Sun Dec 22 05:13:59 UTC 2024 I: starting to build loki/trixie/arm64 on jenkins on '2024-12-22 05:13' Sun Dec 22 05:13:59 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_24/68092/console.log Sun Dec 22 05:13:59 UTC 2024 I: Downloading source for trixie/loki=2.4.7.4-12 --2024-12-22 05:14:00-- http://deb.debian.org/debian/pool/main/l/loki/loki_2.4.7.4-12.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1941 (1.9K) [text/prs.lines.tag] Saving to: ‘loki_2.4.7.4-12.dsc’ 0K . 100% 289M=0s 2024-12-22 05:14:00 (289 MB/s) - ‘loki_2.4.7.4-12.dsc’ saved [1941/1941] Sun Dec 22 05:14:00 UTC 2024 I: loki_2.4.7.4-12.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: loki Binary: loki, loki-doc Architecture: any all Version: 2.4.7.4-12 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/loki Vcs-Git: https://salsa.debian.org/med-team/loki.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: loki deb science optional arch=any loki-doc deb doc optional arch=all Checksums-Sha1: ce7d6ff3ca6159c329ca0f5f6ed633bf265acd33 904260 loki_2.4.7.4.orig.tar.gz 06f163a49053354e5c9e7bb676e45dc5c519d179 29448 loki_2.4.7.4-12.debian.tar.xz Checksums-Sha256: 78bc51f47fb756fcdc9ab55bc4c7dd649ee87aaa6bd9be87eac44e4a8eac9eb5 904260 loki_2.4.7.4.orig.tar.gz 5fb096f238640fdb0a3c6f093af26c450e8ff0910db94870138dda5c1bb6d10e 29448 loki_2.4.7.4-12.debian.tar.xz Files: 7764c55d3c3a33584a6f92740210b677 904260 loki_2.4.7.4.orig.tar.gz 23ef8c23a1aefeedb593172ed9c2f13b 29448 loki_2.4.7.4-12.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmdkXqERHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtH6LA//Q6U+BvJyoZubAlmAQkrfgLfiMvvEXtpO ZFqB5c1t6lAr/farsgyN7It1Wo07t/PnrlhXch14mwq025gXR7D/2RixRbR72SVR If07EJ0PE5VfS/v4TzbP51s74y35FrjJylTlJcea8btBXOLG36kJt6vKuOG5HaJm Go8w3G5fY3Vt5qWgzkn0JGc68jGWFAgPW/AqzJTu0UNUAcic0iSZp5E3vfnZOADV +8Dg8Dkst5heJVxy24YSTBDOTFgoV+AP6Xy1+U91MmhqZsxnnCW/CUKFy5CLCDOh MFn2oBktqdJHxiBbJbiHGZcww9tqlmKkIkttpU7fUyxPGdrUG8aPP0P3FlcRe1wf cKvUboXwJOMrGXD1zhq8vELjIQPRkRV0dF8TYiFidRCuVDrk6vwn3ZSq+5CP/1/d mZAkRHGuhzR0fRXrqiuStt+YmC2EZ8zqORx6n85UMMGOgnCYZCefdnAof9gxGhXL wDnTwNwN4i71PkbAzfeHy25bZ2sDrPcCbdHm+6Y4ghpJ0CyMDHObk+dT9oWFPRkR nYqQgfyGnDwLe5Y3cbnmOzHEMBSxH0ytK/wUrEUGsXHkTMdXY7ok4fJ3eSjIRX/9 Ax1KaBEB72eRUWJmg9r+lzAS/Cuv+eAq75aqZzRIOQ2P81hErJrzMgsItdhuAEhc StO4j/vMwwU= =deFd -----END PGP SIGNATURE----- Sun Dec 22 05:14:00 UTC 2024 I: Checking whether the package is not for us Sun Dec 22 05:14:00 UTC 2024 I: Starting 1st build on remote node codethink04-arm64.debian.net. Sun Dec 22 05:14:00 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Sun Dec 22 05:15:00 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Dec 21 17:14:02 -12 2024 I: pbuilder-time-stamp: 1734844442 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 [loki_2.4.7.4-12.dsc] I: copying [./loki_2.4.7.4.orig.tar.gz] I: copying [./loki_2.4.7.4-12.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Dec 19 17:57:53 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./loki_2.4.7.4-12.dsc: no acceptable signature found dpkg-source: info: extracting loki in loki-2.4.7.4 dpkg-source: info: unpacking loki_2.4.7.4.orig.tar.gz dpkg-source: info: unpacking loki_2.4.7.4-12.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 10_utils.patch dpkg-source: info: applying 10_lex.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying gcc-4.1.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2091857/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='6536ed969c1b4c77a7fb77be6d4da2d9' 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='2091857' 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.ZuUiLHHG/pbuilderrc_BLKf --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.ZuUiLHHG/b1 --logfile b1/build.log loki_2.4.7.4-12.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2091857/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: arm64 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) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20083 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. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{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, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 19.4 MB of archives. After unpacking 77.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-3 [198 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-6 [1130 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-12 [91.4 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-3 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-3 [1532 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Fetched 19.4 MB in 0s (126 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20083 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-3_arm64.deb ... Unpacking gettext-base (0.22.5-3) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-6_arm64.deb ... Unpacking groff-base (1.23.0-6) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-12_arm64.deb ... Unpacking bsdextrautils (2.40.2-12) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-3_all.deb ... Unpacking autopoint (0.22.5-3) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../23-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-3_arm64.deb ... Unpacking gettext (0.22.5-3) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-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 .