Sun Apr 28 19:32:14 UTC 2024 I: starting to build plink2/trixie/i386 on jenkins on '2024-04-28 19:31' Sun Apr 28 19:32:14 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_6/22732/console.log Sun Apr 28 19:32:14 UTC 2024 I: Downloading source for trixie/plink2=2.00~a5.8-231123+dfsg-1 --2024-04-28 19:32:14-- http://deb.debian.org/debian/pool/main/p/plink2/plink2_2.00%7ea5.8-231123%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2155 (2.1K) [text/prs.lines.tag] Saving to: ‘plink2_2.00~a5.8-231123+dfsg-1.dsc’ 0K .. 100% 249M=0s 2024-04-28 19:32:14 (249 MB/s) - ‘plink2_2.00~a5.8-231123+dfsg-1.dsc’ saved [2155/2155] Sun Apr 28 19:32:14 UTC 2024 I: plink2_2.00~a5.8-231123+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: plink2 Binary: plink2 Architecture: any Version: 2.00~a5.8-231123+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Dylan Aïssi Homepage: https://www.cog-genomics.org/plink/2.0/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/plink2 Vcs-Git: https://salsa.debian.org/med-team/plink2.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), help2man, liblapack-dev | liblapack.so, libzstd-dev, zlib1g-dev, libsimde-dev, libdeflate-dev Package-List: plink2 deb science optional arch=any Checksums-Sha1: a556120f1e4b6bf09ccfea44ad3e17ec1c6106dc 1119460 plink2_2.00~a5.8-231123+dfsg.orig.tar.xz e3d7c8b23845c466cbf0bb63cd3402cd8722b936 52288 plink2_2.00~a5.8-231123+dfsg-1.debian.tar.xz Checksums-Sha256: 12700bff139aac4520757e6920addda8efcf84da673cd5bc1c4b800320eb222e 1119460 plink2_2.00~a5.8-231123+dfsg.orig.tar.xz 7bf66afa070435c2b44a4b22931df8f3d8ffd307c7230275c04901ec83e72721 52288 plink2_2.00~a5.8-231123+dfsg-1.debian.tar.xz Files: 978a8223a2fd71fbc76d37f2ac4ba6e8 1119460 plink2_2.00~a5.8-231123+dfsg.orig.tar.xz 2ebf196c340bb24a3e98921457430a80 52288 plink2_2.00~a5.8-231123+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmVnNbMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHzhg//dItmr5jdl7yjmRnd2u8hUax+3n4XIM78 cTg29A+HPXkJ4lzK8BKj4jmPeINvuHipGNU4C4c4n05GjyajWKsUW+/UUY/pV2Pg +58+VZiXviKUaakxFrgHXztSoaeh1H2plC7oWDz2E9hvyStiVVR125H1AlwK6/S5 nibJYUOy6ojlaGky8FnzDp4LFvh4me9gWE6EqAECrb3Ujfq4lnAuGtg3y9qPaGYu yReb+FZzF8eDQgnpDOCXj6dGqmCyVo9WcEcZim5ML5C7r3isftVJA17oJpiX4yCx JEjamLPbGapA/HOoFwJdG4w/s1ticcONfrhBNRzyotIQ/Qy4WENZ1QD6Lm0DvKm3 AQaYam7vVcUDdifLGbtTVKZg2e6/SZ50+wodVIg2qW4HLY3aBYQTVyukV7Qy3zni z0ystjLEPzsv1GclWAgSK9cqZcT8oqp9uZJnqg4DAG9Nc79cVHU6Bgvz8A5w1JGM uRxvkOEDxsfVEcblyfKS3jlp15K30R1UOyXrb/wjrDLwFvSmZXhPzeLTfUoVrGym OpwAOfYkLe0ueVZPlkT77W5ReKkE7Gu5R/Gc7ItgL/P72yFEWLIjLtNJAT2yuSyT QshcTqvSmB5ei+uMhGERoJdwbVImV40atKGHUyPQZQWWdz6ZYHNm3d4Hp7jf1+5d RRVFEh0YvuU= =r4ms -----END PGP SIGNATURE----- Sun Apr 28 19:32:14 UTC 2024 I: Checking whether the package is not for us Sun Apr 28 19:32:14 UTC 2024 I: Starting 1st build on remote node ionos6-i386.debian.net. Sun Apr 28 19:32:14 UTC 2024 I: Preparing to do remote build '1' on ionos6-i386.debian.net. Sun Apr 28 19:48:58 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat May 31 13:55:17 -12 2025 I: pbuilder-time-stamp: 1748742917 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 [plink2_2.00~a5.8-231123+dfsg-1.dsc] I: copying [./plink2_2.00~a5.8-231123+dfsg.orig.tar.xz] I: copying [./plink2_2.00~a5.8-231123+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Nov 29 12:59:31 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./plink2_2.00~a5.8-231123+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting plink2 in plink2-2.00~a5.8-231123+dfsg dpkg-source: info: unpacking plink2_2.00~a5.8-231123+dfsg.orig.tar.xz dpkg-source: info: unpacking plink2_2.00~a5.8-231123+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Fix_Makefile.patch dpkg-source: info: applying use_packaged_libdeflate.patch dpkg-source: info: applying no_atlas.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/5678/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=22 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='25c6f42c006c4c5faa53881105f9721b' 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='5678' 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.3SKgz64Z/pbuilderrc_MKt2 --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.3SKgz64Z/b1 --logfile b1/build.log plink2_2.00~a5.8-231123+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://213.165.73.152:3128' I: uname -a Linux ionos6-i386 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 26 17:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/5678/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), help2man, liblapack-dev | liblapack.so, libzstd-dev, zlib1g-dev, libsimde-dev, libdeflate-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 ... 19884 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 help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev | liblapack.so; however: Package liblapack-dev is not installed. Package liblapack.so is not installed. pbuilder-satisfydepends-dummy depends on libzstd-dev; however: Package libzstd-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. pbuilder-satisfydepends-dummy depends on libdeflate-dev; however: Package libdeflate-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} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} liblapack-dev{a} liblapack3{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsimde-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libzstd-dev{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 libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 42 newly installed, 0 to remove and 0 not upgraded. Need to get 28.9 MB of archives. After