Sat Mar 2 12:00:14 UTC 2024 I: starting to build stacks/trixie/i386 on jenkins on '2024-03-02 12:00' Sat Mar 2 12:00:14 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_8/18984/console.log Sat Mar 2 12:00:14 UTC 2024 I: Downloading source for trixie/stacks=2.66+dfsg-1 --2024-03-02 12:00:15-- http://deb.debian.org/debian/pool/main/s/stacks/stacks_2.66%2bdfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2041 (2.0K) [text/prs.lines.tag] Saving to: ‘stacks_2.66+dfsg-1.dsc’ 0K . 100% 288M=0s 2024-03-02 12:00:15 (288 MB/s) - ‘stacks_2.66+dfsg-1.dsc’ saved [2041/2041] Sat Mar 2 12:00:15 UTC 2024 I: stacks_2.66+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: stacks Binary: stacks Architecture: any Version: 2.66+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille Homepage: https://creskolab.uoregon.edu/stacks/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/stacks Vcs-Git: https://salsa.debian.org/med-team/stacks.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev Package-List: stacks deb science optional arch=any Checksums-Sha1: 385fa639bf9e6404984e3f92390b91f12f70477d 339220 stacks_2.66+dfsg.orig.tar.xz 15689298d93b191899eb8595721abc3532bb2585 12128 stacks_2.66+dfsg-1.debian.tar.xz Checksums-Sha256: ebfe03f3ff69f9e398e891ae055c75d09f0f5e46a4094be5b75268eae410cf95 339220 stacks_2.66+dfsg.orig.tar.xz 10cf0e2485079286ec96d0d3a256c8f89a42670b9d57d932d98c03bac4140f65 12128 stacks_2.66+dfsg-1.debian.tar.xz Files: ad4aa860ad9e955b5add40699f74ee1d 339220 stacks_2.66+dfsg.orig.tar.xz 5f9ede170e0058c49fe7bbf2193676ae 12128 stacks_2.66+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEESjHbWh7kCWyHOZiAkDZJKUwz+bcFAmWvsxUACgkQkDZJKUwz +bec7A/+LNCmJ2yVljOnuonq0j4O5qYS8bjJdwFT0F3lc7oKHQkr/nXar4SVrcfZ iMCgB/4H+9sNKTgOV4GupFmhoBPOhN95aizPqod3zulcyNRDYFZOE+ei1y8RpHHI D6fXMzx3ewQtWO9RyIRWJQqzqZR3fie3Y3becYkYS8OQ86y6yq9LA2wICf6u1Z7s 586SMUSSpbgKIH8+jaJKwy0XC2yM1njJNwIOX95ws2xNdObTtjNqmFNipj4wQqyj AiYQ1+X6vnnCkimIh/GN5lnFCYEdsUC9VH2Y6M+OMR2IoVC3RL/l4PmO5JIc3kNW leFbyes3ZYX6MkOg0jPKuEr1NGEEHGvlWyYyWFjAVbgnbdJ3qKOiaUSGbkaErs+s 5ypyXKH3/HNDRL7dwbevO/Z5FRCD7e7WfiSzEzrhrJvXgMipTcPLA9Xi7e9c3Go3 9U59Txmw70+5JWHxcD6ws5L8pvmCT96OvF4mL07flaDxNBSXlvasuBCcRpsXr6QB 7PkVruQqmCCrkxR6DX+zHjiDp8H5PiEdWmDl+54L0XVxuspunQORcr+gmwJ5XeGM tdP4mSoW5xhFlSnpyTxEuQVTdAo98KW9iwOHsFXRLnz4JJ+it+HXL5+RdFfLmZZk EI2TuFY64YFZrfUchQW/9Oy2xBjuktc9w239bzJaTFjFAjBCTvs= =kWCv -----END PGP SIGNATURE----- Sat Mar 2 12:00:15 UTC 2024 I: Checking whether the package is not for us Sat Mar 2 12:00:15 UTC 2024 I: Starting 1st build on remote node ionos16-i386.debian.net. Sat Mar 2 12:00:15 UTC 2024 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Sat Mar 2 12:02:15 UTC 2024 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Apr 4 06:23:17 -12 2025 I: pbuilder-time-stamp: 1743790997 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: using eatmydata during job I: Copying source file I: copying [stacks_2.66+dfsg-1.dsc] I: copying [./stacks_2.66+dfsg.orig.tar.xz] I: copying [./stacks_2.66+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Jan 23 12:37:41 2024 gpgv: using RSA key 4A31DB5A1EE4096C87399880903649294C33F9B7 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./stacks_2.66+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting stacks in stacks-2.66+dfsg dpkg-source: info: unpacking stacks_2.66+dfsg.orig.tar.xz dpkg-source: info: unpacking stacks_2.66+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying RisR.patch dpkg-source: info: applying script-exe-paths dpkg-source: info: applying use_debian_packaged_htslib.patch dpkg-source: info: applying fix_spelling_errors.patch dpkg-source: info: applying change_program_exit_to_success.patch dpkg-source: info: applying offer_help_option_for_stacks_gdb.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/33069/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='5a1ea66d8b08410ab5fac9abb1f016fd' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='33069' 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.NJcKooLY/pbuilderrc_Pg0X --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.NJcKooLY/b1 --logfile b1/build.log stacks_2.66+dfsg-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos16-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 1 17:49 /bin -> usr/bin I: user script /srv/workspace/pbuilder/33069/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: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-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 ... 