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-12) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-3) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-3) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-3) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-6) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-4) ... 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/loki-2.4.7.4/ && 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 > ../loki_2.4.7.4-12_source.changes dpkg-buildpackage: info: source package loki dpkg-buildpackage: info: source version 2.4.7.4-12 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:4: warning: The macro 'AC_CONFIG_HEADER' is obsolete. configure.in:4: You should run autoupdate. ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from... configure.in:4: the top level configure.in:40: warning: AC_PROG_LEX without either yywrap or noyywrap is obsolete ./lib/autoconf/programs.m4:743: _AC_PROG_LEX is expanded from... ./lib/autoconf/programs.m4:736: AC_PROG_LEX is expanded from... configure.in:40: the top level configure.in:57: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.in:57: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.in:57: the top level configure.in:111: warning: AC_OUTPUT should be used without arguments. configure.in:111: You should run autoupdate. autoheader: warning: autoconf input should be named 'configure.ac', not 'configure.in' debian/rules override_dh_auto_configure-arch make[1]: Entering directory '/build/reproducible-path/loki-2.4.7.4' dh_auto_configure -- --exec_prefix=/build/reproducible-path/loki-2.4.7.4/debian/loki/usr ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --exec_prefix=/build/reproducible-path/loki-2.4.7.4/debian/loki/usr checking whether make sets $(MAKE)... yes checking for DMALLOC library Looking for dmalloc.h in ${prefix}/include and libdmalloc.a in ${prefix}/lib/aarch64-linux-gnu Looking for dmalloc.h in /usr/local/include and libdmalloc.a in /usr/local/lib Looking for dmalloc.h in /usr/include and libdmalloc.a in /usr/lib Looking for dmalloc.h in /build/reproducible-path/loki-2.4.7.4/debian/.debhelper/generated/_source/home/include and libdmalloc.a in /build/reproducible-path/loki-2.4.7.4/debian/.debhelper/generated/_source/home/lib checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for flex... no checking for lex... no checking for bison... no checking for byacc... no checking for ranlib... /usr/bin/ranlib checking for ar... /usr/bin/ar checking for sed... /usr/bin/sed checking for cp... /usr/bin/cp checking for grep... /usr/bin/grep checking for mv... /usr/bin/mv checking for gzip... /usr/bin/gzip checking for chmod... /usr/bin/chmod checking for perl... /usr/bin/perl checking for makedepend... : checking for sin in -lm... yes checking for accept in -lsocket... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for sys/wait.h that is POSIX.1 compatible... yes checking for fcntl.h... yes checking for limits.h... yes checking for values.h... yes checking for unistd.h... (cached) yes checking for sys/systeminfo.h... no checking for mode_t... yes checking for off_t... yes checking for pid_t... yes checking for size_t... yes checking for working alloca.h... yes checking for alloca... yes checking for socklen_t... no checking for an ANSI C-conforming const... yes checking for vprintf... yes checking for memcpy... yes checking for regcomp... yes checking for strtod... yes checking for strtol... yes checking for gethostname... yes checking for popen... yes checking for snprintf... yes checking for atexit... yes checking for memmove... yes configure: creating ./config.status config.status: creating Makefile config.status: creating libsrc/Makefile config.status: creating prepsrc/Makefile config.status: creating prepsrc/compat/Makefile config.status: creating lokisrc/Makefile config.status: creating test/Makefile config.status: creating utils/Makefile config.status: creating include/config.h make[1]: Leaving directory '/build/reproducible-path/loki-2.4.7.4' debian/rules override_dh_auto_configure-indep make[1]: Entering directory '/build/reproducible-path/loki-2.4.7.4' # do nothing here make[1]: Leaving directory '/build/reproducible-path/loki-2.4.7.4' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/loki-2.4.7.4' # nothing to do here make[1]: Leaving directory '/build/reproducible-path/loki-2.4.7.4' dh_auto_build -Nloki-doc make -j12 make[1]: Entering directory '/build/reproducible-path/loki-2.4.7.4' for subdir