I: pbuilder: network access will be disabled during build
I: Current time: Sun Jun 20 13:53:08 +14 2021
I: pbuilder-time-stamp: 1624146788
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bullseye-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 [eigensoft_7.2.1+dfsg-2.dsc]
I: copying [./eigensoft_7.2.1+dfsg.orig.tar.xz]
I: copying [./eigensoft_7.2.1+dfsg-2.debian.tar.xz]
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig._UmmuJqm/trustedkeys.kbx': General error
gpgv: Signature made Thu Jul 23 20:55:26 2020 +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-2.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-2.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: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/10220/tmp/hooks/D01_modify_environment starting
debug: Running on ionos12-i386.
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/10220/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/10220/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]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
BASH_VERSION='5.1.4(1)-release'
BUILDDIR=/build
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=i386
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10'
DIRSTACK=()
DISTRIBUTION=
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=i686
HOST_ARCH=i386
IFS='
'
INVOCATION_ID=f27b7269662c47eba7c4218dd7594210
LANG=C
LANGUAGE=de_CH:de
LC_ALL=C
LD_LIBRARY_PATH=/usr/lib/libeatmydata
LD_PRELOAD=libeatmydata.so
MACHTYPE=i686-pc-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
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=10220
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.5Gr2DOCJ8K/pbuilderrc_ce5D --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.5Gr2DOCJ8K/b2 --logfile b2/build.log --extrapackages usrmerge eigensoft_7.2.1+dfsg-2.dsc'
SUDO_GID=112
SUDO_UID=107
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://78.137.99.97:3128
I: uname -a
Linux i-capture-the-hostname 4.19.0-17-686-pae #1 SMP Debian 4.19.194-1 (2021-06-10) i686 GNU/Linux
I: ls -l /bin
total 5776
-rwxr-xr-x 1 root root 1367848 Feb 25 10:57 bash
-rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2
-rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep
-rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2
-rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore
-rwxr-xr-x 1 root root 38824 Sep 23 2020 cat
-rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp
-rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod
-rwxr-xr-x 1 root root 75752 Sep 23 2020 chown
-rwxr-xr-x 1 root root 157960 Sep 23 2020 cp
-rwxr-xr-x 1 root root 128724 Dec 11 2020 dash
-rwxr-xr-x 1 root root 124904 Sep 23 2020 date
-rwxr-xr-x 1 root root 92172 Sep 23 2020 dd
-rwxr-xr-x 1 root root 100752 Sep 23 2020 df
-rwxr-xr-x 1 root root 153964 Sep 23 2020 dir
-rwxr-xr-x 1 root root 83644 Feb 8 04:38 dmesg
lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname
-rwxr-xr-x 1 root root 34664 Sep 23 2020 echo
-rwxr-xr-x 1 root root 28 Nov 10 2020 egrep
-rwxr-xr-x 1 root root 34664 Sep 23 2020 false
-rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep
-rwxr-xr-x 1 root root 71928 Feb 8 04:38 findmnt
-rwsr-xr-x 1 root root 30112 Feb 27 06:12 fusermount
-rwxr-xr-x 1 root root 210488 Nov 10 2020 grep
-rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip
-rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe
-rwxr-xr-x 1 root root 100952 Mar 3 13:30 gzip
-rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname
-rwxr-xr-x 1 root root 83980 Sep 23 2020 ln
-rwxr-xr-x 1 root root 55572 Feb 8 2020 login
-rwxr-xr-x 1 root root 153964 Sep 23 2020 ls
-rwxr-xr-x 1 root root 153124 Feb 8 04:38 lsblk
-rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir
-rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod
-rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp
-rwxr-xr-x 1 root root 58920 Feb 8 04:38 more
-rwsr-xr-x 1 root root 50720 Feb 8 04:38 mount
-rwxr-xr-x 1 root root 13856 Feb 8 04:38 mountpoint
-rwxr-xr-x 1 root root 157996 Sep 23 2020 mv
lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd
lrwxrwxrwx 1 root root 4 Feb 25 10:57 rbash -> bash
-rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink
-rwxr-xr-x 1 root root 75720 Sep 23 2020 rm
-rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir
-rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts
-rwxr-xr-x 1 root root 125036 Dec 23 2018 sed
lrwxrwxrwx 1 root root 4 Jun 20 13:55 sh -> bash
lrwxrwxrwx 1 root root 4 Jun 18 23:27 sh.distrib -> dash
-rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep
-rwxr-xr-x 1 root root 83880 Sep 23 2020 stty
-rwsr-xr-x 1 root root 79396 Feb 8 04:38 su
-rwxr-xr-x 1 root root 34696 Sep 23 2020 sync
-rwxr-xr-x 1 root root 602584 Feb 17 23:55 tar
-rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile
-rwxr-xr-x 1 root root 108520 Sep 23 2020 touch
-rwxr-xr-x 1 root root 34664 Sep 23 2020 true
