Wed Mar 12 02:28:22 UTC 2025 I: starting to build loki/trixie/amd64 on jenkins on '2025-03-12 02:28'
Wed Mar 12 02:28:22 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_32/35639/console.log
Wed Mar 12 02:28:22 UTC 2025 I: Downloading source for trixie/loki=2.4.7.4-12
--2025-03-12 02:28:22-- 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% 279M=0s
2025-03-12 02:28:22 (279 MB/s) - ‘loki_2.4.7.4-12.dsc’ saved [1941/1941]
Wed Mar 12 02:28:22 UTC 2025 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 <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
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-----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=deFd
-----END PGP SIGNATURE-----
Wed Mar 12 02:28:22 UTC 2025 I: Checking whether the package is not for us
Wed Mar 12 02:28:22 UTC 2025 I: Starting 1st build on remote node ionos5-amd64.debian.net.
Wed Mar 12 02:28:22 UTC 2025 I: Preparing to do remote build '1' on ionos5-amd64.debian.net.
Wed Mar 12 02:29:41 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Mon Apr 13 20:51:20 -12 2026
I: pbuilder-time-stamp: 1776156680
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
dpkg-source: warning: cannot verify inline signature for ./loki_2.4.7.4-12.dsc: unsupported subcommand
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/683893/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='86a1e9a14e0f409eb885eb035c0341c7'
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='683893'
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.thGT05gY/pbuilderrc_1yBJ --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.thGT05gY/b1 --logfile b1/build.log loki_2.4.7.4-12.dsc'
SUDO_GID='110'
SUDO_UID='105'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://213.165.73.152:3128'
I: uname -a
Linux ionos5-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/683893/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 <pbuilder-maint@lists.alioth.debian.org>
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 ... 19800 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} libunistring5{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, 30 newly installed, 0 to remove and 0 not upgraded.
Need to get 20.6 MB of archives. After unpacking 77.9 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-7 [294 kB]
Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB]
Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB]
Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 24 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [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 13.24.1 [920 kB]
Fetched 20.6 MB in 0s (113 MB/s)
Preconfiguring packages ...
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 ... 19800 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_amd64.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:amd64.
Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ...
Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ...
Unpacking gettext-base (0.23.1-1) ...
Selecting previously unselected package libuchardet0:amd64.
Preparing to unpack .../05-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 .../06-groff-base_1.23.0-7_amd64.deb ...
Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.40.4-5_amd64.deb ...
Unpacking bsdextrautils (2.40.4-5) ...
Selecting previously unselected package libpipeline1:amd64.
Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ...
Unpacking libpipeline1:amd64 (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-7_amd64.deb ...
Unpacking m4 (1.4.19-7) ...
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%3a1.17-3_all.deb ...
Unpacking automake (1:1.17-3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ...
Unpacking autopoint (0.23.1-1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ...
Unpacking libdebhelper-perl (13.24.1) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.5.4-4_all.deb ...
Unpacking libtool (2.5.4-4) ...
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_1.14.1-2_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../20-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 .../21-libelf1t64_0.192-4_amd64.deb ...
Unpacking libelf1t64:amd64 (0.192-4) ...
Selecting previously unselected package dwz.
Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ...
Unpacking dwz (0.15-1+b1) ...
Selecting previously unselected package libunistring5:amd64.
Preparing to unpack .../23-libunistring5_1.3-1_amd64.deb ...
Unpacking libunistring5:amd64 (1.3-1) ...
Selecting previously unselected package libicu72:amd64.
Preparing to unpack .../24-libicu72_72.1-6_amd64.deb ...
Unpacking libicu72:amd64 (72.1-6) ...
Selecting previously unselected package libxml2:amd64.
Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b2_amd64.deb ...
Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.23.1-1_amd64.deb ...
Unpacking gettext (0.23.1-1) ...
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_13.24.1_all.deb ...
Unpacking debhelper (13.24.1) ...
Setting up libpipeline1:amd64 (1.5.8-1) ...
Setting up libicu72:amd64 (72.1-6) ...
Setting up bsdextrautils (2.40.4-5) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.24.1) ...
Setting up libmagic1t64:amd64 (1:5.45-3+b1) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-7) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:amd64 (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libunistring5:amd64 (1.3-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up autoconf (2.72-3) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:amd64 (0.0.8-1+b2) ...
Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Setting up automake (1:1.17-3) ...
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 gettext (0.23.1-1) ...
Setting up libtool (2.5.4-4) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
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 (13.24.1) ...