19878 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however: Package libsparsehash-dev is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-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} libbam-dev{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsparsehash-dev{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} samtools{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 51 newly installed, 0 to remove and 0 not upgraded. Need to get 25.9 MB of archives. After unpacking 90.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3 [1195 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-1+b2 [39.6 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.14.1 [85.6 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main i386 libelf1 i386 0.190-1+b1 [182 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1 [118 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.14.1 [890 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg-3+b1 [915 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libbam-dev i386 0.1.19+dfsg-6 [130 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-4+b1 [20.7 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-4+b1 [60.7 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5+b3 [196 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.59.0-1 [82.5 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 libpsl5 i386 0.21.2-1+b1 [59.7 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libssh2-1 i386 1.11.0-4 [224 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 libcurl3-gnutls i386 8.5.0-2 [454 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 libcurl4-gnutls-dev i386 8.5.0-2 [574 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.19-1 [41.9 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 libdeflate-dev i386 1.19-1 [50.5 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libhtscodecs2 i386 1.6.0-1+b1 [68.5 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libhts3 i386 1.19+ds-1 [490 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 liblzma-dev i386 5.4.5-0.3 [304 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 libhts-dev i386 1.19+ds-1 [1660 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libncurses6 i386 6.4+20240113-1 [111 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 samtools i386 1.19.2-1 [680 kB] Fetched 25.9 MB in 1s (50.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19878 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../02-libmagic1_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic1:i386 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-2+b1_i386.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-3_i386.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.39.3-6_i386.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../08-libpipeline1_1.5.7-1+b2_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1+b2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.0-3_i386.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... 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%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.14.1_all.deb ... Unpacking libdebhelper-perl (13.14.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... 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 libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../22-libelf1_0.190-1+b1_i386.deb ... Unpacking libelf1:i386 (0.190-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_i386.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../24-libicu72_72.1-4+b1_i386.deb ... Unpacking libicu72:i386 (72.1-4+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b2_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_i386.deb ... Unpacking gettext (0.21-14+b1) ... 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_13.14.1_all.deb ... Unpacking debhelper (13.14.1) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../30-zlib1g-dev_1%3a1.3.dfsg-3+b1_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.3.dfsg-3+b1) ... Selecting previously unselected package libbam-dev. Preparing to unpack .../31-libbam-dev_0.1.19+dfsg-6_i386.deb ... Unpacking libbam-dev (0.1.19+dfsg-6) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../32-libbrotli1_1.1.0-2+b3_i386.deb ... Unpacking libbrotli1:i386 (1.1.0-2+b3) ... Selecting previously unselected package libsasl2-modules-db:i386. Preparing to unpack .../33-libsasl2-modules-db_2.1.28+dfsg1-4+b1_i386.deb ... Unpacking libsasl2-modules-db:i386 (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libsasl2-2:i386. Preparing to unpack .../34-libsasl2-2_2.1.28+dfsg1-4+b1_i386.deb ... Unpacking libsasl2-2:i386 (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libldap-2.5-0:i386. Preparing to unpack .../35-libldap-2.5-0_2.5.13+dfsg-5+b3_i386.deb ... Unpacking libldap-2.5-0:i386 (2.5.13+dfsg-5+b3) ... Selecting previously unselected package libnghttp2-14:i386. Preparing to unpack .../36-libnghttp2-14_1.59.0-1_i386.deb ... Unpacking libnghttp2-14:i386 (1.59.0-1) ... Selecting previously unselected package libpsl5:i386. Preparing to unpack .../37-libpsl5_0.21.2-1+b1_i386.deb ... Unpacking libpsl5:i386 (0.21.2-1+b1) ... Selecting previously unselected package librtmp1:i386. Preparing to unpack .../38-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_i386.deb ... Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:i386. Preparing to unpack .../39-libssh2-1_1.11.0-4_i386.deb ... Unpacking libssh2-1:i386 (1.11.0-4) ... Selecting previously unselected package libcurl3-gnutls:i386. Preparing to unpack .../40-libcurl3-gnutls_8.5.0-2_i386.deb ... Unpacking libcurl3-gnutls:i386 (8.5.0-2) ... Selecting previously unselected package libcurl4-gnutls-dev:i386. Preparing to unpack .../41-libcurl4-gnutls-dev_8.5.0-2_i386.deb ... Unpacking libcurl4-gnutls-dev:i386 (8.5.0-2) ... Selecting previously unselected package libdeflate0:i386. Preparing to unpack .../42-libdeflate0_1.19-1_i386.deb ... Unpacking libdeflate0:i386 (1.19-1) ... Selecting previously unselected package libdeflate-dev:i386. Preparing to unpack .../43-libdeflate-dev_1.19-1_i386.deb ... Unpacking libdeflate-dev:i386 (1.19-1) ... Selecting previously unselected package libhtscodecs2:i386. Preparing to unpack .../44-libhtscodecs2_1.6.0-1+b1_i386.deb ... Unpacking libhtscodecs2:i386 (1.6.0-1+b1) ... Selecting previously unselected package libhts3:i386. Preparing to unpack .../45-libhts3_1.19+ds-1_i386.deb ... Unpacking libhts3:i386 (1.19+ds-1) ... Selecting previously unselected package liblzma-dev:i386. Preparing to unpack .../46-liblzma-dev_5.4.5-0.3_i386.deb ... Unpacking liblzma-dev:i386 (5.4.5-0.3) ... Selecting previously unselected package libhts-dev:i386. Preparing to unpack .../47-libhts-dev_1.19+ds-1_i386.deb ... Unpacking libhts-dev:i386 (1.19+ds-1) ... Selecting previously unselected package libncurses6:i386. Preparing to unpack .../48-libncurses6_6.4+20240113-1_i386.deb ... Unpacking libncurses6:i386 (6.4+20240113-1) ... Selecting previously unselected package libsparsehash-dev. Preparing to unpack .../49-libsparsehash-dev_2.0.3-2_all.deb ... Unpacking libsparsehash-dev (2.0.3-2) ... Selecting previously unselected package samtools. Preparing to unpack .../50-samtools_1.19.2-1_i386.deb ... Unpacking samtools (1.19.2-1) ... Setting up libhtscodecs2:i386 (1.6.0-1+b1) ... Setting up libpipeline1:i386 (1.5.7-1+b2) ... Setting up libpsl5:i386 (0.21.2-1+b1) ... Setting up libicu72:i386 (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.14.1) ... Setting up libbrotli1:i386 (1.1.0-2+b3) ... Setting up libnghttp2-14:i386 (1.59.0-1) ... Setting up libmagic1:i386 (1:5.45-2+b1) ... Setting up libdeflate0:i386 (1.19-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2+b1) ... Setting up libsparsehash-dev (2.0.3-2) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-4+b1) ... Setting up autotools-dev (20220109.1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:i386 (6.4+20240113-1) ... Setting up autopoint (0.21-14) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-4+b1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:i386 (5.4.5-0.3) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg-3+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:i386 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libssh2-1:i386 (1.11.0-4) ... Setting up libdeflate-dev:i386 (1.19-1) ... Setting up libelf1:i386 (0.190-1+b1) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3+b2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libldap-2.5-0:i386 (2.5.13+dfsg-5+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libbam-dev (0.1.19+dfsg-6) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:i386 (8.5.0-2) ... Setting up libcurl4-gnutls-dev:i386 (8.5.0-2) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3:i386 (1.19+ds-1) ... Setting up libhts-dev:i386 (1.19+ds-1) ... Setting up debhelper (13.14.1) ... Setting up samtools (1.19.2-1) ... Processing triggers for libc-bin (2.37-15) ... 