-rwxr-xr-x 1 root root 17768 Feb 27 06:12 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Feb 8 04:38 umount
-rwxr-xr-x 1 root root 34664 Sep 23 2020 uname
-rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress
-rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir
-rwxr-xr-x 1 root root 63024 Feb 8 04:38 wdctl
lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat
-rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp
-rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff
-rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep
-rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep
-rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce
-rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep
-rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless
-rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore
-rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew
I: user script /srv/workspace/pbuilder/10220/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 <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), 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 ... 19675 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
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} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran{a} gfortran-10{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran-10-dev{a} libgfortran5{a} libgsl-dev{a} libgsl25{a} libgslcblas0{a} libicu67{a} liblapack-dev{a} liblapack3{a} liblapacke{a} liblapacke-dev{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsigsegv2{a} libsub-override-perl{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 libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 46 newly installed, 0 to remove and 0 not upgraded.
Need to get 38.7 MB of archives. After unpacking 156 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB]
Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB]
Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB]
Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB]
Get: 6 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB]
Get: 7 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB]
Get: 8 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB]
Get: 9 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB]
Get: 10 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB]
Get: 11 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB]
Get: 12 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB]
Get: 13 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB]
Get: 14 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get: 15 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB]
Get: 16 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB]
Get: 17 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB]
Get: 18 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB]
Get: 19 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB]
Get: 22 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB]
Get: 23 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB]
Get: 24 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB]
Get: 25 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB]
Get: 26 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-6 [8776 kB]
Get: 27 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB]
Get: 28 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB]
Get: 29 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get: 30 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB]
Get: 32 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB]
Get: 33 http://deb.debian.org/debian bullseye/main i386 libgfortran-10-dev i386 10.2.1-6 [705 kB]
Get: 34 http://deb.debian.org/debian bullseye/main i386 gfortran-10 i386 10.2.1-6 [9642 kB]
Get: 35 http://deb.debian.org/debian bullseye/main i386 gfortran i386 4:10.2.1-1 [1436 B]
Get: 36 http://deb.debian.org/debian bullseye/main i386 libblas3 i386 3.9.0-3 [147 kB]
Get: 37 http://deb.debian.org/debian bullseye/main i386 libblas-dev i386 3.9.0-3 [157 kB]
Get: 38 http://deb.debian.org/debian bullseye/main i386 libgslcblas0 i386 2.6+dfsg-2 [99.2 kB]
Get: 39 http://deb.debian.org/debian bullseye/main i386 libgsl25 i386 2.6+dfsg-2 [911 kB]
Get: 40 http://deb.debian.org/debian bullseye/main i386 libgsl-dev i386 2.6+dfsg-2 [1146 kB]
Get: 41 http://deb.debian.org/debian bullseye/main i386 liblapack3 i386 3.9.0-3 [1960 kB]
Get: 42 http://deb.debian.org/debian bullseye/main i386 liblapack-dev i386 3.9.0-3 [3759 kB]
Get: 43 http://deb.debian.org/debian bullseye/main i386 libtmglib3 i386 3.9.0-3 [125 kB]
Get: 44 http://deb.debian.org/debian bullseye/main i386 liblapacke i386 3.9.0-3 [372 kB]
Get: 45 http://deb.debian.org/debian bullseye/main i386 libtmglib-dev i386 3.9.0-3 [131 kB]
Get: 46 http://deb.debian.org/debian bullseye/main i386 liblapacke-dev i386 3.9.0-3 [338 kB]
Fetched 38.7 MB in 9s (4513 kB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package bsdextrautils.
