Running as unit: rb-build-amd64_7-58799.service ==================================================================================== Thu Jun 5 14:23:35 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_7) on jenkins, called using "ionos11-amd64 ionos15-amd64" as arguments. Thu Jun 5 14:23:35 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-q3zvuGdf" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Jun 5 14:23:35 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Thu Jun 5 14:23:35 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-q5ng0D' Thu Jun 5 14:23:35 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Thu Jun 5 14:23:35 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-zpkPmN' ok, let's check if plink2 is building anywhere yet… ok, plink2 is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of plink2 in trixie on amd64 on jenkins now. 1st build will be done on ionos11-amd64.debian.net. 2nd build will be done on ionos15-amd64.debian.net. ============================================================================= Thu Jun 5 14:23:48 UTC 2025 I: starting to build plink2/trixie/amd64 on jenkins on '2025-06-05 14:23' Thu Jun 5 14:23:48 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_7/58799/console.log 1749133428 amd64 trixie plink2 Thu Jun 5 14:23:48 UTC 2025 I: Downloading source for trixie/plink2=2.00~a6.9-250129+dfsg-1 --2025-06-05 14:23:48-- http://deb.debian.org/debian/pool/main/p/plink2/plink2_2.00%7ea6.9-250129%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2130 (2.1K) [text/prs.lines.tag] Saving to: ‘plink2_2.00~a6.9-250129+dfsg-1.dsc’ 0K .. 100% 255M=0s 2025-06-05 14:23:48 (255 MB/s) - ‘plink2_2.00~a6.9-250129+dfsg-1.dsc’ saved [2130/2130] --2025-06-05 14:23:48-- http://deb.debian.org/debian/pool/main/p/plink2/plink2_2.00%7ea6.9-250129%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2130 (2.1K) [text/prs.lines.tag] Saving to: ‘plink2_2.00~a6.9-250129+dfsg-1.dsc’ 0K .. 100% 255M=0s 2025-06-05 14:23:48 (255 MB/s) - ‘plink2_2.00~a6.9-250129+dfsg-1.dsc’ saved [2130/2130] Thu Jun 5 14:23:48 UTC 2025 I: plink2_2.00~a6.9-250129+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: plink2 Binary: plink2 Architecture: any Version: 2.00~a6.9-250129+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Dylan Aïssi Homepage: https://www.cog-genomics.org/plink/2.0/ Standards-Version: 4.7.0 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: 2babdf35b8ff9ea6c06470f49ec24c37bbce34b1 1569072 plink2_2.00~a6.9-250129+dfsg.orig.tar.xz 50552f38bc33bf30fa4e19a52fee68770c78961c 58480 plink2_2.00~a6.9-250129+dfsg-1.debian.tar.xz Checksums-Sha256: eaf4161cbe095803402b6a6db04b2c65151bedd19cb88617d745ee09237baf2f 1569072 plink2_2.00~a6.9-250129+dfsg.orig.tar.xz f4bb75a2f1f10b5deaaeac2c8e01febe5cbfa4890ce5b769d808db5574ea254f 58480 plink2_2.00~a6.9-250129+dfsg-1.debian.tar.xz Files: 2101c14b95133f26f12f22285cf66c55 1569072 plink2_2.00~a6.9-250129+dfsg.orig.tar.xz dad39f3ed8477974db2d5cf3cf4f42ee 58480 plink2_2.00~a6.9-250129+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEmjwHvQbeL0FugTpdYS7xYT4FD1QFAmemRU8ACgkQYS7xYT4F D1R0uA//dQbT193LUjWJNbAyJO5+Tz93Mc/K2C/UfiwxlloukP+a1d0TDXV15uUh dawdglhC/4VcXFacmjAN605KKYrXLcsgYVGXp/El4binSzkC2k3BmhsZg0wzQZI9 I1fL+bNEU2yPY7mAdRlsIwg/UuAec0gt6zzGAWQ0fLy7ksgtL0BEhEmEnwN2Sx7J FNDvweD1hgLPU/boItjUQk4nq+mkUKnEumXRuHMYNH1JDE7DfoVN8J6Cipumge/x ETHyyfrEZ2AaUmR6EWsUoEupidaJqOlNrcF56IYKYeuyQoFOMQQ0RB4435wocidw peMI2/0DFjLN64sZYB0dg5MOXGb0LZiTWfuOKHAvVTsl1+PxtBSHgnzz3a3uxvAP cgkqw3qZwnbJbyNTY5YBk+EZShiIxqNAonlYei37funX8wYm8cNNMu2InV5tiqjv X2MDBvuaU0vBYz+f89/Lai1zGr1dy9uPJan53Z3h41puHAJyGih2Datw9Af2Xm8e KYE+HUyn89ETyugMPPDtNVQTJGU+9nAclVahMf04mpmbhuf6b7FJlTgOXDug4M5T cVJcInCf8EdZvKxARWPkLbVA2dl4gQkbK5RAtsY8Bh+BA+zo99klJq3Kxt8skmxE s3AKbROPbA6XwRppy8Yt0S5lIkqra5Y5uwM2KsoGW8aIcDGd084= =UXpB -----END PGP SIGNATURE----- Thu Jun 5 14:23:48 UTC 2025 I: Checking whether the package is not for us Thu Jun 5 14:23:48 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net. Thu Jun 5 14:23:48 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Thu Jun 5 14:23:48 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Thu Jun 5 14:23:48 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-UisPJ4' ==================================================================================== Thu Jun 5 14:23:49 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos11-amd64, called using "1 plink2 trixie /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8 2.00~a6.9-250129+dfsg-1" as arguments. Thu Jun 5 14:23:49 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-3DMLYC6k" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Jun 5 14:23:49 UTC 2025 I: Downloading source for trixie/plink2=2.00~a6.9-250129+dfsg-1 Reading package lists... NOTICE: 'plink2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/plink2.git Please use: git clone https://salsa.debian.org/med-team/plink2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1630 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main plink2 2.00~a6.9-250129+dfsg-1 (dsc) [2130 B] Get:2 http://deb.debian.org/debian trixie/main plink2 2.00~a6.9-250129+dfsg-1 (tar) [1569 kB] Get:3 http://deb.debian.org/debian trixie/main plink2 2.00~a6.9-250129+dfsg-1 (diff) [58.5 kB] Fetched 1630 kB in 0s (12.9 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'plink2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/plink2.git Please use: git clone https://salsa.debian.org/med-team/plink2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1630 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main plink2 2.00~a6.9-250129+dfsg-1 (dsc) [2130 B] Get:2 http://deb.debian.org/debian trixie/main plink2 2.00~a6.9-250129+dfsg-1 (tar) [1569 kB] Get:3 http://deb.debian.org/debian trixie/main plink2 2.00~a6.9-250129+dfsg-1 (diff) [58.5 kB] Fetched 1630 kB in 0s (12.9 MB/s) Download complete and in download only mode ============================================================================= Building plink2 in trixie on amd64 on ionos11-amd64 now. Date: Thu Jun 5 14:23:50 UTC 2025 Date UTC: Thu Jun 5 14:23:50 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Jun 5 02:23:50 -12 2025 I: pbuilder-time-stamp: 1749133430 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~a6.9-250129+dfsg-1.dsc] I: copying [./plink2_2.00~a6.9-250129+dfsg.orig.tar.xz] I: copying [./plink2_2.00~a6.9-250129+dfsg-1.debian.tar.xz] I: Extracting source error: the following required arguments were not provided: --keyring Usage: sqv --keyring --cleartext --output For more information, try '--help'. dpkg-source: warning: cannot verify inline signature for ./plink2_2.00~a6.9-250129+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting plink2 in plink2-2.00~a6.9-250129+dfsg dpkg-source: info: unpacking plink2_2.00~a6.9-250129+dfsg.orig.tar.xz dpkg-source: info: unpacking plink2_2.00~a6.9-250129+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/1556179/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=40 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='515326b2868c4f4e908046083fb47d1b' 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='1556179' 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.ukoJ02M8/pbuilderrc_TIEX --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.ukoJ02M8/b1 --logfile b1/build.log plink2_2.00~a6.9-250129+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://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1556179/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 ... 19850 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} liblapack-dev{a} liblapack3{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsimde-dev{a} libtool{a} libuchardet0{a} libunistring5{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, 41 newly installed, 0 to remove and 0 not upgraded. Need to get 21.9 MB of archives. After unpacking 94.2 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+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-8 [1187 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 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 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libblas-dev amd64 3.12.1-2 [170 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.1-2 [4998 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 21.9 MB in 3s (6341 kB/s) Preconfiguring packages ... 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 ... 19850 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-8_amd64.deb ... Unpacking groff-base (1.23.0-8) ... Selecting previously unselected package bsdextrautils. 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Setting up liblapack-dev:amd64 (3.12.1-2) ... 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 (1.14.1-2) ... Setting up groff-base (1.23.0-8) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Processing triggers for libc-bin (2.41-8) ... 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~a6.9-250129+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~a6.9-250129+dfsg-1_source.changes dpkg-buildpackage: info: source package plink2 dpkg-buildpackage: info: source version 2.00~a6.9-250129+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Dylan Aïssi 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~a6.9-250129+dfsg' dh_auto_clean cd build_dynamic && make -j40 clean make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg/build_dynamic' rm -f plink2.1 rm -f pgen_compress.1 make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' mkdir -p /build/reproducible-path/plink2-2.00~a6.9-250129+dfsg/debian/plink2/usr mkdir -p /build/reproducible-path/plink2-2.00~a6.9-250129+dfsg/debian/plink2/usr/lib/plink2 export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+dfsg' cd build_dynamic && make -j40 "INSTALL=install --strip-program=true" SFX=-avx2 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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_htable.cc ../include/plink2_memory.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 ../include/plink2_string.h:24, from ../include/plink2_stats.h:20, from ../plink2_adjust.cc:17: ../plink2_adjust.cc: In function 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)': ../plink2_adjust.cc:812:31: warning: 'line_start' may be used uninitialized [-Wmaybe-uninitialized] 812 | if (unlikely(!TokenLexK0(line_start, col_types, col_skips, relevant_col_ct, token_ptrs, token_slens))) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/plink2_base.h:277:46: note: in definition of macro 'unlikely' 277 | # define unlikely(expr) __builtin_expect(!!(expr), 0) | ^~~~ ../plink2_adjust.cc:805:19: note: 'line_start' was declared here 805 | const char* line_start; | ^~~~~~~~~~ ../plink2_data.cc: In function 'plink2::PglErr plink2::PvarInfoResplitTmp(const uint32_t*, uint32_t, uint32_t, uint32_t, uint32_t, TextStream*, char*, char*)': ../plink2_data.cc:8757:47: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 8757 | const uint32_t info_slen = line_end - line_iter; | ~~~~~~~~~^~~~~~~~~~~ ../plink2_data.cc:8750:15: note: 'line_iter' was declared here 8750 | char* line_iter; | ^~~~~~~~~ ../plink2_fasta.cc: In function 'plink2::PglErr plink2::ProcessFa(const uintptr_t*, const char* const*, const uintptr_t*, const ChrInfo*, const char*, uint32_t, uint32_t, FaFlags, uint32_t, uint32_t, UnsortedVar*, uint32_t*, const char**, AlleleCode*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_fasta.cc:535:38: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 535 | unsigned char ucc = line_iter[0]; | ~~~~~~~~~~~^ ../plink2_fasta.cc:526:13: note: 'line_iter' was declared here 526 | char* line_iter; | ^~~~~~~~~ In file included from ../include/plink2_stats.h:20, from ../plink2_filter.cc:18: In function 'int32_t plink2::tokequal_k(const char*, const char*)', inlined from 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)' at ../plink2_filter.cc:747:27: ../include/plink2_string.h:448:18: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 448 | return memequal(s_read, s_const, s_const_slen) && IsSpaceOrEoln(s_read[s_const_slen]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_filter.cc: In function 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_filter.cc:740:13: note: 'line_iter' was declared here 740 | char* line_iter; | ^~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:28, 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++/14/bits/stl_algo.h:1812:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1900:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, 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:15405:5: /usr/include/c++/14/bits/stl_algo.h:1817:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds=] 1817 | 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:15382:14: note: at offset 128 into object 'parse_table' of size 48 15382 | 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_htable.o plink2_memory.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~a6.9-250129+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~a6.9-250129+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${SIMD}" && export CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a6.9-250129+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -m${SIMD}" && \ make clean ; \ dh_auto_build -- SFX=-${SIMD} ; \ done make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' cd build_dynamic && make -j40 "INSTALL=install --strip-program=true" SFX=-avx make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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_htable.cc ../include/plink2_memory.