in libsrc prepsrc lokisrc utils; do \ (cd $subdir; make depend) \ done make[2]: Entering directory '/build/reproducible-path/loki-2.4.7.4/libsrc' : -I../include/ io_stuff.c ranlib.c genrand.c ran_xtra.c mkbackup.c strsep.c utils.c remember.c peel_utils.c qsort.c min_deg.c bin_tree.c getopt_long.c touch depend make[2]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/libsrc' make[2]: Entering directory '/build/reproducible-path/loki-2.4.7.4/prepsrc' : -I../include control_parse.c control_lex.c check_het.c test_het.c prep.c calc_nrm.c write_report.c prep_utils.c gen_elim.c prep_do_peel_op.c write_data.c touch depend make[2]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/prepsrc' make[2]: Entering directory '/build/reproducible-path/loki-2.4.7.4/lokisrc' : -I../include loki.c loki_peel.c loki_init.c alloc_loki.c loki_sample.c loki_pen.c loki_tlmoves.c meiosis_scan.c loki_identity.c sample_rand.c sample_effects.c loki_setup.c loki_dump.c sample_cens.c handle_res.c print_data.c calc_var_locus.c loki_output.c sample_nu.c loki_complex_peel.c loki_npl.c loki_simple_sample.c loki_simple_peel.c loki_trait_simple_peel.c loki_trait_simple_sample.c get_par_probs.c read_solar_idfile.c peel_to_par.c update_segs.c param_parse.c param_lex.c read_binfiles.c loki_utils.c kinship.c genedrop.c mat_utils.c output_recomb.c seg_pen.c gen_pen.c loki_ibd.c get_founders.c pass_founder_genes.c touch depend make[2]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/lokisrc' make[2]: Entering directory '/build/reproducible-path/loki-2.4.7.4/utils' : -I../include qavg.c hist.c touch depend make[2]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/utils' touch depend for subdir in libsrc prepsrc lokisrc utils; do \ (cd $subdir; make) \ done make[2]: Entering directory '/build/reproducible-path/loki-2.4.7.4/libsrc' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o io_stuff.o io_stuff.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ranlib.o ranlib.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o genrand.o genrand.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ran_xtra.o ran_xtra.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mkbackup.o mkbackup.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o strsep.o strsep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o utils.o utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o remember.o remember.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o peel_utils.o peel_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o qsort.o qsort.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o min_deg.o min_deg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin_tree.o bin_tree.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o getopt_long.o getopt_long.c /usr/bin/ar cr libgen.a io_stuff.o ranlib.o genrand.o ran_xtra.o mkbackup.o strsep.o utils.o remember.o peel_utils.o qsort.o min_deg.o bin_tree.o getopt_long.o /usr/bin/ranlib libgen.a make[2]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/libsrc' make[2]: Entering directory '/build/reproducible-path/loki-2.4.7.4/prepsrc' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o control_parse.o control_parse.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o control_lex.o control_lex.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o read_data.o read_data.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o setup_ped.o setup_ped.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o recode_fact.o recode_fact.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cleanup.o cleanup.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o restrict_data.o restrict_data.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o match_records.o match_records.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o init_fam.o init_fam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o output_data.o output_data.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o get_marker_name.o get_marker_name.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prep.o prep.c setup_ped.c: In function 'setup_pedigree': setup_ped.c:426:83: warning: this statement may fall through [-Wimplicit-fallthrough=] 426 | if(i!=id) { | ^ setup_ped.c:430:74: note: here 430 | default: | ^~~~~~~ setup_ped.c: In function 'check_ymark': setup_ped.c:1135:42: warning: pointer 'list' may be used after 'free' [-Wuse-after-free] 1135 | if(pl->type==LINK_Y) list[ny++]=locus; | ^ setup_ped.c:1127:9: note: call to 'free' here 1127 | free(list); | ^~~~~~~~~~ setup_ped.c:1141:17: warning: pointer 'list' may be used after 'free' [-Wuse-after-free] 1141 | do_yprint(i,list,ny); | ^~~~~~~~~~~~~~~~~~~~ setup_ped.c:1127:9: note: call to 'free' here 1127 | free(list); | ^~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o calc_nrm.o calc_nrm.c lex.yy.c:2062:12: warning: 'input' defined but not used [-Wunused-function] gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o write_report.o write_report.