unpacking 119 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 liblocale-gettext-perl i386 1.07-6+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3+b1 [1195 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 24 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.191-1+b1 [194 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b3 [727 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 help2man i386 1.49.3 [198 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 libblas-dev i386 3.12.0-3 [152 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.20-1 [46.9 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libdeflate-dev i386 1.20-1 [56.0 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14-20240330-1 [735 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 liblapack-dev i386 3.12.0-3 [4400 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libsimde-dev all 0.8.0-1 [458 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 libzstd-dev i386 1.5.5+dfsg2-2 [346 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg-3.1 [915 kB] Fetched 28.9 MB in 0s (94.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19884 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-6+b1_i386.deb ... Unpacking liblocale-gettext-perl (1.07-6+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-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 .../03-libmagic1_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic1:i386 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-2+b1_i386.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../06-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 .../07-groff-base_1.23.0-3+b1_i386.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.39.3-6_i386.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../09-libpipeline1_1.5.7-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.12.0-3_i386.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-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 .../15-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-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 .../20-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 .../21-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 .../22-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../23-libelf1t64_0.191-1+b1_i386.deb ... Unpacking libelf1t64:i386 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../25-libicu72_72.1-4+b1_i386.deb ... Unpacking libicu72:i386 (72.1-4+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.3+b3_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-14+b1_i386.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-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 .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package help2man. Preparing to unpack .../31-help2man_1.49.3_i386.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package libblas3:i386. Preparing to unpack .../32-libblas3_3.12.0-3_i386.deb ... Unpacking libblas3:i386 (3.12.0-3) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/plink2-2.00~a5.8-231123+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 > ../plink2_2.00~a5.8-231123+dfsg-1_source.changes dpkg-buildpackage: info: source package plink2 dpkg-buildpackage: info: source version 2.00~a5.8-231123+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --sourcedirectory=build_dynamic/ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' dh_auto_clean cd build_dynamic && make -j22 clean make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg/build_dynamic' rm -f *.o rm -f plink2 rm -f pgen_compress rm -f pgenlib.a rm -f plink2lib.a rm -f static_pgenlib_test rm -f static_plink2lib_test make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg/build_dynamic' rm -f plink2.1 rm -f pgen_compress.1 make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' dh_autoreconf_clean -O--sourcedirectory=build_dynamic/ dh_clean -O--sourcedirectory=build_dynamic/ debian/rules binary dh binary --sourcedirectory=build_dynamic/ dh_update_autotools_config -O--sourcedirectory=build_dynamic/ dh_autoreconf -O--sourcedirectory=build_dynamic/ dh_auto_configure -O--sourcedirectory=build_dynamic/ debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' mkdir -p /build/reproducible-path/plink2-2.00~a5.8-231123+dfsg/debian/plink2/usr mkdir -p /build/reproducible-path/plink2-2.00~a5.8-231123+dfsg/debian/plink2/usr/lib/plink2 for SIMD in ssse3 sse3 sse2 sse mmx; do \ export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -m${SIMD}" && export CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -m${SIMD}" && \ make clean ; \ dh_auto_build -- SFX=-${SIMD} ; \ done make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' rm -f *.o include/*.o zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o pgenlibr/src/*.a pgenlibr/src/*.o pgenlibr/src/Makevars pgenlibr/src/pgenlibr.so bin/plink2 bin/pgen_compress make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' cd build_dynamic && make -j22 "INSTALL=install --strip-program=true" SFX=-ssse3 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg/build_dynamic' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -mssse3 -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security ../include/SFMT.c -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -mssse3 -std=c++11 -O2 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast ../include/plink2_base.cc ../include/plink2_bits.cc ../include/pgenlib_misc.cc ../include/pgenlib_read.cc ../include/pgenlib_write.cc ../pgen_compress.cc -o pgen_compress-ssse3 echo cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -c cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -mssse3 -std=c++11 -O2 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast ../include/plink2_base.cc ../include/plink2_bits.cc ../include/pgenlib_misc.cc ../include/pgenlib_read.cc ../include/pgenlib_write.cc ../include/plink2_bgzf.cc ../include/plink2_bitmap.cc ../include/plink2_fmath.cc ../include/plink2_stats.cc ../include/plink2_string.cc ../include/plink2_text.cc ../include/plink2_thread.cc ../include/plink2_zstfile.cc ../plink2.cc ../plink2_adjust.cc ../plink2_cmdline.cc ../plink2_common.cc ../plink2_compress_stream.cc ../plink2_data.cc ../plink2_decompress.cc ../plink2_export.cc ../plink2_export_legacy.cc ../plink2_fasta.cc ../plink2_filter.cc ../plink2_glm.cc ../plink2_glm_linear.cc ../plink2_glm_logistic.cc ../plink2_glm_shared.cc ../plink2_help.cc ../plink2_import.cc ../plink2_import_legacy.cc ../plink2_ld.cc ../plink2_matrix.cc ../plink2_matrix_calc.cc ../plink2_merge.cc ../plink2_misc.cc ../plink2_psam.cc ../plink2_pvar.cc ../plink2_random.cc ../plink2_set.cc -c ../plink2.cc: In function 'int main(int, char**)': ../plink2.cc:5307:96: warning: '%s' directive output may be truncated writing up to 2147483635 bytes into a region of size 262098 [-Wformat-truncation=] 5307 | snprintf(g_logbuf, kLogbufSize, "Error: Invalid --export vcf-dosage= argument '%s'.\n", vcf_dosage_start); | ^~ In file included from /usr/include/stdio.h:906, from ../include/plink2_base.h:114, from ../include/plink2_zstfile.h:27, from ../plink2.cc:18: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'int main(int, char**)' at ../plink2.cc:5307:25: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 50 and 2147483685 bytes into a destination of size 262144 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:26, from ../plink2_compress_stream.h:27, from ../plink2_import.cc:19: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1854:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1942:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long long unsigned int*]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'plink2::PglErr plink2::Plink1DosageToPgen(const char*, const char*, const char*, const char*, const Plink1DosageInfo*, const char*, MiscFlags, ImportFlags, uint32_t, FamCol, int32_t, uint32_t, uint32_t, double, uint32_t, char*, char*, ChrInfo*)' at ../plink2_import.cc:15198:5: /usr/include/c++/13/bits/stl_algo.h:1859:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long long unsigned int [6]'} [-Warray-bounds=] 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_import.cc: In function 'plink2::PglErr plink2::Plink1DosageToPgen(const char*, const char*, const char*, const char*, const Plink1DosageInfo*, const char*, MiscFlags, ImportFlags, uint32_t, FamCol, int32_t, uint32_t, uint32_t, double, uint32_t, char*, char*, ChrInfo*)': ../plink2_import.cc:15179:14: note: at offset 128 into object 'parse_table' of size 48 15179 | uint64_t parse_table[6]; | ^~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 ../plink2_cpu.cc -c g++ SFMT.o plink2_base.o plink2_bits.o pgenlib_misc.o pgenlib_read.o pgenlib_write.o plink2_bgzf.o plink2_bitmap.o plink2_fmath.o plink2_stats.o plink2_string.o plink2_text.o plink2_thread.o plink2_zstfile.o plink2.o plink2_adjust.o plink2_cmdline.o plink2_common.o plink2_compress_stream.o plink2_data.o plink2_decompress.o plink2_export.o plink2_export_legacy.o plink2_fasta.o plink2_filter.o plink2_glm.o plink2_glm_linear.o plink2_glm_logistic.o plink2_glm_shared.o plink2_help.o plink2_import.o plink2_import_legacy.o plink2_ld.o plink2_matrix.o plink2_matrix_calc.o plink2_merge.o plink2_misc.o plink2_psam.o plink2_pvar.o plink2_random.o plink2_set.o plink2_cpu.o -o plink2-ssse3 -llapack -lblas -lm -lpthread -lz -lzstd -Wl,-z,relro -Wl,-z,now -ldeflate make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' rm -f *.o include/*.o zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o pgenlibr/src/*.a pgenlibr/src/*.o pgenlibr/src/Makevars pgenlibr/src/pgenlibr.so bin/plink2 bin/pgen_compress make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' cd build_dynamic && make -j22 "INSTALL=install --strip-program=true" SFX=-sse3 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg/build_dynamic' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -msse3 -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security ../include/SFMT.c -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -msse3 -std=c++11 -O2 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast ../include/plink2_base.cc ../include/plink2_bits.cc ../include/pgenlib_misc.cc ../include/pgenlib_read.cc ../include/pgenlib_write.cc ../pgen_compress.cc -o pgen_compress-sse3 echo cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -c cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -msse3 -std=c++11 -O2 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast ../include/plink2_base.cc ../include/plink2_bits.cc ../include/pgenlib_misc.cc ../include/pgenlib_read.cc ../include/pgenlib_write.cc ../include/plink2_bgzf.cc ../include/plink2_bitmap.cc ../include/plink2_fmath.cc ../include/plink2_stats.cc ../include/plink2_string.cc ../include/plink2_text.cc ../include/plink2_thread.cc ../include/plink2_zstfile.cc ../plink2.cc ../plink2_adjust.cc ../plink2_cmdline.cc ../plink2_common.cc ../plink2_compress_stream.cc ../plink2_data.cc ../plink2_decompress.cc ../plink2_export.cc ../plink2_export_legacy.cc ../plink2_fasta.cc ../plink2_filter.cc ../plink2_glm.cc ../plink2_glm_linear.cc ../plink2_glm_logistic.cc ../plink2_glm_shared.cc ../plink2_help.cc ../plink2_import.cc ../plink2_import_legacy.cc ../plink2_ld.cc ../plink2_matrix.cc ../plink2_matrix_calc.cc ../plink2_merge.cc ../plink2_misc.cc ../plink2_psam.cc ../plink2_pvar.cc ../plink2_random.cc ../plink2_set.cc -c ../plink2.cc: In function 'int main(int, char**)': ../plink2.cc:5307:96: warning: '%s' directive output may be truncated writing up to 2147483635 bytes into a region of size 262098 [-Wformat-truncation=] 5307 | snprintf(g_logbuf, kLogbufSize, "Error: Invalid --export vcf-dosage= argument '%s'.