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 ../include/plink2_stats.h:20, from ../plink2_adjust.cc:17: In function 'const char* plink2::FirstPrechar(const char*, uint32_t)', inlined from 'const char* plink2::CurTokenEnd(const char*)' at ../include/plink2_string.h:837:10, inlined from 'const char* plink2::TokenLexK0(const char*, const uint32_t*, const uint32_t*, uint32_t, const char**, uint32_t*)' at ../include/plink2_string.h:1443:46, inlined from 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)' at ../plink2_adjust.cc:812:11: ../include/plink2_string.h:788:17: warning: 'line_start' may be used uninitialized [-Wmaybe-uninitialized] 788 | while (ctou32(*str_iter) >= char_code) { | ^~~~~~~~~ ../plink2_adjust.cc: In function 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)': ../plink2_adjust.cc:805:19: note: 'line_start' was declared here 805 | const char* line_start; | ^~~~~~~~~~ ../plink2_data.cc: In function 'plink2::PglErr plink2::PvarInfoResplitTmp(const uint32_t*, uint32_t, uint32_t, uint32_t, uint32_t, TextStream*, char*, char*)': ../plink2_data.cc:8757:47: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 8757 | const uint32_t info_slen = line_end - line_iter; | ~~~~~~~~~^~~~~~~~~~~ ../plink2_data.cc:8750:15: note: 'line_iter' was declared here 8750 | char* line_iter; | ^~~~~~~~~ ../plink2_fasta.cc: In function 'plink2::PglErr plink2::ProcessFa(const uintptr_t*, const char* const*, const uintptr_t*, const ChrInfo*, const char*, uint32_t, uint32_t, FaFlags, uint32_t, uint32_t, UnsortedVar*, uint32_t*, const char**, AlleleCode*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_fasta.cc:535:38: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 535 | unsigned char ucc = line_iter[0]; | ~~~~~~~~~~~^ ../plink2_fasta.cc:526:13: note: 'line_iter' was declared here 526 | char* line_iter; | ^~~~~~~~~ In file included from ../include/plink2_stats.h:20, from ../plink2_filter.cc:18: In function 'int32_t plink2::tokequal_k(const char*, const char*)', inlined from 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)' at ../plink2_filter.cc:747:27: ../include/plink2_string.h:448:18: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 448 | return memequal(s_read, s_const, s_const_slen) && IsSpaceOrEoln(s_read[s_const_slen]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_filter.cc: In function 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_filter.cc:740:13: note: 'line_iter' was declared here 740 | char* line_iter; | ^~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:28, 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++/14/bits/stl_algo.h:1812:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1900:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, 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:15405:5: /usr/include/c++/14/bits/stl_algo.h:1817:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds=] 1817 | 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:15382:14: note: at offset 128 into object 'parse_table' of size 48 15382 | 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_htable.o plink2_memory.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~a6.9-250129+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' cd build_dynamic && make -j40 "INSTALL=install --strip-program=true" SFX=-sse4.1 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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_htable.cc ../include/plink2_memory.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 ../include/plink2_stats.h:20, from ../plink2_adjust.cc:17: In function 'const char* plink2::FirstPrechar(const char*, uint32_t)', inlined from 'const char* plink2::CurTokenEnd(const char*)' at ../include/plink2_string.h:837:10, inlined from 'const char* plink2::TokenLexK0(const char*, const uint32_t*, const uint32_t*, uint32_t, const char**, uint32_t*)' at ../include/plink2_string.h:1443:46, inlined from 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)' at ../plink2_adjust.cc:812:11: ../include/plink2_string.h:788:17: warning: 'line_start' may be used uninitialized [-Wmaybe-uninitialized] 788 | while (ctou32(*str_iter) >= char_code) { | ^~~~~~~~~ ../plink2_adjust.cc: In function 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)': ../plink2_adjust.cc:805:19: note: 'line_start' was declared here 805 | const char* line_start; | ^~~~~~~~~~ ../plink2_data.cc: In function 'plink2::PglErr plink2::PvarInfoResplitTmp(const uint32_t*, uint32_t, uint32_t, uint32_t, uint32_t, TextStream*, char*, char*)': ../plink2_data.cc:8757:47: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 8757 | const uint32_t info_slen = line_end - line_iter; | ~~~~~~~~~^~~~~~~~~~~ ../plink2_data.cc:8750:15: note: 'line_iter' was declared here 8750 | char* line_iter; | ^~~~~~~~~ ../plink2_fasta.cc: In function 'plink2::PglErr plink2::ProcessFa(const uintptr_t*, const char* const*, const uintptr_t*, const ChrInfo*, const char*, uint32_t, uint32_t, FaFlags, uint32_t, uint32_t, UnsortedVar*, uint32_t*, const char**, AlleleCode*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_fasta.cc:535:38: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 535 | unsigned char ucc = line_iter[0]; | ~~~~~~~~~~~^ ../plink2_fasta.cc:526:13: note: 'line_iter' was declared here 526 | char* line_iter; | ^~~~~~~~~ In file included from ../include/plink2_stats.h:20, from ../plink2_filter.cc:18: In function 'int32_t plink2::tokequal_k(const char*, const char*)', inlined from 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)' at ../plink2_filter.cc:747:27: ../include/plink2_string.h:448:18: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 448 | return memequal(s_read, s_const, s_const_slen) && IsSpaceOrEoln(s_read[s_const_slen]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_filter.cc: In function 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_filter.cc:740:13: note: 'line_iter' was declared here 740 | char* line_iter; | ^~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:28, 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++/14/bits/stl_algo.h:1812:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1900:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, 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:15405:5: /usr/include/c++/14/bits/stl_algo.h:1817:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds=] 1817 | 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:15382:14: note: at offset 128 into object 'parse_table' of size 48 15382 | 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_htable.o plink2_memory.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~a6.9-250129+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' cd build_dynamic && make -j40 "INSTALL=install --strip-program=true" SFX=-ssse3 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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_htable.cc ../include/plink2_memory.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 ../include/plink2_stats.h:20, from ../plink2_adjust.cc:17: In function 'const char* plink2::FirstPrechar(const char*, uint32_t)', inlined from 'const char* plink2::CurTokenEnd(const char*)' at ../include/plink2_string.h:837:10, inlined from 'const char* plink2::TokenLexK0(const char*, const uint32_t*, const uint32_t*, uint32_t, const char**, uint32_t*)' at ../include/plink2_string.h:1443:46, inlined from 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)' at ../plink2_adjust.cc:812:11: ../include/plink2_string.h:788:17: warning: 'line_start' may be used uninitialized [-Wmaybe-uninitialized] 788 | while (ctou32(*str_iter) >= char_code) { | ^~~~~~~~~ ../plink2_adjust.cc: In function 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)': ../plink2_adjust.cc:805:19: note: 'line_start' was declared here 805 | const char* line_start; | ^~~~~~~~~~ ../plink2_data.cc: In function 'plink2::PglErr plink2::PvarInfoResplitTmp(const uint32_t*, uint32_t, uint32_t, uint32_t, uint32_t, TextStream*, char*, char*)': ../plink2_data.cc:8757:47: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 8757 | const uint32_t info_slen = line_end - line_iter; | ~~~~~~~~~^~~~~~~~~~~ ../plink2_data.cc:8750:15: note: 'line_iter' was declared here 8750 | char* line_iter; | ^~~~~~~~~ ../plink2_fasta.cc: In function 'plink2::PglErr plink2::ProcessFa(const uintptr_t*, const char* const*, const uintptr_t*, const ChrInfo*, const char*, uint32_t, uint32_t, FaFlags, uint32_t, uint32_t, UnsortedVar*, uint32_t*, const char**, AlleleCode*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_fasta.cc:535:38: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 535 | unsigned char ucc = line_iter[0]; | ~~~~~~~~~~~^ ../plink2_fasta.cc:526:13: note: 'line_iter' was declared here 526 | char* line_iter; | ^~~~~~~~~ In file included from ../include/plink2_stats.h:20, from ../plink2_filter.cc:18: In function 'int32_t plink2::tokequal_k(const char*, const char*)', inlined from 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)' at ../plink2_filter.cc:747:27: ../include/plink2_string.h:448:18: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 448 | return memequal(s_read, s_const, s_const_slen) && IsSpaceOrEoln(s_read[s_const_slen]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_filter.cc: In function 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_filter.cc:740:13: note: 'line_iter' was declared here 740 | char* line_iter; | ^~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:28, 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++/14/bits/stl_algo.h:1812:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1900:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, 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:15405:5: /usr/include/c++/14/bits/stl_algo.h:1817:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds=] 1817 | 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:15382:14: note: at offset 128 into object 'parse_table' of size 48 15382 | 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_htable.o plink2_memory.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~a6.9-250129+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' cd build_dynamic && make -j40 "INSTALL=install --strip-program=true" SFX=-sse3 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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_htable.cc ../include/plink2_memory.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 ../include/plink2_stats.h:20, from ../plink2_adjust.cc:17: In function 'const char* plink2::FirstPrechar(const char*, uint32_t)', inlined from 'const char* plink2::CurTokenEnd(const char*)' at ../include/plink2_string.h:837:10, inlined from 'const char* plink2::TokenLexK0(const char*, const uint32_t*, const uint32_t*, uint32_t, const char**, uint32_t*)' at ../include/plink2_string.h:1443:46, inlined from 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)' at ../plink2_adjust.cc:812:11: ../include/plink2_string.h:788:17: warning: 'line_start' may be used uninitialized [-Wmaybe-uninitialized] 788 | while (ctou32(*str_iter) >= char_code) { | ^~~~~~~~~ ../plink2_adjust.cc: In function 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)': ../plink2_adjust.cc:805:19: note: 'line_start' was declared here 805 | const char* line_start; | ^~~~~~~~~~ ../plink2_data.cc: In function 'plink2::PglErr plink2::PvarInfoResplitTmp(const uint32_t*, uint32_t, uint32_t, uint32_t, uint32_t, TextStream*, char*, char*)': ../plink2_data.cc:8757:47: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 8757 | const uint32_t info_slen = line_end - line_iter; | ~~~~~~~~~^~~~~~~~~~~ ../plink2_data.cc:8750:15: note: 'line_iter' was declared here 8750 | char* line_iter; | ^~~~~~~~~ ../plink2_fasta.cc: In function 'plink2::PglErr plink2::ProcessFa(const uintptr_t*, const char* const*, const uintptr_t*, const ChrInfo*, const char*, uint32_t, uint32_t, FaFlags, uint32_t, uint32_t, UnsortedVar*, uint32_t*, const char**, AlleleCode*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_fasta.cc:535:38: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 535 | unsigned char ucc = line_iter[0]; | ~~~~~~~~~~~^ ../plink2_fasta.cc:526:13: note: 'line_iter' was declared here 526 | char* line_iter; | ^~~~~~~~~ In file included from ../include/plink2_stats.h:20, from ../plink2_filter.cc:18: In function 'int32_t plink2::tokequal_k(const char*, const char*)', inlined from 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)' at ../plink2_filter.cc:747:27: ../include/plink2_string.h:448:18: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 448 | return memequal(s_read, s_const, s_const_slen) && IsSpaceOrEoln(s_read[s_const_slen]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_filter.cc: In function 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_filter.cc:740:13: note: 'line_iter' was declared here 740 | char* line_iter; | ^~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:28, 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++/14/bits/stl_algo.h:1812:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1900:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, 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:15405:5: /usr/include/c++/14/bits/stl_algo.h:1817:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds=] 1817 | 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:15382:14: note: at offset 128 into object 'parse_table' of size 48 15382 | 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_htable.o plink2_memory.