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prep_utils.o prep_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gen_elim.o gen_elim.c write_report.c: In function 'WriteReport': write_report.c:286:28: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] 286 | if(!elem->type&(ST_MODEL|ST_TRAIT)) continue; | ^~~~~~~~~~~ write_report.c:300:28: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] 300 | if(!elem->type&(ST_MODEL|ST_TRAIT)) continue; | ^~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prep_do_peel_op.o prep_do_peel_op.c gen_elim.c: In function 'min_degree': gen_elim.c:1075:31: warning: variable 'best_fg' set but not used [-Wunused-but-set-variable] 1075 | int x,i1,k1,k2,*trans,best_fg=0; | ^~~~~~~ gen_elim.c: In function 'find_sequence': gen_elim.c:1156:24: warning: variable 'mark' set but not used [-Wunused-but-set-variable] 1156 | struct Marker *mark; | ^~~~ gen_elim.c:1155:31: warning: variable 'order1' set but not used [-Wunused-but-set-variable] 1155 | int *g_perm,*order=0,*order1; | ^~~~~~ gen_elim.c: In function 'logical_peel': gen_elim.c:1268:24: warning: variable 'mark' set but not used [-Wunused-but-set-variable] 1268 | struct Marker *mark; | ^~~~ gen_elim.c:1266:34: warning: variable 'pp1' set but not used [-Wunused-but-set-variable] 1266 | struct Peelseq_Head *pp,*pp1; | ^~~ prep_do_peel_op.c: In function 'do_peel_op': prep_do_peel_op.c:238:26: warning: variable 'fill' set but not used [-Wunused-but-set-variable] 238 | double max_terms,fill; | ^~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o write_data.o write_data.c control_lex.l: In function 'yy_orig_lex': control_lex.l:106:11: warning: '__builtin_strncpy' specified bound 4096 equals destination size [-Wstringop-truncation] 106 | (void)strncpy(linebuf,yytext+1,LINEBUFSIZE); | ^ control_lex.l:95:11: warning: '__builtin_strncpy' specified bound 4096 equals destination size [-Wstringop-truncation] 95 | (void)strncpy(linebuf,yytext,LINEBUFSIZE); | ^ /usr/bin/ar cr libprep.a control_parse.o control_lex.o read_data.o setup_ped.o recode_fact.o cleanup.o restrict_data.o match_records.o init_fam.o output_data.o get_marker_name.o /usr/bin/ranlib libprep.a (cd compat; make) make[3]: Entering directory '/build/reproducible-path/loki-2.4.7.4/prepsrc/compat' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../../include -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o compat.o compat.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../../include -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o merlin.o merlin.c merlin.c: In function 'process_qtdt': merlin.c:59:60: warning: parameter 'error_check' set but not used [-Wunused-but-set-parameter] 59 | int process_qtdt(int argc,char *argv[],char **LogFile,int *error_check,loki_time *lt) | ~~~~~^~~~~~~~~~~ merlin.c:162:38: warning: this statement may fall through [-Wimplicit-fallthrough=] 162 | nmark++; | ~~~~~^~ merlin.c:163:26: note: here 163 | case 'A': | ^~~~ /usr/bin/ar cr libcompat.a compat.o merlin.o /usr/bin/ranlib libcompat.a make[3]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/prepsrc/compat' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -o prep prep.o calc_nrm.o write_report.o prep_utils.o gen_elim.o prep_do_peel_op.o write_data.o -Wl,-z,relro -Wl,-z,now -L. -L../libsrc -lprep -lgen -Lcompat -lcompat -lm make[2]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/prepsrc' make[2]: Entering directory '/build/reproducible-path/loki-2.4.7.4/lokisrc' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o param_parse.o param_parse.c gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -DYY_NO_UNPUT param_lex.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o read_binfiles.o read_binfiles.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_utils.o loki_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kinship.o kinship.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o genedrop.o genedrop.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mat_utils.o mat_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o output_recomb.o output_recomb.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seg_pen.o seg_pen.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gen_pen.o gen_pen.c gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -DIBD_COMPRESS_PROG=\"/usr/bin/gzip\" loki_ibd.