\n", vcf_dosage_start); | ^~ In file included from /usr/include/stdio.h:906, from ../include/plink2_base.h:114, from ../include/plink2_zstfile.h:27, from ../plink2.cc:18: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'int main(int, char**)' at ../plink2.cc:5307:25: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 50 and 2147483685 bytes into a destination of size 262144 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:26, from ../plink2_compress_stream.h:27, from ../plink2_import.cc:19: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1854:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1942:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long long unsigned int*]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'plink2::PglErr plink2::Plink1DosageToPgen(const char*, const char*, const char*, const char*, const Plink1DosageInfo*, const char*, MiscFlags, ImportFlags, uint32_t, FamCol, int32_t, uint32_t, uint32_t, double, uint32_t, char*, char*, ChrInfo*)' at ../plink2_import.cc:15198:5: /usr/include/c++/13/bits/stl_algo.h:1859:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long long unsigned int [6]'} [-Warray-bounds=] 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_import.cc: In function 'plink2::PglErr plink2::Plink1DosageToPgen(const char*, const char*, const char*, const char*, const Plink1DosageInfo*, const char*, MiscFlags, ImportFlags, uint32_t, FamCol, int32_t, uint32_t, uint32_t, double, uint32_t, char*, char*, ChrInfo*)': ../plink2_import.cc:15179:14: note: at offset 128 into object 'parse_table' of size 48 15179 | uint64_t parse_table[6]; | ^~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 ../plink2_cpu.cc -c g++ SFMT.o plink2_base.o plink2_bits.o pgenlib_misc.o pgenlib_read.o pgenlib_write.o plink2_bgzf.o plink2_bitmap.o plink2_fmath.o plink2_stats.o plink2_string.o plink2_text.o plink2_thread.o plink2_zstfile.o plink2.o plink2_adjust.o plink2_cmdline.o plink2_common.o plink2_compress_stream.o plink2_data.o plink2_decompress.o plink2_export.o plink2_export_legacy.o plink2_fasta.o plink2_filter.o plink2_glm.o plink2_glm_linear.o plink2_glm_logistic.o plink2_glm_shared.o plink2_help.o plink2_import.o plink2_import_legacy.o plink2_ld.o plink2_matrix.o plink2_matrix_calc.o plink2_merge.o plink2_misc.o plink2_psam.o plink2_pvar.o plink2_random.o plink2_set.o plink2_cpu.o -o plink2-sse3 -llapack -lblas -lm -lpthread -lz -lzstd -Wl,-z,relro -Wl,-z,now -ldeflate make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' rm -f *.o include/*.o zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o pgenlibr/src/*.a pgenlibr/src/*.o pgenlibr/src/Makevars pgenlibr/src/pgenlibr.so bin/plink2 bin/pgen_compress make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' cd build_dynamic && make -j22 "INSTALL=install --strip-program=true" SFX=-sse2 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg/build_dynamic' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -msse2 -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security ../include/SFMT.c -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -msse2 -std=c++11 -O2 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast ../include/plink2_base.cc ../include/plink2_bits.cc ../include/pgenlib_misc.cc ../include/pgenlib_read.cc ../include/pgenlib_write.cc ../pgen_compress.cc -o pgen_compress-sse2 echo cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -c cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -msse2 -std=c++11 -O2 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast ../include/plink2_base.cc ../include/plink2_bits.cc ../include/pgenlib_misc.cc ../include/pgenlib_read.cc ../include/pgenlib_write.cc ../include/plink2_bgzf.cc ../include/plink2_bitmap.cc ../include/plink2_fmath.cc ../include/plink2_stats.cc ../include/plink2_string.cc ../include/plink2_text.cc ../include/plink2_thread.cc ../include/plink2_zstfile.cc ../plink2.cc ../plink2_adjust.cc ../plink2_cmdline.cc ../plink2_common.cc ../plink2_compress_stream.cc ../plink2_data.cc ../plink2_decompress.cc ../plink2_export.cc ../plink2_export_legacy.cc ../plink2_fasta.cc ../plink2_filter.cc ../plink2_glm.cc ../plink2_glm_linear.cc ../plink2_glm_logistic.cc ../plink2_glm_shared.cc ../plink2_help.cc ../plink2_import.cc ../plink2_import_legacy.cc ../plink2_ld.cc ../plink2_matrix.cc ../plink2_matrix_calc.cc ../plink2_merge.cc ../plink2_misc.cc ../plink2_psam.cc ../plink2_pvar.cc ../plink2_random.cc ../plink2_set.cc -c ../plink2.cc: In function 'int main(int, char**)': ../plink2.cc:5307:96: warning: '%s' directive output may be truncated writing up to 2147483635 bytes into a region of size 262098 [-Wformat-truncation=] 5307 | snprintf(g_logbuf, kLogbufSize, "Error: Invalid --export vcf-dosage= argument '%s'.