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~a6.9-250129+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' cd build_dynamic && make -j40 "INSTALL=install --strip-program=true" SFX=-sse2 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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_htable.cc ../include/plink2_memory.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 ../include/plink2_stats.h:20, from ../plink2_adjust.cc:17: In function 'const char* plink2::FirstPrechar(const char*, uint32_t)', inlined from 'const char* plink2::CurTokenEnd(const char*)' at ../include/plink2_string.h:837:10, inlined from 'const char* plink2::TokenLexK0(const char*, const uint32_t*, const uint32_t*, uint32_t, const char**, uint32_t*)' at ../include/plink2_string.h:1443:46, inlined from 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)' at ../plink2_adjust.cc:812:11: ../include/plink2_string.h:788:17: warning: 'line_start' may be used uninitialized [-Wmaybe-uninitialized] 788 | while (ctou32(*str_iter) >= char_code) { | ^~~~~~~~~ ../plink2_adjust.cc: In function 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)': ../plink2_adjust.cc:805:19: note: 'line_start' was declared here 805 | const char* line_start; | ^~~~~~~~~~ ../plink2_data.cc: In function 'plink2::PglErr plink2::PvarInfoResplitTmp(const uint32_t*, uint32_t, uint32_t, uint32_t, uint32_t, TextStream*, char*, char*)': ../plink2_data.cc:8757:47: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 8757 | const uint32_t info_slen = line_end - line_iter; | ~~~~~~~~~^~~~~~~~~~~ ../plink2_data.cc:8750:15: note: 'line_iter' was declared here 8750 | char* line_iter; | ^~~~~~~~~ ../plink2_fasta.cc: In function 'plink2::PglErr plink2::ProcessFa(const uintptr_t*, const char* const*, const uintptr_t*, const ChrInfo*, const char*, uint32_t, uint32_t, FaFlags, uint32_t, uint32_t, UnsortedVar*, uint32_t*, const char**, AlleleCode*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_fasta.cc:535:38: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 535 | unsigned char ucc = line_iter[0]; | ~~~~~~~~~~~^ ../plink2_fasta.cc:526:13: note: 'line_iter' was declared here 526 | char* line_iter; | ^~~~~~~~~ In file included from ../include/plink2_stats.h:20, from ../plink2_filter.cc:18: In function 'int32_t plink2::tokequal_k(const char*, const char*)', inlined from 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)' at ../plink2_filter.cc:747:27: ../include/plink2_string.h:448:18: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 448 | return memequal(s_read, s_const, s_const_slen) && IsSpaceOrEoln(s_read[s_const_slen]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_filter.cc: In function 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_filter.cc:740:13: note: 'line_iter' was declared here 740 | char* line_iter; | ^~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:28, 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++/14/bits/stl_algo.h:1812:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1900:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, 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:15405:5: /usr/include/c++/14/bits/stl_algo.h:1817:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds=] 1817 | 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:15382:14: note: at offset 128 into object 'parse_table' of size 48 15382 | 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_htable.o plink2_memory.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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+dfsg/debian/plink2/usr/bin cd /build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' dh_installdocs -O--sourcedirectory=build_dynamic/ debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+dfsg' dh_installchangelogs debian/upstream.docs/upstream.changelog make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a6.9-250129+dfsg' dh_installexamples -O--sourcedirectory=build_dynamic/ debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+dfsg' dh_installman debian/plink2.1 dh_installman pgen_compress.1 make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-3), " make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a6.9-250129+dfsg' dh_md5sums -O--sourcedirectory=build_dynamic/ dh_builddeb -O--sourcedirectory=build_dynamic/ dpkg-deb: building package 'plink2-dbgsym' in '../plink2-dbgsym_2.00~a6.9-250129+dfsg-1_amd64.deb'. dpkg-deb: building package 'plink2' in '../plink2_2.00~a6.9-250129+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../plink2_2.00~a6.9-250129+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/1556179 and its subdirectories I: Current time: Thu Jun 5 03:11:31 -12 2025 I: pbuilder-time-stamp: 1749136291 Thu Jun 5 15:11:31 UTC 2025 I: Signing ./b1/plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo as plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo.asc Thu Jun 5 15:11:31 UTC 2025 I: Signed ./b1/plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo as ./b1/plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo.asc Thu Jun 5 15:11:31 UTC 2025 - build #1 for plink2/trixie/amd64 on ionos11-amd64 done. Starting cleanup. All cleanup done. Thu Jun 5 15:11:31 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-3DMLYC6k, removing. /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Jun 5 15:11 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jun 5 14:23 b2 -rw-r--r-- 1 jenkins jenkins 2130 Feb 7 18:30 plink2_2.00~a6.9-250129+dfsg-1.dsc -rw------- 1 jenkins jenkins 3304 Jun 5 14:23 rbuildlog.64dUZtM /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/b1: total 42572 -rw-r--r-- 1 jenkins jenkins 89457 Jun 5 15:11 build.log -rw-r--r-- 1 jenkins jenkins 39097964 Jun 5 15:11 plink2-dbgsym_2.00~a6.9-250129+dfsg-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 58480 Jun 5 15:11 plink2_2.00~a6.9-250129+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2130 Jun 5 15:11 plink2_2.00~a6.9-250129+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 5336 Jun 5 15:11 plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6218 Jun 5 15:11 plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1775 Jun 5 15:11 plink2_2.00~a6.9-250129+dfsg-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 2736596 Jun 5 15:11 plink2_2.00~a6.9-250129+dfsg-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1941 Jun 5 15:11 plink2_2.00~a6.9-250129+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 1569072 Jun 5 15:11 plink2_2.00~a6.9-250129+dfsg.orig.tar.xz /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/b2: total 0 Thu Jun 5 15:11:32 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jun 5 02:23:50 -12 2025 I: pbuilder-time-stamp: 1749133430 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~a6.9-250129+dfsg-1.dsc] I: copying [./plink2_2.00~a6.9-250129+dfsg.orig.tar.xz] I: copying [./plink2_2.00~a6.9-250129+dfsg-1.debian.tar.xz] I: Extracting source error: the following required arguments were not provided: --keyring Usage: sqv --keyring --cleartext --output For more information, try '--help'. dpkg-source: warning: cannot verify inline signature for ./plink2_2.00~a6.9-250129+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting plink2 in plink2-2.00~a6.9-250129+dfsg dpkg-source: info: unpacking plink2_2.00~a6.9-250129+dfsg.orig.tar.xz dpkg-source: info: unpacking plink2_2.00~a6.9-250129+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/1556179/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=40 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='515326b2868c4f4e908046083fb47d1b' 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='1556179' 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.ukoJ02M8/pbuilderrc_TIEX --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.ukoJ02M8/b1 --logfile b1/build.log plink2_2.00~a6.9-250129+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://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1556179/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 ... 19850 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} liblapack-dev{a} liblapack3{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsimde-dev{a} libtool{a} libuchardet0{a} libunistring5{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, 41 newly installed, 0 to remove and 0 not upgraded. Need to get 21.9 MB of archives. After unpacking 94.2 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+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-8 [1187 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 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 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libblas-dev amd64 3.12.1-2 [170 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.1-2 [4998 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 21.9 MB in 3s (6341 kB/s) Preconfiguring packages ... 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 ... 19850 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-8_amd64.deb ... Unpacking groff-base (1.23.0-8) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.41-5_amd64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... 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 libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../22-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../24-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-2_amd64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package help2man. Preparing to unpack .../30-help2man_1.49.3_amd64.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../31-libblas3_3.12.1-2_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-2) ... Selecting previously unselected package libblas-dev:amd64. Preparing to unpack .../32-libblas-dev_3.12.1-2_amd64.deb ... Unpacking libblas-dev:amd64 (3.12.1-2) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../33-libdeflate0_1.23-2_amd64.deb ... Unpacking libdeflate0:amd64 (1.23-2) ... Selecting previously unselected package libdeflate-dev:amd64. Preparing to unpack .../34-libdeflate-dev_1.23-2_amd64.deb ... Unpacking libdeflate-dev:amd64 (1.23-2) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../35-libgfortran5_14.2.0-19_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-19) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../36-liblapack3_3.12.1-2_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-2) ... Selecting previously unselected package liblapack-dev:amd64. Preparing to unpack .../37-liblapack-dev_3.12.1-2_amd64.deb ... Unpacking liblapack-dev:amd64 (3.12.1-2) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../38-libsimde-dev_0.8.2-3_all.deb ... Unpacking libsimde-dev (0.8.2-3) ... Selecting previously unselected package libzstd-dev:amd64. Preparing to unpack .../39-libzstd-dev_1.5.7+dfsg-1_amd64.deb ... Unpacking libzstd-dev:amd64 (1.5.7+dfsg-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../40-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libsimde-dev (0.8.2-3) ... Setting up libzstd-dev:amd64 (1.5.7+dfsg-1) ... Setting up bsdextrautils (2.41-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-2) ... 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 libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libdeflate-dev:amd64 (1.23-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libblas-dev:amd64 (3.12.1-2) ... 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 (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:amd64 (3.12.1-2) ... 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 (0.23.1-2) ... Setting up libtool (2.5.4-4) ... 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 (3.12.1-2) ... 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 (1.14.1-2) ... Setting up groff-base (1.23.0-8) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Processing triggers for libc-bin (2.41-8) ... 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~a6.9-250129+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~a6.9-250129+dfsg-1_source.changes dpkg-buildpackage: info: source package plink2 dpkg-buildpackage: info: source version 2.00~a6.9-250129+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Dylan Aïssi 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~a6.9-250129+dfsg' dh_auto_clean cd build_dynamic && make -j40 clean make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg/build_dynamic' rm -f plink2.1 rm -f pgen_compress.1 make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' mkdir -p /build/reproducible-path/plink2-2.00~a6.9-250129+dfsg/debian/plink2/usr mkdir -p /build/reproducible-path/plink2-2.00~a6.9-250129+dfsg/debian/plink2/usr/lib/plink2 export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+dfsg' cd build_dynamic && make -j40 "INSTALL=install --strip-program=true" SFX=-avx2 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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_htable.cc ../include/plink2_memory.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 ../include/plink2_string.h:24, from ../include/plink2_stats.h:20, from ../plink2_adjust.cc:17: ../plink2_adjust.cc: In function 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)': ../plink2_adjust.cc:812:31: warning: 'line_start' may be used uninitialized [-Wmaybe-uninitialized] 812 | if (unlikely(!TokenLexK0(line_start, col_types, col_skips, relevant_col_ct, token_ptrs, token_slens))) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/plink2_base.h:277:46: note: in definition of macro 'unlikely' 277 | # define unlikely(expr) __builtin_expect(!!