Tue May 7 07:18:03 UTC 2024 I: starting to build plink2/trixie/amd64 on jenkins on '2024-05-07 07:17' Tue May 7 07:18:03 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_28/19526/console.log Tue May 7 07:18:03 UTC 2024 I: Downloading source for trixie/plink2=2.00~a5.8-231123+dfsg-1 --2024-05-07 07:18:04-- 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% 303M=0s 2024-05-07 07:18:04 (303 MB/s) - ‘plink2_2.00~a5.8-231123+dfsg-1.dsc’ saved [2155/2155] Tue May 7 07:18:04 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----- Tue May 7 07:18:04 UTC 2024 I: Checking whether the package is not for us Tue May 7 07:18:04 UTC 2024 I: Starting 1st build on remote node ionos15-amd64.debian.net. Tue May 7 07:18:04 UTC 2024 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Tue May 7 07:35:20 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 9 01:41:07 -12 2025 I: pbuilder-time-stamp: 1749476467 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [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/143431/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='9bee375ee84f4e9388eef12ca1c2b032' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='143431' 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.eQJclvWk/pbuilderrc_NEdG --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.eQJclvWk/b1 --logfile b1/build.log plink2_2.00~a5.8-231123+dfsg-1.dsc' SUDO_GID='111' SUDO_UID='106' 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 ionos15-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 8 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/143431/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19698 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} libmagic1t64{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 29.5 MB of archives. After unpacking 124 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 liblocale-gettext-perl amd64 1.07-7 [15.0 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 24 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libblas-dev amd64 3.12.0-3 [159 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.20-1 [54.5 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.0-3 [4880 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.2-1 [465 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.5+dfsg2-2 [358 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Fetched 29.5 MB in 1s (49.6 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 ... 19698 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7) ... 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%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_amd64.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:amd64. Preparing to unpack .../23-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../25-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-14+b1_amd64.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_amd64.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../32-libblas3_3.12.0-3_amd64.deb ... Unpacking libblas3:amd64 (3.12.0-3) ... Selecting previously unselected package libblas-dev:amd64. Preparing to unpack .../33-libblas-dev_3.12.0-3_amd64.deb ... Unpacking libblas-dev:amd64 (3.12.0-3) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../34-libdeflate0_1.20-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.20-1) ... Selecting previously unselected package libdeflate-dev:amd64. Preparing to unpack .../35-libdeflate-dev_1.20-1_amd64.deb ... Unpacking libdeflate-dev:amd64 (1.20-1) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../36-libgfortran5_14-20240330-1_amd64.deb ... Unpacking libgfortran5:amd64 (14-20240330-1) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../37-liblapack3_3.12.0-3_amd64.deb ... Unpacking liblapack3:amd64 (3.12.0-3) ... Selecting previously unselected package liblapack-dev:amd64. Preparing to unpack .../38-liblapack-dev_3.12.0-3_amd64.deb ... Unpacking liblapack-dev:amd64 (3.12.0-3) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../39-libsimde-dev_0.8.2-1_all.deb ... Unpacking libsimde-dev (0.8.2-1) ... Selecting previously unselected package libzstd-dev:amd64. Preparing to unpack .../40-libzstd-dev_1.5.5+dfsg2-2_amd64.deb ... Unpacking libzstd-dev:amd64 (1.5.5+dfsg2-2) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../41-zlib1g-dev_1%3a1.3.dfsg-3.1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libsimde-dev (0.8.2-1) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up libzstd-dev:amd64 (1.5.5+dfsg2-2) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up autopoint (0.21-14) ... Setting up libgfortran5:amd64 (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libdeflate-dev:amd64 (1.20-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up liblocale-gettext-perl (1.07-7) ... Setting up libblas-dev:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode 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 liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up liblapack-dev:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-7) ... 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/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 amd64 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 -j42 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 export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -mavx2 -mbmi -mbmi2 -mlzcnt -mfma" \ && export CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -mavx2 -mbmi -mbmi2 -mlzcnt -mfma" \ && make clean \ ; dh_auto_build -- SFX=-avx2 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 -j42 "INSTALL=install --strip-program=true" SFX=-avx2 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -mavx2 -mbmi -mbmi2 -mlzcnt -mfma -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -mavx2 -mbmi -mbmi2 -mlzcnt -mfma -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-avx2 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -mavx2 -mbmi -mbmi2 -mlzcnt -mfma -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 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 unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = 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 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 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 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 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-avx2 -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' for SIMD in avx sse4.1 ssse3 sse3 sse2 ; do \ export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a5.8-231123+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -j42 "INSTALL=install --strip-program=true" SFX=-avx 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -mavx -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -mavx -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-avx 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -mavx -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 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 unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = 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 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 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 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 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-avx -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 -j42 "INSTALL=install --strip-program=true" SFX=-sse4.1 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -msse4.1 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -msse4.1 -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-sse4.1 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -msse4.1 -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 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 unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = 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 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 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 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 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-sse4.1 -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 -j42 "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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = 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 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 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 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 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 -j42 "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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = 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 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 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 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 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 -j42 "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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = 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 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 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 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 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' help2man --no-discard-stderr --name="whole genome SNP analysis" build_dynamic//pgen_compress-sse2 > 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 avx2 avx sse4.1 ssse3 sse3 sse2 ; 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 (= 0.8.2-1), " 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' in '../plink2_2.00~a5.8-231123+dfsg-1_amd64.deb'. dpkg-deb: building package 'plink2-dbgsym' in '../plink2-dbgsym_2.00~a5.8-231123+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../plink2_2.00~a5.8-231123+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../plink2_2.00~a5.8-231123+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: 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/143431 and its subdirectories I: Current time: Mon Jun 9 01:58:19 -12 2025 I: pbuilder-time-stamp: 1749477499 Tue May 7 07:35:21 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Tue May 7 07:35:21 UTC 2024 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Tue May 7 08:05:42 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Tue May 7 08:05:43 UTC 2024 I: plink2_2.00~a5.8-231123+dfsg-1_amd64.changes: Format: 1.8 Date: Wed, 29 Nov 2023 13:45:30 +0100 Source: plink2 Binary: plink2 plink2-dbgsym Architecture: amd64 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: 603255c14221f2b3f7b7042b2319f948ff2afe0a 36676076 plink2-dbgsym_2.00~a5.8-231123+dfsg-1_amd64.deb da2f777930736f10d23df43bde30e076f8b9af92 5593 plink2_2.00~a5.8-231123+dfsg-1_amd64.buildinfo 93145d30a1bf9be523d2b8aecedba278ce1e0e17 2529032 plink2_2.00~a5.8-231123+dfsg-1_amd64.deb Checksums-Sha256: 812ba755ac13547a572001668840703f3abf1c44f6fc4c488f20bb087402566e 36676076 plink2-dbgsym_2.00~a5.8-231123+dfsg-1_amd64.deb 15191bb6eecaf8098ea73dbf5d3c231017ec2ce44f30966cf322cc541a860833 5593 plink2_2.00~a5.8-231123+dfsg-1_amd64.buildinfo fee73179460a98319136f39aa6bb9bd752363350cddac515919ca14c421eb112 2529032 plink2_2.00~a5.8-231123+dfsg-1_amd64.deb Files: 7aee74e17f93603d775865228b64905f 36676076 debug optional plink2-dbgsym_2.00~a5.8-231123+dfsg-1_amd64.deb 007a5bb0e9d30d8d58a225722f3d9879 5593 science optional plink2_2.00~a5.8-231123+dfsg-1_amd64.buildinfo eb1512ca11cc00da92eb8d80315f6177 2529032 science optional plink2_2.00~a5.8-231123+dfsg-1_amd64.deb Tue May 7 08:05:44 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_28-19526.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.eQJclvWk/plink2_2.00~a5.8-231123+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.eQJclvWk/plink2_2.00~a5.8-231123+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.eQJclvWk/plink2_2.00~a5.8-231123+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.eQJclvWk/b1/plink2_2.00~a5.8-231123+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.eQJclvWk/b2/plink2_2.00~a5.8-231123+dfsg-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.764s) 0.764s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.418s) 0.418s 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: 1.103s CPU time consumed: 1.103s Tue May 7 08:05:45 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Tue May 7 08:05:45 UTC 2024 I: plink2 from trixie built successfully and reproducibly on amd64. Tue May 7 08:05:47 UTC 2024 I: Submitting .buildinfo files to external archives: Tue May 7 08:05:47 UTC 2024 I: Submitting 8.0K b1/plink2_2.00~a5.8-231123+dfsg-1_amd64.buildinfo.asc Tue May 7 08:05:47 UTC 2024 I: Submitting 8.0K b2/plink2_2.00~a5.8-231123+dfsg-1_amd64.buildinfo.asc Tue May 7 08:05:48 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue May 7 08:05:48 UTC 2024 I: Done submitting .buildinfo files. Tue May 7 08:05:48 UTC 2024 I: Removing signed plink2_2.00~a5.8-231123+dfsg-1_amd64.buildinfo.asc files: removed './b1/plink2_2.00~a5.8-231123+dfsg-1_amd64.buildinfo.asc' removed './b2/plink2_2.00~a5.8-231123+dfsg-1_amd64.buildinfo.asc'