Running as unit: rb-build-amd64_10-31063.service ==================================================================================== Fri Feb 21 15:20:49 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_10) on jenkins, called using "ionos5-amd64 ionos1-amd64" as arguments. Fri Feb 21 15:20:49 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-YsHZ5Cxe" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Feb 21 15:20:49 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Fri Feb 21 15:20:49 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-qrqKCC' Fri Feb 21 15:20:50 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Fri Feb 21 15:20:50 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-sZ4Dzb' ok, let's check if samtools-legacy is building anywhere yet… ok, samtools-legacy is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of samtools-legacy in trixie on amd64 on jenkins now. 1st build will be done on ionos5-amd64.debian.net. 2nd build will be done on ionos1-amd64.debian.net. ============================================================================= Fri Feb 21 15:21:07 UTC 2025 I: starting to build samtools-legacy/trixie/amd64 on jenkins on '2025-02-21 15:20' Fri Feb 21 15:21:07 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_10/31063/console.log 1740151267 amd64 trixie samtools-legacy Fri Feb 21 15:21:07 UTC 2025 I: Downloading source for trixie/samtools-legacy=0.1.19+dfsg-6 --2025-02-21 15:21:07-- http://deb.debian.org/debian/pool/main/s/samtools-legacy/samtools-legacy_0.1.19%2bdfsg-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2135 (2.1K) [text/prs.lines.tag] Saving to: ‘samtools-legacy_0.1.19+dfsg-6.dsc’ 0K .. 100% 360M=0s 2025-02-21 15:21:07 (360 MB/s) - ‘samtools-legacy_0.1.19+dfsg-6.dsc’ saved [2135/2135] --2025-02-21 15:21:07-- http://deb.debian.org/debian/pool/main/s/samtools-legacy/samtools-legacy_0.1.19%2bdfsg-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2135 (2.1K) [text/prs.lines.tag] Saving to: ‘samtools-legacy_0.1.19+dfsg-6.dsc’ 0K .. 100% 360M=0s 2025-02-21 15:21:07 (360 MB/s) - ‘samtools-legacy_0.1.19+dfsg-6.dsc’ saved [2135/2135] Fri Feb 21 15:21:07 UTC 2025 I: samtools-legacy_0.1.19+dfsg-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: samtools-legacy Binary: libbam-dev Architecture: any Version: 0.1.19+dfsg-6 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy Homepage: https://www.htslib.org/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/samtools-legacy Vcs-Git: https://salsa.debian.org/med-team/samtools-legacy.git Testsuite: autopkgtest Testsuite-Triggers: build-essential, samtools Build-Depends: debhelper-compat (= 13), libncurses5-dev, zlib1g-dev Package-List: libbam-dev deb libdevel optional arch=any Checksums-Sha1: 5fd99dde7fbf878d1bb3e7793a378ed6177b5c65 370876 samtools-legacy_0.1.19+dfsg.orig.tar.xz da47214b090f515ad7d74dfdc6d0a28ce694d1b8 9120 samtools-legacy_0.1.19+dfsg-6.debian.tar.xz Checksums-Sha256: 485c3dfb668465449b393c5fd3b217f5262bb3f686232f6fddbc22d3c7b2f0bf 370876 samtools-legacy_0.1.19+dfsg.orig.tar.xz ddb68478725e1a02f78996217b044b0dd01672272721a2aa2edc25c9d0b32841 9120 samtools-legacy_0.1.19+dfsg-6.debian.tar.xz Files: 89dc3cc456c90901f7314580f1787ebb 370876 samtools-legacy_0.1.19+dfsg.orig.tar.xz 3e59dc229661dae8e511933490573c04 9120 samtools-legacy_0.1.19+dfsg-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmO/vx0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGz8Q//ftHuGVQvG522JKyUa2x2Ay7XzkkgDtg+ IB4RoFcytAJbyJAtPzMgXbyjVy/NN0O6g3ux2NCMY8m/yzA7rpsRdJ8bomvvLMS/ bNsHB4J1zAzOCrTgRG6rbI8nPpwO5bg20P9GzHjuPsRVrB+jJq9Tf8NKcvwwti90 zZdoj8l/KOHaB2OfY6/1zPJwzoNZb8auLcUiDLEbKGadzdSbb8jQvXwQIYKGjiya iG42zGF/elbsiZP9ivWJQgjApQP59IDsAQ0WKCr0ZRlY3jJ8GwR8CnNoG4fcdQo1 rDxwlf73VS7BAsyp/yNvqMelxI5x+f3056djZ/sobKwt2dS9NOnE4DyHxUiaNwD4 udMmV/az/4ahHmV/LqQetwRNHbCd8Yj6Cu9SsAlecNJfH2/dMmCfkTIVjXsdPnc1 LGYagS8AUBkPsMPbm+RdLcs3GIguB5C9Rpy23Z9xiC+fv/fmK0c3rej4cIqCrjpP FrR6GhgPef5pteBj1wkAqxthHT/5ewvX4dm24cBKcZNvMH4oSgQ/qHTYONZTQpQE jWzJBd0KjjUzMjCrAYI69s5+evFhvSb9YBVEBYwX0w0Qga3khwwicIifPaOEGDjN K4w4h1R7SgWIJK3+CMRL5nCvFoX/LxmqqTxjiVa2g5pmmwrffyC4g0TcuEyQ7LB4 ErMxr0Ums1Q= =ovjK -----END PGP SIGNATURE----- Fri Feb 21 15:21:07 UTC 2025 I: Checking whether the package is not for us Fri Feb 21 15:21:07 UTC 2025 I: Starting 1st build on remote node ionos5-amd64.debian.net. Fri Feb 21 15:21:07 UTC 2025 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Fri Feb 21 15:21:07 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Fri Feb 21 15:21:07 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-s8Qd28' ==================================================================================== Thu Mar 26 21:44:08 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos5-amd64, called using "1 samtools-legacy trixie /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P 0.1.19+dfsg-6" as arguments. Thu Mar 26 21:44:08 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-2ybG2YPT" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Mar 26 21:44:08 UTC 2026 I: Downloading source for trixie/samtools-legacy=0.1.19+dfsg-6 Reading package lists... NOTICE: 'samtools-legacy' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/samtools-legacy.git Please use: git clone https://salsa.debian.org/med-team/samtools-legacy.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 382 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main samtools-legacy 0.1.19+dfsg-6 (dsc) [2135 B] Get:2 http://deb.debian.org/debian trixie/main samtools-legacy 0.1.19+dfsg-6 (tar) [371 kB] Get:3 http://deb.debian.org/debian trixie/main samtools-legacy 0.1.19+dfsg-6 (diff) [9120 B] Fetched 382 kB in 0s (8106 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'samtools-legacy' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/samtools-legacy.git Please use: git clone https://salsa.debian.org/med-team/samtools-legacy.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 382 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main samtools-legacy 0.1.19+dfsg-6 (dsc) [2135 B] Get:2 http://deb.debian.org/debian trixie/main samtools-legacy 0.1.19+dfsg-6 (tar) [371 kB] Get:3 http://deb.debian.org/debian trixie/main samtools-legacy 0.1.19+dfsg-6 (diff) [9120 B] Fetched 382 kB in 0s (8106 kB/s) Download complete and in download only mode ============================================================================= Building samtools-legacy in trixie on amd64 on ionos5-amd64 now. Date: Thu Mar 26 21:44:08 UTC 2026 Date UTC: Thu Mar 26 21:44:08 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Mar 26 09:44:08 -12 2026 I: pbuilder-time-stamp: 1774561448 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [samtools-legacy_0.1.19+dfsg-6.dsc] I: copying [./samtools-legacy_0.1.19+dfsg.orig.tar.xz] I: copying [./samtools-legacy_0.1.19+dfsg-6.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./samtools-legacy_0.1.19+dfsg-6.dsc: unsupported subcommand dpkg-source: info: extracting samtools-legacy in samtools-legacy-0.1.19+dfsg dpkg-source: info: unpacking samtools-legacy_0.1.19+dfsg.orig.tar.xz dpkg-source: info: unpacking samtools-legacy_0.1.19+dfsg-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_example_makefile.patch dpkg-source: info: applying fix_segfault_with_small_ref.patch dpkg-source: info: applying fix_coverage_cap.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying gcc-11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/965005/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=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='f35b345c7e3142269e668378652ba1c3' 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='965005' 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.FLVhuF0P/pbuilderrc_liGq --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/b1 --logfile b1/build.log samtools-legacy_0.1.19+dfsg-6.