(expr), 0) | ^~~~ ../plink2_adjust.cc:805:19: note: 'line_start' was declared here 805 | const char* line_start; | ^~~~~~~~~~ ../plink2_data.cc: In function 'plink2::PglErr plink2::PvarInfoResplitTmp(const uint32_t*, uint32_t, uint32_t, uint32_t, uint32_t, TextStream*, char*, char*)': ../plink2_data.cc:8757:47: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 8757 | const uint32_t info_slen = line_end - line_iter; | ~~~~~~~~~^~~~~~~~~~~ ../plink2_data.cc:8750:15: note: 'line_iter' was declared here 8750 | char* line_iter; | ^~~~~~~~~ ../plink2_fasta.cc: In function 'plink2::PglErr plink2::ProcessFa(const uintptr_t*, const char* const*, const uintptr_t*, const ChrInfo*, const char*, uint32_t, uint32_t, FaFlags, uint32_t, uint32_t, UnsortedVar*, uint32_t*, const char**, AlleleCode*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_fasta.cc:535:38: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 535 | unsigned char ucc = line_iter[0]; | ~~~~~~~~~~~^ ../plink2_fasta.cc:526:13: note: 'line_iter' was declared here 526 | char* line_iter; | ^~~~~~~~~ In file included from ../include/plink2_stats.h:20, from ../plink2_filter.cc:18: In function 'int32_t plink2::tokequal_k(const char*, const char*)', inlined from 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)' at ../plink2_filter.cc:747:27: ../include/plink2_string.h:448:18: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 448 | return memequal(s_read, s_const, s_const_slen) && IsSpaceOrEoln(s_read[s_const_slen]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_filter.cc: In function 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_filter.cc:740:13: note: 'line_iter' was declared here 740 | char* line_iter; | ^~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:28, 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++/14/bits/stl_algo.h:1812:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1900:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, 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:15405:5: /usr/include/c++/14/bits/stl_algo.h:1817:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds=] 1817 | 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:15382:14: note: at offset 128 into object 'parse_table' of size 48 15382 | 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_htable.o plink2_memory.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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+dfsg' cd build_dynamic && make -j40 "INSTALL=install --strip-program=true" SFX=-avx make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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_htable.cc ../include/plink2_memory.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 ../include/plink2_stats.h:20, from ../plink2_adjust.cc:17: In function 'const char* plink2::FirstPrechar(const char*, uint32_t)', inlined from 'const char* plink2::CurTokenEnd(const char*)' at ../include/plink2_string.h:837:10, inlined from 'const char* plink2::TokenLexK0(const char*, const uint32_t*, const uint32_t*, uint32_t, const char**, uint32_t*)' at ../include/plink2_string.h:1443:46, inlined from 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)' at ../plink2_adjust.cc:812:11: ../include/plink2_string.h:788:17: warning: 'line_start' may be used uninitialized [-Wmaybe-uninitialized] 788 | while (ctou32(*str_iter) >= char_code) { | ^~~~~~~~~ ../plink2_adjust.cc: In function 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)': ../plink2_adjust.cc:805:19: note: 'line_start' was declared here 805 | const char* line_start; | ^~~~~~~~~~ ../plink2_data.cc: In function 'plink2::PglErr plink2::PvarInfoResplitTmp(const uint32_t*, uint32_t, uint32_t, uint32_t, uint32_t, TextStream*, char*, char*)': ../plink2_data.cc:8757:47: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 8757 | const uint32_t info_slen = line_end - line_iter; | ~~~~~~~~~^~~~~~~~~~~ ../plink2_data.cc:8750:15: note: 'line_iter' was declared here 8750 | char* line_iter; | ^~~~~~~~~ ../plink2_fasta.cc: In function 'plink2::PglErr plink2::ProcessFa(const uintptr_t*, const char* const*, const uintptr_t*, const ChrInfo*, const char*, uint32_t, uint32_t, FaFlags, uint32_t, uint32_t, UnsortedVar*, uint32_t*, const char**, AlleleCode*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_fasta.cc:535:38: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 535 | unsigned char ucc = line_iter[0]; | ~~~~~~~~~~~^ ../plink2_fasta.cc:526:13: note: 'line_iter' was declared here 526 | char* line_iter; | ^~~~~~~~~ In file included from ../include/plink2_stats.h:20, from ../plink2_filter.cc:18: In function 'int32_t plink2::tokequal_k(const char*, const char*)', inlined from 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)' at ../plink2_filter.cc:747:27: ../include/plink2_string.h:448:18: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 448 | return memequal(s_read, s_const, s_const_slen) && IsSpaceOrEoln(s_read[s_const_slen]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_filter.cc: In function 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_filter.cc:740:13: note: 'line_iter' was declared here 740 | char* line_iter; | ^~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:28, 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++/14/bits/stl_algo.h:1812:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1900:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, 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:15405:5: /usr/include/c++/14/bits/stl_algo.h:1817:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds=] 1817 | 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:15382:14: note: at offset 128 into object 'parse_table' of size 48 15382 | 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_htable.o plink2_memory.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~a6.9-250129+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' cd build_dynamic && make -j40 "INSTALL=install --strip-program=true" SFX=-sse4.1 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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_htable.cc ../include/plink2_memory.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 ../include/plink2_stats.h:20, from ../plink2_adjust.cc:17: In function 'const char* plink2::FirstPrechar(const char*, uint32_t)', inlined from 'const char* plink2::CurTokenEnd(const char*)' at ../include/plink2_string.h:837:10, inlined from 'const char* plink2::TokenLexK0(const char*, const uint32_t*, const uint32_t*, uint32_t, const char**, uint32_t*)' at ../include/plink2_string.h:1443:46, inlined from 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)' at ../plink2_adjust.cc:812:11: ../include/plink2_string.h:788:17: warning: 'line_start' may be used uninitialized [-Wmaybe-uninitialized] 788 | while (ctou32(*str_iter) >= char_code) { | ^~~~~~~~~ ../plink2_adjust.cc: In function 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)': ../plink2_adjust.cc:805:19: note: 'line_start' was declared here 805 | const char* line_start; | ^~~~~~~~~~ ../plink2_data.cc: In function 'plink2::PglErr plink2::PvarInfoResplitTmp(const uint32_t*, uint32_t, uint32_t, uint32_t, uint32_t, TextStream*, char*, char*)': ../plink2_data.cc:8757:47: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 8757 | const uint32_t info_slen = line_end - line_iter; | ~~~~~~~~~^~~~~~~~~~~ ../plink2_data.cc:8750:15: note: 'line_iter' was declared here 8750 | char* line_iter; | ^~~~~~~~~ ../plink2_fasta.cc: In function 'plink2::PglErr plink2::ProcessFa(const uintptr_t*, const char* const*, const uintptr_t*, const ChrInfo*, const char*, uint32_t, uint32_t, FaFlags, uint32_t, uint32_t, UnsortedVar*, uint32_t*, const char**, AlleleCode*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_fasta.cc:535:38: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 535 | unsigned char ucc = line_iter[0]; | ~~~~~~~~~~~^ ../plink2_fasta.cc:526:13: note: 'line_iter' was declared here 526 | char* line_iter; | ^~~~~~~~~ In file included from ../include/plink2_stats.h:20, from ../plink2_filter.cc:18: In function 'int32_t plink2::tokequal_k(const char*, const char*)', inlined from 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)' at ../plink2_filter.cc:747:27: ../include/plink2_string.h:448:18: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 448 | return memequal(s_read, s_const, s_const_slen) && IsSpaceOrEoln(s_read[s_const_slen]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_filter.cc: In function 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_filter.cc:740:13: note: 'line_iter' was declared here 740 | char* line_iter; | ^~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:28, 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++/14/bits/stl_algo.h:1812:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1900:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, 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:15405:5: /usr/include/c++/14/bits/stl_algo.h:1817:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds=] 1817 | 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:15382:14: note: at offset 128 into object 'parse_table' of size 48 15382 | 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_htable.o plink2_memory.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~a6.9-250129+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' cd build_dynamic && make -j40 "INSTALL=install --strip-program=true" SFX=-ssse3 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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_htable.cc ../include/plink2_memory.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 ../include/plink2_stats.h:20, from ../plink2_adjust.cc:17: In function 'const char* plink2::FirstPrechar(const char*, uint32_t)', inlined from 'const char* plink2::CurTokenEnd(const char*)' at ../include/plink2_string.h:837:10, inlined from 'const char* plink2::TokenLexK0(const char*, const uint32_t*, const uint32_t*, uint32_t, const char**, uint32_t*)' at ../include/plink2_string.h:1443:46, inlined from 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)' at ../plink2_adjust.cc:812:11: ../include/plink2_string.h:788:17: warning: 'line_start' may be used uninitialized [-Wmaybe-uninitialized] 788 | while (ctou32(*str_iter) >= char_code) { | ^~~~~~~~~ ../plink2_adjust.cc: In function 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)': ../plink2_adjust.cc:805:19: note: 'line_start' was declared here 805 | const char* line_start; | ^~~~~~~~~~ ../plink2_data.cc: In function 'plink2::PglErr plink2::PvarInfoResplitTmp(const uint32_t*, uint32_t, uint32_t, uint32_t, uint32_t, TextStream*, char*, char*)': ../plink2_data.cc:8757:47: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 8757 | const uint32_t info_slen = line_end - line_iter; | ~~~~~~~~~^~~~~~~~~~~ ../plink2_data.cc:8750:15: note: 'line_iter' was declared here 8750 | char* line_iter; | ^~~~~~~~~ ../plink2_fasta.cc: In function 'plink2::PglErr plink2::ProcessFa(const uintptr_t*, const char* const*, const uintptr_t*, const ChrInfo*, const char*, uint32_t, uint32_t, FaFlags, uint32_t, uint32_t, UnsortedVar*, uint32_t*, const char**, AlleleCode*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_fasta.cc:535:38: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 535 | unsigned char ucc = line_iter[0]; | ~~~~~~~~~~~^ ../plink2_fasta.cc:526:13: note: 'line_iter' was declared here 526 | char* line_iter; | ^~~~~~~~~ In file included from ../include/plink2_stats.h:20, from ../plink2_filter.cc:18: In function 'int32_t plink2::tokequal_k(const char*, const char*)', inlined from 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)' at ../plink2_filter.cc:747:27: ../include/plink2_string.h:448:18: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 448 | return memequal(s_read, s_const, s_const_slen) && IsSpaceOrEoln(s_read[s_const_slen]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_filter.cc: In function 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_filter.cc:740:13: note: 'line_iter' was declared here 740 | char* line_iter; | ^~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:28, 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++/14/bits/stl_algo.h:1812:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1900:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, 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:15405:5: /usr/include/c++/14/bits/stl_algo.h:1817:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds=] 1817 | 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:15382:14: note: at offset 128 into object 'parse_table' of size 48 15382 | 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_htable.o plink2_memory.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~a6.9-250129+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' cd build_dynamic && make -j40 "INSTALL=install --strip-program=true" SFX=-sse3 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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_htable.cc ../include/plink2_memory.