I: pbuilder: network access will be disabled during build I: Current time: Sat Mar 1 21:58:35 +14 2025 I: pbuilder-time-stamp: 1740815915 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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~a3.5-220809+dfsg-1.dsc] I: copying [./plink2_2.00~a3.5-220809+dfsg.orig.tar.xz] I: copying [./plink2_2.00~a3.5-220809+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Dec 12 08:51:20 2022 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~a3.5-220809+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting plink2 in plink2-2.00~a3.5-220809+dfsg dpkg-source: info: unpacking plink2_2.00~a3.5-220809+dfsg.orig.tar.xz dpkg-source: info: unpacking plink2_2.00~a3.5-220809+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 baseline I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1589894/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Mar 1 07:58 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1589894/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1589894/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=9b906a91aad345409ae2abd44d71df4e LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1589894 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.n7leymYR/pbuilderrc_KfRv --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.n7leymYR/b2 --logfile b2/build.log plink2_2.00~a3.5-220809+dfsg-1.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 23 2023 more -rwsr-xr-x 1 root root 59704 Mar 23 2023 mount -rwxr-xr-x 1 root root 18744 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 9 Mar 1 07:58 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 23 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 23 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/1589894/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, libatlas-base-dev, liblapack-dev, libzstd-dev (>= 1.4.4), 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 ... 18148 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 libatlas-base-dev; however: Package libatlas-base-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on libzstd-dev (>= 1.4.4); 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} libatlas-base-dev{a} libatlas3-base{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{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 35.3 MB of archives. After unpacking 155 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 help2man amd64 1.49.3 [198 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libatlas3-base amd64 3.10.3-13 [3305 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libatlas-base-dev amd64 3.10.3-13 [3510 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libdeflate-dev amd64 1.14-1 [53.3 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 liblapack-dev amd64 3.11.0-2 [4631 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libsimde-dev all 0.7.4~rc2-2 [377 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libzstd-dev amd64 1.5.4+dfsg2-5 [354 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Fetched 35.3 MB in 1s (38.5 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 ... 18148 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-5_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... 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_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... 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_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... 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 libelf1:amd64. Preparing to unpack .../23-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../25-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.3~deb12u1_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Selecting previously unselected package gettext. 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Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-12) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libdeflate-dev:amd64 (1.14-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Setting up liblocale-gettext-perl (1.07-5) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libatlas3-base:amd64 (3.10.3-13) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/atlas/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 libtool (2.4.7-5) ... Setting up libatlas-base-dev:amd64 (3.10.3-13) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/atlas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/atlas/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up liblapack3:amd64 (3.11.0-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up liblapack-dev:amd64 (3.11.0-2) ... Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9+deb12u3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1589894/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bookworm I: user script /srv/workspace/pbuilder/1589894/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/plink2-2.00~a3.5-220809+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../plink2_2.00~a3.5-220809+dfsg-1_source.changes dpkg-buildpackage: info: source package plink2 dpkg-buildpackage: info: source version 2.00~a3.5-220809+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~a3.5-220809+dfsg' dh_auto_clean cd build_dynamic && make -j16 clean make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a3.5-220809+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~a3.5-220809+dfsg/build_dynamic' rm -f plink2.1 rm -f pgen_compress.1 make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a3.5-220809+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~a3.5-220809+dfsg' mkdir -p /build/reproducible-path/plink2-2.00~a3.5-220809+dfsg/debian/plink2/usr mkdir -p /build/reproducible-path/plink2-2.00~a3.5-220809+dfsg/debian/plink2/usr/lib/plink2 export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -mavx2 -mbmi -mbmi2 -mlzcnt -mfma" \ && export CFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -mavx2 -mbmi -mbmi2 -mlzcnt -mfma" \ && make clean \ ; dh_auto_build -- SFX=-avx2 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg' rm -f *.o include/*.o zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o bin/plink2 bin/pgen_compress