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o get_founders.o get_founders.c param_lex.c: In function 'yy_get_next_buffer': param_lex.c:641:32: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 641 | for ( n = 0; n < max_size && \ | ^ param_lex.c:1161:17: note: in expansion of macro 'YY_INPUT' 1161 | YY_INPUT( (&YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[number_to_move]), | ^~~~~~~~ param_lex.c: At top level: param_lex.c:1301:16: warning: 'input' defined but not used [-Wunused-function] 1301 | static int input (void) | ^~~~~ param_lex.c:1260:17: warning: 'yyunput' defined but not used [-Wunused-function] 1260 | static void yyunput (int c, register char * yy_bp ) | ^~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o pass_founder_genes.o pass_founder_genes.c loki_ibd.c: In function 'SetupIBD': loki_ibd.c:215:102: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=] 215 | fprintf(stderr,"Asked for 2*n_locations*n_pairs*sizeof(int)=2*%d*%d*%d=%d bytes\n",j,np,sizeof(int),2*j*np*sizeof(int)); | ~^ ~~~~~~~~~~~ | | | | int long unsigned int | %ld loki_ibd.c:215:105: warning: format '%d' expects argument of type 'int', but argument 6 has type 'long unsigned int' [-Wformat=] 215 | fprintf(stderr,"Asked for 2*n_locations*n_pairs*sizeof(int)=2*%d*%d*%d=%d bytes\n",j,np,sizeof(int),2*j*np*sizeof(int)); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld gen_pen.c: In function 'calc_degree': gen_pen.c:321:31: warning: variable 'k2' set but not used [-Wunused-but-set-variable] 321 | int i1,j,j1,j2,k=0,k1,k2; | ^~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki.o loki.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_peel.o loki_peel.c pass_founder_genes.c: In function 'pass_founder_genes': pass_founder_genes.c:35:47: warning: variable 'locus1' set but not used [-Wunused-but-set-variable] 35 | int i,i1,j,s,**genes,**seg,comp,cs,nc,locus1; | ^~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_init.o loki_init.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alloc_loki.o alloc_loki.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_sample.o loki_sample.c param_lex.l: In function 'yylex': param_lex.l:91:11: warning: 'strncpy' specified bound 512 equals destination size [-Wstringop-truncation] 91 | (void)strncpy(linebuf,yytext+1,512); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ param_lex.l:64:11: warning: 'strncpy' specified bound 512 equals destination size [-Wstringop-truncation] 64 | (void)strncpy(linebuf,yytext,512); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ loki_init.c: In function 'InitValues': loki_init.c:125:38: warning: this statement may fall through [-Wimplicit-fallthrough=] 125 | tau_beta[mod]*=residual_var[mod]; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ loki_init.c:126:18: note: here 126 | case 1: | ^~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_pen.o loki_pen.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_tlmoves.o loki_tlmoves.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o meiosis_scan.o meiosis_scan.c pass_founder_genes.c: In function 'pass_founder_genes2': pass_founder_genes.c:447:44: warning: 'g[0]' may be used uninitialized [-Wmaybe-uninitialized] 447 | for(s=0;s<2;s++) if(genes[s][i]!=g[s]) { | ^ pass_founder_genes.c:426:32: note: 'g[0]' was declared here 426 | int i,i1,j,k,s,**genes,g[2],fg=0,*hap; | ^ pass_founder_genes.c:447:44: warning: 'g[1]' may be used uninitialized [-Wmaybe-uninitialized] 447 | for(s=0;s<2;s++) if(genes[s][i]!=g[s]) { | ^ pass_founder_genes.c:426:32: note: 'g[1]' was declared here 426 | int i,i1,j,k,s,**genes,g[2],fg=0,*hap; | ^ loki_tlmoves.c: In function 'sample_mpos': loki_tlmoves.c:152:36: warning: variable 'idd' set but not used [-Wunused-but-set-variable] 152 | int i,j,locus,k2=-1,k3,ids,idd,sx,**seg,s,s1; | ^~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_identity.o loki_identity.c loki_peel.c: In function 'peel_locus': loki_peel.c:427:43: warning: 'z' may be used uninitialized [-Wmaybe-uninitialized] 427 | if(z== -DBL_MAX) { | ^ loki_peel.c:145:26: note: 'z' was declared here 145 | double like=0.0,like1,z,z1,theta,Mtp[2],Ptp[2],*pos,*eff,**count,*tpp,*freq1,*count1; | ^ meiosis_scan.c: In function 'meiosis_scan': meiosis_scan.c:162:76: warning: variable 'n_comp1' set but not used [-Wunused-but-set-variable] 162 | int sex,kid,**seg,**seg1,kid1,nkids1,*kids1,lffg,symflag,n_qtl,qtl,n_comp1; | ^~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_rand.o sample_rand.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_effects.o sample_effects.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_setup.o loki_setup.c loki_tlmoves.c:210:61: warning: 'x' may be used uninitialized [-Wmaybe-uninitialized] 210 | r=.5*(1.0-exp(.02*(x-x1))); | ~~^~~~ loki_tlmoves.c:153:48: note: 'x' was declared here 153 | double pp[2][50],ct1[2][50],ct2[2][50],x,x1,r,z,z1; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_dump.o loki_dump.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_cens.o sample_cens.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o handle_res.o handle_res.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o print_data.o print_data.