Processing triggers for libc-bin (2.40-7) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/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 <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
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=x86_64-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/x86_64-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/x86_64-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 -j42
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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prep.o prep.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 -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o calc_nrm.o calc_nrm.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gen_elim.o gen_elim.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 -fcf-protection -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
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 -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o write_data.o write_data.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;
| ^~~~~~~~~~~
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;
| ^~~~
lex.yy.c:2062:12: warning: 'input' defined but not used [-Wunused-function]
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;
| ^~~
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);
| ^~~~~~~~~~
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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o get_founders.o get_founders.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 -fcf-protection -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 -fcf-protection -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
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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_peel.o loki_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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_sample.o loki_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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o meiosis_scan.o meiosis_scan.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 -fcf-protection -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 -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_identity.o loki_identity.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_setup.o loki_setup.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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
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 -fcf-protection -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 -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_output.o loki_output.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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
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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o update_segs.o update_segs.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]),
| ^~~~~~~~
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;
| ^~
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;
| ^~~
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 )
| ^~~~~~~
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;
| ^~~~~~
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:
| ^~~~
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;
| ^~~~
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_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:
| ^~~~
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;
| ^~~~~~~~~
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;
| ^~~~~~~
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_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;
| ^
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;
| ^
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;
| ^
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;
| ^~
/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_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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -j42 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
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_amd64.deb'.
dpkg-deb: building package 'loki-dbgsym' in '../loki-dbgsym_2.4.7.4-12_amd64.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_amd64.buildinfo
dpkg-genchanges --build=binary -O../loki_2.4.7.4-12_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: 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/683893 and its subdirectories
I: Current time: Mon Apr 13 20:52:37 -12 2026
I: pbuilder-time-stamp: 1776156757
Wed Mar 12 02:29:42 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net.
Wed Mar 12 02:29:42 UTC 2025 I: Preparing to do remote build '2' on ionos11-amd64.debian.net.
Wed Mar 12 02:31:35 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net.
Wed Mar 12 02:31:35 UTC 2025 I: loki_2.4.7.4-12_amd64.changes:
Format: 1.8
Date: Thu, 19 Dec 2024 18:36:19 +0100
Source: loki
Binary: loki loki-dbgsym loki-doc
Architecture: amd64 all
Version: 2.4.7.4-12
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
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:
6c37c1c7fa87ecbb393f4cdcc0f8ff688296600e 716036 loki-dbgsym_2.4.7.4-12_amd64.deb
3bb1e62bca71b80a7c2f34ebabfc369181f9df32 224192 loki-doc_2.4.7.4-12_all.deb
08253b40427caad3ea7528d1b207a9b336df177f 5125 loki_2.4.7.4-12_amd64.buildinfo
694e7994d46f5c4b23db56fff6982612cb4bd75c 372132 loki_2.4.7.4-12_amd64.deb
Checksums-Sha256:
6abd0030bc6be502015af4e1ac4aa4af9c9ba75920876520e0cdcaac3781ad80 716036 loki-dbgsym_2.4.7.4-12_amd64.deb
bd5261db10fd419de220b49ca749f3c1037d34233942297f474e2d0e961b38c2 224192 loki-doc_2.4.7.4-12_all.deb
4b505df00845fc373e57113a2d76a72caea5dd133ebd390e68ab9f9aa76580e4 5125 loki_2.4.7.4-12_amd64.buildinfo
2f27f96c63e83fe9c6990043aa0b89d63830363d702ae70fa7feaf6fa2501f08 372132 loki_2.4.7.4-12_amd64.deb
Files:
e3eb8d66b16ea526190a95a65b1236df 716036 debug optional loki-dbgsym_2.4.7.4-12_amd64.deb
2dd7ba8e613746a951d337643bb537be 224192 doc optional loki-doc_2.4.7.4-12_all.deb
a1a896a58b316167665fe98bdccd9abd 5125 science optional loki_2.4.7.4-12_amd64.buildinfo
1ecf93607bf65c2dd5ff5c4a33050da8 372132 science optional loki_2.4.7.4-12_amd64.deb
Wed Mar 12 02:31:36 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-amd64_32-35639.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.thGT05gY/loki_2.4.7.4-12.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.thGT05gY/loki_2.4.7.4-12.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.thGT05gY/loki_2.4.7.4-12.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.thGT05gY/b1/loki_2.4.7.4-12_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.thGT05gY/b2/loki_2.4.7.4-12_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: 0.003s)
0.003s 2 calls outputs
0.000s 1 call cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 219ms
CPU time consumed: 219ms
Wed Mar 12 02:31:37 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Wed Mar 12 02:31:37 UTC 2025 I: loki from trixie built successfully and reproducibly on amd64.
Wed Mar 12 02:31:38 UTC 2025 I: Submitting .buildinfo files to external archives:
Wed Mar 12 02:31:38 UTC 2025 I: Submitting 8.0K b1/loki_2.4.7.4-12_amd64.buildinfo.asc
Wed Mar 12 02:31:40 UTC 2025 I: Submitting 8.0K b2/loki_2.4.7.4-12_amd64.buildinfo.asc
Wed Mar 12 02:31:41 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Wed Mar 12 02:31:41 UTC 2025 I: Done submitting .buildinfo files.
Wed Mar 12 02:31:41 UTC 2025 I: Removing signed loki_2.4.7.4-12_amd64.buildinfo.asc files:
removed './b1/loki_2.4.7.4-12_amd64.buildinfo.asc'
removed './b2/loki_2.4.7.4-12_amd64.buildinfo.asc'