\n", vcf_dosage_start); | ^~ In file included from /usr/include/stdio.h:906, from ../include/plink2_base.h:114, from ../include/plink2_zstfile.h:27, from ../plink2.cc:18: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'int main(int, char**)' at ../plink2.cc:5307:25: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 50 and 2147483685 bytes into a destination of size 262144 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:26, from ../plink2_compress_stream.h:27, from ../plink2_import.cc:19: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1854:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1942:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long long unsigned int*]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'plink2::PglErr plink2::Plink1DosageToPgen(const char*, const char*, const char*, const char*, const Plink1DosageInfo*, const char*, MiscFlags, ImportFlags, uint32_t, FamCol, int32_t, uint32_t, uint32_t, double, uint32_t, char*, char*, ChrInfo*)' at ../plink2_import.cc:15198:5: /usr/include/c++/13/bits/stl_algo.h:1859:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long long unsigned int [6]'} [-Warray-bounds=] 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_import.cc: In function 'plink2::PglErr plink2::Plink1DosageToPgen(const char*, const char*, const char*, const char*, const Plink1DosageInfo*, const char*, MiscFlags, ImportFlags, uint32_t, FamCol, int32_t, uint32_t, uint32_t, double, uint32_t, char*, char*, ChrInfo*)': ../plink2_import.cc:15179:14: note: at offset 128 into object 'parse_table' of size 48 15179 | uint64_t parse_table[6]; | ^~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 ../plink2_cpu.cc -c g++ SFMT.o plink2_base.o plink2_bits.o pgenlib_misc.o pgenlib_read.o pgenlib_write.o plink2_bgzf.o plink2_bitmap.o plink2_fmath.o plink2_stats.o plink2_string.o plink2_text.o plink2_thread.o plink2_zstfile.o plink2.o plink2_adjust.o plink2_cmdline.o plink2_common.o plink2_compress_stream.o plink2_data.o plink2_decompress.o plink2_export.o plink2_export_legacy.o plink2_fasta.o plink2_filter.o plink2_glm.o plink2_glm_linear.o plink2_glm_logistic.o plink2_glm_shared.o plink2_help.o plink2_import.o plink2_import_legacy.o plink2_ld.o plink2_matrix.o plink2_matrix_calc.o plink2_merge.o plink2_misc.o plink2_psam.o plink2_pvar.o plink2_random.o plink2_set.o plink2_cpu.o -o plink2-sse2 -llapack -lblas -lm -lpthread -lz -lzstd -Wl,-z,relro -Wl,-z,now -ldeflate make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' rm -f *.o include/*.o zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o pgenlibr/src/*.a pgenlibr/src/*.o pgenlibr/src/Makevars pgenlibr/src/pgenlibr.so bin/plink2 bin/pgen_compress make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' cd build_dynamic && make -j22 "INSTALL=install --strip-program=true" SFX=-sse make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg/build_dynamic' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -msse -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security ../include/SFMT.c -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -msse -std=c++11 -O2 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast ../include/plink2_base.cc ../include/plink2_bits.cc ../include/pgenlib_misc.cc ../include/pgenlib_read.cc ../include/pgenlib_write.cc ../pgen_compress.cc -o pgen_compress-sse echo cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -c cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -msse -std=c++11 -O2 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast ../include/plink2_base.cc ../include/plink2_bits.cc ../include/pgenlib_misc.cc ../include/pgenlib_read.cc ../include/pgenlib_write.cc ../include/plink2_bgzf.cc ../include/plink2_bitmap.cc ../include/plink2_fmath.cc ../include/plink2_stats.cc ../include/plink2_string.cc ../include/plink2_text.cc ../include/plink2_thread.cc ../include/plink2_zstfile.cc ../plink2.cc ../plink2_adjust.cc ../plink2_cmdline.cc ../plink2_common.cc ../plink2_compress_stream.cc ../plink2_data.cc ../plink2_decompress.cc ../plink2_export.cc ../plink2_export_legacy.cc ../plink2_fasta.cc ../plink2_filter.cc ../plink2_glm.cc ../plink2_glm_linear.cc ../plink2_glm_logistic.cc ../plink2_glm_shared.cc ../plink2_help.cc ../plink2_import.cc ../plink2_import_legacy.cc ../plink2_ld.cc ../plink2_matrix.cc ../plink2_matrix_calc.cc ../plink2_merge.cc ../plink2_misc.cc ../plink2_psam.cc ../plink2_pvar.cc ../plink2_random.cc ../plink2_set.cc -c ../plink2.cc: In function 'int main(int, char**)': ../plink2.cc:5307:96: warning: '%s' directive output may be truncated writing up to 2147483635 bytes into a region of size 262098 [-Wformat-truncation=] 5307 | snprintf(g_logbuf, kLogbufSize, "Error: Invalid --export vcf-dosage= argument '%s'.\n", vcf_dosage_start); | ^~ In file included from /usr/include/stdio.h:906, from ../include/plink2_base.h:114, from ../include/plink2_zstfile.h:27, from ../plink2.cc:18: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'int main(int, char**)' at ../plink2.cc:5307:25: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 50 and 2147483685 bytes into a destination of size 262144 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:26, from ../plink2_compress_stream.h:27, from ../plink2_import.cc:19: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1854:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1942:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long long unsigned int*]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'plink2::PglErr plink2::Plink1DosageToPgen(const char*, const char*, const char*, const char*, const Plink1DosageInfo*, const char*, MiscFlags, ImportFlags, uint32_t, FamCol, int32_t, uint32_t, uint32_t, double, uint32_t, char*, char*, ChrInfo*)' at ../plink2_import.cc:15198:5: /usr/include/c++/13/bits/stl_algo.h:1859:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long