Mon Jul 27 02:19:09 UTC 2020 I: starting to build loki/buster/arm64 on jenkins on '2020-07-27 02:18' Mon Jul 27 02:19:09 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_10/17915/console.log Mon Jul 27 02:19:09 UTC 2020 I: Downloading source for buster/loki=2.4.7.4-8 --2020-07-27 02:19:09-- http://deb.debian.org/debian/pool/main/l/loki/loki_2.4.7.4-8.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1909 (1.9K) Saving to: ‘loki_2.4.7.4-8.dsc’ 0K . 100% 197M=0s 2020-07-27 02:19:09 (197 MB/s) - ‘loki_2.4.7.4-8.dsc’ saved [1909/1909] Mon Jul 27 02:19:09 UTC 2020 I: loki_2.4.7.4-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: loki Binary: loki, loki-doc Architecture: any all Version: 2.4.7.4-8 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/loki Vcs-Git: https://salsa.debian.org/med-team/loki.git Build-Depends: debhelper (>= 11~) 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 6580fa7a5a3fc06d7669dae5dd4bf8c1f1bb97f0 23912 loki_2.4.7.4-8.debian.tar.xz Checksums-Sha256: 78bc51f47fb756fcdc9ab55bc4c7dd649ee87aaa6bd9be87eac44e4a8eac9eb5 904260 loki_2.4.7.4.orig.tar.gz 02b3277fbba549b48351df614ff12204c21f449482f3d71eecc2a2ca76b171ae 23912 loki_2.4.7.4-8.debian.tar.xz Files: 7764c55d3c3a33584a6f92740210b677 904260 loki_2.4.7.4.orig.tar.gz 167c3b32c549c33f0b454e747278aa02 23912 loki_2.4.7.4-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlvAK+0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFTTg/+Pmce39wKe5Q+kiLcQSprwU/zEjCb22kG /nje3KGvNFN1BeUZXcPpRCIJ0IQHRE/KZNKWYUSsVGMSewFD4ScITDtYHVcsGLr4 zL/cMUGHU+bnRrWP0h7WtgP3zMw3P768c4JO8WGgo0Jrdjv+aeLCzL/RUVFA1O0K V54o4dXMoZFsWDiWsdDoofj/DyRABoi0w6lgDii90f3EBtg/TPEBzheuJenanurl dXlxiqYnoVutuuDpl0Hsxuvj7N0X00ARwQDPErC9eDlYEyYz0e4Aef/7mritngOh IdArYNrGse0GTUgZQcltmxAv3iwVtmID6zY8H/+UWfDS3WkiS4A8ZeDgKGvVbqds bRqwajjLqRUrlIl0yM1hRd/jCwnfapVTurQ0YD4ZTCHGvMhve+k7dIc7Tr2J80o7 XnvVLN6kXoD1Fk2tRK9aCef0bCEi8vaYvsVW9g6j7Jv42fNzbCyK3X8MJkGovNi4 jTDf7c+dvqaiAX2xZMJtjzYOx4tUTSBsQn0GbUOSI18yImstmOms01S1CWZJ/LMd jeSGuSJkMP8ZuxjGpMap4kKYnuFTvKt5CjIPoj4tpY/7VxQAReHQfFZoP29DUlaB aeFan7vnA0SLpGwHWcv93JT3iLzvgFEjfnDF5ia7reHJdUrFH1XhGH8agfIKeJC/ X1oaBe6onlE= =NZu2 -----END PGP SIGNATURE----- Mon Jul 27 02:19:09 UTC 2020 I: Checking whether the package is not for us Mon Jul 27 02:19:09 UTC 2020 I: Starting 1st build on remote node codethink-sled11-arm64.debian.net. Mon Jul 27 02:19:09 UTC 2020 I: Preparing to do remote build '1' on codethink-sled11-arm64.debian.net. Mon Jul 27 02:20:44 UTC 2020 I: Deleting $TMPDIR on codethink-sled11-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Aug 28 20:42:17 -12 2021 I: pbuilder-time-stamp: 1630226537 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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_2.4.7.4-8.dsc] I: copying [./loki_2.4.7.4.orig.tar.gz] I: copying [./loki_2.4.7.4-8.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu Oct 11 17:06:53 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./loki_2.4.7.4-8.dsc 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_2.4.7.4-8.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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3583/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='3583' 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/tmp.RIRtqFg6x9/pbuilderrc_Nfcb --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RIRtqFg6x9/b1 --logfile b1/build.log loki_2.4.7.4-8.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink-sled11-arm64 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 28 02:49 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/3583/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 (>= 11~) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19168 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 (>= 11~); however: Package debhelper 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} bsdmainutils{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} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{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 libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 18.6 MB of archives. After unpacking 69.