78 | int creadlen = 0, readlen, creadlen2, readlen2; | ^~~~~~~~ +g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-get-unique getUnique.o -lhts -lz 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); @@ -1003,13 +1040,13 @@ EM.cpp:635:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 635 | system(command); | ~~~~~~^~~~~~~~~ -g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-get-unique getUnique.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2wig bam2wig.o wiggle.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2readdepth bam2readdepth.o wiggle.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-sam-validator samValidator.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-scan-for-paired-end-reads scanForPairedEndReads.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-tbam2gbam tbam2gbam.o SamHeader.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-parse-alignments parseIt.o -lhts -lz +g++ -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o 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=] @@ -1042,6 +1079,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +g++ -Wl,-z,relro -Wl,-z,now -o rsem-synthesis-reference-transcripts synthesisRef.o 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); @@ -1070,8 +1108,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -Wl,-z,relro -Wl,-z,now -o rsem-synthesis-reference-transcripts synthesisRef.o -g++ -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o 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); @@ -1367,6 +1403,20 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/include/x86_64-linux-gnu/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 ()); + | ~~~~~~~~~~~~~~~~~ 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=] @@ -1436,20 +1486,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/include/x86_64-linux-gnu/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); @@ -1767,7 +1803,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg' dh_auto_install -- BOOST=/usr/include prefix="/usr" - make -j40 install DESTDIR=/build/reproducible-path/rsem-1.3.3\+dfsg/debian/rsem AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=/usr + make -j42 install DESTDIR=/build/reproducible-path/rsem-1.3.3\+dfsg/debian/rsem AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=/usr make[2]: Entering directory '/build/reproducible-path/rsem-1.3.3+dfsg' install --strip-program=true -p rsem-extract-reference-transcripts /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-extract-reference-transcripts ; install --strip-program=true -p rsem-synthesis-reference-transcripts /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-synthesis-reference-transcripts ; install --strip-program=true -p rsem-preref /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-preref ; install --strip-program=true -p rsem-build-read-index /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-build-read-index ; install --strip-program=true -p rsem-simulate-reads /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-simulate-reads ; install --strip-program=true -p rsem-parse-alignments /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-parse-alignments ; install --strip-program=true -p rsem-run-em /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-run-em ; install --strip-program=true -p rsem-tbam2gbam /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-tbam2gbam ; install --strip-program=true -p rsem-bam2wig /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-bam2wig ; install --strip-program=true -p rsem-bam2readdepth /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-bam2readdepth ; install --strip-program=true -p rsem-get-unique /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-get-unique ; install --strip-program=true -p rsem-sam-validator /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-sam-validator ; install --strip-program=true -p rsem-scan-for-paired-end-reads /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-scan-for-paired-end-reads ; install --strip-program=true -p rsem-run-gibbs /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-run-gibbs ; install --strip-program=true -p rsem-calculate-credibility-intervals /build/reproducible-path/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-calculate-credibility-intervals ; install: WARNING: ignoring --strip-program option as -s option was not specified @@ -1825,8 +1861,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'rsem-dbgsym' in '../rsem-dbgsym_1.3.3+dfsg-3_amd64.deb'. dpkg-deb: building package 'rsem' in '../rsem_1.3.3+dfsg-3_amd64.deb'. +dpkg-deb: building package 'rsem-dbgsym' in '../rsem-dbgsym_1.3.3+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../rsem_1.3.3+dfsg-3_amd64.buildinfo dpkg-genchanges --build=binary -O../rsem_1.3.3+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1834,12 +1870,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/757674/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/757674/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/3005475 and its subdirectories -I: Current time: Tue Sep 16 02:57:14 -12 2025 -I: pbuilder-time-stamp: 1758034634 +I: removing directory /srv/workspace/pbuilder/757674 and its subdirectories +I: Current time: Tue Oct 20 11:22:02 +14 2026 +I: pbuilder-time-stamp: 1792444922 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/rsem_1.3.3+dfsg-3.diff: 76.7% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/rsem_1.3.3+dfsg-3.diff.gz b2/build.log: 89.0% -- replaced with stdout Compressing the 1st log... b1/build.log: 89.3% -- replaced with stdout Tue Sep 16 14:59:06 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_rsem_forky_amd64_1758034746 + touch /var/log/reproducible-builds/diffoscope_stamp_rsem_forky_amd64_1758034746 + RESULT=0 + systemd-run '--description=diffoscope on rsem/1.3.3+dfsg-3 in forky/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_5-56371 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv --run-session -c jenkins-reproducible-forky-diffoscope-e5295522-5b5b-4c7b-bb85-1c7c76fa9430 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/dbd-tmp-dGkZska ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/rsem_1.3.3+dfsg-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/rsem_1.3.3+dfsg-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/rsem_1.3.3+dfsg-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/b1/rsem_1.3.3+dfsg-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/b2/rsem_1.3.3+dfsg-3_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_5-56371.service; invocation ID: 57deb3351d124a239bf453c760bc379c # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/rsem_1.3.3+dfsg-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/rsem_1.3.3+dfsg-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/rsem_1.3.3+dfsg-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/b1/rsem_1.3.3+dfsg-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.2FHTgyNv/b2/rsem_1.3.3+dfsg-3_amd64.changes ## command (total time: 0.013s) 0.013s 1 call cmp (internal) ## has_same_content_as (total time: 0.013s) 0.013s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.015s) 0.015s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 231ms CPU time consumed: 188ms Memory peak: 17.6M (swap: 0B) _ __ ___ ___ _ __ ___ | '__/ __|/ _ \ '_ ` _ \ | | \__ \ __/ | | | | | |_| |___/\___|_| |_| |_| Tue Sep 16 15:06:36 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Tue Sep 16 15:06:36 UTC 2025 I: rsem from forky built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-16 15:06:37] INFO: Starting at 2025-09-16 15:06:37.270954 [2025-09-16 15:06:37] INFO: Generating the pages of 1 package(s) [2025-09-16 15:06:37] CRITICAL: https://tests.reproducible-builds.org/debian/forky/amd64/rsem didn't produce a buildlog, even though it has been built. [2025-09-16 15:06:37] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/rsem didn't produce a buildlog, even though it has been built. [2025-09-16 15:06:37] INFO: Finished at 2025-09-16 15:06:37.787801, took: 0:00:00.516853 Tue Sep 16 15:06:37 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/forky/amd64/rsem.html Tue Sep 16 15:06:37 UTC 2025 I: Removing signed rsem_1.3.3+dfsg-3_amd64.buildinfo.asc files: removed './b1/rsem_1.3.3+dfsg-3_amd64.buildinfo.asc' removed './b2/rsem_1.3.3+dfsg-3_amd64.buildinfo.asc' 1758035197 amd64 forky rsem Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/rsem_1.3.3+dfsg-3.rbuild.log: 87.7% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/rsem_1.3.3+dfsg-3.rbuild.log.gz [2025-09-16 15:06:38] INFO: Starting at 2025-09-16 15:06:38.131132 [2025-09-16 15:06:38] INFO: Generating the pages of 1 package(s) [2025-09-16 15:06:38] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/rsem didn't produce a buildlog, even though it has been built. [2025-09-16 15:06:38] INFO: Finished at 2025-09-16 15:06:38.554035, took: 0:00:00.422906 All cleanup done. Tue Sep 16 15:06:38 UTC 2025 - total duration: 0h 15m 35s. Tue Sep 16 15:06:38 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-Vz4y0foR, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 15min 37.739s CPU time consumed: 5.171s Memory peak: 213M (swap: 0B)