long unsigned int [6]'} [-Warray-bounds=] 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_import.cc: In function 'plink2::PglErr plink2::Plink1DosageToPgen(const char*, const char*, const char*, const char*, const Plink1DosageInfo*, const char*, MiscFlags, ImportFlags, uint32_t, FamCol, int32_t, uint32_t, uint32_t, double, uint32_t, char*, char*, ChrInfo*)': ../plink2_import.cc:15179:14: note: at offset 128 into object 'parse_table' of size 48 15179 | uint64_t parse_table[6]; | ^~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 ../plink2_cpu.cc -c g++ SFMT.o plink2_base.o plink2_bits.o pgenlib_misc.o pgenlib_read.o pgenlib_write.o plink2_bgzf.o plink2_bitmap.o plink2_fmath.o plink2_stats.o plink2_string.o plink2_text.o plink2_thread.o plink2_zstfile.o plink2.o plink2_adjust.o plink2_cmdline.o plink2_common.o plink2_compress_stream.o plink2_data.o plink2_decompress.o plink2_export.o plink2_export_legacy.o plink2_fasta.o plink2_filter.o plink2_glm.o plink2_glm_linear.o plink2_glm_logistic.o plink2_glm_shared.o plink2_help.o plink2_import.o plink2_import_legacy.o plink2_ld.o plink2_matrix.o plink2_matrix_calc.o plink2_merge.o plink2_misc.o plink2_psam.o plink2_pvar.o plink2_random.o plink2_set.o plink2_cpu.o -o plink2-sse -llapack -lblas -lm -lpthread -lz -lzstd -Wl,-z,relro -Wl,-z,now -ldeflate make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' rm -f *.o include/*.o zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o pgenlibr/src/*.a pgenlibr/src/*.o pgenlibr/src/Makevars pgenlibr/src/pgenlibr.so bin/plink2 bin/pgen_compress make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' cd build_dynamic && make -j22 "INSTALL=install --strip-program=true" SFX=-mmx make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg/build_dynamic' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -mmmx -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security ../include/SFMT.c -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -mmmx -std=c++11 -O2 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast ../include/plink2_base.cc ../include/plink2_bits.cc ../include/pgenlib_misc.cc ../include/pgenlib_read.cc ../include/pgenlib_write.cc ../pgen_compress.cc -o pgen_compress-mmx echo cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -c cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -mmmx -std=c++11 -O2 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast ../include/plink2_base.cc ../include/plink2_bits.cc ../include/pgenlib_misc.cc ../include/pgenlib_read.cc ../include/pgenlib_write.cc ../include/plink2_bgzf.cc ../include/plink2_bitmap.cc ../include/plink2_fmath.cc ../include/plink2_stats.cc ../include/plink2_string.cc ../include/plink2_text.cc ../include/plink2_thread.cc ../include/plink2_zstfile.cc ../plink2.cc ../plink2_adjust.cc ../plink2_cmdline.cc ../plink2_common.cc ../plink2_compress_stream.cc ../plink2_data.cc ../plink2_decompress.cc ../plink2_export.cc ../plink2_export_legacy.cc ../plink2_fasta.cc ../plink2_filter.cc ../plink2_glm.cc ../plink2_glm_linear.cc ../plink2_glm_logistic.cc ../plink2_glm_shared.cc ../plink2_help.cc ../plink2_import.cc ../plink2_import_legacy.cc ../plink2_ld.cc ../plink2_matrix.cc ../plink2_matrix_calc.cc ../plink2_merge.cc ../plink2_misc.cc ../plink2_psam.cc ../plink2_pvar.cc ../plink2_random.cc ../plink2_set.cc -c ../plink2.cc: In function 'int main(int, char**)': ../plink2.cc:5307:96: warning: '%s' directive output may be truncated writing up to 2147483635 bytes into a region of size 262098 [-Wformat-truncation=] 5307 | snprintf(g_logbuf, kLogbufSize, "Error: Invalid --export vcf-dosage= argument '%s'.\n", vcf_dosage_start); | ^~ In file included from /usr/include/stdio.h:906, from ../include/plink2_base.h:114, from ../include/plink2_zstfile.h:27, from ../plink2.cc:18: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'int main(int, char**)' at ../plink2.cc:5307:25: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 50 and 2147483685 bytes into a destination of size 262144 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:26, from ../plink2_compress_stream.h:27, from ../plink2_import.cc:19: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1854:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1942:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long long unsigned int*]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'plink2::PglErr plink2::Plink1DosageToPgen(const char*, const char*, const char*, const char*, const Plink1DosageInfo*, const char*, MiscFlags, ImportFlags, uint32_t, FamCol, int32_t, uint32_t, uint32_t, double, uint32_t, char*, char*, ChrInfo*)' at ../plink2_import.cc:15198:5: /usr/include/c++/13/bits/stl_algo.h:1859:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long long unsigned int [6]'} [-Warray-bounds=] 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_import.cc: In function 'plink2::PglErr plink2::Plink1DosageToPgen(const char*, const char*, const char*, const char*, const Plink1DosageInfo*, const char*, MiscFlags, ImportFlags, uint32_t, FamCol, int32_t, uint32_t, uint32_t, double, uint32_t, char*, char*, ChrInfo*)': ../plink2_import.cc:15179:14: note: at offset 128 into object 'parse_table' of size 48 15179 | uint64_t parse_table[6]; | ^~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 ../plink2_cpu.cc -c g++ SFMT.o plink2_base.o plink2_bits.o pgenlib_misc.o pgenlib_read.o pgenlib_write.o plink2_bgzf.o plink2_bitmap.o plink2_fmath.o plink2_stats.o plink2_string.o plink2_text.o plink2_thread.o plink2_zstfile.o plink2.o plink2_adjust.o plink2_cmdline.o