I: pbuilder: network access will be disabled during build I: Current time: Thu Jun 11 06:19:39 +14 2020 I: pbuilder-time-stamp: 1591805979 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 [eigensoft_7.2.1+dfsg-1.dsc] I: copying [./eigensoft_7.2.1+dfsg.orig.tar.xz] I: copying [./eigensoft_7.2.1+dfsg-1.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 Tue Jul 17 04:17:17 2018 +14 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 ./eigensoft_7.2.1+dfsg-1.dsc dpkg-source: info: extracting eigensoft in eigensoft-7.2.1+dfsg dpkg-source: info: unpacking eigensoft_7.2.1+dfsg.orig.tar.xz dpkg-source: info: unpacking eigensoft_7.2.1+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying blas.patch dpkg-source: info: applying lapacke.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4392/tmp/hooks/D01_modify_environment starting debug: Running on jtx1b. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/4392/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/4392/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=e9051e7af8b24a19805e7e8b44fb8dfd LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=4392 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.Zrr18YojOV/pbuilderrc_FD5e --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Zrr18YojOV/b2 --logfile b2/build.log eigensoft_7.2.1+dfsg-1.dsc' SUDO_GID=114 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:8000/ I: uname -a Linux i-capture-the-hostname 4.19.0-9-arm64 #1 SMP Debian 4.19.118-2 (2020-04-29) aarch64 GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 18 2019 bash -rwxr-xr-x 3 root root 26052 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 22432 Mar 1 2019 cat -rwxr-xr-x 1 root root 38868 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 38836 Mar 1 2019 chmod -rwxr-xr-x 1 root root 42972 Mar 1 2019 chown -rwxr-xr-x 1 root root 88376 Mar 1 2019 cp -rwxr-xr-x 1 root root 75516 Jan 18 2019 dash -rwxr-xr-x 1 root root 71648 Mar 1 2019 date -rwxr-xr-x 1 root root 51212 Mar 1 2019 dd -rwxr-xr-x 1 root root 55672 Mar 1 2019 df -rwxr-xr-x 1 root root 88444 Mar 1 2019 dir -rwxr-xr-x 1 root root 54872 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 18260 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 23 09:38 fusermount -rwxr-xr-x 1 root root 124508 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 6 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 27 2018 hostname -rwxr-xr-x 1 root root 43044 Mar 1 2019 ln -rwxr-xr-x 1 root root 34932 Jul 27 2018 login -rwxr-xr-x 1 root root 88444 Mar 1 2019 ls -rwxr-xr-x 1 root root 67036 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 47168 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 43040 Mar 1 2019 mknod -rwxr-xr-x 1 root root 26552 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 10 2019 more -rwsr-xr-x 1 root root 34268 Jan 10 2019 mount -rwxr-xr-x 1 root root 9688 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 84284 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Mar 1 2019 readlink -rwxr-xr-x 1 root root 42968 Mar 1 2019 rm -rwxr-xr-x 1 root root 26496 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jun 11 06:19 sh -> bash lrwxrwxrwx 1 root root 4 Jun 10 22:27 sh.distrib -> dash -rwxr-xr-x 1 root root 22384 Mar 1 2019 sleep -rwxr-xr-x 1 root root 51124 Mar 1 2019 stty -rwsr-xr-x 1 root root 42472 Jan 10 2019 su -rwxr-xr-x 1 root root 22392 Mar 1 2019 sync -rwxr-xr-x 1 root root 283324 Apr 24 2019 tar -rwxr-xr-x 1 root root 9808 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 63464 Mar 1 2019 touch -rwxr-xr-x 1 root root 18260 Mar 1 2019 true -rwxr-xr-x 1 root root 9636 Apr 23 09:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 10 2019 umount -rwxr-xr-x 1 root root 22380 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 88444 Mar 1 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/4392/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: armhf 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~), gfortran, libblas-dev, liblapack-dev, liblapacke-dev, libgsl-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 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. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapacke-dev; however: Package liblapacke-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran{a} gfortran-8{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran-8-dev{a} libgfortran5{a} libglib2.0-0{a} libgsl-dev{a} libgsl23{a} libgslcblas0{a} libicu63{a} liblapack-dev{a} liblapack3{a} liblapacke{a} liblapacke-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{a} libtmglib-dev{a} libtmglib3{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, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 31.9 MB of archives. After unpacking 107 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 10 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 11 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 12 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 13 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 14 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 24 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 30 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 31 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main armhf libgfortran5 armhf 8.3.0-6 [213 kB] Get: 35 http://deb.debian.org/debian buster/main armhf libgfortran-8-dev armhf 8.3.0-6 [260 kB] Get: 36 http://deb.debian.org/debian buster/main armhf gfortran-8 armhf 8.3.0-6 [7219 kB] Get: 37 http://deb.debian.org/debian buster/main armhf gfortran armhf 4:8.3.0-1 [1424 B] Get: 38 http://deb.debian.org/debian buster/main armhf libblas3 armhf 3.8.0-2 [109 kB] Get: 39 http://deb.debian.org/debian buster/main armhf libblas-dev armhf 3.8.0-2 [117 kB] Get: 40 http://deb.debian.org/debian buster/main armhf libgslcblas0 armhf 2.5+dfsg-6 [79.1 kB] Get: 41 http://deb.debian.org/debian buster/main armhf libgsl23 armhf 2.5+dfsg-6 [718 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libgsl-dev armhf 2.5+dfsg-6 [903 kB] Get: 43 http://deb.debian.org/debian buster/main armhf liblapack3 armhf 3.8.0-2 [1631 kB] Get: 44 http://deb.debian.org/debian buster/main armhf liblapack-dev armhf 3.8.0-2 [1680 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libtmglib3 armhf 3.8.0-2 [97.2 kB] Get: 46 http://deb.debian.org/debian buster/main armhf liblapacke armhf 3.8.0-2 [301 kB] Get: 47 http://deb.debian.org/debian buster/main armhf libtmglib-dev armhf 3.8.0-2 [100 kB] Get: 48 http://deb.debian.org/debian buster/main armhf liblapacke-dev armhf 3.8.0-2 [288 kB] Fetched 31.9 MB in 4s (9102 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (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 ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_armhf.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_armhf.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_armhf.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_armhf.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../11-libsigsegv2_2.12-2_armhf.deb ... Unpacking libsigsegv2:armhf (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_armhf.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. 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Setting up liblapack-dev:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode Setting up liblapacke:armhf (3.8.0-2) ... Setting up libtmglib-dev:armhf (3.8.0-2) ... Setting up po-debconf (1.0.21) ... Setting up liblapacke-dev:armhf (3.8.0-2) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up debhelper (12.1.1) ... 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/eigensoft-7.2.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package eigensoft dpkg-buildpackage: info: source version 7.2.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/eigensoft-7.2.1+dfsg' dh_clean /usr/bin/make -C src clobber make[2]: Entering directory '/build/eigensoft-7.2.1+dfsg/src' rm -f *.o */*.o */*.a nicksrc/*.o eigensrc/*.o ksrc/*.o rm -f baseprog convertf mergeit pca smshrink eigensrc/pcatoy eigensrc/smartrel eigensrc/smarteigenstrat eigensrc/twstats eigensrc/eigenstrat eigensrc/eigenstratQTL eigensrc/smartpca cd ../bin/ ; rm -f baseprog convertf mergeit pca smshrink pcatoy smartrel smarteigenstrat twstats eigenstrat eigenstratQTL smartpca ; cd ../src make[2]: Leaving directory '/build/eigensoft-7.2.1+dfsg/src' make[1]: Leaving directory '/build/eigensoft-7.2.1+dfsg' debian/rules build dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build make[1]: Entering directory '/build/eigensoft-7.2.1+dfsg' /usr/bin/make DEBUG_OPTIONS=-g -C src all make[2]: Entering directory '/build/eigensoft-7.2.1+dfsg/src' cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o baseprog.o baseprog.c cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcio.o mcio.c mcio.c: In function 'getgenos': mcio.c:1368:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system (cmd); ^~~~~~~~~~~~ In file included from ../include/statsubs.h:6, from ../include/nicklib.h:4, from ../include/admutils.h:2, from ../include/mcio.h:11, from mcio.c:3: mcio.c: In function 'getindivs': ../include/strsubs.h:83:54: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] #define ZALLOC(item,n,type) if ((item = (type *)calloc((n),sizeof(type))) == NULL) \ ^~~~~~~~~~~~~~~~~~~~~~~~ mcio.c:952:3: note: in expansion of macro 'ZALLOC' ZALLOC (indivmarkers, nindiv, Indiv *); ^~~~~~ In file included from ../include/strsubs.h:1, from ../include/vsubs.h:5, from ../include/mcio.h:10, from mcio.c:3: /usr/include/stdlib.h:541:14: note: in a call to allocation function 'calloc' declared here extern void *calloc (size_t __nmemb, size_t __size) ^~~~~~ cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o egsubs.o egsubs.c cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o admutils.o admutils.c admutils.c: In function 'setid2pops': admutils.c:1256:31: warning: format '%s' expects a matching 'char *' argument [-Wformat=] printf ("(setid2pops): %s not found\n"); ~^ cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o h2d.o h2d.c cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/exclude.o eigensrc/exclude.c /usr/bin/make -C nicksrc make[3]: Entering directory '/build/eigensoft-7.2.1+dfsg/src/nicksrc' cc -I../../include -D_GNU_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gauss.o gauss.c cc -I../../include -D_GNU_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gds.o gds.c cc -I../../include -D_GNU_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o getpars.o getpars.c cc -I../../include -D_GNU_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o linsubs.o linsubs.c cc -I../../include -D_GNU_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sortit.o sortit.c cc -I../../include -D_GNU_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o statsubs.o statsubs.c cc -I../../include -D_GNU_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o strsubs.o strsubs.c cc -I../../include -D_GNU_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vsubs.o vsubs.c cc -I../../include -D_GNU_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o xsearch.o xsearch.c cc -I../../include -D_GNU_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o twtable.o twtable.c ar -r libnick.a gauss.o gds.o getpars.o linsubs.o sortit.o statsubs.o strsubs.o vsubs.o xsearch.o twtable.o ar: creating libnick.a make[3]: Leaving directory '/build/eigensoft-7.2.1+dfsg/src/nicksrc' cc -Wl,-z,relro -Wl,-z,now baseprog.o mcio.o egsubs.o admutils.o h2d.o eigensrc/exclude.o nicksrc/libnick.a -lgsl -lblas -lm -llapacke -llapack -lpthread -o baseprog cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convertf.o convertf.c convertf.c: In function 'main': convertf.c:257:5: warning: implicit declaration of function 'setfamilypopnames'; did you mean 'setgenotypename'? [-Wimplicit-function-declaration] setfamilypopnames (YES); ^~~~~~~~~~~~~~~~~ setgenotypename cc -Wl,-z,relro -Wl,-z,now convertf.o mcio.o egsubs.o admutils.o h2d.o eigensrc/exclude.o nicksrc/libnick.a -lgsl -lblas -lm -llapacke -llapack -lpthread -o convertf cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mergeit.o mergeit.c cc -Wl,-z,relro -Wl,-z,now mergeit.o mcio.o admutils.o nicksrc/libnick.a -lgsl -lblas -lm -llapacke -llapack -lpthread -o mergeit cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o pca.o pca.c pca.c: In function 'main': pca.c:102:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%c", &Xchar); ^~~~~~~~~~~~~~~~~~~~~~~~~ pca.c:167:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%c", &Xchar); ^~~~~~~~~~~~~~~~~~~~~~~~~ pca.c:190:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%c", &Xchar); /* should be \n character */ ^~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/eigsubs.o eigensrc/eigsubs.c cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/eigx.o eigensrc/eigx.c cc -Wl,-z,relro -Wl,-z,now pca.o eigensrc/eigsubs.o eigensrc/eigx.o nicksrc/libnick.a -lgsl -lblas -lm -llapacke -llapack -lpthread -o pca cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smshrink.o smshrink.c smshrink.c: In function 'main': smshrink.c:624:5: warning: implicit declaration of function 'setid2pops'; did you mean 'setsdpos'? [-Wimplicit-function-declaration] setid2pops (id2pops, indivmarkers, numindivs); ^~~~~~~~~~ setsdpos smshrink.c:774:5: warning: implicit declaration of function 'kjg_fpca' [-Wimplicit-function-declaration] kjg_fpca (numeigs, fastdim, fastiter, evals, evecs); ^~~~~~~~ smshrink.c:578:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system (buff); ^~~~~~~~~~~~~ cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/smartsubs.o eigensrc/smartsubs.c cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o twsubs.o twsubs.c cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o qpsubs.o qpsubs.c cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regsubs.o regsubs.c cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gval.o gval.c gval.c: In function 'setgval': gval.c:67:5: warning: implicit declaration of function 'getcolxz'; did you mean 'get_ncols'? [-Wimplicit-function-declaration] getcolxz (cc, cupt, xindex, xtypes, nrows, i, xmean, xfancy, &n0, &n1); ^~~~~~~~ get_ncols cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ksrc/kjg_fpca.o ksrc/kjg_fpca.c ksrc/kjg_fpca.c: In function 'kjg_fpca': ksrc/kjg_fpca.c:31:14: warning: implicit declaration of function 'get_ncols'; did you mean 'gethpos'? [-Wimplicit-function-declaration] size_t m = get_ncols (); ^~~~~~~~~ gethpos