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Fetched 18.6 MB in 1s (20.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_arm64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../11-libsigsegv2_2.12-2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_arm64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../22-libelf1_0.176-1.1_arm64.deb ... Unpacking libelf1:arm64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.12-3_arm64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../24-libglib2.0-0_2.58.3-2+deb10u2_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:arm64. Preparing to unpack .../25-libicu63_63.1-6+deb10u1_arm64.deb ... Unpacking libicu63:arm64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../26-libxml2_2.9.4+dfsg1-7+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:arm64. 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Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:arm64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/loki-2.4.7.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package loki dpkg-buildpackage: info: source version 2.4.7.4-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' debian/rules override_dh_auto_configure-arch make[1]: Entering directory '/build/loki-2.4.7.4' dh_auto_configure -- --exec_prefix=/build/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-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --libexecdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --exec_prefix=/build/loki-2.4.7.4/debian/loki/usr configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking 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 /nonexistent/first-build/include and libdmalloc.a in /nonexistent/first-build/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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... 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... /bin/sed checking for cp... /bin/cp checking for grep... /bin/grep checking for mv... /bin/mv checking for gzip... /bin/gzip checking for chmod... /bin/chmod checking for perl... /usr/bin/perl checking for makedepend... : checking for sin in -lm... yes checking for accept in -lsocket... no checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... (cached) /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/wait.h that is POSIX.1 compatible... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking values.h usability... yes checking values.h presence... yes checking for values.h... yes checking for unistd.h... (cached) yes checking sys/systeminfo.h usability... no checking sys/systeminfo.h presence... no 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... yes checking for an ANSI C-conforming const... yes checking for vprintf... yes checking for _doprnt... no 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 configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking make[1]: Leaving directory '/build/loki-2.4.7.4' debian/rules override_dh_auto_configure-indep make[1]: Entering directory '/build/loki-2.4.7.4' # do nothing here make[1]: Leaving directory '/build/loki-2.4.7.4' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/loki-2.4.7.4' # nothing to do here make[1]: Leaving directory '/build/loki-2.4.7.4' dh_auto_build -Nloki-doc make -j8 make[1]: Entering directory '/build/loki-2.4.7.4' for subdir in libsrc prepsrc lokisrc utils; do \ (cd $subdir; make depend) \ done make[2]: Entering directory '/build/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/loki-2.4.7.4/libsrc' make[2]: Entering directory '/build/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/loki-2.4.7.4/prepsrc' make[2]: Entering directory '/build/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/loki-2.4.7.4/lokisrc' make[2]: Entering directory '/build/loki-2.4.7.4/utils' : -I../include qavg.c hist.c touch depend make[2]: Leaving directory '/build/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/loki-2.4.7.4/libsrc' gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/loki-2.4.7.4/libsrc' make[2]: Entering directory '/build/loki-2.4.7.4/prepsrc' gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o match_records.o match_records.c lex.yy.c:2062:12: warning: 'input' defined but not used [-Wunused-function] setup_ped.c: In function 'setup_pedigree': setup_ped.c:426:13: warning: this statement may fall through [-Wimplicit-fallthrough=] if(i!