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/965005/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), libncurses5-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19809 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 libncurses5-dev; however: Package libncurses5-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev 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} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 21.9 MB of archives. After unpacking 82.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5+20250125-2 [105 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libncurses-dev amd64 6.5+20250125-2 [353 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 21.9 MB in 3s (8202 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19809 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-3_amd64.deb ... Unpacking bsdextrautils (2.40.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_amd64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-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 .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-1_amd64.deb ... Unpacking libunistring5:amd64 (1.3-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-6_amd64.deb ... Unpacking libicu72:amd64 (72.1-6) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_amd64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-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 .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../30-libncurses6_6.5+20250125-2_amd64.deb ... Unpacking libncurses6:amd64 (6.5+20250125-2) ... Selecting previously unselected package libncurses-dev:amd64. Preparing to unpack .../31-libncurses-dev_6.5+20250125-2_amd64.deb ... Unpacking libncurses-dev:amd64 (6.5+20250125-2) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../32-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libicu72:amd64 (72.1-6) ... Setting up bsdextrautils (2.40.4-3) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libncurses6:amd64 (6.5+20250125-2) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up libncurses-dev:amd64 (6.5+20250125-2) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.1) ... Processing triggers for libc-bin (2.40-6) ... 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/samtools-legacy-0.1.19+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 > ../samtools-legacy_0.1.19+dfsg-6_source.changes dpkg-buildpackage: info: source package samtools-legacy dpkg-buildpackage: info: source version 0.1.19+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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/samtools-legacy-0.1.19+dfsg' make[2]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib make[2]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[2]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so* make[2]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' make[2]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a make[2]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' make[1]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+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/samtools-legacy-0.1.19+dfsg' dh_auto_build -- all all-recur razip lib CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2" make -j42 "INSTALL=install --strip-program=true" all all-recur razip lib "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2" make[2]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[4]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o razf.c: In function 'razf_flush': razf.c:221:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:234:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 234 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function '_razf_write': razf.c:201:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function 'razf_close': razf.c:804:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:805:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 805 | write(rz->x.fpw, &rz->out, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:808:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 808 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:810:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 810 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function 'razf_end_flush': razf.c:258:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 258 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function 'save_zindex': razf.c:96:19: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | if(is_be) write(fd, &rz->index->size, sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:99:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | write(fd, &v32, sizeof(uint32_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:106:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 106 | write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:107:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c: In function 'bam_index_load_core': bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 366 | fread(p->list, 16, p->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from knetfile.c:46: knetfile.c: In function 'kftp_send_cmd': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:236:9: note: in expansion of macro 'netwrite' 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); | ^~~~~~~~ knetfile.c: In function 'khttp_connect_file': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:415:9: note: in expansion of macro 'netwrite' 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ razip.c: In function 'main': razip.c:131:33: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | write(f_dst, buffer, c); | ^~~~~~~~~~~~~~~~~~~~~~~ razip.c: In function 'write_open': razip.c:32:25: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | scanf("%c", &c); | ^~~~~~~~~~~~~~~ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o razf.c: In function 'razf_flush': razf.c:221:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:234:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 234 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function '_razf_write': razf.c:201:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o razf.c: In function 'razf_close': razf.c:804:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:805:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 805 | write(rz->x.fpw, &rz->out, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:808:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 808 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:810:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 810 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function 'razf_end_flush': razf.c:258:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 258 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function 'save_zindex': razf.c:96:19: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | if(is_be) write(fd, &rz->index->size, sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:99:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | write(fd, &v32, sizeof(uint32_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:106:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 106 | write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:107:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o bam_index.c: In function 'bam_index_load_core': bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 366 | fread(p->list, 16, p->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from knetfile.c:46: knetfile.c: In function 'kftp_send_cmd': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:236:9: note: in expansion of macro 'netwrite' 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); | ^~~~~~~~ knetfile.c: In function 'khttp_connect_file': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:415:9: note: in expansion of macro 'netwrite' 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz bam_index.c: In function 'bam_index_load_core': bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 366 | fread(p->list, 16, p->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[4]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o ar: `u' modifier ignored since `D' is the default (see `U') ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' make[3]: Nothing to be done for 'lib'. make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' make[4]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' make[4]: Nothing to be done for 'lib'. make[4]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' make[2]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[1]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' /usr/bin/make -C examples all make[2]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/examples' ../samtools faidx ex1.fa ../samtools import ex1.fa.fai ex1.sam.gz ex1.bam [sam_header_read2] 2 sequences loaded. ../samtools index ex1.bam ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam [samopen] SAM header is present: 2 sequences. ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam [samopen] SAM header is present: 2 sequences. (echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg ../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam ../samtools rmdup ex1f.bam ex1f-rmduppe.bam [bam_rmdup_core] processing reference seq1... [bam_rmdup_core] processing reference seq2... [bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1' [bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b' ../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam [bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1' [bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b' ../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf [mpileup] 1 samples in 1 input files Set max per-file depth to 8000 cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread -Wl,-z,relro # You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa' make[2]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/examples' make[1]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/libbam-dev/ dh_install dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' dh_installchangelogs NEWS make[1]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' 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 dpkg-gencontrol: warning: Depends field of package libbam-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'libbam-dev' in '../libbam-dev_0.1.19+dfsg-6_amd64.deb'. dpkg-genbuildinfo --build=binary -O../samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo dpkg-genchanges --build=binary -O../samtools-legacy_0.1.19+dfsg-6_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/965005 and its subdirectories I: Current time: Thu Mar 26 09:44:59 -12 2026 I: pbuilder-time-stamp: 1774561499 Thu Mar 26 21:44:59 UTC 2026 I: Signing ./b1/samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo as samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo.asc Thu Mar 26 21:45:00 UTC 2026 I: Signed ./b1/samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo as ./b1/samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo.asc Thu Mar 26 21:45:00 UTC 2026 - build #1 for samtools-legacy/trixie/amd64 on ionos5-amd64 done. Starting cleanup. All cleanup done. Thu Mar 26 21:45:00 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-2ybG2YPT, removing. /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Feb 21 15:22 b1 drwxr-xr-x 2 jenkins jenkins 4096 Feb 21 15:21 b2 -rw------- 1 jenkins jenkins 3319 Feb 21 15:21 rbuildlog.dGPRYFb -rw-r--r-- 1 jenkins jenkins 2135 Jan 12 2023 samtools-legacy_0.1.19+dfsg-6.dsc /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/b1: total 244 -rw-r--r-- 1 jenkins jenkins 82616 Feb 21 15:22 build.log -rw-r--r-- 1 jenkins jenkins 119848 Feb 21 15:22 libbam-dev_0.1.19+dfsg-6_amd64.deb -rw-r--r-- 1 jenkins jenkins 9120 Feb 21 15:22 samtools-legacy_0.1.19+dfsg-6.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2135 Feb 21 15:22 samtools-legacy_0.1.19+dfsg-6.dsc -rw-r--r-- 1 jenkins jenkins 4799 Feb 21 15:22 samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 5681 Feb 21 15:22 samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1398 Feb 21 15:22 samtools-legacy_0.1.19+dfsg-6_amd64.changes -rw-r--r-- 1 jenkins jenkins 1585 Feb 21 15:22 samtools-legacy_0.1.19+dfsg-6_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/b2: total 0 Fri Feb 21 15:22:00 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Mar 26 09:44:08 -12 2026 I: pbuilder-time-stamp: 1774561448 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [samtools-legacy_0.1.19+dfsg-6.dsc] I: copying [./samtools-legacy_0.1.19+dfsg.orig.tar.xz] I: copying [./samtools-legacy_0.1.19+dfsg-6.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./samtools-legacy_0.1.19+dfsg-6.dsc: unsupported subcommand dpkg-source: info: extracting samtools-legacy in samtools-legacy-0.1.19+dfsg dpkg-source: info: unpacking samtools-legacy_0.1.19+dfsg.orig.tar.xz dpkg-source: info: unpacking samtools-legacy_0.1.19+dfsg-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_example_makefile.patch dpkg-source: info: applying fix_segfault_with_small_ref.patch dpkg-source: info: applying fix_coverage_cap.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying gcc-11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/965005/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=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='f35b345c7e3142269e668378652ba1c3' 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='965005' 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.FLVhuF0P/pbuilderrc_liGq --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/b1 --logfile b1/build.log samtools-legacy_0.1.19+dfsg-6.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/965005/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), libncurses5-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19809 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 libncurses5-dev; however: Package libncurses5-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev 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} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 21.9 MB of archives. After unpacking 82.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5+20250125-2 [105 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libncurses-dev amd64 6.5+20250125-2 [353 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 21.9 MB in 3s (8202 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19809 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-3_amd64.deb ... Unpacking bsdextrautils (2.40.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_amd64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-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 .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-1_amd64.deb ... Unpacking libunistring5:amd64 (1.3-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-6_amd64.deb ... Unpacking libicu72:amd64 (72.1-6) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_amd64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-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 .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../30-libncurses6_6.5+20250125-2_amd64.deb ... Unpacking libncurses6:amd64 (6.5+20250125-2) ... Selecting previously unselected package libncurses-dev:amd64. Preparing to unpack .../31-libncurses-dev_6.5+20250125-2_amd64.deb ... Unpacking libncurses-dev:amd64 (6.5+20250125-2) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../32-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libicu72:amd64 (72.1-6) ... Setting up bsdextrautils (2.40.4-3) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libncurses6:amd64 (6.5+20250125-2) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up libncurses-dev:amd64 (6.5+20250125-2) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.1) ... Processing triggers for libc-bin (2.40-6) ... 