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 ../include/plink2_stats.h:20, from ../plink2_adjust.cc:17: In function 'const char* plink2::FirstPrechar(const char*, uint32_t)', inlined from 'const char* plink2::CurTokenEnd(const char*)' at ../include/plink2_string.h:837:10, inlined from 'const char* plink2::TokenLexK0(const char*, const uint32_t*, const uint32_t*, uint32_t, const char**, uint32_t*)' at ../include/plink2_string.h:1443:46, inlined from 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)' at ../plink2_adjust.cc:812:11: ../include/plink2_string.h:788:17: warning: 'line_start' may be used uninitialized [-Wmaybe-uninitialized] 788 | while (ctou32(*str_iter) >= char_code) { | ^~~~~~~~~ ../plink2_adjust.cc: In function 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)': ../plink2_adjust.cc:805:19: note: 'line_start' was declared here 805 | const char* line_start; | ^~~~~~~~~~ ../plink2_data.cc: In function 'plink2::PglErr plink2::PvarInfoResplitTmp(const uint32_t*, uint32_t, uint32_t, uint32_t, uint32_t, TextStream*, char*, char*)': ../plink2_data.cc:8757:47: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 8757 | const uint32_t info_slen = line_end - line_iter; | ~~~~~~~~~^~~~~~~~~~~ ../plink2_data.cc:8750:15: note: 'line_iter' was declared here 8750 | char* line_iter; | ^~~~~~~~~ ../plink2_fasta.cc: In function 'plink2::PglErr plink2::ProcessFa(const uintptr_t*, const char* const*, const uintptr_t*, const ChrInfo*, const char*, uint32_t, uint32_t, FaFlags, uint32_t, uint32_t, UnsortedVar*, uint32_t*, const char**, AlleleCode*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_fasta.cc:535:38: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 535 | unsigned char ucc = line_iter[0]; | ~~~~~~~~~~~^ ../plink2_fasta.cc:526:13: note: 'line_iter' was declared here 526 | char* line_iter; | ^~~~~~~~~ In file included from ../include/plink2_stats.h:20, from ../plink2_filter.cc:18: In function 'int32_t plink2::tokequal_k(const char*, const char*)', inlined from 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)' at ../plink2_filter.cc:747:27: ../include/plink2_string.h:448:18: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 448 | return memequal(s_read, s_const, s_const_slen) && IsSpaceOrEoln(s_read[s_const_slen]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_filter.cc: In function 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_filter.cc:740:13: note: 'line_iter' was declared here 740 | char* line_iter; | ^~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:28, 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++/14/bits/stl_algo.h:1812:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1900:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, 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:15405:5: /usr/include/c++/14/bits/stl_algo.h:1817:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds=] 1817 | 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:15382:14: note: at offset 128 into object 'parse_table' of size 48 15382 | 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_htable.o plink2_memory.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~a6.9-250129+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' cd build_dynamic && make -j40 "INSTALL=install --strip-program=true" SFX=-sse2 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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_htable.cc ../include/plink2_memory.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 ../include/plink2_stats.h:20, from ../plink2_adjust.cc:17: In function 'const char* plink2::FirstPrechar(const char*, uint32_t)', inlined from 'const char* plink2::CurTokenEnd(const char*)' at ../include/plink2_string.h:837:10, inlined from 'const char* plink2::TokenLexK0(const char*, const uint32_t*, const uint32_t*, uint32_t, const char**, uint32_t*)' at ../include/plink2_string.h:1443:46, inlined from 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)' at ../plink2_adjust.cc:812:11: ../include/plink2_string.h:788:17: warning: 'line_start' may be used uninitialized [-Wmaybe-uninitialized] 788 | while (ctou32(*str_iter) >= char_code) { | ^~~~~~~~~ ../plink2_adjust.cc: In function 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)': ../plink2_adjust.cc:805:19: note: 'line_start' was declared here 805 | const char* line_start; | ^~~~~~~~~~ ../plink2_data.cc: In function 'plink2::PglErr plink2::PvarInfoResplitTmp(const uint32_t*, uint32_t, uint32_t, uint32_t, uint32_t, TextStream*, char*, char*)': ../plink2_data.cc:8757:47: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 8757 | const uint32_t info_slen = line_end - line_iter; | ~~~~~~~~~^~~~~~~~~~~ ../plink2_data.cc:8750:15: note: 'line_iter' was declared here 8750 | char* line_iter; | ^~~~~~~~~ ../plink2_fasta.cc: In function 'plink2::PglErr plink2::ProcessFa(const uintptr_t*, const char* const*, const uintptr_t*, const ChrInfo*, const char*, uint32_t, uint32_t, FaFlags, uint32_t, uint32_t, UnsortedVar*, uint32_t*, const char**, AlleleCode*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_fasta.cc:535:38: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 535 | unsigned char ucc = line_iter[0]; | ~~~~~~~~~~~^ ../plink2_fasta.cc:526:13: note: 'line_iter' was declared here 526 | char* line_iter; | ^~~~~~~~~ In file included from ../include/plink2_stats.h:20, from ../plink2_filter.cc:18: In function 'int32_t plink2::tokequal_k(const char*, const char*)', inlined from 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)' at ../plink2_filter.cc:747:27: ../include/plink2_string.h:448:18: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 448 | return memequal(s_read, s_const, s_const_slen) && IsSpaceOrEoln(s_read[s_const_slen]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_filter.cc: In function 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_filter.cc:740:13: note: 'line_iter' was declared here 740 | char* line_iter; | ^~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:28, 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++/14/bits/stl_algo.h:1812:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1900:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, 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:15405:5: /usr/include/c++/14/bits/stl_algo.h:1817:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds=] 1817 | 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:15382:14: note: at offset 128 into object 'parse_table' of size 48 15382 | 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_htable.o plink2_memory.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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+dfsg/debian/plink2/usr/bin cd /build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' dh_installdocs -O--sourcedirectory=build_dynamic/ debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+dfsg' dh_installchangelogs debian/upstream.docs/upstream.changelog make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a6.9-250129+dfsg' dh_installexamples -O--sourcedirectory=build_dynamic/ debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+dfsg' dh_installman debian/plink2.1 dh_installman pgen_compress.1 make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-3), " make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a6.9-250129+dfsg' dh_md5sums -O--sourcedirectory=build_dynamic/ dh_builddeb -O--sourcedirectory=build_dynamic/ dpkg-deb: building package 'plink2-dbgsym' in '../plink2-dbgsym_2.00~a6.9-250129+dfsg-1_amd64.deb'. dpkg-deb: building package 'plink2' in '../plink2_2.00~a6.9-250129+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../plink2_2.00~a6.9-250129+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/1556179 and its subdirectories I: Current time: Thu Jun 5 03:11:31 -12 2025 I: pbuilder-time-stamp: 1749136291 Thu Jun 5 15:11:32 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Thu Jun 5 15:11:32 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Thu Jun 5 15:11:32 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Thu Jun 5 15:11:32 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-7oO4yc' ==================================================================================== Wed Jul 8 21:34:33 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "2 plink2 trixie /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8 2.00~a6.9-250129+dfsg-1" as arguments. Wed Jul 8 21:34:33 UTC 2026 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-O2OCyFrM" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Jul 8 21:34:33 UTC 2026 I: Downloading source for trixie/plink2=2.00~a6.9-250129+dfsg-1 Reading package lists... NOTICE: 'plink2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/plink2.git Please use: git clone https://salsa.debian.org/med-team/plink2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1630 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main plink2 2.00~a6.9-250129+dfsg-1 (dsc) [2130 B] Get:2 http://deb.debian.org/debian trixie/main plink2 2.00~a6.9-250129+dfsg-1 (tar) [1569 kB] Get:3 http://deb.debian.org/debian trixie/main plink2 2.00~a6.9-250129+dfsg-1 (diff) [58.5 kB] Fetched 1630 kB in 0s (20.7 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'plink2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/plink2.git Please use: git clone https://salsa.debian.org/med-team/plink2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1630 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main plink2 2.00~a6.9-250129+dfsg-1 (dsc) [2130 B] Get:2 http://deb.debian.org/debian trixie/main plink2 2.00~a6.9-250129+dfsg-1 (tar) [1569 kB] Get:3 http://deb.debian.org/debian trixie/main plink2 2.00~a6.9-250129+dfsg-1 (diff) [58.5 kB] Fetched 1630 kB in 0s (20.7 MB/s) Download complete and in download only mode ============================================================================= Re-Building plink2 in trixie on amd64 on ionos15-amd64 now. Date: Wed Jul 8 21:34:33 UTC 2026 Date UTC: Wed Jul 8 21:34:33 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8 + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/pbuilderrc_OUoI + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' plink2 = debian-installer -o plink2 = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' plink2 = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/pbuilderrc_OUoI --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/b2 --logfile b2/build.log plink2_2.00~a6.9-250129+dfsg-1.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Jul 9 11:34:33 +14 2026 I: pbuilder-time-stamp: 1783546473 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~a6.9-250129+dfsg-1.dsc] I: copying [./plink2_2.00~a6.9-250129+dfsg.orig.tar.xz] I: copying [./plink2_2.00~a6.9-250129+dfsg-1.debian.tar.xz] I: Extracting source error: the following required arguments were not provided: --keyring Usage: sqv --keyring --cleartext --output For more information, try '--help'. dpkg-source: warning: cannot verify inline signature for ./plink2_2.00~a6.9-250129+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting plink2 in plink2-2.00~a6.9-250129+dfsg dpkg-source: info: unpacking plink2_2.00~a6.9-250129+dfsg.orig.tar.xz dpkg-source: info: unpacking plink2_2.00~a6.9-250129+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/1646424/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-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 Jul 8 21:34 /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/1646424/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1646424/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=5664b4d3de52415abe911ea99558db3d 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=1646424 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.ukoJ02M8/pbuilderrc_OUoI --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/b2 --logfile b2/build.log plink2_2.00~a6.9-250129+dfsg-1.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.12.22+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.22-1~bpo12+1 (2025-04-25) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1646424/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 ... 19850 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} liblapack-dev{a} liblapack3{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsimde-dev{a} libtool{a} libuchardet0{a} libunistring5{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, 41 newly installed, 0 to remove and 0 not upgraded. Need to get 21.9 MB of archives. After unpacking 94.2 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+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-8 [1187 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 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 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libblas-dev amd64 3.12.1-2 [170 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.1-2 [4998 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 21.9 MB in 0s (88.2 MB/s) Preconfiguring packages ... 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 ... 19850 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-8_amd64.deb ... Unpacking groff-base (1.23.0-8) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.41-5_amd64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... 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 libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../22-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../24-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-2_amd64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package help2man. Preparing to unpack .../30-help2man_1.49.3_amd64.