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/stacks-2.66+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 > ../stacks_2.66+dfsg-1_source.changes dpkg-buildpackage: info: source package stacks dpkg-buildpackage: info: source version 2.66+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Lance Lin dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/stacks-2.66+dfsg' dh_clean rm -f ./constants.php make[1]: Leaving directory '/build/reproducible-path/stacks-2.66+dfsg' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:28: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:28: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:28: the top level configure.ac:20: installing 'config/ar-lib' configure.ac:15: installing 'config/compile' configure.ac:42: installing 'config/config.guess' configure.ac:42: installing 'config/config.sub' configure.ac:7: installing 'config/install-sh' configure.ac:7: installing 'config/missing' Makefile.am: installing 'config/depcomp' parallel-tests: installing 'config/test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/stacks-2.66+dfsg' dh_auto_configure -- --enable-sparsehash --enable-bam \ --with-bam-include-path=/usr/include/samtools \ --with-bam-lib-path=/usr/lib ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-sparsehash --enable-bam --with-bam-include-path=/usr/include/samtools --with-bam-lib-path=/usr/lib checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking whether g++ supports C++11 features by default... yes checking for ranlib... ranlib checking for ar... ar checking the archiver (ar) interface... ar checking for omp_set_num_threads in -lgomp... yes checking for gzread in -lz... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for float.h... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for gcc option to support OpenMP... -fopenmp checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether closedir returns void... no checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for floor... no checking for memset... yes checking for pow... no checking for sqrt... no checking for clock_gettime... yes checking for functional regular expressions... yes checking for gawk... (cached) mawk checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/stacks-2.66+dfsg' dh_auto_build make -j16 make[1]: Entering directory '/build/reproducible-path/stacks-2.66+dfsg' make all-recursive make[2]: Entering directory '/build/reproducible-path/stacks-2.66+dfsg' make[3]: Entering directory '/build/reproducible-path/stacks-2.66+dfsg' g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks.o src/ustacks.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/aln_utils.o src/aln_utils.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/BamI.o src/BamI.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/catalog_utils.o src/catalog_utils.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cmb.o src/cmb.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/constants.o src/constants.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNANSeq.o src/DNANSeq.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNASeq4.o src/DNASeq4.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNASeq.o src/DNASeq.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/gzFasta.o src/gzFasta.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/input.o src/input.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmers.o src/kmers.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/locus.o src/locus.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/log_utils.o src/log_utils.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/MetaPopInfo.o src/MetaPopInfo.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/models.o src/models.cc src/MetaPopInfo.cc: In member function 'void MetaPopInfo::fill_pop_indexes(std::map >&) const': src/MetaPopInfo.cc:427:30: warning: narrowing conversion of 'i' from 'std::size_t' {aka 'unsigned int'} to 'int' [-Wnarrowing] 427 | pop_indexes.insert( {i, {pops_[i].first_sample, pops_[i].last_sample}} ); | ^ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mstack.o src/mstack.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mst.o src/mst.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/nucleotides.o src/nucleotides.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/renz.o src/renz.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Seq.o src/Seq.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sql_utilities.o src/sql_utilities.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/stacks.o src/stacks.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/utils.o src/utils.