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o calc_var_locus.o calc_var_locus.c loki_tlmoves.c: In function 'get_tl_position': loki_tlmoves.c:623:17: warning: 'z' may be used uninitialized [-Wmaybe-uninitialized] 623 | prior[i]+=z; | ^~ loki_tlmoves.c:606:16: note: 'z' was declared here 606 | double z,z1,z2,map_length; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_output.o loki_output.c loki_output.c: In function 'OutputSample': loki_output.c:345:17: warning: this statement may fall through [-Wimplicit-fallthrough=] 345 | OutputSample_2(fptr,lp); | ^~~~~~~~~~~~~~~~~~~~~~~ loki_output.c:346:10: note: here 346 | case OUTPUT_VERSION_2_3: | ^~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_nu.o sample_nu.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_complex_peel.o loki_complex_peel.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_npl.o loki_npl.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_simple_sample.o loki_simple_sample.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_simple_peel.o loki_simple_peel.c loki_complex_peel.c: In function 'loki_complex_peelop': loki_complex_peel.c:458:169: warning: format '%d' expects argument of type 'int', but argument 8 has type 'long unsigned int' [-Wformat=] 458 | (void)fprintf(stderr,"\nToo many individuals in output R-Function for marker %s\nn_peel = %d, n_all = %d, n_bits1 = %d, required size = %d, LONG_BIT = %d\n",marker[locus].name,n_peel,n_all,n_bits1,n_peel*n_bits1,LK_LONG_BIT); | ~^ | | | int | %ld loki_complex_peel.c:379:16: warning: variable 'max_terms' set but not used [-Wunused-but-set-variable] 379 | double max_terms,*tp,prob=0.0,z,p1,Konst=0.0; | ^~~~~~~~~ loki_simple_sample.c: In function 'loki_simple_sample': loki_simple_sample.c:25:58: warning: variable 'tpp2' set but not used [-Wunused-but-set-variable] 25 | double *tp,p1,p2,z,z1,prob=0.0,pp[4],*tmp,*tpp1,*tpp2; | ^~~~ loki_simple_sample.c:25:52: warning: variable 'tpp1' set but not used [-Wunused-but-set-variable] 25 | double *tp,p1,p2,z,z1,prob=0.0,pp[4],*tmp,*tpp1,*tpp2; | ^~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_trait_simple_peel.o loki_trait_simple_peel.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_trait_simple_sample.o loki_trait_simple_sample.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o get_par_probs.o get_par_probs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o read_solar_idfile.o read_solar_idfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o peel_to_par.o peel_to_par.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o update_segs.o update_segs.c /usr/bin/ar cr libloki.a param_parse.o param_lex.o read_binfiles.o loki_utils.o kinship.o genedrop.o mat_utils.o output_recomb.o seg_pen.o gen_pen.o loki_ibd.o get_founders.o pass_founder_genes.o /usr/bin/ranlib libloki.a loki_simple_peel.c: In function 'loki_simple_peelop': loki_simple_peel.c:601:54: warning: 'cm[0]' may be used uninitialized [-Wmaybe-uninitialized] 601 | id_set2[i]=(cm[X_MAT]&a1)?lump[X_MAT]:i; | ~~~~~~~~~~^~~~ loki_simple_peel.c:27:28: note: 'cm[0]' was declared here 27 | lk_ulong a,b,a1,b1,cm[2],*tmp_idx,*tmp_idx1,*cmm[2],mask; | ^~ loki_simple_peel.c:600:54: warning: 'cm[1]' may be used uninitialized [-Wmaybe-uninitialized] 600 | id_set1[i]=(cm[X_PAT]&a1)?l:i1; | ~~~~~~~~~~^~~~ loki_simple_peel.c:27:28: note: 'cm[1]' was declared here 27 | lk_ulong a,b,a1,b1,cm[2],*tmp_idx,*tmp_idx1,*cmm[2],mask; | ^~ loki_simple_peel.c: In function 'loki_simple_peelop_x': loki_simple_peel.c:1279:54: warning: 'cm[0]' may be used uninitialized [-Wmaybe-uninitialized] 1279 | id_set2[i]=(cm[X_MAT]&a1)?lump[X_MAT]:i; | ~~~~~~~~~~^~~~ loki_simple_peel.c:723:28: note: 'cm[0]' was declared here 723 | lk_ulong a,b,a1,b1,cm[2],*tmp_idx,*tmp_idx1,*cmm[2],mask; | ^~ loki_simple_peel.c:1278:54: warning: 'cm[1]' may be used uninitialized [-Wmaybe-uninitialized] 1278 | id_set1[i]=(cm[X_PAT]&a1)?l:i1; | ~~~~~~~~~~^~~~ loki_simple_peel.c:723:28: note: 'cm[1]' was declared here 723 | lk_ulong a,b,a1,b1,cm[2],*tmp_idx,*tmp_idx1,*cmm[2],mask; | ^~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -o loki loki.o loki_peel.o loki_init.o alloc_loki.o loki_sample.o loki_pen.o loki_tlmoves.o meiosis_scan.o loki_identity.o sample_rand.o sample_effects.o loki_setup.o loki_dump.o sample_cens.o handle_res.o print_data.o calc_var_locus.o loki_output.o sample_nu.o loki_complex_peel.o loki_npl.o loki_simple_sample.o loki_simple_peel.o loki_trait_simple_peel.o loki_trait_simple_sample.o get_par_probs.o read_solar_idfile.o peel_to_par.o update_segs.o -Wl,-z,relro -Wl,-z,now -L. -L../libsrc -lloki -lgen -lm make[2]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/lokisrc' make[2]: Entering directory '/build/reproducible-path/loki-2.4.7.4/utils' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -o qavg qavg.c -Wl,-z,relro -Wl,-z,now -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -o hist hist.c -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/utils' make[1]: Leaving directory '/build/reproducible-path/loki-2.4.7.4' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/loki-2.4.7.4' cd test; if [ -f Makefile ] ; then make ; fi make[2]: Entering directory '/build/reproducible-path/loki-2.4.7.4/test' /usr/bin/sed s+SED+/usr/bin/sed+g