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../31-libblas3_3.12.1-2_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-2) ... Selecting previously unselected package libblas-dev:amd64. Preparing to unpack .../32-libblas-dev_3.12.1-2_amd64.deb ... Unpacking libblas-dev:amd64 (3.12.1-2) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../33-libdeflate0_1.23-2_amd64.deb ... Unpacking libdeflate0:amd64 (1.23-2) ... Selecting previously unselected package libdeflate-dev:amd64. Preparing to unpack .../34-libdeflate-dev_1.23-2_amd64.deb ... Unpacking libdeflate-dev:amd64 (1.23-2) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../35-libgfortran5_14.2.0-19_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-19) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../36-liblapack3_3.12.1-2_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-2) ... Selecting previously unselected package liblapack-dev:amd64. Preparing to unpack .../37-liblapack-dev_3.12.1-2_amd64.deb ... Unpacking liblapack-dev:amd64 (3.12.1-2) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../38-libsimde-dev_0.8.2-3_all.deb ... Unpacking libsimde-dev (0.8.2-3) ... Selecting previously unselected package libzstd-dev:amd64. Preparing to unpack .../39-libzstd-dev_1.5.7+dfsg-1_amd64.deb ... Unpacking libzstd-dev:amd64 (1.5.7+dfsg-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../40-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libsimde-dev (0.8.2-3) ... Setting up libzstd-dev:amd64 (1.5.7+dfsg-1) ... Setting up bsdextrautils (2.41-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-2) ... 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 libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libdeflate-dev:amd64 (1.23-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libblas-dev:amd64 (3.12.1-2) ... 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 (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:amd64 (3.12.1-2) ... 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 (0.23.1-2) ... Setting up libtool (2.5.4-4) ... 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 (3.12.1-2) ... 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 (1.14.1-2) ... Setting up groff-base (1.23.0-8) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Processing triggers for libc-bin (2.41-8) ... 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/1646424/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/1646424/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg-1_source.changes dpkg-buildpackage: info: source package plink2 dpkg-buildpackage: info: source version 2.00~a6.9-250129+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Dylan Aïssi 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~a6.9-250129+dfsg' dh_auto_clean cd build_dynamic && make -j42 clean make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg/build_dynamic' rm -f plink2.1 rm -f pgen_compress.1 make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' mkdir -p /build/reproducible-path/plink2-2.00~a6.9-250129+dfsg/debian/plink2/usr mkdir -p /build/reproducible-path/plink2-2.00~a6.9-250129+dfsg/debian/plink2/usr/lib/plink2 export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+dfsg' cd build_dynamic && make -j42 "INSTALL=install --strip-program=true" SFX=-avx2 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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_htable.cc ../include/plink2_memory.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 ../include/plink2_string.h:24, from ../include/plink2_stats.h:20, from ../plink2_adjust.cc:17: ../plink2_adjust.cc: In function 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)': ../plink2_adjust.cc:812:31: warning: 'line_start' may be used uninitialized [-Wmaybe-uninitialized] 812 | if (unlikely(!TokenLexK0(line_start, col_types, col_skips, relevant_col_ct, token_ptrs, token_slens))) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/plink2_base.h:277:46: note: in definition of macro 'unlikely' 277 | # define unlikely(expr) __builtin_expect(!!(expr), 0) | ^~~~ ../plink2_adjust.cc:805:19: note: 'line_start' was declared here 805 | const char* line_start; | ^~~~~~~~~~ ../plink2_data.cc: In function 'plink2::PglErr plink2::PvarInfoResplitTmp(const uint32_t*, uint32_t, uint32_t, uint32_t, uint32_t, TextStream*, char*, char*)': ../plink2_data.cc:8757:47: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 8757 | const uint32_t info_slen = line_end - line_iter; | ~~~~~~~~~^~~~~~~~~~~ ../plink2_data.cc:8750:15: note: 'line_iter' was declared here 8750 | char* line_iter; | ^~~~~~~~~ ../plink2_fasta.cc: In function 'plink2::PglErr plink2::ProcessFa(const uintptr_t*, const char* const*, const uintptr_t*, const ChrInfo*, const char*, uint32_t, uint32_t, FaFlags, uint32_t, uint32_t, UnsortedVar*, uint32_t*, const char**, AlleleCode*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_fasta.cc:535:38: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 535 | unsigned char ucc = line_iter[0]; | ~~~~~~~~~~~^ ../plink2_fasta.cc:526:13: note: 'line_iter' was declared here 526 | char* line_iter; | ^~~~~~~~~ In file included from ../include/plink2_stats.h:20, from ../plink2_filter.cc:18: In function 'int32_t plink2::tokequal_k(const char*, const char*)', inlined from 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)' at ../plink2_filter.cc:747:27: ../include/plink2_string.h:448:18: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 448 | return memequal(s_read, s_const, s_const_slen) && IsSpaceOrEoln(s_read[s_const_slen]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_filter.cc: In function 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_filter.cc:740:13: note: 'line_iter' was declared here 740 | char* line_iter; | ^~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:28, 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++/14/bits/stl_algo.h:1812:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1900:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, 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:15405:5: /usr/include/c++/14/bits/stl_algo.h:1817:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds=] 1817 | 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:15382:14: note: at offset 128 into object 'parse_table' of size 48 15382 | 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_htable.o plink2_memory.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~a6.9-250129+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~a6.9-250129+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${SIMD}" && export CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/plink2-2.00~a6.9-250129+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I/usr/include/simde -DIGNORE_BUNDLED_LIBDEFLATE -m${SIMD}" && \ make clean ; \ dh_auto_build -- SFX=-${SIMD} ; \ done make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' cd build_dynamic && make -j42 "INSTALL=install --strip-program=true" SFX=-avx make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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_htable.cc ../include/plink2_memory.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 ../include/plink2_stats.h:20, from ../plink2_adjust.cc:17: In function 'const char* plink2::FirstPrechar(const char*, uint32_t)', inlined from 'const char* plink2::CurTokenEnd(const char*)' at ../include/plink2_string.h:837:10, inlined from 'const char* plink2::TokenLexK0(const char*, const uint32_t*, const uint32_t*, uint32_t, const char**, uint32_t*)' at ../include/plink2_string.h:1443:46, inlined from 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)' at ../plink2_adjust.cc:812:11: ../include/plink2_string.h:788:17: warning: 'line_start' may be used uninitialized [-Wmaybe-uninitialized] 788 | while (ctou32(*str_iter) >= char_code) { | ^~~~~~~~~ ../plink2_adjust.cc: In function 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)': ../plink2_adjust.cc:805:19: note: 'line_start' was declared here 805 | const char* line_start; | ^~~~~~~~~~ ../plink2_data.cc: In function 'plink2::PglErr plink2::PvarInfoResplitTmp(const uint32_t*, uint32_t, uint32_t, uint32_t, uint32_t, TextStream*, char*, char*)': ../plink2_data.cc:8757:47: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 8757 | const uint32_t info_slen = line_end - line_iter; | ~~~~~~~~~^~~~~~~~~~~ ../plink2_data.cc:8750:15: note: 'line_iter' was declared here 8750 | char* line_iter; | ^~~~~~~~~ ../plink2_fasta.cc: In function 'plink2::PglErr plink2::ProcessFa(const uintptr_t*, const char* const*, const uintptr_t*, const ChrInfo*, const char*, uint32_t, uint32_t, FaFlags, uint32_t, uint32_t, UnsortedVar*, uint32_t*, const char**, AlleleCode*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_fasta.cc:535:38: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 535 | unsigned char ucc = line_iter[0]; | ~~~~~~~~~~~^ ../plink2_fasta.cc:526:13: note: 'line_iter' was declared here 526 | char* line_iter; | ^~~~~~~~~ In file included from ../include/plink2_stats.h:20, from ../plink2_filter.cc:18: In function 'int32_t plink2::tokequal_k(const char*, const char*)', inlined from 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)' at ../plink2_filter.cc:747:27: ../include/plink2_string.h:448:18: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 448 | return memequal(s_read, s_const, s_const_slen) && IsSpaceOrEoln(s_read[s_const_slen]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_filter.cc: In function 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_filter.cc:740:13: note: 'line_iter' was declared here 740 | char* line_iter; | ^~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:28, 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++/14/bits/stl_algo.h:1812:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1900:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, 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:15405:5: /usr/include/c++/14/bits/stl_algo.h:1817:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds=] 1817 | 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:15382:14: note: at offset 128 into object 'parse_table' of size 48 15382 | 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_htable.o plink2_memory.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~a6.9-250129+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' cd build_dynamic && make -j42 "INSTALL=install --strip-program=true" SFX=-sse4.1 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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_htable.cc ../include/plink2_memory.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 ../include/plink2_stats.h:20, from ../plink2_adjust.cc:17: In function 'const char* plink2::FirstPrechar(const char*, uint32_t)', inlined from 'const char* plink2::CurTokenEnd(const char*)' at ../include/plink2_string.h:837:10, inlined from 'const char* plink2::TokenLexK0(const char*, const uint32_t*, const uint32_t*, uint32_t, const char**, uint32_t*)' at ../include/plink2_string.h:1443:46, inlined from 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)' at ../plink2_adjust.cc:812:11: ../include/plink2_string.h:788:17: warning: 'line_start' may be used uninitialized [-Wmaybe-uninitialized] 788 | while (ctou32(*str_iter) >= char_code) { | ^~~~~~~~~ ../plink2_adjust.cc: In function 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)': ../plink2_adjust.cc:805:19: note: 'line_start' was declared here 805 | const char* line_start; | ^~~~~~~~~~ ../plink2_data.cc: In function 'plink2::PglErr plink2::PvarInfoResplitTmp(const uint32_t*, uint32_t, uint32_t, uint32_t, uint32_t, TextStream*, char*, char*)': ../plink2_data.cc:8757:47: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 8757 | const uint32_t info_slen = line_end - line_iter; | ~~~~~~~~~^~~~~~~~~~~ ../plink2_data.cc:8750:15: note: 'line_iter' was declared here 8750 | char* line_iter; | ^~~~~~~~~ ../plink2_fasta.cc: In function 'plink2::PglErr plink2::ProcessFa(const uintptr_t*, const char* const*, const uintptr_t*, const ChrInfo*, const char*, uint32_t, uint32_t, FaFlags, uint32_t, uint32_t, UnsortedVar*, uint32_t*, const char**, AlleleCode*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_fasta.cc:535:38: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 535 | unsigned char ucc = line_iter[0]; | ~~~~~~~~~~~^ ../plink2_fasta.cc:526:13: note: 'line_iter' was declared here 526 | char* line_iter; | ^~~~~~~~~ In file included from ../include/plink2_stats.h:20, from ../plink2_filter.cc:18: In function 'int32_t plink2::tokequal_k(const char*, const char*)', inlined from 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)' at ../plink2_filter.cc:747:27: ../include/plink2_string.h:448:18: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 448 | return memequal(s_read, s_const, s_const_slen) && IsSpaceOrEoln(s_read[s_const_slen]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_filter.cc: In function 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_filter.cc:740:13: note: 'line_iter' was declared here 740 | char* line_iter; | ^~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:28, 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++/14/bits/stl_algo.h:1812:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1900:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, 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:15405:5: /usr/include/c++/14/bits/stl_algo.h:1817:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds=] 1817 | 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:15382:14: note: at offset 128 into object 'parse_table' of size 48 15382 | 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_htable.o plink2_memory.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~a6.9-250129+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' cd build_dynamic && make -j42 "INSTALL=install --strip-program=true" SFX=-ssse3 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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_htable.cc ../include/plink2_memory.