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Vcf.o src/Vcf.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks.o src/cstacks.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks.o src/sstacks.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags.o src/process_radtags.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clean.o src/clean.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/file_io.o src/file_io.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/write.o src/write.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_shortreads.o src/process_shortreads.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmer_filter.o src/kmer_filter.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clone_filter.o src/clone_filter.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations.o src/populations.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/bootstrap.o src/bootstrap.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/export_formats.o src/export_formats.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mapping_utils.o src/mapping_utils.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotype_dictionaries.o src/genotype_dictionaries.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/PopSum.o src/PopSum.cc src/export_formats.cc: In member function 'virtual int PhylipVarAllExport::post_processing()': src/export_formats.cc:2375:21: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::size_t' {aka 'unsigned int'} [-Wformat=] 2375 | sprintf(s, "%11lu", this->_seq_len); | ~~~~^ ~~~~~~~~~~~~~~ | | | | | std::size_t {aka unsigned int} | long unsigned int | %11u g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Hwp.o src/Hwp.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks.o src/phasedstacks.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/tsv2bam.o src/tsv2bam.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/gstacks.o src/gstacks.cc src/Hwp.cc: In member function 'void HWMatrix::dump_matrix()': src/Hwp.cc:383:43: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'std::size_t' {aka 'unsigned int'} [-Wformat=] 383 | snprintf(buf, id_len, "%*lu ", padding, this->_g[i][j]); | ~~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int std::size_t {aka unsigned int} | %*u g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/debruijn.o src/debruijn.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/SuffixTree.o src/SuffixTree.cc rm -f libcore.a ar cru libcore.a src/aln_utils.o src/BamI.o src/catalog_utils.o src/cmb.o src/constants.o src/DNANSeq.o src/DNASeq4.o src/DNASeq.o src/gzFasta.o src/input.o src/kmers.o src/locus.o src/log_utils.o src/MetaPopInfo.o src/models.o src/mstack.o src/mst.o src/nucleotides.o src/renz.o src/Seq.o src/sql_utilities.o src/stacks.o src/utils.o src/Vcf.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcore.a rm -f libclean.a ar cru libclean.a src/clean.o src/file_io.o src/write.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libclean.a g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o process_shortreads src/process_shortreads.o -lhts libcore.a libclean.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o kmer_filter src/kmer_filter.o -lhts libcore.a libclean.a -lz -lgomp src/gstacks.cc: In member function 'bool LocusProcessor::align_reads_to_contig(SuffixTree*, GappedAln*, DNASeq4&, AlignRes&) const': src/gstacks.cc:1365:32: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wformat=] 1365 | snprintf(c, id_len, "%luM", query.length()); | ~~^ ~~~~~~~~~~~~~~ | | | | | std::__cxx11::basic_string::size_type {aka unsigned int} | long unsigned int | %u src/gstacks.cc: In member function 'std::size_t LocusProcessor::find_locus_overlap(SuffixTree*, GappedAln*, const DNASeq4&, std::string&) const': src/gstacks.cc:1551:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::size_t' {aka 'unsigned int'} [-Wformat=] 1551 | snprintf(buf, id_len, "%luM", alns.front().aln_len); | ~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int std::size_t {aka unsigned int} | %u g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o clone_filter src/clone_filter.o -lhts libcore.a libclean.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o ustacks src/ustacks.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o sstacks src/sstacks.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o cstacks src/cstacks.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o process_radtags src/process_radtags.o -lhts libcore.a libclean.