Thu Aug 6 01:43:10 UTC 2020 I: starting to build loki/buster/i386 on jenkins on '2020-08-06 01:42' Thu Aug 6 01:43:10 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_2/11061/console.log Thu Aug 6 01:43:10 UTC 2020 I: Downloading source for buster/loki=2.4.7.4-8 --2020-08-06 01:43:11-- 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% 203M=0s 2020-08-06 01:43:11 (203 MB/s) - ‘loki_2.4.7.4-8.dsc’ saved [1909/1909] Thu Aug 6 01:43:11 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----- Thu Aug 6 01:43:11 UTC 2020 I: Checking whether the package is not for us Thu Aug 6 01:43:11 UTC 2020 I: Starting 1st build on remote node profitbricks-build6-i386.debian.net. Thu Aug 6 01:43:11 UTC 2020 I: Preparing to do remote build '1' on profitbricks-build6-i386.debian.net. Thu Aug 6 01:43:42 UTC 2020 I: Deleting $TMPDIR on profitbricks-build6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 7 20:06:11 -12 2021 I: pbuilder-time-stamp: 1631088371 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: using eatmydata during job 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 '/root/.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/27381/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=18' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='34c908f91ff3454284b3199e789fa968' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='27381' 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.t3Cyhf61Rc/pbuilderrc_8FzU --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.t3Cyhf61Rc/b1 --logfile b1/build.log loki_2.4.7.4-8.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux profitbricks-build6-i386 4.19.0-10-amd64 #1 SMP Debian 4.19.132-1 (2020-07-24) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1302248 Apr 17 2019 bash -rwxr-xr-x 3 root root 38280 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38280 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 38280 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 17768 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 38692 Feb 28 2019 cat -rwxr-xr-x 1 root root 75588 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 63268 Feb 28 2019 chmod -rwxr-xr-x 1 root root 75588 Feb 28 2019 chown -rwxr-xr-x 1 root root 153732 Feb 28 2019 cp -rwxr-xr-x 1 root root 132820 Jan 17 2019 dash -rwxr-xr-x 1 root root 120676 Feb 28 2019 date -rwxr-xr-x 1 root root 92040 Feb 28 2019 dd -rwxr-xr-x 1 root root 100620 Feb 28 2019 df -rwxr-xr-x 1 root root 149736 Feb 28 2019 dir -rwxr-xr-x 1 root root 79412 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 34532 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 34532 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 67700 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 30112 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 206392 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 100952 Jan 5 2019 gzip -rwxr-xr-x 1 root root 21916 Sep 26 2018 hostname -rwxr-xr-x 1 root root 79752 Feb 28 2019 ln -rwxr-xr-x 1 root root 55400 Jul 26 2018 login -rwxr-xr-x 1 root root 149736 Feb 28 2019 ls -rwxr-xr-x 1 root root 112032 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 87972 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 79748 Feb 28 2019 mknod -rwxr-xr-x 1 root root 46916 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 42348 Jan 9 2019 more -rwsr-xr-x 1 root root 50592 Jan 9 2019 mount -rwxr-xr-x 1 root root 13724 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 157832 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 38660 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 46852 Feb 28 2019 readlink -rwxr-xr-x 1 root root 75588 Feb 28 2019 rm -rwxr-xr-x 1 root root 42756 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 22276 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Sep 7 02:47 sh -> dash -rwxr-xr-x 1 root root 34532 Feb 28 2019 sleep -rwxr-xr-x 1 root root 79652 Feb 28 2019 stty -rwsr-xr-x 1 root root 71072 Jan 9 2019 su -rwxr-xr-x 1 root root 34564 Feb 28 2019 sync -rwxr-xr-x 1 root root 504024 Apr 23 2019 tar -rwxr-xr-x 1 root root 13860 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 104292 Feb 28 2019 touch -rwxr-xr-x 1 root root 34532 Feb 28 2019 true -rwxr-xr-x 1 root root 17768 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30108 Jan 9 2019 umount -rwxr-xr-x 1 root root 34532 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 149736 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34208 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/27381/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: i386 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 ... 19234 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 19.4 MB of archives. After unpacking 70.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 10 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 11 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 12 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 14 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 24 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 25 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6+deb10u1 [8451 kB] Get: 27 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 29 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 30 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 31 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Fetched 19.4 MB in 0s (77.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19234 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../04-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_i386.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_i386.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic1:i386 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_i386.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_i386.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../11-libsigsegv2_2.12-2_i386.deb ... Unpacking libsigsegv2:i386 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_i386.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:i386. Preparing to unpack .../22-libelf1_0.176-1.1_i386.deb ... Unpacking libelf1:i386 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.12-3_i386.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../24-libglib2.0-0_2.58.3-2+deb10u2_i386.deb ... Unpacking libglib2.0-0:i386 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:i386. Preparing to unpack .../25-libicu63_63.1-6+deb10u1_i386.deb ... Unpacking libicu63:i386 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../26-libxml2_2.9.4+dfsg1-7+b3_i386.deb ... Unpacking libxml2:i386 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:i386. Preparing to unpack .../27-libcroco3_0.6.12-3_i386.deb ... Unpacking libcroco3:i386 (0.6.12-3) ... 