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 ../include/plink2_stats.h:20, from ../plink2_adjust.cc:17: In function 'const char* plink2::FirstPrechar(const char*, uint32_t)', inlined from 'const char* plink2::CurTokenEnd(const char*)' at ../include/plink2_string.h:837:10, inlined from 'const char* plink2::TokenLexK0(const char*, const uint32_t*, const uint32_t*, uint32_t, const char**, uint32_t*)' at ../include/plink2_string.h:1443:46, inlined from 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)' at ../plink2_adjust.cc:812:11: ../include/plink2_string.h:788:17: warning: 'line_start' may be used uninitialized [-Wmaybe-uninitialized] 788 | while (ctou32(*str_iter) >= char_code) { | ^~~~~~~~~ ../plink2_adjust.cc: In function 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)': ../plink2_adjust.cc:805:19: note: 'line_start' was declared here 805 | const char* line_start; | ^~~~~~~~~~ ../plink2_data.cc: In function 'plink2::PglErr plink2::PvarInfoResplitTmp(const uint32_t*, uint32_t, uint32_t, uint32_t, uint32_t, TextStream*, char*, char*)': ../plink2_data.cc:8757:47: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 8757 | const uint32_t info_slen = line_end - line_iter; | ~~~~~~~~~^~~~~~~~~~~ ../plink2_data.cc:8750:15: note: 'line_iter' was declared here 8750 | char* line_iter; | ^~~~~~~~~ ../plink2_fasta.cc: In function 'plink2::PglErr plink2::ProcessFa(const uintptr_t*, const char* const*, const uintptr_t*, const ChrInfo*, const char*, uint32_t, uint32_t, FaFlags, uint32_t, uint32_t, UnsortedVar*, uint32_t*, const char**, AlleleCode*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_fasta.cc:535:38: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 535 | unsigned char ucc = line_iter[0]; | ~~~~~~~~~~~^ ../plink2_fasta.cc:526:13: note: 'line_iter' was declared here 526 | char* line_iter; | ^~~~~~~~~ In file included from ../include/plink2_stats.h:20, from ../plink2_filter.cc:18: In function 'int32_t plink2::tokequal_k(const char*, const char*)', inlined from 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)' at ../plink2_filter.cc:747:27: ../include/plink2_string.h:448:18: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 448 | return memequal(s_read, s_const, s_const_slen) && IsSpaceOrEoln(s_read[s_const_slen]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_filter.cc: In function 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_filter.cc:740:13: note: 'line_iter' was declared here 740 | char* line_iter; | ^~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:28, 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++/14/bits/stl_algo.h:1812:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1900:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, 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:15405:5: /usr/include/c++/14/bits/stl_algo.h:1817:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds=] 1817 | 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:15382:14: note: at offset 128 into object 'parse_table' of size 48 15382 | 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_htable.o plink2_memory.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~a6.9-250129+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' cd build_dynamic && make -j42 "INSTALL=install --strip-program=true" SFX=-sse3 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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_htable.cc ../include/plink2_memory.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 ../include/plink2_stats.h:20, from ../plink2_adjust.cc:17: In function 'const char* plink2::FirstPrechar(const char*, uint32_t)', inlined from 'const char* plink2::CurTokenEnd(const char*)' at ../include/plink2_string.h:837:10, inlined from 'const char* plink2::TokenLexK0(const char*, const uint32_t*, const uint32_t*, uint32_t, const char**, uint32_t*)' at ../include/plink2_string.h:1443:46, inlined from 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)' at ../plink2_adjust.cc:812:11: ../include/plink2_string.h:788:17: warning: 'line_start' may be used uninitialized [-Wmaybe-uninitialized] 788 | while (ctou32(*str_iter) >= char_code) { | ^~~~~~~~~ ../plink2_adjust.cc: In function 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)': ../plink2_adjust.cc:805:19: note: 'line_start' was declared here 805 | const char* line_start; | ^~~~~~~~~~ ../plink2_data.cc: In function 'plink2::PglErr plink2::PvarInfoResplitTmp(const uint32_t*, uint32_t, uint32_t, uint32_t, uint32_t, TextStream*, char*, char*)': ../plink2_data.cc:8757:47: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 8757 | const uint32_t info_slen = line_end - line_iter; | ~~~~~~~~~^~~~~~~~~~~ ../plink2_data.cc:8750:15: note: 'line_iter' was declared here 8750 | char* line_iter; | ^~~~~~~~~ ../plink2_fasta.cc: In function 'plink2::PglErr plink2::ProcessFa(const uintptr_t*, const char* const*, const uintptr_t*, const ChrInfo*, const char*, uint32_t, uint32_t, FaFlags, uint32_t, uint32_t, UnsortedVar*, uint32_t*, const char**, AlleleCode*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_fasta.cc:535:38: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 535 | unsigned char ucc = line_iter[0]; | ~~~~~~~~~~~^ ../plink2_fasta.cc:526:13: note: 'line_iter' was declared here 526 | char* line_iter; | ^~~~~~~~~ In file included from ../include/plink2_stats.h:20, from ../plink2_filter.cc:18: In function 'int32_t plink2::tokequal_k(const char*, const char*)', inlined from 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)' at ../plink2_filter.cc:747:27: ../include/plink2_string.h:448:18: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 448 | return memequal(s_read, s_const, s_const_slen) && IsSpaceOrEoln(s_read[s_const_slen]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_filter.cc: In function 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_filter.cc:740:13: note: 'line_iter' was declared here 740 | char* line_iter; | ^~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:28, 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++/14/bits/stl_algo.h:1812:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1900:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, 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:15405:5: /usr/include/c++/14/bits/stl_algo.h:1817:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds=] 1817 | 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:15382:14: note: at offset 128 into object 'parse_table' of size 48 15382 | 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_htable.o plink2_memory.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~a6.9-250129+dfsg/build_dynamic' make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' cd build_dynamic && make -j42 "INSTALL=install --strip-program=true" SFX=-sse2 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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_htable.cc ../include/plink2_memory.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 ../include/plink2_stats.h:20, from ../plink2_adjust.cc:17: In function 'const char* plink2::FirstPrechar(const char*, uint32_t)', inlined from 'const char* plink2::CurTokenEnd(const char*)' at ../include/plink2_string.h:837:10, inlined from 'const char* plink2::TokenLexK0(const char*, const uint32_t*, const uint32_t*, uint32_t, const char**, uint32_t*)' at ../include/plink2_string.h:1443:46, inlined from 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)' at ../plink2_adjust.cc:812:11: ../include/plink2_string.h:788:17: warning: 'line_start' may be used uninitialized [-Wmaybe-uninitialized] 788 | while (ctou32(*str_iter) >= char_code) { | ^~~~~~~~~ ../plink2_adjust.cc: In function 'plink2::PglErr plink2::AdjustFile(const AdjustFileInfo*, double, double, uint32_t, char*, char*)': ../plink2_adjust.cc:805:19: note: 'line_start' was declared here 805 | const char* line_start; | ^~~~~~~~~~ ../plink2_data.cc: In function 'plink2::PglErr plink2::PvarInfoResplitTmp(const uint32_t*, uint32_t, uint32_t, uint32_t, uint32_t, TextStream*, char*, char*)': ../plink2_data.cc:8757:47: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 8757 | const uint32_t info_slen = line_end - line_iter; | ~~~~~~~~~^~~~~~~~~~~ ../plink2_data.cc:8750:15: note: 'line_iter' was declared here 8750 | char* line_iter; | ^~~~~~~~~ ../plink2_fasta.cc: In function 'plink2::PglErr plink2::ProcessFa(const uintptr_t*, const char* const*, const uintptr_t*, const ChrInfo*, const char*, uint32_t, uint32_t, FaFlags, uint32_t, uint32_t, UnsortedVar*, uint32_t*, const char**, AlleleCode*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_fasta.cc:535:38: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 535 | unsigned char ucc = line_iter[0]; | ~~~~~~~~~~~^ ../plink2_fasta.cc:526:13: note: 'line_iter' was declared here 526 | char* line_iter; | ^~~~~~~~~ In file included from ../include/plink2_stats.h:20, from ../plink2_filter.cc:18: In function 'int32_t plink2::tokequal_k(const char*, const char*)', inlined from 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)' at ../plink2_filter.cc:747:27: ../include/plink2_string.h:448:18: warning: 'line_iter' may be used uninitialized [-Wmaybe-uninitialized] 448 | return memequal(s_read, s_const, s_const_slen) && IsSpaceOrEoln(s_read[s_const_slen]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../plink2_filter.cc: In function 'plink2::PglErr plink2::RmDup(const uintptr_t*, const ChrInfo*, const uint32_t*, const char* const*, const uint32_t*, const uint32_t*, const uintptr_t*, const char* const*, const uintptr_t*, const float*, const uintptr_t*, const uintptr_t*, const char* const*, const char*, const double*, const char*, uint32_t, uint32_t, uint32_t, uint32_t, uintptr_t, uint32_t, RmDupMode, uint32_t, uint32_t, PgenReader*, uintptr_t*, uint32_t*, char*, char*)': ../plink2_filter.cc:740:13: note: 'line_iter' was declared here 740 | char* line_iter; | ^~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../include/plink2_string.h:30, from ../plink2_cmdline.h:28, 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++/14/bits/stl_algo.h:1812:5, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = long unsigned int*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1900:5, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = long unsigned int*]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, 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:15405:5: /usr/include/c++/14/bits/stl_algo.h:1817:32: warning: array subscript 16 is outside array bounds of 'uint64_t [6]' {aka 'long unsigned int [6]'} [-Warray-bounds=] 1817 | 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:15382:14: note: at offset 128 into object 'parse_table' of size 48 15382 | 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_htable.o plink2_memory.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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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~a6.9-250129+dfsg/debian/plink2/usr/bin cd /build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' dh_installdocs -O--sourcedirectory=build_dynamic/ debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+dfsg' dh_installchangelogs debian/upstream.docs/upstream.changelog make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a6.9-250129+dfsg' dh_installexamples -O--sourcedirectory=build_dynamic/ debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+dfsg' dh_installman debian/plink2.1 dh_installman pgen_compress.1 make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-3), " make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a6.9-250129+dfsg' dh_md5sums -O--sourcedirectory=build_dynamic/ dh_builddeb -O--sourcedirectory=build_dynamic/ dpkg-deb: building package 'plink2' in '../plink2_2.00~a6.9-250129+dfsg-1_amd64.deb'. dpkg-deb: building package 'plink2-dbgsym' in '../plink2-dbgsym_2.00~a6.9-250129+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../plink2_2.00~a6.9-250129+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/1646424/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1646424/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/1646424 and its subdirectories I: Current time: Thu Jul 9 12:03:09 +14 2026 I: pbuilder-time-stamp: 1783548189 + false + set +x Wed Jul 8 22:03:09 UTC 2026 I: Signing ./b2/plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo as plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo.asc Wed Jul 8 22:03:09 UTC 2026 I: Signed ./b2/plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo as ./b2/plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo.asc Wed Jul 8 22:03:09 UTC 2026 - build #2 for plink2/trixie/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Wed Jul 8 22:03:09 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-O2OCyFrM, removing. /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8: total 108 drwxr-xr-x 2 jenkins jenkins 4096 Jun 5 15:11 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jun 5 15:40 b2 -rw-r--r-- 1 jenkins jenkins 2130 Feb 7 18:30 plink2_2.00~a6.9-250129+dfsg-1.dsc -rw------- 1 jenkins jenkins 93050 Jun 5 15:11 rbuildlog.64dUZtM /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/b1: total 42632 -rw-r--r-- 1 jenkins jenkins 89457 Jun 5 15:11 build.log -rw-r--r-- 1 jenkins jenkins 39097964 Jun 5 15:11 plink2-dbgsym_2.00~a6.9-250129+dfsg-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 58480 Jun 5 15:11 plink2_2.00~a6.9-250129+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2130 