loki_test.in|/usr/bin/sed s+PREP+../prepsrc/prep+g|\ /usr/bin/sed s+LOKI+../lokisrc/loki+g|/usr/bin/sed s+GREP+/usr/bin/grep+g > tmp cp tmp loki_test && chmod 755 loki_test /usr/bin/sed s+COMPRESS+/usr/bin/gzip+g control_gaw9.in > tmp cp tmp control_gaw9 JV test 1 ... OK JV test 2 ... OK JV censored data test ... OK LM sample test ... OK Major gene test ... OK GAW9 test ... OK JV restart test ... OK make[2]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/test' make[1]: Leaving directory '/build/reproducible-path/loki-2.4.7.4' dh_auto_test -Nloki create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/reproducible-path/loki-2.4.7.4' dh_auto_install -a make -j12 install DESTDIR=/build/reproducible-path/loki-2.4.7.4/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/loki-2.4.7.4' for subdir in libsrc prepsrc lokisrc utils; do \ (cd $subdir; make) \ done make[3]: Entering directory '/build/reproducible-path/loki-2.4.7.4/libsrc' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/libsrc' make[3]: Entering directory '/build/reproducible-path/loki-2.4.7.4/prepsrc' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/prepsrc' make[3]: Entering directory '/build/reproducible-path/loki-2.4.7.4/lokisrc' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/lokisrc' make[3]: Entering directory '/build/reproducible-path/loki-2.4.7.4/utils' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/utils' for subdir in prepsrc lokisrc utils; do \ (cd $subdir; make install) \ done make[3]: Entering directory '/build/reproducible-path/loki-2.4.7.4/prepsrc' mkdir ../bin for file in prep; do \ /usr/bin/cp $file /build/reproducible-path/loki-2.4.7.4/debian/loki/usr/bin/; \ /usr/bin/chmod 755 /build/reproducible-path/loki-2.4.7.4/debian/loki/usr/bin/$file ; \ done make[3]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/prepsrc' make[3]: Entering directory '/build/reproducible-path/loki-2.4.7.4/lokisrc' for file in loki; do \ /usr/bin/cp $file /build/reproducible-path/loki-2.4.7.4/debian/loki/usr/bin/; \ /usr/bin/chmod 755 /build/reproducible-path/loki-2.4.7.4/debian/loki/usr/bin/$file ; \ done make[3]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/lokisrc' make[3]: Entering directory '/build/reproducible-path/loki-2.4.7.4/utils' for file in ext count dist freq sort_error; do \ /usr/bin/sed 's!+PERLPROG+!/usr/bin/perl!' $file.in > /build/reproducible-path/loki-2.4.7.4/debian/loki/usr/bin/loki_$file; \ /usr/bin/chmod 755 /build/reproducible-path/loki-2.4.7.4/debian/loki/usr/bin/loki_$file; \ done for file in qavg hist; do \ /usr/bin/cp $file /build/reproducible-path/loki-2.4.7.4/debian/loki/usr/bin/; \ /usr/bin/chmod 755 /build/reproducible-path/loki-2.4.7.4/debian/loki/usr/bin/$file ; \ done make[3]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/utils' make[2]: Leaving directory '/build/reproducible-path/loki-2.4.7.4' make install prefix=/build/reproducible-path/loki-2.4.7.4/debian/loki/usr bindir=/build/reproducible-path/loki-2.4.7.4/debian/loki/usr/bin LDFLAGS="-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/loki-2.4.7.4' for subdir in libsrc prepsrc lokisrc utils; do \ (cd $subdir; make) \ done make[3]: Entering directory '/build/reproducible-path/loki-2.4.7.4/libsrc' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/libsrc' make[3]: Entering directory '/build/reproducible-path/loki-2.4.7.4/prepsrc' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/prepsrc' make[3]: Entering directory '/build/reproducible-path/loki-2.4.7.4/lokisrc' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/lokisrc' make[3]: Entering directory '/build/reproducible-path/loki-2.4.7.4/utils' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/utils' for subdir in prepsrc lokisrc utils; do \ (cd $subdir; make install) \ done make[3]: Entering directory '/build/reproducible-path/loki-2.4.7.4/prepsrc' for file in prep; do \ /usr/bin/cp $file /build/reproducible-path/loki-2.4.7.4/debian/loki/usr/bin/; \ /usr/bin/chmod 755 /build/reproducible-path/loki-2.4.7.4/debian/loki/usr/bin/$file ; \ done make[3]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/prepsrc' make[3]: Entering directory '/build/reproducible-path/loki-2.4.7.4/lokisrc' for file in loki; do \ /usr/bin/cp $file /build/reproducible-path/loki-2.4.7.4/debian/loki/usr/bin/; \ /usr/bin/chmod 755 /build/reproducible-path/loki-2.4.7.4/debian/loki/usr/bin/$file ; \ done make[3]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/lokisrc' make[3]: Entering directory '/build/reproducible-path/loki-2.4.7.4/utils' for file in ext count dist freq sort_error; do \ /usr/bin/sed 's!+PERLPROG+!