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o phasedstacks src/phasedstacks.o -lhts libcore.a -lz -lgomp rm -f libpop.a ar cru libpop.a src/bootstrap.o src/export_formats.o src/mapping_utils.o src/genotype_dictionaries.o src/PopSum.o src/Hwp.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpop.a g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o tsv2bam src/tsv2bam.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o populations src/populations.o -lhts libcore.a libpop.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.66+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o gstacks src/gstacks.o src/debruijn.o src/SuffixTree.o -lhts libcore.a -lz -lgomp make[3]: Leaving directory '/build/reproducible-path/stacks-2.66+dfsg' make[2]: Leaving directory '/build/reproducible-path/stacks-2.66+dfsg' make[1]: Leaving directory '/build/reproducible-path/stacks-2.66+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/stacks-2.66+dfsg' if [ -e /usr/share/automake-1.16/tap-driver.sh ] ; then \ ln -s /usr/share/automake-1.16/tap-driver.sh tests/tap-driver.sh ; \ else \ echo "Make sure /usr/share/automake-*/tap-driver.sh exists and is linked" ; \ false ; \ fi # dh_auto_test rm tests/tap-driver.sh # FIXME: Does not work even after this trick. See # https://groups.google.com/forum/#!msg/stacks-users/TA2tMEqb4Mg/pQy4fUCYi9kJ true make[1]: Leaving directory '/build/reproducible-path/stacks-2.66+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/stacks-2.66+dfsg' dh_auto_install --no-parallel make -j1 install DESTDIR=/build/reproducible-path/stacks-2.66\+dfsg/debian/stacks AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/stacks-2.66+dfsg' make[3]: Entering directory '/build/reproducible-path/stacks-2.66+dfsg' make[4]: Entering directory '/build/reproducible-path/stacks-2.66+dfsg' /usr/bin/mkdir -p '/build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin' /usr/bin/install -c ustacks cstacks sstacks process_radtags process_shortreads kmer_filter clone_filter populations phasedstacks tsv2bam gstacks '/build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin' /usr/bin/mkdir -p '/build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin' /usr/bin/install -c scripts/denovo_map.pl scripts/ref_map.pl scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-gdb scripts/stacks-samtools-tview scripts/stacks-count-reads-per-sample-per-locus scripts/stacks-hist2d-loci-samples-coverage '/build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin' make install-data-hook make[5]: Entering directory '/build/reproducible-path/stacks-2.66+dfsg' sed -e 's,_VERSION_,2.66,' -e 's,_BINDIR_,/usr/libexec/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin/denovo_map.pl > /build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin/denovo_map.pl.subst mv /build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin/denovo_map.pl.subst /build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin/denovo_map.pl chmod +x /build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin/denovo_map.pl sed -e 's,_VERSION_,2.66,' -e 's,_BINDIR_,/usr/libexec/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin/ref_map.pl > /build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin/ref_map.pl.subst mv /build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin/ref_map.pl.subst /build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin/ref_map.pl chmod +x /build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin/ref_map.pl sed -i.bkp -e 's,_VERSION_,2.66,' /build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments sed -i.bkp -e 's,_VERSION_,2.66,' /build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin/stacks-samtools-tview rm -f /build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments.bkp rm -f /build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin/stacks-samtools-tview.bkp chmod +x /build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments chmod +x /build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin/stacks-dist-extract chmod +x /build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/bin/stacks-gdb make[5]: Leaving directory '/build/reproducible-path/stacks-2.66+dfsg' make[4]: Leaving directory '/build/reproducible-path/stacks-2.66+dfsg' make[3]: Leaving directory '/build/reproducible-path/stacks-2.66+dfsg' make[2]: Leaving directory '/build/reproducible-path/stacks-2.66+dfsg' make[1]: Leaving directory '/build/reproducible-path/stacks-2.66+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/stacks-2.66+dfsg' mkdir -p debian/stacks/usr/libexec/stacks mv debian/stacks/usr/bin debian/stacks/usr/libexec/stacks cd debian/stacks/usr/libexec/stacks/bin && \ for f in *.pl ; do \ ln -s "$f" "`basename $f .pl`" ; \ sed -i '1s?