Jun 5 15:11 plink2_2.00~a6.9-250129+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 5336 Jun 5 15:11 plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6218 Jun 5 15:11 plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1775 Jun 5 15:11 plink2_2.00~a6.9-250129+dfsg-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 2736596 Jun 5 15:11 plink2_2.00~a6.9-250129+dfsg-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1941 Jun 5 15:11 plink2_2.00~a6.9-250129+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 1569072 Jun 5 15:11 plink2_2.00~a6.9-250129+dfsg.orig.tar.xz /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/b2: total 42576 -rw-r--r-- 1 jenkins jenkins 91400 Jun 5 15:40 build.log -rw-r--r-- 1 jenkins jenkins 39097964 Jun 5 15:40 plink2-dbgsym_2.00~a6.9-250129+dfsg-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 58480 Jun 5 15:40 plink2_2.00~a6.9-250129+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2130 Jun 5 15:40 plink2_2.00~a6.9-250129+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 5347 Jun 5 15:40 plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6229 Jun 5 15:40 plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1775 Jun 5 15:40 plink2_2.00~a6.9-250129+dfsg-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 2736596 Jun 5 15:40 plink2_2.00~a6.9-250129+dfsg-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1941 Jun 5 15:40 plink2_2.00~a6.9-250129+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 1569072 Jun 5 15:40 plink2_2.00~a6.9-250129+dfsg.orig.tar.xz Thu Jun 5 15:40:10 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Thu Jun 5 15:40:10 UTC 2025 I: plink2_2.00~a6.9-250129+dfsg-1_amd64.changes: Format: 1.8 Date: Fri, 07 Feb 2025 18:00:04 +0100 Source: plink2 Binary: plink2 plink2-dbgsym Architecture: amd64 Version: 2.00~a6.9-250129+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Dylan Aïssi Description: plink2 - whole-genome association analysis toolset Closes: 1048822 Changes: plink2 (2.00~a6.9-250129+dfsg-1) unstable; urgency=medium . * New upstream version 2.00~a6.9-250129+dfsg * Update string in watch file * Refresh patches * Update upstream changelog * Fix invalid-dep3-format-patch-wrong-last-update * Standards-Version: 4.7.0 (no changes needed) * Fix superfluous-file-pattern * Add a clean target (Closes: #1048822) Checksums-Sha1: 99eb0da07839b5de66a6f33be1d67a273624f679 39097964 plink2-dbgsym_2.00~a6.9-250129+dfsg-1_amd64.deb 198618fe880c987c299873bc5f5ce0360c5c52ad 5336 plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo 178056c2eb9a1b6b8af195968e806d1f2976421a 2736596 plink2_2.00~a6.9-250129+dfsg-1_amd64.deb Checksums-Sha256: 3b128566291c42e375349064e7646f492e5d70954a43c4bb633d36758fa1a009 39097964 plink2-dbgsym_2.00~a6.9-250129+dfsg-1_amd64.deb 7b114f0566fd4fd903f7e74efe5a866681a54d43de8648c2deb6b2020c0d9bf5 5336 plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo a0dc1c02f561e86a54c54ed1076d1c9297ebed0edf00ca9223e534b6b624403c 2736596 plink2_2.00~a6.9-250129+dfsg-1_amd64.deb Files: 5bc11a101e7f8b6c26906f37b0b653a3 39097964 debug optional plink2-dbgsym_2.00~a6.9-250129+dfsg-1_amd64.deb 4fa2e84648aa716229b74606625b9136 5336 science optional plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo 3f4f4c6eb9128c02c5e490d810b55b17 2736596 science optional plink2_2.00~a6.9-250129+dfsg-1_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/plink2_2.00~a6.9-250129+dfsg-1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/plink2_2.00~a6.9-250129+dfsg-1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/plink2_2.00~a6.9-250129+dfsg-1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/plink2_2.00~a6.9-250129+dfsg-1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/amd64/plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/plink2_2.00~a6.9-250129+dfsg-1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-06-05 15:11:32.026768328 +0000 +++ b2/build.log 2025-06-05 15:40:10.161934429 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jun 5 02:23:50 -12 2025 -I: pbuilder-time-stamp: 1749133430 +I: Current time: Thu Jul 9 11:34:33 +14 2026 +I: pbuilder-time-stamp: 1783546473 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ 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/1556179/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1646424/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 Jul 8 21:34 /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/1646424/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1646424/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=40 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='515326b2868c4f4e908046083fb47d1b' - 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='1556179' - PS1='# ' - PS2='> ' + INVOCATION_ID=5664b4d3de52415abe911ea99558db3d + 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=1646424 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.ukoJ02M8/pbuilderrc_TIEX --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.ukoJ02M8/b1 --logfile b1/build.log plink2_2.00~a6.9-250129+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://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/pbuilderrc_OUoI --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/b2 --logfile b2/build.log plink2_2.00~a6.9-250129+dfsg-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.22+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.22-1~bpo12+1 (2025-04-25) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1556179/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1646424/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -167,7 +199,7 @@ Get: 39 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 21.9 MB in 3s (6341 kB/s) +Fetched 21.9 MB in 0s (88.2 MB/s) Preconfiguring packages ... 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 ... 19850 files and directories currently installed.) @@ -350,7 +382,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/1646424/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1646424/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg-1_source.changes dpkg-buildpackage: info: source package plink2 dpkg-buildpackage: info: source version 2.00~a6.9-250129+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -362,7 +398,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+dfsg' dh_auto_clean - cd build_dynamic && make -j40 clean + cd build_dynamic && make -j42 clean make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+dfsg/build_dynamic' rm -f *.o rm -f plink2 @@ -393,7 +429,7 @@ make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' - cd build_dynamic && make -j40 "INSTALL=install --strip-program=true" SFX=-avx2 + cd build_dynamic && make -j42 "INSTALL=install --strip-program=true" SFX=-avx2 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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 @@ -467,7 +503,7 @@ make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' - cd build_dynamic && make -j40 "INSTALL=install --strip-program=true" SFX=-avx + cd build_dynamic && make -j42 "INSTALL=install --strip-program=true" SFX=-avx make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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 @@ -536,7 +572,7 @@ make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' - cd build_dynamic && make -j40 "INSTALL=install --strip-program=true" SFX=-sse4.1 + cd build_dynamic && make -j42 "INSTALL=install --strip-program=true" SFX=-sse4.1 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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 @@ -605,7 +641,7 @@ make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' - cd build_dynamic && make -j40 "INSTALL=install --strip-program=true" SFX=-ssse3 + cd build_dynamic && make -j42 "INSTALL=install --strip-program=true" SFX=-ssse3 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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 @@ -674,7 +710,7 @@ make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' - cd build_dynamic && make -j40 "INSTALL=install --strip-program=true" SFX=-sse3 + cd build_dynamic && make -j42 "INSTALL=install --strip-program=true" SFX=-sse3 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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 @@ -743,7 +779,7 @@ make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+dfsg' - cd build_dynamic && make -j40 "INSTALL=install --strip-program=true" SFX=-sse2 + cd build_dynamic && make -j42 "INSTALL=install --strip-program=true" SFX=-sse2 make[2]: Entering directory '/build/reproducible-path/plink2-2.00~a6.9-250129+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~a6.9-250129+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~a6.9-250129+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 @@ -856,8 +892,8 @@ make[1]: Leaving directory '/build/reproducible-path/plink2-2.00~a6.9-250129+dfsg' dh_md5sums -O--sourcedirectory=build_dynamic/ dh_builddeb -O--sourcedirectory=build_dynamic/ -dpkg-deb: building package 'plink2-dbgsym' in '../plink2-dbgsym_2.00~a6.9-250129+dfsg-1_amd64.deb'. dpkg-deb: building package 'plink2' in '../plink2_2.00~a6.9-250129+dfsg-1_amd64.deb'. +dpkg-deb: building package 'plink2-dbgsym' in '../plink2-dbgsym_2.00~a6.9-250129+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../plink2_2.00~a6.9-250129+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -865,12 +901,14 @@ 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/1646424/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1646424/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/1556179 and its subdirectories -I: Current time: Thu Jun 5 03:11:31 -12 2025 -I: pbuilder-time-stamp: 1749136291 +I: removing directory /srv/workspace/pbuilder/1646424 and its subdirectories +I: Current time: Thu Jul 9 12:03:09 +14 2026 +I: pbuilder-time-stamp: 1783548189 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/plink2_2.00~a6.9-250129+dfsg-1.diff: 80.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/plink2_2.00~a6.9-250129+dfsg-1.diff.gz b2/build.log: 89.4% -- replaced with stdout Compressing the 1st log... b1/build.log: 90.0% -- replaced with stdout Thu Jun 5 15:40:11 UTC 2025 I: diffoscope 297 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_plink2_trixie_amd64_1749138011 + touch /var/log/reproducible-builds/diffoscope_stamp_plink2_trixie_amd64_1749138011 + RESULT=0 + systemd-run '--description=diffoscope on plink2/2.00~a6.9-250129+dfsg-1 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_7-58799 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8 --run-session -c jenkins-reproducible-trixie-diffoscope-1b97240e-02b7-40b5-9172-8509c93a0aec -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/dbd-tmp-hkXfTU5 ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/plink2_2.00~a6.9-250129+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/plink2_2.00~a6.9-250129+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/plink2_2.00~a6.9-250129+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/b1/plink2_2.00~a6.9-250129+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/b2/plink2_2.00~a6.9-250129+dfsg-1_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_7-58799.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/plink2_2.00~a6.9-250129+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/plink2_2.00~a6.9-250129+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/plink2_2.00~a6.9-250129+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/b1/plink2_2.00~a6.9-250129+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ukoJ02M8/b2/plink2_2.00~a6.9-250129+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 diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.002s) 0.002s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 158ms CPU time consumed: 160ms _ _ _ ____ _ __ | (_)_ __ | | _|___ \ | '_ \| | | '_ \| |/ / __) | | |_) | | | | | | < / __/ | .__/|_|_|_| |_|_|\_\_____| |_| Thu Jun 5 15:40:12 UTC 2025 I: diffoscope 297 found no differences in the changes files, and a .buildinfo file also exists. Thu Jun 5 15:40:12 UTC 2025 I: plink2 from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-06-05 15:40:13] INFO: Starting at 2025-06-05 15:40:13.227627 [2025-06-05 15:40:13] INFO: Generating the pages of 1 package(s) [2025-06-05 15:40:13] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/plink2 didn't produce a buildlog, even though it has been built. [2025-06-05 15:40:13] INFO: Finished at 2025-06-05 15:40:13.438889, took: 0:00:00.211264 Thu Jun 5 15:40:13 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/plink2.html Thu Jun 5 15:40:13 UTC 2025 I: Removing signed plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo.asc files: removed './b1/plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo.asc' removed './b2/plink2_2.00~a6.9-250129+dfsg-1_amd64.buildinfo.asc' 1749138013 amd64 trixie plink2 Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/plink2_2.00~a6.9-250129+dfsg-1.rbuild.log: 87.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/plink2_2.00~a6.9-250129+dfsg-1.rbuild.log.gz [2025-06-05 15:40:13] INFO: Starting at 2025-06-05 15:40:13.694225 [2025-06-05 15:40:13] INFO: Generating the pages of 1 package(s) [2025-06-05 15:40:13] INFO: Finished at 2025-06-05 15:40:13.896703, took: 0:00:00.202480 All cleanup done. Thu Jun 5 15:40:13 UTC 2025 - total duration: 1h 16m 37s. Thu Jun 5 15:40:13 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-q3zvuGdf, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1h 16min 38.853s CPU time consumed: 4.949s