/usr/bin/perl!' $file.in > /build/reproducible-path/loki-2.4.7.4/debian/loki/usr/bin/loki_$file; \ /usr/bin/chmod 755 /build/reproducible-path/loki-2.4.7.4/debian/loki/usr/bin/loki_$file; \ done for file in qavg hist; do \ /usr/bin/cp $file /build/reproducible-path/loki-2.4.7.4/debian/loki/usr/bin/; \ /usr/bin/chmod 755 /build/reproducible-path/loki-2.4.7.4/debian/loki/usr/bin/$file ; \ done make[3]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/utils' make[2]: Leaving directory '/build/reproducible-path/loki-2.4.7.4' make[1]: Leaving directory '/build/reproducible-path/loki-2.4.7.4' debian/rules override_dh_auto_install-indep make[1]: Entering directory '/build/reproducible-path/loki-2.4.7.4' # nothing to do here make[1]: Leaving directory '/build/reproducible-path/loki-2.4.7.4' dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman-arch make[1]: Entering directory '/build/reproducible-path/loki-2.4.7.4' dh_installman -a for man in hist.1 loki_count.1 loki_dist.1 loki_ext.1 loki_freq.1 loki_sort_error.1 prep.1 qavg.1 ; do \ ln -s loki.1.gz debian/loki/usr/share/man/man1/${man}.gz ; \ done make[1]: Leaving directory '/build/reproducible-path/loki-2.4.7.4' dh_installman -Nloki dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package loki: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package loki: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'loki' in '../loki_2.4.7.4-12_arm64.deb'. dpkg-deb: building package 'loki-dbgsym' in '../loki-dbgsym_2.4.7.4-12_arm64.deb'. dpkg-deb: building package 'loki-doc' in '../loki-doc_2.4.7.4-12_all.deb'. dpkg-genbuildinfo --build=binary -O../loki_2.4.7.4-12_arm64.buildinfo dpkg-genchanges --build=binary -O../loki_2.4.7.4-12_arm64.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: not including original 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/2091857 and its subdirectories I: Current time: Sat Dec 21 17:14:59 -12 2024 I: pbuilder-time-stamp: 1734844499 Sun Dec 22 05:15:01 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Sun Dec 22 05:15:01 UTC 2024 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Sun Dec 22 05:16:07 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Sun Dec 22 05:16:08 UTC 2024 I: loki_2.4.7.4-12_arm64.changes: Format: 1.8 Date: Thu, 19 Dec 2024 18:36:19 +0100 Source: loki Binary: loki loki-dbgsym loki-doc Architecture: arm64 all Version: 2.4.7.4-12 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: loki - MCMC linkage analysis on general pedigrees loki-doc - MCMC linkage analysis on general pedigrees (PS manual) Closes: 1090794 Changes: loki (2.4.7.4-12) unstable; urgency=medium . * Fix gcc-14 build issue Closes: #1090794 * Standards-Version: 4.7.0 (routine-update) Checksums-Sha1: fdc6c0aa10b8ad8c0deae358856faaa4b93dea89 700796 loki-dbgsym_2.4.7.4-12_arm64.deb 3bb1e62bca71b80a7c2f34ebabfc369181f9df32 224192 loki-doc_2.4.7.4-12_all.deb c3b76000a8769bb3f78166bb18266ba0b27e1fa7 5245 loki_2.4.7.4-12_arm64.buildinfo 1eb614e2f604b1937c338915de3e56aac82a3582 334756 loki_2.4.7.4-12_arm64.deb Checksums-Sha256: 63d4702d44b5bbcf1bc3dd70027224030359f04a8fc6d4eeed2fa1107af5a2fd 700796 loki-dbgsym_2.4.7.4-12_arm64.deb bd5261db10fd419de220b49ca749f3c1037d34233942297f474e2d0e961b38c2 224192 loki-doc_2.4.7.4-12_all.deb 1ea84d85e156e175057755e1c171ea13f6fab15f9327e087d9797005810a91a9 5245 loki_2.4.7.4-12_arm64.buildinfo d9f9d178d45485dc74eb120b4ebfa907430909e465b200b18def3b3f7f7c73b1 334756 loki_2.4.7.4-12_arm64.deb Files: 45c76c9e22a6ebce636d43dcdba2ccfe 700796 debug optional loki-dbgsym_2.4.7.4-12_arm64.deb 2dd7ba8e613746a951d337643bb537be 224192 doc optional loki-doc_2.4.7.4-12_all.deb 7ddbbca1d06fe7c39714d8a606281c32 5245 science optional loki_2.4.7.4-12_arm64.buildinfo dc91c5b0e639314c9d2c9df102595a48 334756 science optional loki_2.4.7.4-12_arm64.deb Sun Dec 22 05:16:09 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_24-68092.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ZuUiLHHG/loki_2.4.7.4-12.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ZuUiLHHG/loki_2.4.7.4-12.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ZuUiLHHG/loki_2.4.7.4-12.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ZuUiLHHG/b1/loki_2.4.7.4-12_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ZuUiLHHG/b2/loki_2.4.7.4-12_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.342s) 0.342s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.026s) 0.026s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 639ms CPU time consumed: 637ms Sun Dec 22 05:16:10 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Sun Dec 22 05:16:10 UTC 2024 I: loki from trixie built successfully and reproducibly on arm64. Sun Dec 22 05:16:11 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Dec 22 05:16:11 UTC 2024 I: Submitting 8.0K b1/loki_2.4.7.4-12_arm64.buildinfo.asc Sun Dec 22 05:16:12 UTC 2024 I: Submitting 8.0K b2/loki_2.4.7.4-12_arm64.buildinfo.asc Sun Dec 22 05:16:12 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Dec 22 05:16:12 UTC 2024 I: Done submitting .buildinfo files. Sun Dec 22 05:16:12 UTC 2024 I: Removing signed loki_2.4.7.4-12_arm64.buildinfo.asc files: removed './b1/loki_2.4.7.4-12_arm64.buildinfo.asc' removed './b2/loki_2.4.7.4-12_arm64.buildinfo.asc'