=id) { ^ setup_ped.c:430:11: note: here default: ^~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prep_utils.o prep_utils.c write_report.c: In function 'WriteReport': write_report.c:286:7: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] if(!elem->type&(ST_MODEL|ST_TRAIT)) continue; ^~~~~~~~~~~ write_report.c:300:7: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] if(!elem->type&(ST_MODEL|ST_TRAIT)) continue; ^~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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:1075:24: warning: variable 'best_fg' set but not used [-Wunused-but-set-variable] int x,i1,k1,k2,*trans,best_fg=0; ^~~~~~~ gen_elim.c: In function 'find_sequence': gen_elim.c:1156:17: warning: variable 'mark' set but not used [-Wunused-but-set-variable] struct Marker *mark; ^~~~ gen_elim.c:1155:24: warning: variable 'order1' set but not used [-Wunused-but-set-variable] int *g_perm,*order=0,*order1; ^~~~~~ prep_do_peel_op.c: In function 'do_peel_op': prep_do_peel_op.c:238:19: warning: variable 'fill' set but not used [-Wunused-but-set-variable] double max_terms,fill; ^~~~ gen_elim.c: In function 'logical_peel': gen_elim.c:1268:17: warning: variable 'mark' set but not used [-Wunused-but-set-variable] struct Marker *mark; ^~~~ gen_elim.c:1266:27: warning: variable 'pp1' set but not used [-Wunused-but-set-variable] struct Peelseq_Head *pp,*pp1; ^~~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o write_data.o write_data.c /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/loki-2.4.7.4/prepsrc/compat' gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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] int process_qtdt(int argc,char *argv[],char **LogFile,int *error_check,loki_time *lt) ~~~~~^~~~~~~~~~~ merlin.c:162:10: warning: this statement may fall through [-Wimplicit-fallthrough=] nmark++; ~~~~~^~ merlin.c:163:5: note: here case 'A': ^~~~ /usr/bin/ar cr libcompat.a compat.o merlin.o /usr/bin/ranlib libcompat.a make[3]: Leaving directory '/build/loki-2.4.7.4/prepsrc/compat' gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/loki-2.4.7.4/prepsrc' make[2]: Entering directory '/build/loki-2.4.7.4/lokisrc' gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -DYY_NO_UNPUT param_lex.c gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seg_pen.o seg_pen.c param_lex.c: In function 'yy_get_next_buffer': param_lex.c:641:18: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] for ( n = 0; n < max_size && \ ^ param_lex.c:1161:3: note: in expansion of macro 'YY_INPUT' YY_INPUT( (&YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[number_to_move]), ^~~~~~~~ At top level: param_lex.c:1301:16: warning: 'input' defined but not used [-Wunused-function] static int input (void) ^~~~~ param_lex.c:1260:17: warning: 'yyunput' defined but not used [-Wunused-function] static void yyunput (int c, register char * yy_bp ) ^~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gen_pen.o gen_pen.c gen_pen.c: In function 'calc_degree': gen_pen.c:321:24: warning: variable 'k2' set but not used [-Wunused-but-set-variable] int i1,j,j1,j2,k=0,k1,k2; ^~ gcc -c -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -DIBD_COMPRESS_PROG=\"/bin/gzip\" loki_ibd.c gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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:215:74: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=] 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)); ~^ ~~~~~~~~~~~ %ld loki_ibd.c:215:77: warning: format '%d' expects argument of type 'int', but argument 6 has type 'long unsigned int' [-Wformat=] 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)); ~^ ~~~~~~~~~~~~~~~~~~ %ld pass_founder_genes.c: In function 'pass_founder_genes': pass_founder_genes.c:35:40: warning: variable 'locus1' set but not used [-Wunused-but-set-variable] int i,i1,j,s,**genes,**seg,comp,cs,nc,locus1; ^~~~~~ param_lex.c: In