^#!/usr/bin/env.*perl?#!/usr/bin/perl?' $f ; \ done dh_install make[1]: Leaving directory '/build/reproducible-path/stacks-2.66+dfsg' dh_installdocs dh_installchangelogs dh_perl debian/rules override_dh_link make[1]: Entering directory '/build/reproducible-path/stacks-2.66+dfsg' dh_link mkdir -p debian/stacks/usr/libexec/debian-med/bin cd debian/stacks/usr/libexec/debian-med/bin && \ for f in `ls /build/reproducible-path/stacks-2.66+dfsg/debian/stacks/usr/libexec/stacks/bin` ; do \ ln -s ../../stacks/bin/$f ; \ done make[1]: Leaving directory '/build/reproducible-path/stacks-2.66+dfsg' 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: package stacks: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package stacks: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'stacks-dbgsym' in '../stacks-dbgsym_2.66+dfsg-1_i386.deb'. dpkg-deb: building package 'stacks' in '../stacks_2.66+dfsg-1_i386.deb'. dpkg-genbuildinfo --build=binary -O../stacks_2.66+dfsg-1_i386.buildinfo dpkg-genchanges --build=binary -O../stacks_2.66+dfsg-1_i386.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: including full 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/33069 and its subdirectories I: Current time: Fri Apr 4 06:25:13 -12 2025 I: pbuilder-time-stamp: 1743791113 Sat Mar 2 12:02:16 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net. Sat Mar 2 12:02:16 UTC 2024 I: Preparing to do remote build '2' on ionos12-i386.debian.net. Sat Mar 2 12:08:18 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. Sat Mar 2 12:08:18 UTC 2024 I: stacks_2.66+dfsg-1_i386.changes: Format: 1.8 Date: Tue, 23 Jan 2024 19:32:21 +0700 Source: stacks Binary: stacks stacks-dbgsym Architecture: i386 Version: 2.66+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Lance Lin Description: stacks - pipeline for building loci from short-read DNA sequences Changes: stacks (2.66+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream version * d/patches: Refresh patches (change_program_exit_to_success.patch, fix_spelling_errors.patch, script-exe-paths) Checksums-Sha1: aba2abc0c77dc263597fe26d532249f1d1612ed8 28244756 stacks-dbgsym_2.66+dfsg-1_i386.deb a3cb17e5ff4388d2093f02ae8f59b1f28b4502fa 6226 stacks_2.66+dfsg-1_i386.buildinfo 0f071476cf1e6adfd21d51b7c5827d0e73248e6b 1262868 stacks_2.66+dfsg-1_i386.deb Checksums-Sha256: 2e1b3367e989d7b2eabd9ea5ec82d16f5adbbbf65f17e4e79d7fa3136c901d59 28244756 stacks-dbgsym_2.66+dfsg-1_i386.deb 44875a2600bc69623e7520d1dee5abd99586beabafa08561cc73c04d7c67d80f 6226 stacks_2.66+dfsg-1_i386.buildinfo 7a048176bd275e78a0751e9095116956cb62c320d275210c88513fedff4b394b 1262868 stacks_2.66+dfsg-1_i386.deb Files: fe3ca9f2598f807cca125436bb23da55 28244756 debug optional stacks-dbgsym_2.66+dfsg-1_i386.deb 3ee54f67c3c3c16f8b3a0de6169efcd6 6226 science optional stacks_2.66+dfsg-1_i386.buildinfo 043d09fa076ee6bcdbac37f4f5e906ca 1262868 science optional stacks_2.66+dfsg-1_i386.deb Sat Mar 2 12:08:20 UTC 2024 I: diffoscope 258 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.NJcKooLY/stacks_2.66+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.NJcKooLY/stacks_2.66+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.NJcKooLY/stacks_2.66+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.NJcKooLY/b1/stacks_2.66+dfsg-1_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.NJcKooLY/b2/stacks_2.66+dfsg-1_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.605s) 0.605s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.309s) 0.309s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Sat Mar 2 12:08:21 UTC 2024 I: diffoscope 258 found no differences in the changes files, and a .buildinfo file also exists. Sat Mar 2 12:08:21 UTC 2024 I: stacks from trixie built successfully and reproducibly on i386. Sat Mar 2 12:08:23 UTC 2024 I: Submitting .buildinfo files to external archives: Sat Mar 2 12:08:23 UTC 2024 I: Submitting 8.0K b1/stacks_2.66+dfsg-1_i386.buildinfo.asc Sat Mar 2 12:08:24 UTC 2024 I: Submitting 8.0K b2/stacks_2.66+dfsg-1_i386.buildinfo.asc Sat Mar 2 12:08:25 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Mar 2 12:08:25 UTC 2024 I: Done submitting .buildinfo files. Sat Mar 2 12:08:25 UTC 2024 I: Removing signed stacks_2.66+dfsg-1_i386.buildinfo.asc files: removed './b1/stacks_2.66+dfsg-1_i386.buildinfo.asc' removed './b2/stacks_2.66+dfsg-1_i386.buildinfo.asc'