Mon Jul 12 16:25:16 UTC 2021 I: starting to build eigensoft/buster/amd64 on jenkins on '2021-07-12 16:25' Mon Jul 12 16:25:16 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_8/66110/console.log Mon Jul 12 16:25:17 UTC 2021 I: Downloading source for buster/eigensoft=7.2.1+dfsg-1 --2021-07-12 16:25:17-- http://deb.debian.org/debian/pool/main/e/eigensoft/eigensoft_7.2.1+dfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2127 (2.1K) Saving to: ‘eigensoft_7.2.1+dfsg-1.dsc’ 0K .. 100% 258M=0s 2021-07-12 16:25:17 (258 MB/s) - ‘eigensoft_7.2.1+dfsg-1.dsc’ saved [2127/2127] Mon Jul 12 16:25:17 UTC 2021 I: eigensoft_7.2.1+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: eigensoft Binary: eigensoft Architecture: any Version: 7.2.1+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Homepage: http://www.hsph.harvard.edu/faculty/alkes-price/software/ Standards-Version: 4.1.5 Vcs-Browser: https://salsa.debian.org/med-team/eigensoft Vcs-Git: https://salsa.debian.org/med-team/eigensoft.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~), gfortran, libblas-dev, liblapack-dev, liblapacke-dev, libgsl-dev Package-List: eigensoft deb science optional arch=any Checksums-Sha1: e0f2a73c97afe1f69d59840ab65ee3c3ff567173 170148 eigensoft_7.2.1+dfsg.orig.tar.xz b3f276d41be79d006a5e07c9d2158587a869ba42 5816 eigensoft_7.2.1+dfsg-1.debian.tar.xz Checksums-Sha256: 182e2f030d08ea5350b3e7a2636dfcc1f23a174266de9f4c87134ad7f85fb008 170148 eigensoft_7.2.1+dfsg.orig.tar.xz eb3e0622a1de58a7bf8b42b8e41c2bc5ea7fd79c625857020f4a3aa0d6407628 5816 eigensoft_7.2.1+dfsg-1.debian.tar.xz Files: a20c83aeb532f9689716c7a03bf1f3e5 170148 eigensoft_7.2.1+dfsg.orig.tar.xz 4801e171d2e2ccbb5403334c29154d95 5816 eigensoft_7.2.1+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAltMqO0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHKpw//Vp+Vu1dBi9fWtZyCIZtt5eqV5Vpuoq4F 9otOxPMd5cFNgDywl3f4nfAwZOs0wN/kfMgM2ySv2SpeVvCQGpJYW4ATLA8IWn4z Edvn4IRO2Cmgi3dGGp20NizDDY0OSwaMlk+XSNZcKEEzxOgUP2zR+rOYX78ge73H ldD+ZsLBmRmpKBJVe78HHwRufvKfnLLdYRKabpDmciTJk9Hk79EwWUK8xxW0wVWb 5ebMvkmjhTpw8P/iuc3X/4nPo8Iej5mKh1hkAyfxuC4Vv3AVMyTTDMe4tOIcWJ4o lLBlQRthGgzN1+ToZF5t78wd3hwLBeu2wQim540UzGKrnPrJfqFe6ckoiUJvlrwH PRsCqsVGcWipHHBGq/fDQmFCRwoHNDl7aJyT0xXKzc6IJbKgGupkCRiXQPQ99dI+ BNc8SRe+hx/FSRu/FnJIDjcnd7VsrVSX8aIkXbR06hbasXg48BXtlL0Ihz11vkXB YsnKBkZou4mrsr8loMJCdCoPHENTe0In0c+IvaSKqkIMhHAdJPEXVndaGIKqm2fq ljMRUMVZl148B26f8/mnLMRSTFN/Pv1FQ1mA8qJuIm8bSKVHVaUvRrJ7CNaEdWvo 0mqw3mv0sTYU1dFSG64BEivledXtUQkF5ZY9Q0FVh85a4GLE/r1SOoZ4R17cU7QS D4vIBc8I7m8= =eVLB -----END PGP SIGNATURE----- Mon Jul 12 16:25:17 UTC 2021 I: Checking whether the package is not for us Mon Jul 12 16:25:17 UTC 2021 I: Starting 1st build on remote node ionos15-amd64.debian.net. Mon Jul 12 16:25:17 UTC 2021 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Mon Jul 12 16:26:06 UTC 2021 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Aug 14 10:48:19 -12 2022 I: pbuilder-time-stamp: 1660517299 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 Mon Jul 16 02:17:17 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 ./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/11233/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='e85d93fcc2b24078946281e7a192c514' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='11233' 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.nBJGUPxDyt/pbuilderrc_XDHW --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.nBJGUPxDyt/b1 --logfile b1/build.log eigensoft_7.2.1+dfsg-1.dsc' SUDO_GID='111' SUDO_UID='106' 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 ionos15-amd64 5.10.0-0.bpo.7-amd64 #1 SMP Debian 5.10.40-1~bpo10+1 (2021-06-04) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 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 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 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 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 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 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 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 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 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 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 9 02:47 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 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/11233/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team 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 ... 