ksrc/kjg_fpca.c:32:14: warning: implicit declaration of function 'get_nrows'; did you mean 'gethpos'? [-Wimplicit-function-declaration] size_t n = get_nrows (); ^~~~~~~~~ gethpos ksrc/kjg_fpca.c: In function 'kjg_fpca_XTXA': ksrc/kjg_fpca.c:118:11: warning: implicit declaration of function 'kjg_geno_get_normalized_rows' [-Wimplicit-function-declaration] r = kjg_geno_get_normalized_rows (i, KJG_FPCA_ROWS, Y); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ksrc/kjg_gsl.o ksrc/kjg_gsl.c ksrc/kjg_gsl.c: In function 'kjg_gsl_matrix_fscanf': ksrc/kjg_gsl.c:38:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (stream, "%lg", &x); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -Wl,-z,relro -Wl,-z,now smshrink.o eigensrc/eigsubs.o eigensrc/exclude.o eigensrc/smartsubs.o eigensrc/eigx.o twsubs.o mcio.o qpsubs.o admutils.o egsubs.o regsubs.o gval.o nicksrc/libnick.a ksrc/kjg_fpca.o ksrc/kjg_gsl.o -lgsl -lblas -lm -llapacke -llapack -lpthread -o smshrink cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/pcatoy.o eigensrc/pcatoy.c cc -Wl,-z,relro -Wl,-z,now eigensrc/pcatoy.o eigensrc/eigsubs.o eigensrc/eigx.o nicksrc/libnick.a -lgsl -lblas -lm -llapacke -llapack -lpthread -o eigensrc/pcatoy cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/smartrel.o eigensrc/smartrel.c cc -Wl,-z,relro -Wl,-z,now eigensrc/smartrel.o twsubs.o mcio.o qpsubs.o admutils.o egsubs.o regsubs.o eigensrc/eigsubs.o eigensrc/eigx.o eigensrc/smartsubs.o nicksrc/libnick.a -lgsl -lblas -lm -llapacke -llapack -lpthread -o eigensrc/smartrel cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/smarteigenstrat.o eigensrc/smarteigenstrat.c eigensrc/smarteigenstrat.c: In function 'readpcafile': eigensrc/smarteigenstrat.c:332:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fppca, "%d", &K); ^~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/smarteigenstrat.c:339:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fppca, "%lf", &tempdouble); /* eigenvalues */ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/smarteigenstrat.c:342:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fppca, "%lf", &V[NSAMPLES * n + k]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/smarteigenstrat.c:360:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fppca, "%lf", &tempdouble); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -Wl,-z,relro -Wl,-z,now eigensrc/smarteigenstrat.o mcio.o admutils.o nicksrc/libnick.a -lgsl -lblas -lm -llapacke -llapack -lpthread -o eigensrc/smarteigenstrat cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/twstats.o eigensrc/twstats.c cc -Wl,-z,relro -Wl,-z,now eigensrc/twstats.o nicksrc/libnick.a -lgsl -lblas -lm -llapacke -llapack -lpthread -o eigensrc/twstats cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now eigensrc/eigenstrat.c -lgsl -lblas -lm -llapacke -llapack -lpthread -o eigensrc/eigenstrat eigensrc/eigenstrat.c: In function 'main': eigensrc/eigenstrat.c:86:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%c", &Xchar); ^~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstrat.c:123:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fppca, "%d", &K); ^~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstrat.c:130:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fppca, "%lf", &tempdouble); /* eigenvalues */ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstrat.c:133:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fppca, "%lf", &V[NSAMPLES * n + k]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstrat.c:151:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fppca, "%lf", &tempdouble); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstrat.c:165:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fppheno, "%c", &Xchar); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstrat.c:188:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fppheno, "%c", &Xchar); /* should be end of file */ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstrat.c:244:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%c", &Xchar); ^~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstrat.c:267:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%c", &Xchar); /* should be \n character */ ^~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now eigensrc/eigenstratQTL.c -lgsl -lblas -lm -llapacke -llapack -lpthread -o eigensrc/eigenstratQTL eigensrc/eigenstratQTL.c: In function 'main': eigensrc/eigenstratQTL.c:86:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%c", &Xchar); ^~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstratQTL.c:123:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fppca, "%d", &K); ^~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstratQTL.c:130:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fppca, "%lf", &tempdouble); /* eigenvalues */ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstratQTL.c:133:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fppca, "%lf", &V[NSAMPLES * n + k]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstratQTL.c:151:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fppca, "%lf", &tempdouble); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstratQTL.c:172:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fppheno, "%lf", &iscase[n]); /* QTL phenotype */ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstratQTL.c:174:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fppheno, "%lf", &tempdouble); /* to check # entries */ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstratQTL.c:227:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%c", &Xchar); ^~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstratQTL.c:250:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%c", &Xchar); /* should be \n character */ ^~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -ffile-prefix-map=/build/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/smartpca.o eigensrc/smartpca.c eigensrc/smartpca.c: In function 'main': eigensrc/smartpca.c:644:5: warning: implicit declaration of function 'setid2pops'; did you mean 'setsdpos'? [-Wimplicit-function-declaration] setid2pops (id2pops, indivmarkers, numindivs); ^~~~~~~~~~ setsdpos eigensrc/smartpca.c:809:5: warning: implicit declaration of function 'kjg_fpca' [-Wimplicit-function-declaration] kjg_fpca (numeigs, fastdim, fastiter, evals, evecs); ^~~~~~~~ eigensrc/smartpca.c:597:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system (buff); ^~~~~~~~~~~~~ cc -Wl,-z,relro -Wl,-z,now eigensrc/smartpca.o eigensrc/eigsubs.o eigensrc/exclude.o eigensrc/smartsubs.o eigensrc/eigx.o mcio.o qpsubs.o admutils.o egsubs.o regsubs.o gval.o nicksrc/libnick.a ksrc/kjg_fpca.o ksrc/kjg_gsl.o -lgsl -lblas -lm -llapacke -llapack -lpthread -o eigensrc/smartpca make[2]: Leaving directory '/build/eigensoft-7.2.1+dfsg/src' cd src && make install make[2]: Entering directory '/build/eigensoft-7.2.1+dfsg/src' mv baseprog convertf mergeit pca smshrink eigensrc/pcatoy eigensrc/smartrel eigensrc/smarteigenstrat eigensrc/twstats eigensrc/eigenstrat eigensrc/eigenstratQTL eigensrc/smartpca ../bin make[2]: Leaving directory '/build/eigensoft-7.2.1+dfsg/src' make[1]: Leaving directory '/build/eigensoft-7.2.1+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_install make[1]: Entering directory '/build/eigensoft-7.2.1+dfsg' dh_install find debian/eigensoft/usr/share/ -type f -empty -delete # file consists only from single line with wrong interpreter find debian/eigensoft/usr/share/ -type f -name HGDP.X.perl -delete # Fix wrappers and drop *.perl extension in /usr/bin while keeping # the original name in /usr/lib/debian-med/bin mkdir -p debian/eigensoft/usr/lib/debian-med/bin for pl in evec2pca-ped evec2pca smarteigenstrat smartpca ; do \ rm debian/eigensoft/usr/bin/${pl} ; \ sed -i \ -e "s?\(command[[:space:]]*=[[:space:]]*\"\)\(${pl}\)?\1/usr/lib/eigensoft/\2?" \ -e "s?\(cmd[[:space:]]*=[[:space:]]*\"\)\(${pl}\)?\1/usr/lib/eigensoft/\2?" \ -e "s?\(cmd[[:space:]]*=[[:space:]]*\"\)\(evec2pca.*\)\.perl?\1?" \ -e "s?\(${pl}\)\.perl?\1?" \ debian/eigensoft/usr/bin/${pl}.perl ; \ cp -a debian/eigensoft/usr/bin/${pl}.perl debian/eigensoft/usr/bin/${pl} ; \ mv debian/eigensoft/usr/bin/${pl}.perl debian/eigensoft/usr/lib/debian-med/bin ; \ done rm: cannot remove 'debian/eigensoft/usr/bin/evec2pca-ped': No such file or directory rm: cannot remove 'debian/eigensoft/usr/bin/evec2pca': No such file or directory rm debian/eigensoft/usr/bin/gc.perl make[1]: Leaving directory '/build/eigensoft-7.2.1+dfsg' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/eigensoft-7.2.1+dfsg' dh_fixperms find debian/*/usr/share/eigensoft -type f -name "*.perl" -exec chmod +x \{\} \; make[1]: Leaving directory '/build/eigensoft-7.2.1+dfsg' dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/pcatoy debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/bin/pca debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/bin/smshrink debian/eigensoft/usr/bin/eigenstratQTL debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/mergeit were not linked against libblas.so.3 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'eigensoft' in '../eigensoft_7.2.1+dfsg-1_armhf.deb'. dpkg-deb: building package 'eigensoft-dbgsym' in '../eigensoft-dbgsym_7.2.1+dfsg-1_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../eigensoft_7.2.1+dfsg-1_armhf.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: user script /srv/workspace/pbuilder/4392/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/4392/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/4392 and its subdirectories I: Current time: Thu Jun 11 06:22:13 +14 2020 I: pbuilder-time-stamp: 1591806133