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/samtools-legacy-0.1.19+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 > ../samtools-legacy_0.1.19+dfsg-6_source.changes dpkg-buildpackage: info: source package samtools-legacy dpkg-buildpackage: info: source version 0.1.19+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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/samtools-legacy-0.1.19+dfsg' make[2]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib make[2]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[2]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so* make[2]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' make[2]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a make[2]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' make[1]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+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/samtools-legacy-0.1.19+dfsg' dh_auto_build -- all all-recur razip lib CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2" make -j42 "INSTALL=install --strip-program=true" all all-recur razip lib "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2" make[2]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[4]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o razf.c: In function 'razf_flush': razf.c:221:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:234:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 234 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function '_razf_write': razf.c:201:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function 'razf_close': razf.c:804:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:805:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 805 | write(rz->x.fpw, &rz->out, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:808:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 808 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:810:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 810 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function 'razf_end_flush': razf.c:258:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 258 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function 'save_zindex': razf.c:96:19: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | if(is_be) write(fd, &rz->index->size, sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:99:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | write(fd, &v32, sizeof(uint32_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:106:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 106 | write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:107:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c: In function 'bam_index_load_core': bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 366 | fread(p->list, 16, p->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from knetfile.c:46: knetfile.c: In function 'kftp_send_cmd': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:236:9: note: in expansion of macro 'netwrite' 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); | ^~~~~~~~ knetfile.c: In function 'khttp_connect_file': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:415:9: note: in expansion of macro 'netwrite' 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ razip.c: In function 'main': razip.c:131:33: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | write(f_dst, buffer, c); | ^~~~~~~~~~~~~~~~~~~~~~~ razip.c: In function 'write_open': razip.c:32:25: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | scanf("%c", &c); | ^~~~~~~~~~~~~~~ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o razf.c: In function 'razf_flush': razf.c:221:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:234:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 234 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function '_razf_write': razf.c:201:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o razf.c: In function 'razf_close': razf.c:804:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:805:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 805 | write(rz->x.fpw, &rz->out, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:808:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 808 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:810:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 810 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function 'razf_end_flush': razf.c:258:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 258 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function 'save_zindex': razf.c:96:19: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | if(is_be) write(fd, &rz->index->size, sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:99:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | write(fd, &v32, sizeof(uint32_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:106:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 106 | write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:107:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o bam_index.c: In function 'bam_index_load_core': bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 366 | fread(p->list, 16, p->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from knetfile.c:46: knetfile.c: In function 'kftp_send_cmd': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:236:9: note: in expansion of macro 'netwrite' 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); | ^~~~~~~~ knetfile.c: In function 'khttp_connect_file': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:415:9: note: in expansion of macro 'netwrite' 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz bam_index.c: In function 'bam_index_load_core': bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 366 | fread(p->list, 16, p->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[4]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o ar: `u' modifier ignored since `D' is the default (see `U') ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' make[3]: Nothing to be done for 'lib'. make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' make[4]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' make[4]: Nothing to be done for 'lib'. make[4]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' make[2]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[1]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' /usr/bin/make -C examples all make[2]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/examples' ../samtools faidx ex1.fa ../samtools import ex1.fa.fai ex1.sam.gz ex1.bam [sam_header_read2] 2 sequences loaded. ../samtools index ex1.bam ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam [samopen] SAM header is present: 2 sequences. ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam [samopen] SAM header is present: 2 sequences. (echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg ../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam ../samtools rmdup ex1f.bam ex1f-rmduppe.bam [bam_rmdup_core] processing reference seq1... [bam_rmdup_core] processing reference seq2... [bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1' [bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b' ../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam [bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1' [bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b' ../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf [mpileup] 1 samples in 1 input files Set max per-file depth to 8000 cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread -Wl,-z,relro # You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa' make[2]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/examples' make[1]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/libbam-dev/ dh_install dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' dh_installchangelogs NEWS make[1]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' 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 dpkg-gencontrol: warning: Depends field of package libbam-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'libbam-dev' in '../libbam-dev_0.1.19+dfsg-6_amd64.deb'. dpkg-genbuildinfo --build=binary -O../samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo dpkg-genchanges --build=binary -O../samtools-legacy_0.1.19+dfsg-6_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/965005 and its subdirectories I: Current time: Thu Mar 26 09:44:59 -12 2026 I: pbuilder-time-stamp: 1774561499 Fri Feb 21 15:22:01 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Fri Feb 21 15:22:01 UTC 2025 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Fri Feb 21 15:22:01 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Fri Feb 21 15:22:01 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-X4NTSq' ==================================================================================== Fri Feb 21 15:22:02 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "2 samtools-legacy trixie /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P 0.1.19+dfsg-6" as arguments. Fri Feb 21 15:22:02 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-Xzmoh7r2" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Feb 21 15:22:02 UTC 2025 I: Downloading source for trixie/samtools-legacy=0.1.19+dfsg-6 Reading package lists... NOTICE: 'samtools-legacy' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/samtools-legacy.git Please use: git clone https://salsa.debian.org/med-team/samtools-legacy.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 382 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main samtools-legacy 0.1.19+dfsg-6 (dsc) [2135 B] Get:2 http://deb.debian.org/debian trixie/main samtools-legacy 0.1.19+dfsg-6 (tar) [371 kB] Get:3 http://deb.debian.org/debian trixie/main samtools-legacy 0.1.19+dfsg-6 (diff) [9120 B] Fetched 382 kB in 0s (4232 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'samtools-legacy' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/samtools-legacy.git Please use: git clone https://salsa.debian.org/med-team/samtools-legacy.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 382 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main samtools-legacy 0.1.19+dfsg-6 (dsc) [2135 B] Get:2 http://deb.debian.org/debian trixie/main samtools-legacy 0.1.19+dfsg-6 (tar) [371 kB] Get:3 http://deb.debian.org/debian trixie/main samtools-legacy 0.1.19+dfsg-6 (diff) [9120 B] Fetched 382 kB in 0s (4232 kB/s) Download complete and in download only mode ============================================================================= Re-Building samtools-legacy in trixie on amd64 on ionos1-amd64 now. Date: Fri Feb 21 15:22:03 UTC 2025 Date UTC: Fri Feb 21 15:22:03 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/pbuilderrc_oSn3 + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' samtools-legacy = debian-installer -o samtools-legacy = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' samtools-legacy = u-boot ']' + case "${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.FLVhuF0P/pbuilderrc_oSn3 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/b2 --logfile b2/build.log samtools-legacy_0.1.19+dfsg-6.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: Sat Feb 22 05:22:03 +14 2025 I: pbuilder-time-stamp: 1740151323 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [samtools-legacy_0.1.19+dfsg-6.dsc] I: copying [./samtools-legacy_0.1.19+dfsg.orig.tar.xz] I: copying [./samtools-legacy_0.1.19+dfsg-6.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./samtools-legacy_0.1.19+dfsg-6.dsc: unsupported subcommand dpkg-source: info: extracting samtools-legacy in samtools-legacy-0.1.19+dfsg dpkg-source: info: unpacking samtools-legacy_0.1.19+dfsg.orig.tar.xz dpkg-source: info: unpacking samtools-legacy_0.1.19+dfsg-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_example_makefile.patch dpkg-source: info: applying fix_segfault_with_small_ref.patch dpkg-source: info: applying fix_coverage_cap.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying gcc-11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2037828/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-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 Feb 21 15:22 /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/2037828/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2037828/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]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(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=20 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=0392a99263ac4a04ae73b2c89dfc2b9c 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=2037828 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.FLVhuF0P/pbuilderrc_oSn3 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/b2 --logfile b2/build.log samtools-legacy_0.1.19+dfsg-6.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2037828/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), libncurses5-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19809 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 libncurses5-dev; however: Package libncurses5-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev 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} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 21.9 MB of archives. After unpacking 82.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5+20250125-2 [105 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libncurses-dev amd64 6.5+20250125-2 [353 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 21.9 MB in 3s (6337 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19809 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-3_amd64.deb ... Unpacking bsdextrautils (2.40.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_amd64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-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 .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-1_amd64.deb ... Unpacking libunistring5:amd64 (1.3-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-6_amd64.deb ... Unpacking libicu72:amd64 (72.1-6) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_amd64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-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 .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../30-libncurses6_6.5+20250125-2_amd64.deb ... Unpacking libncurses6:amd64 (6.5+20250125-2) ... Selecting previously unselected package libncurses-dev:amd64. Preparing to unpack .../31-libncurses-dev_6.5+20250125-2_amd64.deb ... Unpacking libncurses-dev:amd64 (6.5+20250125-2) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../32-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libicu72:amd64 (72.1-6) ... Setting up bsdextrautils (2.40.4-3) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libncurses6:amd64 (6.5+20250125-2) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up libncurses-dev:amd64 (6.5+20250125-2) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.1) ... Processing triggers for libc-bin (2.40-6) ... 