19195 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 37.1 MB of archives. After unpacking 146 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libgfortran-8-dev amd64 8.3.0-6 [616 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 gfortran-8 amd64 8.3.0-6 [9375 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 gfortran amd64 4:8.3.0-1 [1432 B] Get: 38 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libblas-dev amd64 3.8.0-2 [154 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libgslcblas0 amd64 2.5+dfsg-6 [101 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libgsl23 amd64 2.5+dfsg-6 [880 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libgsl-dev amd64 2.5+dfsg-6 [1063 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 liblapack-dev amd64 3.8.0-2 [2140 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libtmglib3 amd64 3.8.0-2 [128 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 liblapacke amd64 3.8.0-2 [367 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 libtmglib-dev amd64 3.8.0-2 [129 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 liblapacke-dev amd64 3.8.0-2 [325 kB] Fetched 37.1 MB in 0s (79.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. 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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" HOME="/nonexistent/first-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 amd64 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 [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-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/bin/eigenstrat debian/eigensoft/usr/bin/pcatoy debian/eigensoft/usr/bin/eigenstratQTL debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/pca debian/eigensoft/usr/bin/mergeit debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/bin/smshrink debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/bin/twstats 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_amd64.deb'. dpkg-deb: building package 'eigensoft-dbgsym' in '../eigensoft-dbgsym_7.2.1+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../eigensoft_7.2.1+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/11233 and its subdirectories I: Current time: Sun Aug 14 10:49:07 -12 2022 I: pbuilder-time-stamp: 1660517347 Mon Jul 12 16:26:06 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Mon Jul 12 16:26:07 UTC 2021 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Mon Jul 12 16:27:16 UTC 2021 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Mon Jul 12 16:27:16 UTC 2021 I: eigensoft_7.2.1+dfsg-1_amd64.changes: Format: 1.8 Date: Mon, 16 Jul 2018 16:10:33 +0200 Source: eigensoft Binary: eigensoft eigensoft-dbgsym Architecture: amd64 Version: 7.2.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: eigensoft - reduction of population bias for genetic analyses Changes: eigensoft (7.2.1+dfsg-1) unstable; urgency=medium . [ Steffen Moeller ] * debian/upstream/metadata; Added references to registries and paper . [ Andreas Tille ] * New upstream version * d/watch: Source is now on Github * d/rules: Do not parse d/changelog * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.5 Checksums-Sha1: 25d011bc839090fb1fb33f65fe5e26d89bfc8cc1 1328620 eigensoft-dbgsym_7.2.1+dfsg-1_amd64.deb 8b0f627f2617ee8b720d8d919da26b6da4434438 5130 eigensoft_7.2.1+dfsg-1_amd64.buildinfo b1a35985334de2f58c626ed1c0f9bd19ab94b892 382256 eigensoft_7.2.1+dfsg-1_amd64.deb Checksums-Sha256: 85452bcb72e4807ae3f5a35dee74048f70fdaa9f00fa135ad5d6d98022e2aa7a 1328620 eigensoft-dbgsym_7.2.1+dfsg-1_amd64.deb 311f2883c64c77252196ed496245688b05dc15b32b9775a8c5d1f21ca370176e 5130 eigensoft_7.2.1+dfsg-1_amd64.buildinfo 9a7bf8f50bff75ea84fc0749393ec9d2b701817932bb3d33131eaccdb0417a72 382256 eigensoft_7.2.1+dfsg-1_amd64.deb Files: cfd38b4f15b0939d951b6577c4f62fc0 1328620 debug optional eigensoft-dbgsym_7.2.1+dfsg-1_amd64.deb 81e8635848eda898147f42fac88296b3 5130 science optional eigensoft_7.2.1+dfsg-1_amd64.buildinfo 52a241a1a05985b749e4f795801f56ea 382256 science optional eigensoft_7.2.1+dfsg-1_amd64.deb Mon Jul 12 16:27:17 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.nBJGUPxDyt/eigensoft_7.2.1+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.nBJGUPxDyt/eigensoft_7.2.1+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.nBJGUPxDyt/eigensoft_7.2.1+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.nBJGUPxDyt/b1/eigensoft_7.2.1+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.nBJGUPxDyt/b2/eigensoft_7.2.1+dfsg-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.259s) 0.259s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.041s) 0.041s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Jul 12 16:27:19 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Mon Jul 12 16:27:19 UTC 2021 I: eigensoft from buster built successfully and reproducibly on amd64. Mon Jul 12 16:27:20 UTC 2021 I: Submitting .buildinfo files to external archives: Mon Jul 12 16:27:20 UTC 2021 I: Submitting 8.0K b1/eigensoft_7.2.1+dfsg-1_amd64.buildinfo.asc Mon Jul 12 16:27:21 UTC 2021 I: Submitting 8.0K b2/eigensoft_7.2.1+dfsg-1_amd64.buildinfo.asc Mon Jul 12 16:27:21 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jul 12 16:27:21 UTC 2021 I: Done submitting .buildinfo files. Mon Jul 12 16:27:21 UTC 2021 I: Removing signed eigensoft_7.2.1+dfsg-1_amd64.buildinfo.asc files: removed './b1/eigensoft_7.2.1+dfsg-1_amd64.buildinfo.asc' removed './b2/eigensoft_7.2.1+dfsg-1_amd64.buildinfo.asc'