function 'yylex': param_lex.l:91:11: warning: 'strncpy' specified bound 512 equals destination size [-Wstringop-truncation] (void)strncpy(linebuf,yytext+1,512); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ param_lex.l:64:11: warning: 'strncpy' specified bound 512 equals destination size [-Wstringop-truncation] (void)strncpy(linebuf,yytext,512); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alloc_loki.o alloc_loki.c loki_init.c: In function 'InitValues': loki_init.c:125:17: warning: this statement may fall through [-Wimplicit-fallthrough=] tau_beta[mod]*=residual_var[mod]; ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ loki_init.c:126:4: note: here case 1: ^~~~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_pen.o loki_pen.c loki_peel.c: In function 'peel_locus': loki_peel.c:434:11: warning: 'z' may be used uninitialized in this function [-Wmaybe-uninitialized] like1+=z; ~~~~~^~~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_tlmoves.o loki_tlmoves.c loki_tlmoves.c: In function 'sample_mpos': loki_tlmoves.c:152:29: warning: variable 'idd' set but not used [-Wunused-but-set-variable] int i,j,locus,k2=-1,k3,ids,idd,sx,**seg,s,s1; ^~~ loki_tlmoves.c:210:26: warning: 'x' may be used uninitialized in this function [-Wmaybe-uninitialized] r=.5*(1.0-exp(.02*(x-x1))); ~~^~~~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o meiosis_scan.o meiosis_scan.c meiosis_scan.c: In function 'meiosis_scan': meiosis_scan.c:162:69: warning: variable 'n_comp1' set but not used [-Wunused-but-set-variable] int sex,kid,**seg,**seg1,kid1,nkids1,*kids1,lffg,symflag,n_qtl,qtl,n_comp1; ^~~~~~~ loki_tlmoves.c: In function 'get_tl_position': loki_tlmoves.c:623:10: warning: 'z' may be used uninitialized in this function [-Wmaybe-uninitialized] prior[i]+=z; ^~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_nu.o sample_nu.c loki_output.c: In function 'OutputSample': loki_output.c:345:3: warning: this statement may fall through [-Wimplicit-fallthrough=] OutputSample_2(fptr,lp); ^~~~~~~~~~~~~~~~~~~~~~~ loki_output.c:346:3: note: here case OUTPUT_VERSION_2_3: ^~~~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 loki_complex_peel.c: In function 'loki_complex_peelop': loki_complex_peel.c:458:155: warning: format '%d' expects argument of type 'int', but argument 8 has type 'long unsigned int' [-Wformat=] (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); ~^ %ld loki_complex_peel.c:379:9: warning: variable 'max_terms' set but not used [-Wunused-but-set-variable] double max_terms,*tp,prob=0.0,z,p1,Konst=0.0; ^~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 loki_simple_sample.c: In function 'loki_simple_sample': loki_simple_sample.c:25:51: warning: variable 'tpp2' set but not used [-Wunused-but-set-variable] double *tp,p1,p2,z,z1,prob=0.0,pp[4],*tmp,*tpp1,*tpp2; ^~~~ loki_simple_sample.c:25:45: warning: variable 'tpp1' set but not used [-Wunused-but-set-variable] double *tp,p1,p2,z,z1,prob=0.0,pp[4],*tmp,*tpp1,*tpp2; ^~~~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 loki_simple_peel.c: In function 'loki_simple_peelop': loki_simple_peel.c:601:26: warning: 'cm[0]' may be used uninitialized in this function [-Wmaybe-uninitialized] id_set2[i]=(cm[X_MAT]&a1)?lump[X_MAT]:i; ~~~~~~~~~~^~~~ loki_simple_peel.c:600:26: warning: 'cm[1]' may be used uninitialized in this function [-Wmaybe-uninitialized] id_set1[i]=(cm[X_PAT]&a1)?l:i1; ~~~~~~~~~~^~~~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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_x': loki_simple_peel.c:1278:26: warning: 'cm[1]' may be used uninitialized in this function [-Wmaybe-uninitialized] id_set1[i]=(cm[X_PAT]&a1)?l:i1; ~~~~~~~~~~^~~~ loki_simple_peel.c:1279:26: warning: 'cm[0]' may be used uninitialized in this function [-Wmaybe-uninitialized] id_set2[i]=(cm[X_MAT]&a1)?lump[X_MAT]:i; ~~~~~~~~~~^~~~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/loki-2.4.7.4/lokisrc' make[2]: Entering directory '/build/loki-2.4.7.4/utils' gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -o qavg qavg.c -Wl,-z,relro -Wl,-z,now -lm gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/loki-2.4.7.4/utils' make[1]: Leaving directory '/build/loki-2.4.7.4' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_installdirs debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/loki-2.4.7.4' dh_auto_install -a make -j8 install DESTDIR=/build/loki-2.4.7.4/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/loki-2.4.7.4' for subdir in libsrc prepsrc lokisrc utils; do \ (cd $subdir; make) \ done make[3]: Entering directory '/build/loki-2.4.7.4/libsrc' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/loki-2.4.7.4/libsrc' make[3]: Entering directory '/build/loki-2.4.7.4/prepsrc' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/loki-2.4.7.4/prepsrc' make[3]: Entering directory '/build/loki-2.4.7.4/lokisrc' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/loki-2.4.7.4/lokisrc' make[3]: Entering directory '/build/loki-2.4.7.4/utils' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/loki-2.4.7.4/utils' for subdir in prepsrc lokisrc utils; do \ (cd $subdir; make install) \ done make[3]: Entering directory '/build/loki-2.4.7.4/prepsrc' mkdir ../bin for file in prep; do \ /bin/cp $file /build/loki-2.4.7.4/debian/loki/usr/bin/; \ /bin/chmod 755 /build/loki-2.4.7.4/debian/loki/usr/bin/$file ; \ done make[3]: Leaving directory '/build/loki-2.4.7.4/prepsrc' make[3]: Entering directory '/build/loki-2.4.7.4/lokisrc' for file in loki; do \ /bin/cp $file /build/loki-2.4.7.4/debian/loki/usr/bin/; \ /bin/chmod 755 /build/loki-2.4.7.4/debian/loki/usr/bin/$file ; \ done make[3]: Leaving directory '/build/loki-2.4.7.4/lokisrc' make[3]: Entering directory '/build/loki-2.4.7.4/utils' for file in ext count dist freq sort_error; do \ /bin/sed 's!+PERLPROG+!/usr/bin/perl!' $file.in > /build/loki-2.4.7.4/debian/loki/usr/bin/loki_$file; \ /bin/chmod 755 /build/loki-2.4.7.4/debian/loki/usr/bin/loki_$file; \ done for file in qavg hist; do \ /bin/cp $file /build/loki-2.4.7.4/debian/loki/usr/bin/; \ /bin/chmod 755 /build/loki-2.4.7.4/debian/loki/usr/bin/$file ; \ done make[3]: Leaving directory '/build/loki-2.4.7.4/utils' make[2]: Leaving directory '/build/loki-2.4.7.4' make install prefix=/build/loki-2.4.7.4/debian/loki/usr bindir=/build/loki-2.4.7.4/debian/loki/usr/bin LDFLAGS="-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/loki-2.4.7.4' for subdir in libsrc prepsrc lokisrc utils; do \ (cd $subdir; make) \ done make[3]: Entering directory '/build/loki-2.4.7.4/libsrc' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/loki-2.4.7.4/libsrc' make[3]: Entering directory '/build/loki-2.4.7.4/prepsrc' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/loki-2.4.7.4/prepsrc' make[3]: Entering directory '/build/loki-2.4.7.4/lokisrc' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/loki-2.4.7.4/lokisrc' make[3]: Entering directory '/build/loki-2.4.7.4/utils' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/loki-2.4.7.4/utils' for subdir in prepsrc lokisrc utils; do \ (cd $subdir; make install) \ done make[3]: Entering directory '/build/loki-2.4.7.4/prepsrc' for file in prep; do \ /bin/cp $file /build/loki-2.4.7.4/debian/loki/usr/bin/; \ /bin/chmod 755 /build/loki-2.4.7.4/debian/loki/usr/bin/$file ; \ done make[3]: Leaving directory '/build/loki-2.4.7.4/prepsrc' make[3]: Entering directory '/build/loki-2.4.7.4/lokisrc' for file in loki; do \ /bin/cp $file /build/loki-2.4.7.4/debian/loki/usr/bin/; \ /bin/chmod 755 /build/loki-2.4.7.4/debian/loki/usr/bin/$file ; \ done make[3]: Leaving directory '/build/loki-2.4.7.4/lokisrc' make[3]: Entering directory '/build/loki-2.4.7.4/utils' for file in ext count dist freq sort_error; do \ /bin/sed 's!+PERLPROG+!