(Reading database ...
(Reading database ... 5%
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19675 files and directories currently installed.)
Preparing to unpack .../00-bsdextrautils_2.36.1-7_i386.deb ...
Unpacking bsdextrautils (2.36.1-7) ...
Selecting previously unselected package libuchardet0:i386.
Preparing to unpack .../01-libuchardet0_0.0.7-1_i386.deb ...
Unpacking libuchardet0:i386 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../02-groff-base_1.22.4-6_i386.deb ...
Unpacking groff-base (1.22.4-6) ...
Selecting previously unselected package libpipeline1:i386.
Preparing to unpack .../03-libpipeline1_1.5.3-1_i386.deb ...
Unpacking libpipeline1:i386 (1.5.3-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../04-man-db_2.9.4-2_i386.deb ...
Unpacking man-db (2.9.4-2) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ...
Unpacking sensible-utils (0.0.14) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_i386.deb ...
Unpacking libmagic-mgc (1:5.39-3) ...
Selecting previously unselected package libmagic1:i386.
Preparing to unpack .../07-libmagic1_1%3a5.39-3_i386.deb ...
Unpacking libmagic1:i386 (1:5.39-3) ...
Selecting previously unselected package file.
Preparing to unpack .../08-file_1%3a5.39-3_i386.deb ...
Unpacking file (1:5.39-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../09-gettext-base_0.21-4_i386.deb ...
Unpacking gettext-base (0.21-4) ...
Selecting previously unselected package libsigsegv2:i386.
Preparing to unpack .../10-libsigsegv2_2.13-1_i386.deb ...
Unpacking libsigsegv2:i386 (2.13-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../11-m4_1.4.18-5_i386.deb ...
Unpacking m4 (1.4.18-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../12-autoconf_2.69-14_all.deb ...
Unpacking autoconf (2.69-14) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ...
Unpacking autotools-dev (20180224.1+nmu1) ...
Selecting previously unselected package automake.
Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ...
Unpacking automake (1:1.16.3-2) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../15-autopoint_0.21-4_all.deb ...
Unpacking autopoint (0.21-4) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../16-libdebhelper-perl_13.3.4_all.deb ...
Unpacking libdebhelper-perl (13.3.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../17-libtool_2.4.6-15_all.deb ...
Unpacking libtool (2.4.6-15) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../18-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ...
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The following additional packages will be installed:
libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl
The following NEW packages will be installed:
libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge
0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded.