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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 i386 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=i686-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/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-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/i386-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 -j18 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 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 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 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: ^~~~~~~ lex.yy.c:2062:12: warning: 'input' defined but not used [-Wunused-function] 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 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; ^~~~~~~~~~~ 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; ^~~~~~ 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; ^~~ 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; ^~~~ /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 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 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 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 param_lex.c: In function 'yy_get_next_buffer': param_lex.c:641:18: warning: comparison of integer expressions of different signedness: 'int' and '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]), ^~~~~~~~ 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 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; ^~~~~~ 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 loki_sample.o loki_sample.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 -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_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_tlmoves.o loki_tlmoves.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 meiosis_scan.o meiosis_scan.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_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 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; ^~~ 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 sample_effects.o sample_effects.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; ^~~~~~~ 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 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 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 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 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: ^~~~ 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_complex_peel.o loki_complex_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_npl.o loki_npl.c loki_complex_peel.c: In function 'loki_complex_peelop': 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_simple_sample.o loki_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 loki_simple_peel.o loki_simple_peel.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_trait_simple_peel.o loki_trait_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_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 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; ~~~~~~~~~~^~~~ 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; ~~~~~~~~~~^~~~ /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 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 -j18 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_i386.deb'. dpkg-deb: building package 'loki' in '../loki_2.4.7.4-8_i386.deb'. dpkg-deb: building package 'loki-doc' in '../loki-doc_2.4.7.4-8_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../loki_2.4.7.4-8_i386.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/27381 and its subdirectories I: Current time: Tue Sep 7 20:06:41 -12 2021 I: pbuilder-time-stamp: 1631088401 Thu Aug 6 01:43:42 UTC 2020 I: 1st build successful. Starting 2nd build on remote node profitbricks-build2-i386.debian.net. Thu Aug 6 01:43:42 UTC 2020 I: Preparing to do remote build '2' on profitbricks-build2-i386.debian.net. Thu Aug 6 01:48:38 UTC 2020 I: Deleting $TMPDIR on profitbricks-build2-i386.debian.net. Thu Aug 6 01:48:38 UTC 2020 I: loki_2.4.7.4-8_i386.changes: Format: 1.8 Date: Fri, 12 Oct 2018 07:04:58 +0200 Source: loki Binary: loki loki-dbgsym loki-doc Architecture: i386 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: c61577476770acf03e9f9ac71a4608f629c07ae5 724832 loki-dbgsym_2.4.7.4-8_i386.deb e4fd1501564bda540da4e3bce270992cf3c76457 225460 loki-doc_2.4.7.4-8_all.deb b9b478896df6736128f95b9d78fc3d4d7ec63e7f 4848 loki_2.4.7.4-8_i386.buildinfo 202640085d40738f3f613e38dff9376829085b3b 354924 loki_2.4.7.4-8_i386.deb Checksums-Sha256: 3c8ef25af3524a03c2e0ff0a869f746163394b2febff6b61c98bc4bb0714eb37 724832 loki-dbgsym_2.4.7.4-8_i386.deb 8bc3b533087c410c56262d1bda00f621d792808d6132b24c3e3f92f61b88d36b 225460 loki-doc_2.4.7.4-8_all.deb 58d8a6ead8459d11b967b8407a9fb8768be1a291d32fd9471f5b28b2833135f8 4848 loki_2.4.7.4-8_i386.buildinfo 56558b80231cca02cec17d170631e067a828027abfa60adf0a633bbcd561c8ca 354924 loki_2.4.7.4-8_i386.deb Files: 73a76bc6aa64b5acfcb753197028d4c2 724832 debug optional loki-dbgsym_2.4.7.4-8_i386.deb 4a28bf9196d03bc7ade1172634dd9903 225460 doc optional loki-doc_2.4.7.4-8_all.deb 19de63b1132dddb472eeecff9bcbe51f 4848 science optional loki_2.4.7.4-8_i386.buildinfo 8148c555ab357a213e997a20a14f592d 354924 science optional loki_2.4.7.4-8_i386.deb Thu Aug 6 01:48:39 UTC 2020 I: diffoscope 154 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.t3Cyhf61Rc/loki_2.4.7.4-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.t3Cyhf61Rc/loki_2.4.7.4-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.t3Cyhf61Rc/loki_2.4.7.4-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.t3Cyhf61Rc/b1/loki_2.4.7.4-8_i386.changes /srv/reproducible-results/rbuild-debian/tmp.t3Cyhf61Rc/b2/loki_2.4.7.4-8_i386.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: 0.237s) 0.236s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.044s) 0.043s 10 calls diffoscope.comparators.binary.FilesystemFile 0.001s 8 calls abc.DotChangesFile Thu Aug 6 01:48:41 UTC 2020 I: diffoscope 154 found no differences in the changes files, and a .buildinfo file also exists. Thu Aug 6 01:48:41 UTC 2020 I: loki from buster built successfully and reproducibly on i386. Thu Aug 6 01:48:42 UTC 2020 I: Submitting .buildinfo files to external archives: Thu Aug 6 01:48:42 UTC 2020 I: Submitting 8.0K b1/loki_2.4.7.4-8_i386.buildinfo.asc Thu Aug 6 01:48:43 UTC 2020 I: Submitting 8.0K b2/loki_2.4.7.4-8_i386.buildinfo.asc Thu Aug 6 01:48:44 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Aug 6 01:48:44 UTC 2020 I: Done submitting .buildinfo files. Thu Aug 6 01:48:44 UTC 2020 I: Removing signed loki_2.4.7.4-8_i386.buildinfo.asc files: removed './b1/loki_2.4.7.4-8_i386.buildinfo.asc' removed './b2/loki_2.4.7.4-8_i386.buildinfo.asc'