plink2_common.o plink2_compress_stream.o plink2_data.o plink2_decompress.o plink2_export.o plink2_export_legacy.o plink2_fasta.o plink2_filter.o plink2_glm.o plink2_glm_linear.o plink2_glm_logistic.o plink2_glm_shared.o plink2_help.o plink2_import.o plink2_import_legacy.o plink2_ld.o plink2_matrix.o plink2_matrix_calc.o plink2_merge.o plink2_misc.o plink2_psam.o plink2_pvar.o plink2_random.o plink2_set.o plink2_cpu.o -o plink2-mmx -llapack -lblas -lm -lpthread -lz -lzstd -Wl,-z,relro -Wl,-z,now -ldeflate make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg/build_dynamic' dh_auto_build -- SFX=-plain cd build_dynamic && make -j22 "INSTALL=install --strip-program=true" SFX=-plain make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg/build_dynamic' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security ../include/SFMT.c -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -std=c++11 -O2 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast ../include/plink2_base.cc ../include/plink2_bits.cc ../include/pgenlib_misc.cc ../include/pgenlib_read.cc ../include/pgenlib_write.cc ../pgen_compress.cc -o pgen_compress-plain echo cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -c cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -std=c++11 -O2 -DZSTD_MULTITHREAD -DIGNORE_BUNDLED_ZSTD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast ../include/plink2_base.cc ../include/plink2_bits.cc ../include/pgenlib_misc.cc ../include/pgenlib_read.cc ../include/pgenlib_write.cc ../include/plink2_bgzf.cc ../include/plink2_bitmap.cc ../include/plink2_fmath.cc ../include/plink2_stats.cc ../include/plink2_string.cc ../include/plink2_text.cc ../include/plink2_thread.cc ../include/plink2_zstfile.cc ../plink2.cc ../plink2_adjust.cc ../plink2_cmdline.cc ../plink2_common.cc ../plink2_compress_stream.cc ../plink2_data.cc ../plink2_decompress.cc ../plink2_export.cc ../plink2_export_legacy.cc ../plink2_fasta.cc ../plink2_filter.cc ../plink2_glm.cc ../plink2_glm_linear.cc ../plink2_glm_logistic.cc ../plink2_glm_shared.cc ../plink2_help.cc ../plink2_import.cc ../plink2_import_legacy.cc ../plink2_ld.cc ../plink2_matrix.cc ../plink2_matrix_calc.cc ../plink2_merge.cc ../plink2_misc.cc ../plink2_psam.cc ../plink2_pvar.cc ../plink2_random.cc ../plink2_set.cc -c ../plink2.cc: In function 'int main(int, char**)': ../plink2.cc:5307:96: warning: '%s' directive output may be truncated writing up to 2147483635 bytes into a region of size 262098 [-Wformat-truncation=] 5307 | snprintf(g_logbuf, kLogbufSize, "Error: Invalid --export vcf-dosage= argument '%s'.\n", vcf_dosage_start); | ^~ In file included from /usr/include/stdio.h:906, from ../include/plink2_base.h:114, from ../include/plink2_zstfile.h:27, from ../plink2.cc:18: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'int main(int, char**)' at ../plink2.cc:5307:25: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 50 and 2147483685 bytes into a destination of size 262144 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:26, from ../plink2_compress_stream.h:27, from ../plink2_import.cc:19: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1854:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1942:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long long unsigned int*]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'plink2::PglErr plink2::Plink1DosageToPgen(const char*, const char*, const char*, const char*, const Plink1DosageInfo*, const char*, MiscFlags, ImportFlags, uint32_t, FamCol, int32_t, uint32_t, uint32_t, double, uint32_t, char*, char*, ChrInfo*)' at ../plink2_import.cc:15198:5: /usr/include/c++/13/bits/stl_algo.h:1859:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long long unsigned int [6]'} [-Warray-bounds=] 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_import.cc: In function 'plink2::PglErr plink2::Plink1DosageToPgen(const char*, const char*, const char*, const char*, const Plink1DosageInfo*, const char*, MiscFlags, ImportFlags, uint32_t, FamCol, int32_t, uint32_t, uint32_t, double, uint32_t, char*, char*, ChrInfo*)': ../plink2_import.cc:15179:14: note: at offset 128 into object 'parse_table' of size 48 15179 | uint64_t parse_table[6]; | ^~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 ../plink2_cpu.cc -c g++ SFMT.o plink2_base.o plink2_bits.o pgenlib_misc.o pgenlib_read.o pgenlib_write.o plink2_bgzf.o plink2_bitmap.o plink2_fmath.o plink2_stats.o plink2_string.o plink2_text.o plink2_thread.o plink2_zstfile.o plink2.o plink2_adjust.o plink2_cmdline.o plink2_common.o plink2_compress_stream.o plink2_data.o plink2_decompress.o plink2_export.o plink2_export_legacy.o plink2_fasta.o plink2_filter.o plink2_glm.o plink2_glm_linear.o plink2_glm_logistic.o plink2_glm_shared.o plink2_help.o plink2_import.o plink2_import_legacy.o plink2_ld.o plink2_matrix.o plink2_matrix_calc.o plink2_merge.o plink2_misc.o plink2_psam.o plink2_pvar.o plink2_random.o plink2_set.o plink2_cpu.o -o plink2-plain -llapack -lblas -lm -lpthread -lz -lzstd -Wl,-z,relro -Wl,-z,now -ldeflate make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg/build_dynamic' help2man --no-discard-stderr --name="whole genome SNP analysis" build_dynamic//pgen_compress-plain > pgen_compress.1 make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' dh_auto_test -O--sourcedirectory=build_dynamic/ create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=build_dynamic/ dh_prep -O--sourcedirectory=build_dynamic/ debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' dh_install debian/bin/simd-dispatch /usr/lib/plink2/ for SIMD in ssse3 sse3 sse2 