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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-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
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 binary
dh binary
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 -fdebug-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 -fdebug-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]
1368 | 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=]
83 | #define ZALLOC(item,n,type) if ((item = (type *)calloc((n),sizeof(type))) == NULL) \
| ^~~~~~~~~~~~~~~~~~~~~~~~
mcio.c:952:3: note: in expansion of macro 'ZALLOC'
952 | 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:542:14: note: in a call to allocation function 'calloc' declared here
542 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
In file included from /usr/include/stdio.h:867,
from ../include/mcio.h:4,
from mcio.c:3:
In function 'printf',
inlined from 'outfiles' at mcio.c:3159:5:
/usr/include/i386-linux-gnu/bits/stdio2.h:107:10: warning: '%s' directive argument is null [-Wformat-overflow=]
107 | return __printf_chk (__USE_FORTIFY_LEVEL - 1, __fmt, __va_arg_pack ());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-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 -fdebug-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=]
1256 | printf ("(setid2pops): %s not found\n");
| ~^
| |
| char *
cc -g -O2 -fdebug-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 -fdebug-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 -fdebug-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' [-Wimplicit-function-declaration]
257 | setfamilypopnames (YES);
| ^~~~~~~~~~~~~~~~~
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 -fdebug-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 -fdebug-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]
102 | fscanf (fp, "%c", &Xchar);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
pca.c:167:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
167 | fscanf (fp, "%c", &Xchar);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
pca.c:190:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
190 | fscanf (fp, "%c", &Xchar); /* should be \n character */
| ^~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-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 -fdebug-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 -fdebug-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]
624 | setid2pops (id2pops, indivmarkers, numindivs);
| ^~~~~~~~~~
| setsdpos
smshrink.c:774:5: warning: implicit declaration of function 'kjg_fpca' [-Wimplicit-function-declaration]
774 | 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]
578 | system (buff);
| ^~~~~~~~~~~~~
cc -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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' [-Wimplicit-function-declaration]
67 | getcolxz (cc, cupt, xindex, xtypes, nrows, i, xmean, xfancy, &n0, &n1);
| ^~~~~~~~
cc -g -O2 -fdebug-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' [-Wimplicit-function-declaration]
31 | size_t m = get_ncols ();
| ^~~~~~~~~
ksrc/kjg_fpca.c:32:14: warning: implicit declaration of function 'get_nrows' [-Wimplicit-function-declaration]
32 | size_t n = get_nrows ();
| ^~~~~~~~~
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]
118 | r = kjg_geno_get_normalized_rows (i, KJG_FPCA_ROWS, Y);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-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]
38 | 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 -fdebug-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 -fdebug-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 -fdebug-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]
332 | fscanf (fppca, "%d", &K);
| ^~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/smarteigenstrat.c:339:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
339 | fscanf (fppca, "%lf", &tempdouble); /* eigenvalues */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/smarteigenstrat.c:342:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
342 | 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]
360 | 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 -fdebug-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 -fdebug-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]
86 | fscanf (fp, "%c", &Xchar);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:123:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
123 | fscanf (fppca, "%d", &K);
| ^~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:130:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
130 | fscanf (fppca, "%lf", &tempdouble); /* eigenvalues */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:133:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
133 | 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]
151 | fscanf (fppca, "%lf", &tempdouble);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:165:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
165 | fscanf (fppheno, "%c", &Xchar);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:188:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
188 | 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]
244 | fscanf (fp, "%c", &Xchar);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:267:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
267 | fscanf (fp, "%c", &Xchar); /* should be \n character */
| ^~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-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]
86 | fscanf (fp, "%c", &Xchar);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:123:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
123 | fscanf (fppca, "%d", &K);
| ^~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:130:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
130 | fscanf (fppca, "%lf", &tempdouble); /* eigenvalues */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:133:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
133 | 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]
151 | fscanf (fppca, "%lf", &tempdouble);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:172:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
172 | 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]
174 | 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]
227 | fscanf (fp, "%c", &Xchar);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:250:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
250 | fscanf (fp, "%c", &Xchar); /* should be \n character */
| ^~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-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]
644 | setid2pops (id2pops, indivmarkers, numindivs);
| ^~~~~~~~~~
| setsdpos
eigensrc/smartpca.c:809:5: warning: implicit declaration of function 'kjg_fpca' [-Wimplicit-function-declaration]
809 | 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]
597 | 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
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_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/eigensoft/usr/bin/smshrink debian/eigensoft/usr/lib/eigensoft/smartpca 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-dbgsym' in '../eigensoft-dbgsym_7.2.1+dfsg-2_i386.deb'.
dpkg-deb: building package 'eigensoft' in '../eigensoft_7.2.1+dfsg-2_i386.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genchanges --build=binary >../eigensoft_7.2.1+dfsg-2_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: user script /srv/workspace/pbuilder/10220/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/10220/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/10220 and its subdirectories
I: Current time: Sun Jun 20 13:57:52 +14 2021
I: pbuilder-time-stamp: 1624147072