make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg' cd build_dynamic && make -j16 "INSTALL=install --strip-program=true" SFX=-avx2 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg/build_dynamic' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -mavx2 -mbmi -mbmi2 -mlzcnt -mfma -O2 -std=gnu99 -DZSTD_MULTITHREAD -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~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -mavx2 -mbmi -mbmi2 -mlzcnt -mfma -std=c++11 -O2 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast -I../simde ../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 -Wall -Wextra -Wshadow -Wformat-security -I../zstd/lib -I../zstd/lib/common -c cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -I../zstd/lib -I../zstd/lib/common -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -mavx2 -mbmi -mbmi2 -mlzcnt -mfma -std=c++11 -O2 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast -I../simde ../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++/12/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++/12/bits/stl_algo.h:1844:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1932:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, 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:15040:5: /usr/include/c++/12/bits/stl_algo.h:1849:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds] 1849 | 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:15021:14: note: at offset 128 into object 'parse_table' of size 48 15021 | 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 -lcblas -latlas -lm -lpthread -lz -lzstd -Wl,-z,relro -Wl,-z,now -ldeflate make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a3.5-220809+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~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -m${SIMD}" && export CFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -m${SIMD}" && \ make clean ; \ dh_auto_build -- SFX=-${SIMD} ; \ done make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg' rm -f *.o include/*.o zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o bin/plink2 bin/pgen_compress make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg' cd build_dynamic && make -j16 "INSTALL=install --strip-program=true" SFX=-avx make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg/build_dynamic' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -mavx -O2 -std=gnu99 -DZSTD_MULTITHREAD -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~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -mavx -std=c++11 -O2 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast -I../simde ../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 -Wall -Wextra -Wshadow -Wformat-security -I../zstd/lib -I../zstd/lib/common -c cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -I../zstd/lib -I../zstd/lib/common -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -mavx -std=c++11 -O2 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast -I../simde ../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++/12/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++/12/bits/stl_algo.h:1844:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1932:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, 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:15040:5: /usr/include/c++/12/bits/stl_algo.h:1849:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds] 1849 | 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:15021:14: note: at offset 128 into object 'parse_table' of size 48 15021 | 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 -lcblas -latlas -lm -lpthread -lz -lzstd -Wl,-z,relro -Wl,-z,now -ldeflate make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg' rm -f *.o include/*.o zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o bin/plink2 bin/pgen_compress make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg' cd build_dynamic && make -j16 "INSTALL=install --strip-program=true" SFX=-sse4.1 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg/build_dynamic' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -msse4.1 -O2 -std=gnu99 -DZSTD_MULTITHREAD -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~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -msse4.1 -std=c++11 -O2 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast -I../simde ../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 -Wall -Wextra -Wshadow -Wformat-security -I../zstd/lib -I../zstd/lib/common -c cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -I../zstd/lib -I../zstd/lib/common -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -msse4.1 -std=c++11 -O2 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast -I../simde ../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++/12/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++/12/bits/stl_algo.h:1844:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1932:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, 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:15040:5: /usr/include/c++/12/bits/stl_algo.h:1849:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds] 1849 | 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:15021:14: note: at offset 128 into object 'parse_table' of size 48 15021 | 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 -lcblas -latlas -lm -lpthread -lz -lzstd -Wl,-z,relro -Wl,-z,now -ldeflate make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg' rm -f *.o include/*.o zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o bin/plink2 bin/pgen_compress make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg' cd build_dynamic && make -j16 "INSTALL=install --strip-program=true" SFX=-ssse3 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg/build_dynamic' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -mssse3 -O2 -std=gnu99 -DZSTD_MULTITHREAD -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~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -mssse3 -std=c++11 -O2 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast -I../simde ../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 -Wall -Wextra -Wshadow -Wformat-security -I../zstd/lib -I../zstd/lib/common -c cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -I../zstd/lib -I../zstd/lib/common -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -mssse3 -std=c++11 -O2 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast -I../simde ../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++/12/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++/12/bits/stl_algo.h:1844:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1932:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, 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:15040:5: /usr/include/c++/12/bits/stl_algo.h:1849:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds] 1849 | 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:15021:14: note: at offset 128 into object 'parse_table' of size 48 15021 | 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 -lcblas -latlas -lm -lpthread -lz -lzstd -Wl,-z,relro -Wl,-z,now -ldeflate make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg' rm -f *.o include/*.o zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o bin/plink2 bin/pgen_compress make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg' cd build_dynamic && make -j16 "INSTALL=install --strip-program=true" SFX=-sse3 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg/build_dynamic' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -msse3 -O2 -std=gnu99 -DZSTD_MULTITHREAD -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~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -msse3 -std=c++11 -O2 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast -I../simde ../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 -Wall -Wextra -Wshadow -Wformat-security -I../zstd/lib -I../zstd/lib/common -c cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -I../zstd/lib -I../zstd/lib/common -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -msse3 -std=c++11 -O2 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast -I../simde ../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++/12/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++/12/bits/stl_algo.h:1844:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1932:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, 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:15040:5: /usr/include/c++/12/bits/stl_algo.h:1849:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds] 1849 | 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:15021:14: note: at offset 128 into object 'parse_table' of size 48 15021 | 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 -lcblas -latlas -lm -lpthread -lz -lzstd -Wl,-z,relro -Wl,-z,now -ldeflate make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg' rm -f *.o include/*.o zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o bin/plink2 bin/pgen_compress make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg' cd build_dynamic && make -j16 "INSTALL=install --strip-program=true" SFX=-sse2 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg/build_dynamic' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -msse2 -O2 -std=gnu99 -DZSTD_MULTITHREAD -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~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -msse2 -std=c++11 -O2 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast -I../simde ../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 -Wall -Wextra -Wshadow -Wformat-security -I../zstd/lib -I../zstd/lib/common -c cc -O2 -std=gnu99 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -I../zstd/lib -I../zstd/lib/common -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -msse2 -std=c++11 -O2 -DZSTD_MULTITHREAD -Wall -Wextra -Wshadow -Wformat-security -Wold-style-cast -I../simde ../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++/12/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++/12/bits/stl_algo.h:1844:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1932:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, 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:15040:5: /usr/include/c++/12/bits/stl_algo.h:1849:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds] 1849 | 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:15021:14: note: at offset 128 into object 'parse_table' of size 48 15021 | 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 -lcblas -latlas -lm -lpthread -lz -lzstd -Wl,-z,relro -Wl,-z,now -ldeflate make[2]: Leaving directory '/build/reproducible-path/plink2-2.00~a3.5-220809+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~a3.5-220809+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~a3.5-220809+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~a3.5-220809+dfsg/debian/plink2/usr/bin cd /build/reproducible-path/plink2-2.00~a3.5-220809+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~a3.5-220809+dfsg' dh_installdocs -O--sourcedirectory=build_dynamic/ debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg' dh_installchangelogs debian/upstream.docs/upstream.changelog make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg' dh_installexamples -O--sourcedirectory=build_dynamic/ debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg' dh_installman debian/plink2.1 dh_installman pgen_compress.1 make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a3.5-220809+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~a3.5-220809+dfsg' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.4~rc2-2), " make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a3.5-220809+dfsg' dh_md5sums -O--sourcedirectory=build_dynamic/ dh_builddeb -O--sourcedirectory=build_dynamic/ dpkg-deb: building package 'plink2-dbgsym' in '../plink2-dbgsym_2.00~a3.5-220809+dfsg-1_amd64.deb'. dpkg-deb: building package 'plink2' in '../plink2_2.00~a3.5-220809+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../plink2_2.00~a3.5-220809+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../plink2_2.00~a3.5-220809+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: user script /srv/workspace/pbuilder/1589894/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1589894/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1589894 and its subdirectories I: Current time: Sat Mar 1 22:40:06 +14 2025 I: pbuilder-time-stamp: 1740818406