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/2037828/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2037828/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/samtools-legacy-0.1.19+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 > ../samtools-legacy_0.1.19+dfsg-6_source.changes dpkg-buildpackage: info: source package samtools-legacy dpkg-buildpackage: info: source version 0.1.19+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j20 clean make[1]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[2]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib make[2]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[2]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so* make[2]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' make[2]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a make[2]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' make[1]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+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/samtools-legacy-0.1.19+dfsg' dh_auto_build -- all all-recur razip lib CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2" make -j20 "INSTALL=install --strip-program=true" all all-recur razip lib "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2" make[2]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o make[4]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o razip.c: In function 'main': razip.c:131:33: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | write(f_dst, buffer, c); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o razip.c: In function 'write_open': razip.c:32:25: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | scanf("%c", &c); | ^~~~~~~~~~~~~~~ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o bam_index.c: In function 'bam_index_load_core': bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 366 | fread(p->list, 16, p->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o In file included from knetfile.c:46: knetfile.c: In function 'kftp_send_cmd': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:236:9: note: in expansion of macro 'netwrite' 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); | ^~~~~~~~ knetfile.c: In function 'khttp_connect_file': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:415:9: note: in expansion of macro 'netwrite' 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ razf.c: In function 'razf_flush': razf.c:221:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:234:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 234 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function '_razf_write': razf.c:201:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function 'razf_close': razf.c:804:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:805:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 805 | write(rz->x.fpw, &rz->out, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:808:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 808 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:810:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 810 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function 'razf_end_flush': razf.c:258:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 258 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function 'save_zindex': razf.c:96:19: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | if(is_be) write(fd, &rz->index->size, sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:99:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | write(fd, &v32, sizeof(uint32_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:106:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 106 | write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:107:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o bam_index.c: In function 'bam_index_load_core': bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 366 | fread(p->list, 16, p->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o bam_index.c: In function 'bam_index_load_core': bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 366 | fread(p->list, 16, p->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o ar: `u' modifier ignored since `D' is the default (see `U') ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[4]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' make[3]: Nothing to be done for 'lib'. make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' make[4]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' make[4]: Nothing to be done for 'lib'. make[4]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/misc' make[2]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[1]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' /usr/bin/make -C examples all make[2]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/examples' ../samtools faidx ex1.fa ../samtools import ex1.fa.fai ex1.sam.gz ex1.bam [sam_header_read2] 2 sequences loaded. ../samtools index ex1.bam ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam [samopen] SAM header is present: 2 sequences. ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam [samopen] SAM header is present: 2 sequences. (echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg ../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam ../samtools rmdup ex1f.bam ex1f-rmduppe.bam [bam_rmdup_core] processing reference seq1... [bam_rmdup_core] processing reference seq2... [bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1' [bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b' ../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam [bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1' [bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b' ../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf [mpileup] 1 samples in 1 input files Set max per-file depth to 8000 cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread -Wl,-z,relro # You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa' make[2]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/examples' make[1]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/libbam-dev/ dh_install dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' dh_installchangelogs NEWS make[1]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' 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 dpkg-gencontrol: warning: Depends field of package libbam-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'libbam-dev' in '../libbam-dev_0.1.19+dfsg-6_amd64.deb'. dpkg-genbuildinfo --build=binary -O../samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo dpkg-genchanges --build=binary -O../samtools-legacy_0.1.19+dfsg-6_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/2037828/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2037828/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/2037828 and its subdirectories I: Current time: Sat Feb 22 05:24:27 +14 2025 I: pbuilder-time-stamp: 1740151467 + false + set +x Fri Feb 21 15:24:27 UTC 2025 I: Signing ./b2/samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo as samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo.asc Fri Feb 21 15:24:27 UTC 2025 I: Signed ./b2/samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo as ./b2/samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo.asc Fri Feb 21 15:24:27 UTC 2025 - build #2 for samtools-legacy/trixie/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Fri Feb 21 15:24:27 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-Xzmoh7r2, removing. /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P: total 104 drwxr-xr-x 2 jenkins jenkins 4096 Feb 21 15:22 b1 drwxr-xr-x 2 jenkins jenkins 4096 Feb 21 15:24 b2 -rw------- 1 jenkins jenkins 86221 Feb 21 15:22 rbuildlog.dGPRYFb -rw-r--r-- 1 jenkins jenkins 2135 Jan 12 2023 samtools-legacy_0.1.19+dfsg-6.dsc /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/b1: total 252 -rw-r--r-- 1 jenkins jenkins 82616 Feb 21 15:22 build.log -rw-r--r-- 1 jenkins jenkins 119848 Feb 21 15:22 libbam-dev_0.1.19+dfsg-6_amd64.deb -rw-r--r-- 1 jenkins jenkins 9120 Feb 21 15:22 samtools-legacy_0.1.19+dfsg-6.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2135 Feb 21 15:22 samtools-legacy_0.1.19+dfsg-6.dsc -rw-r--r-- 1 jenkins jenkins 4799 Feb 21 15:22 samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 5681 Feb 21 15:22 samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1398 Feb 21 15:22 samtools-legacy_0.1.19+dfsg-6_amd64.changes -rw-r--r-- 1 jenkins jenkins 1585 Feb 21 15:22 samtools-legacy_0.1.19+dfsg-6_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/b2: total 236 -rw-r--r-- 1 jenkins jenkins 76678 Feb 21 15:24 build.log -rw-r--r-- 1 jenkins jenkins 119848 Feb 21 15:24 libbam-dev_0.1.19+dfsg-6_amd64.deb -rw-r--r-- 1 jenkins jenkins 9120 Feb 21 15:24 samtools-legacy_0.1.19+dfsg-6.