plain ; do \ dh_install build_dynamic/plink2-${SIMD} usr/lib/plink2/ ; \ dh_install build_dynamic/pgen_compress-${SIMD} usr/lib/plink2/ ; \ done mkdir -p /build/reproducible-path/plink2-2.00~a5.8-231123+dfsg/debian/plink2/usr/bin cd /build/reproducible-path/plink2-2.00~a5.8-231123+dfsg/debian/plink2/usr/bin \ && for prog in plink2 pgen_compress ; do \ ln -s ../lib/plink2/simd-dispatch ${prog} ; done make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' dh_installdocs -O--sourcedirectory=build_dynamic/ debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' dh_installchangelogs debian/upstream.docs/upstream.changelog make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' dh_installexamples -O--sourcedirectory=build_dynamic/ debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' dh_installman debian/plink2.1 dh_installman pgen_compress.1 make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' dh_installsystemduser -O--sourcedirectory=build_dynamic/ dh_perl -O--sourcedirectory=build_dynamic/ dh_link -O--sourcedirectory=build_dynamic/ dh_strip_nondeterminism -O--sourcedirectory=build_dynamic/ dh_compress -O--sourcedirectory=build_dynamic/ dh_fixperms -O--sourcedirectory=build_dynamic/ dh_missing -O--sourcedirectory=build_dynamic/ dh_dwz -a -O--sourcedirectory=build_dynamic/ dh_strip -a -O--sourcedirectory=build_dynamic/ dh_makeshlibs -a -O--sourcedirectory=build_dynamic/ dh_shlibdeps -a -O--sourcedirectory=build_dynamic/ dh_installdeb -O--sourcedirectory=build_dynamic/ debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.0-1), " make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg' dh_md5sums -O--sourcedirectory=build_dynamic/ dh_builddeb -O--sourcedirectory=build_dynamic/ dpkg-deb: building package 'plink2-dbgsym' in '../plink2-dbgsym_2.00~a5.8-231123+dfsg-1_i386.deb'. dpkg-deb: building package 'plink2' in '../plink2_2.00~a5.8-231123+dfsg-1_i386.deb'. dpkg-genbuildinfo --build=binary -O../plink2_2.00~a5.8-231123+dfsg-1_i386.buildinfo dpkg-genchanges --build=binary -O../plink2_2.00~a5.8-231123+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/5678 and its subdirectories I: Current time: Sat May 31 14:11:56 -12 2025 I: pbuilder-time-stamp: 1748743917 Sun Apr 28 19:48:59 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net. Sun Apr 28 19:48:59 UTC 2024 I: Preparing to do remote build '2' on ionos12-i386.debian.net. Sun Apr 28 20:44:20 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. Sun Apr 28 20:44:21 UTC 2024 I: plink2_2.00~a5.8-231123+dfsg-1_i386.changes: Format: 1.8 Date: Wed, 29 Nov 2023 13:45:30 +0100 Source: plink2 Binary: plink2 plink2-dbgsym Architecture: i386 Version: 2.00~a5.8-231123+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: plink2 - whole-genome association analysis toolset Closes: 1056683 Changes: plink2 (2.00~a5.8-231123+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream version * Drop libatlas-base-dev Build-Depends Closes: #1056683 * Add Build-Depends alternative: liblapack-dev | liblapack.so * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: 33ef8e9d86effc945e1bc2eb49971b16e8b2df69 21089724 plink2-dbgsym_2.00~a5.8-231123+dfsg-1_i386.deb acc87f20def89b0709bf81ec6b98ec43e9bcda7b 5539 plink2_2.00~a5.8-231123+dfsg-1_i386.buildinfo 195bd29a453546f7746363274061ab9e433ab1f5 1708912 plink2_2.00~a5.8-231123+dfsg-1_i386.deb Checksums-Sha256: 4cb54df726fa69bdd7275c78dcd41262501850147505a938a87556cb047b0656 21089724 plink2-dbgsym_2.00~a5.8-231123+dfsg-1_i386.deb 34b2f79863440624ff54009176b8e8027101b7db22b500f4f04f43be35c56d0d 5539 plink2_2.00~a5.8-231123+dfsg-1_i386.buildinfo b2733bb3020b9a4045719bb74dba58d1b4b1248dda95f37c433f05b8bb116aed 1708912 plink2_2.00~a5.8-231123+dfsg-1_i386.deb Files: d8ca10ad9a830fe600b7b62f54a28faa 21089724 debug optional plink2-dbgsym_2.00~a5.8-231123+dfsg-1_i386.deb b19d85ef901acb21f44906159a8b8514 5539 science optional plink2_2.00~a5.8-231123+dfsg-1_i386.buildinfo 98d8960e2e39c3ed24b18e77d63da4c9 1708912 science optional plink2_2.00~a5.8-231123+dfsg-1_i386.deb Sun Apr 28 20:44:22 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_6-22732.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.3SKgz64Z/plink2_2.00~a5.8-231123+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.3SKgz64Z/plink2_2.00~a5.8-231123+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.3SKgz64Z/plink2_2.00~a5.8-231123+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.3SKgz64Z/b1/plink2_2.00~a5.8-231123+dfsg-1_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.3SKgz64Z/b2/plink2_2.00~a5.8-231123+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: 0.576s) 0.576s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.255s) 0.255s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 903ms CPU time consumed: 897ms Sun Apr 28 20:44:23 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Sun Apr 28 20:44:23 UTC 2024 I: plink2 from trixie built successfully and reproducibly on i386. Sun Apr 28 20:44:24 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Apr 28 20:44:24 UTC 2024 I: Submitting 8.0K b1/plink2_2.00~a5.8-231123+dfsg-1_i386.buildinfo.asc Sun Apr 28 20:44:26 UTC 2024 I: Submitting 8.0K b2/plink2_2.00~a5.8-231123+dfsg-1_i386.buildinfo.asc Sun Apr 28 20:44:27 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Apr 28 20:44:27 UTC 2024 I: Done submitting .buildinfo files. Sun Apr 28 20:44:27 UTC 2024 I: Removing signed plink2_2.00~a5.8-231123+dfsg-1_i386.buildinfo.asc files: removed './b1/plink2_2.00~a5.8-231123+dfsg-1_i386.buildinfo.asc' removed './b2/plink2_2.00~a5.8-231123+dfsg-1_i386.buildinfo.asc'