/usr/bin/perl!' $file.in > /build/loki-2.4.7.4/debian/loki/usr/bin/loki_$file; \ /bin/chmod 755 /build/loki-2.4.7.4/debian/loki/usr/bin/loki_$file; \ done for file in qavg hist; do \ /bin/cp $file /build/loki-2.4.7.4/debian/loki/usr/bin/; \ /bin/chmod 755 /build/loki-2.4.7.4/debian/loki/usr/bin/$file ; \ done make[3]: Leaving directory '/build/loki-2.4.7.4/utils' make[2]: Leaving directory '/build/loki-2.4.7.4' make[1]: Leaving directory '/build/loki-2.4.7.4' debian/rules override_dh_auto_install-indep make[1]: Entering directory '/build/loki-2.4.7.4' # nothing to do here make[1]: Leaving directory '/build/loki-2.4.7.4' dh_installdocs dh_installchangelogs debian/rules override_dh_installman-arch make[1]: Entering directory '/build/loki-2.4.7.4' dh_installman -a for man in check_het.1 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/loki-2.4.7.4' dh_installman -Nloki dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps 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-dbgsym' in '../loki-dbgsym_2.4.7.4-8_arm64.deb'. dpkg-deb: building package 'loki-doc' in '../loki-doc_2.4.7.4-8_all.deb'. dpkg-deb: building package 'loki' in '../loki_2.4.7.4-8_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../loki_2.4.7.4-8_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) 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/3583 and its subdirectories I: Current time: Sat Aug 28 20:43:40 -12 2021 I: pbuilder-time-stamp: 1630226620 Mon Jul 27 02:20:45 UTC 2020 I: 1st build successful. Starting 2nd build on remote node codethink-sled12-arm64.debian.net. Mon Jul 27 02:20:45 UTC 2020 I: Preparing to do remote build '2' on codethink-sled12-arm64.debian.net. Mon Jul 27 02:22:07 UTC 2020 I: Deleting $TMPDIR on codethink-sled12-arm64.debian.net. Mon Jul 27 02:22:08 UTC 2020 I: loki_2.4.7.4-8_arm64.changes: Format: 1.8 Date: Fri, 12 Oct 2018 07:04:58 +0200 Source: loki Binary: loki loki-dbgsym loki-doc Architecture: arm64 all Version: 2.4.7.4-8 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) Changes: loki (2.4.7.4-8) unstable; urgency=medium . * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 * hardening=+all * Fix spelling Checksums-Sha1: 5f3e744a24c081db42df0331ec9563bff16363fe 773384 loki-dbgsym_2.4.7.4-8_arm64.deb e4fd1501564bda540da4e3bce270992cf3c76457 225460 loki-doc_2.4.7.4-8_all.deb 3cd815033b60720d9b7ef10793ea3811ac2c29e5 4790 loki_2.4.7.4-8_arm64.buildinfo 7773d146411fc9232e34bad364d64c32a8496578 323784 loki_2.4.7.4-8_arm64.deb Checksums-Sha256: ab109acfe39b180baef0749d213358ff13c5e645fe617f513182999e106064a2 773384 loki-dbgsym_2.4.7.4-8_arm64.deb 8bc3b533087c410c56262d1bda00f621d792808d6132b24c3e3f92f61b88d36b 225460 loki-doc_2.4.7.4-8_all.deb 439091c84ffe5269f8a90d6e15ba807dc416309bc52ff4a9f16cebe531c26cf2 4790 loki_2.4.7.4-8_arm64.buildinfo 506e1eb060455ef4e7bba8f8c35b3d7145903b7e86d2d204725c8f0cc229829d 323784 loki_2.4.7.4-8_arm64.deb Files: 5d4c18a551f4b7096475318de749dc36 773384 debug optional loki-dbgsym_2.4.7.4-8_arm64.deb 4a28bf9196d03bc7ade1172634dd9903 225460 doc optional loki-doc_2.4.7.4-8_all.deb a3c88afc6d37dfd2825de54d74191f0c 4790 science optional loki_2.4.7.4-8_arm64.buildinfo 65fa7e659baac5758446ed79dc372902 323784 science optional loki_2.4.7.4-8_arm64.deb Mon Jul 27 02:22:10 UTC 2020 I: diffoscope 153 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.RIRtqFg6x9/loki_2.4.7.4-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.RIRtqFg6x9/loki_2.4.7.4-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.RIRtqFg6x9/loki_2.4.7.4-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.RIRtqFg6x9/b1/loki_2.4.7.4-8_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.RIRtqFg6x9/b2/loki_2.4.7.4-8_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: 0.285s) 0.285s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.043s) 0.043s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Jul 27 02:22:11 UTC 2020 I: diffoscope 153 found no differences in the changes files, and a .buildinfo file also exists. Mon Jul 27 02:22:11 UTC 2020 I: loki from buster built successfully and reproducibly on arm64. Mon Jul 27 02:22:12 UTC 2020 I: Submitting .buildinfo files to external archives: Mon Jul 27 02:22:12 UTC 2020 I: Submitting 8.0K b1/loki_2.4.7.4-8_arm64.buildinfo.asc Mon Jul 27 02:22:14 UTC 2020 I: Submitting 8.0K b2/loki_2.4.7.4-8_arm64.buildinfo.asc Mon Jul 27 02:22:14 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jul 27 02:22:14 UTC 2020 I: Done submitting .buildinfo files. Mon Jul 27 02:22:14 UTC 2020 I: Removing signed loki_2.4.7.4-8_arm64.buildinfo.asc files: removed './b1/loki_2.4.7.4-8_arm64.buildinfo.asc' removed './b2/loki_2.4.7.4-8_arm64.buildinfo.asc'