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2135 Feb 21 15:24 samtools-legacy_0.1.19+dfsg-6.dsc -rw-r--r-- 1 jenkins jenkins 4790 Feb 21 15:24 samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 5672 Feb 21 15:24 samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1398 Feb 21 15:24 samtools-legacy_0.1.19+dfsg-6_amd64.changes -rw-r--r-- 1 jenkins jenkins 1585 Feb 21 15:24 samtools-legacy_0.1.19+dfsg-6_source.changes Fri Feb 21 15:24:28 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Fri Feb 21 15:24:29 UTC 2025 I: samtools-legacy_0.1.19+dfsg-6_amd64.changes: Format: 1.8 Date: Mon, 12 Dec 2022 17:30:33 +0100 Source: samtools-legacy Binary: libbam-dev Architecture: amd64 Version: 0.1.19+dfsg-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format Closes: 1015655 Changes: samtools-legacy (0.1.19+dfsg-6) unstable; urgency=medium . * Team upload. * Revert: Add missing build dependency on dh addon. * Disable LTO Closes: #1015655 * d/watch: Provide sensible upstream tarball name * Standards-Version: 4.6.1 (routine-update) * Remove trailing whitespace in debian/rules (routine-update) Checksums-Sha1: ae250d65c4ec59f24b006bd85f1a2acfc6d7ca84 119848 libbam-dev_0.1.19+dfsg-6_amd64.deb c49ca1bef8652bc93922f5a80e48cd7bcd7eba1f 4799 samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo Checksums-Sha256: a7a4f73909cfd4ece671e69da8b9f4296cbb262cca6f0b66e00a0a9fd5268f7c 119848 libbam-dev_0.1.19+dfsg-6_amd64.deb bb5490a5d923ef4dd8a1b2bb32241d3f9df41bec489c1d7d44e58872cb6ddac3 4799 samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo Files: f08cbc233a41be5c69fb66c1889794d4 119848 libdevel optional libbam-dev_0.1.19+dfsg-6_amd64.deb d058931364864ceaedbab941f206a20f 4799 science optional samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/samtools-legacy_0.1.19+dfsg-6.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/samtools-legacy_0.1.19+dfsg-6.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/samtools-legacy_0.1.19+dfsg-6.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/samtools-legacy_0.1.19+dfsg-6.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/amd64/samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/samtools-legacy_0.1.19+dfsg-6.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-02-21 15:22:00.865227800 +0000 +++ b2/build.log 2025-02-21 15:24:28.482576410 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Mar 26 09:44:08 -12 2026 -I: pbuilder-time-stamp: 1774561448 +I: Current time: Sat Feb 22 05:22:03 +14 2025 +I: pbuilder-time-stamp: 1740151323 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying gcc-11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/965005/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2037828/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 Feb 21 15:22 /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/2037828/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2037828/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=42 ' - DISTRIBUTION='trixie' - 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]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(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=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='f35b345c7e3142269e668378652ba1c3' - 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='965005' - PS1='# ' - PS2='> ' + INVOCATION_ID=0392a99263ac4a04ae73b2c89dfc2b9c + 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=2037828 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.FLVhuF0P/pbuilderrc_liGq --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/b1 --logfile b1/build.log samtools-legacy_0.1.19+dfsg-6.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.FLVhuF0P/pbuilderrc_oSn3 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/b2 --logfile b2/build.log samtools-legacy_0.1.19+dfsg-6.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/965005/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2037828/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -146,7 +178,7 @@ Get: 31 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5+20250125-2 [105 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libncurses-dev amd64 6.5+20250125-2 [353 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 21.9 MB in 3s (8202 kB/s) +Fetched 21.9 MB in 3s (6337 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19809 files and directories currently installed.) @@ -293,7 +325,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/samtools-legacy-0.1.19+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 > ../samtools-legacy_0.1.19+dfsg-6_source.changes +I: user script /srv/workspace/pbuilder/2037828/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2037828/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/samtools-legacy-0.1.19+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 > ../samtools-legacy_0.1.19+dfsg-6_source.changes dpkg-buildpackage: info: source package samtools-legacy dpkg-buildpackage: info: source version 0.1.19+dfsg-6 dpkg-buildpackage: info: source distribution unstable @@ -303,7 +339,7 @@ debian/rules clean dh clean dh_auto_clean - make -j42 clean + make -j20 clean make[1]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[2]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib @@ -324,7 +360,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' dh_auto_build -- all all-recur razip lib CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2" - make -j42 "INSTALL=install --strip-program=true" all all-recur razip lib "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2" + make -j20 "INSTALL=install --strip-program=true" all all-recur razip lib "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2" make[2]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o @@ -338,80 +374,40 @@ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o make[4]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o -razf.c: In function 'razf_flush': -razf.c:221:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -razf.c:234:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 234 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -razf.c: In function '_razf_write': -razf.c:201:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -razf.c: In function 'razf_close': -razf.c:804:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -razf.c:805:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 805 | write(rz->x.fpw, &rz->out, sizeof(int64_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -razf.c:808:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 808 | write(rz->x.fpw, &v64, sizeof(int64_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -razf.c:810:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 810 | write(rz->x.fpw, &v64, sizeof(int64_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -razf.c: In function 'razf_end_flush': -razf.c:258:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 258 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -razf.c: In function 'save_zindex': -razf.c:96:19: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 96 | if(is_be) write(fd, &rz->index->size, sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -razf.c:99:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 99 | write(fd, &v32, sizeof(uint32_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -razf.c:106:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 106 | write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -razf.c:107:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +razip.c: In function 'main': +razip.c:131:33: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 131 | write(f_dst, buffer, c); + | ^~~~~~~~~~~~~~~~~~~~~~~ +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o +razip.c: In function 'write_open': +razip.c:32:25: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 32 | scanf("%c", &c); + | ^~~~~~~~~~~~~~~ +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o bam_index.c: In function 'bam_index_load_core': bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); @@ -437,6 +433,9 @@ bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o In file included from knetfile.c:46: knetfile.c: In function 'kftp_send_cmd': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -452,15 +451,6 @@ knetfile.c:415:9: note: in expansion of macro 'netwrite' 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ -razip.c: In function 'main': -razip.c:131:33: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 131 | write(f_dst, buffer, c); - | ^~~~~~~~~~~~~~~~~~~~~~~ -razip.c: In function 'write_open': -razip.c:32:25: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 32 | scanf("%c", &c); - | ^~~~~~~~~~~~~~~ -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o razf.c: In function 'razf_flush': razf.c:221:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); @@ -472,8 +462,6 @@ razf.c:201:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o razf.c: In function 'razf_close': razf.c:804:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); @@ -504,15 +492,8 @@ razf.c:107:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o bam_index.c: In function 'bam_index_load_core': bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); @@ -538,45 +519,26 @@ bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from knetfile.c:46: -knetfile.c: In function 'kftp_send_cmd': -knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) - | ^~~~~~~~~~~~~~~~~~~ -knetfile.c:236:9: note: in expansion of macro 'netwrite' - 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); - | ^~~~~~~~ -knetfile.c: In function 'khttp_connect_file': -knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) - | ^~~~~~~~~~~~~~~~~~~ -knetfile.c:415:9: note: in expansion of macro 'netwrite' - 415 | netwrite(fp->fd, buf, l); - | ^~~~~~~~ -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz bam_index.c: In function 'bam_index_load_core': bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); @@ -602,6 +564,13 @@ bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o +ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o +ar: `u' modifier ignored since `D' is the default (see `U') ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' @@ -622,10 +591,12 @@ make[4]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[4]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o -ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o -ar: `u' modifier ignored since `D' is the default (see `U') +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' @@ -655,8 +626,8 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz @@ -726,12 +697,14 @@ 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/2037828/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2037828/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/965005 and its subdirectories -I: Current time: Thu Mar 26 09:44:59 -12 2026 -I: pbuilder-time-stamp: 1774561499 +I: removing directory /srv/workspace/pbuilder/2037828 and its subdirectories +I: Current time: Sat Feb 22 05:24:27 +14 2025 +I: pbuilder-time-stamp: 1740151467 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/samtools-legacy_0.1.19+dfsg-6.diff: 90.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/samtools-legacy_0.1.19+dfsg-6.diff.gz b2/build.log: 88.1% -- replaced with stdout Compressing the 1st log... b1/build.log: 89.7% -- replaced with stdout Fri Feb 21 15:24:29 UTC 2025 I: diffoscope 288 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_samtools-legacy_trixie_amd64_1740151469 + touch /var/log/reproducible-builds/diffoscope_stamp_samtools-legacy_trixie_amd64_1740151469 + RESULT=0 + systemd-run '--description=diffoscope on samtools-legacy/0.1.19+dfsg-6 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_10-31063 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P --run-session -c jenkins-reproducible-trixie-diffoscope-74f0371c-d682-4a5e-91d1-7453f0891ae5 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/dbd-tmp-lEEEGW7 ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/samtools-legacy_0.1.19+dfsg-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/samtools-legacy_0.1.19+dfsg-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/samtools-legacy_0.1.19+dfsg-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/b1/samtools-legacy_0.1.19+dfsg-6_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/b2/samtools-legacy_0.1.19+dfsg-6_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_10-31063.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/samtools-legacy_0.1.19+dfsg-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/samtools-legacy_0.1.19+dfsg-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/samtools-legacy_0.1.19+dfsg-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/b1/samtools-legacy_0.1.19+dfsg-6_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.FLVhuF0P/b2/samtools-legacy_0.1.19+dfsg-6_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 228ms CPU time consumed: 229ms _ _ _ ___ __ _ _ __ ___ | |_ ___ ___ | |___ | | ___ __ _ __ _ ___ _ _ / __|/ _` | '_ ` _ \| __/ _ \ / _ \| / __|_____| |/ _ \/ _` |/ _` |/ __| | | | \__ \ (_| | | | | | | || (_) | (_) | \__ \_____| | __/ (_| | (_| | (__| |_| | |___/\__,_|_| |_| |_|\__\___/ \___/|_|___/ |_|\___|\__, |\__,_|\___|\__, | |___/ |___/ Fri Feb 21 15:24:30 UTC 2025 I: diffoscope 288 found no differences in the changes files, and a .buildinfo file also exists. Fri Feb 21 15:24:30 UTC 2025 I: samtools-legacy from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-02-21 15:24:31] INFO: Starting at 2025-02-21 15:24:31.018604 [2025-02-21 15:24:31] INFO: Generating the pages of 1 package(s) [2025-02-21 15:24:31] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/samtools-legacy didn't produce a buildlog, even though it has been built. [2025-02-21 15:24:31] INFO: Finished at 2025-02-21 15:24:31.479520, took: 0:00:00.460926 Fri Feb 21 15:24:31 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/samtools-legacy.html Fri Feb 21 15:24:31 UTC 2025 I: Submitting .buildinfo files to external archives: Fri Feb 21 15:24:31 UTC 2025 I: Submitting 8.0K b1/samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo.asc https://buildinfo.debian.net/c49ca1bef8652bc93922f5a80e48cd7bcd7eba1f/samtools-legacy_0.1.19+dfsg-6_amd64 Fri Feb 21 15:24:32 UTC 2025 I: Submitting 8.0K b2/samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo.asc https://buildinfo.debian.net/07997e959f2c47c53bb6d5a0e2844812d6c0fa6d/samtools-legacy_0.1.19+dfsg-6_amd64 Fri Feb 21 15:24:33 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Feb 21 15:24:33 UTC 2025 I: Done submitting .buildinfo files. Fri Feb 21 15:24:33 UTC 2025 I: Removing signed samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo.asc files: removed './b1/samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo.asc' removed './b2/samtools-legacy_0.1.19+dfsg-6_amd64.buildinfo.asc' 1740151473 amd64 trixie samtools-legacy Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/samtools-legacy_0.1.19+dfsg-6.rbuild.log: 87.2% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/samtools-legacy_0.1.19+dfsg-6.rbuild.log.gz [2025-02-21 15:24:33] INFO: Starting at 2025-02-21 15:24:33.696411 [2025-02-21 15:24:33] INFO: Generating the pages of 1 package(s) [2025-02-21 15:24:34] INFO: Finished at 2025-02-21 15:24:34.114085, took: 0:00:00.417681 All cleanup done. Fri Feb 21 15:24:34 UTC 2025 - total duration: 0h 3m 41s. Fri Feb 21 15:24:34 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-YsHZ5Cxe, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 3min 44.639s CPU time consumed: 6.930s