https://launchpad.net/ubuntu/+archive/test-rebuild-20220617-kinetic/+build/23990306 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-039 5.4.0-121-generic #137-Ubuntu SMP Wed Jun 15 13:35:38 UTC 2022 aarch64 Buildd toolchain package versions: launchpad-buildd_215~563~ubuntu20.04.1 python3-lpbuildd_215~563~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.4 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 4 Jul 14:00:47 ntpdate[1821]: adjust time server 10.211.37.1 offset -0.002740 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=kinetic --arch=armhf PACKAGEBUILD-23990306 --image-type chroot /home/buildd/filecache-default/e7574466887b0df41a9ed814007609e88584b937 Creating target for build PACKAGEBUILD-23990306 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=kinetic --arch=armhf PACKAGEBUILD-23990306 Starting target for build PACKAGEBUILD-23990306 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=kinetic --arch=armhf PACKAGEBUILD-23990306 'deb http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic main' 'deb http://ftpmaster.internal/ubuntu kinetic main universe' Overriding sources.list in build-PACKAGEBUILD-23990306 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=kinetic --arch=armhf PACKAGEBUILD-23990306 Adding trusted keys to build-PACKAGEBUILD-23990306 pub rsa1024/1E9377A2BA9EF27F 2009-10-22 [SC] Key fingerprint = 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid Launchpad Toolchain builds RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=kinetic --arch=armhf PACKAGEBUILD-23990306 Updating target for build PACKAGEBUILD-23990306 Get:1 http://ftpmaster.internal/ubuntu kinetic InRelease [267 kB] Get:2 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic InRelease [23.8 kB] Get:3 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main armhf Packages [4256 B] Get:4 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main Translation-en [4132 B] Get:5 http://ftpmaster.internal/ubuntu kinetic/main armhf Packages [1326 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/universe armhf Packages [13.3 MB] Get:8 http://ftpmaster.internal/ubuntu kinetic/universe Translation-en [5747 kB] Fetched 21.2 MB in 6s (3621 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libfdisk1 util-linux-extra The following packages will be upgraded: adduser apt base-files binutils binutils-arm-linux-gnueabihf binutils-common bsdutils cpp-11 dash dpkg dpkg-dev e2fsprogs fakeroot g++-11 gcc-11 gcc-11-base gcc-12-base init init-system-helpers libapparmor1 libapt-pkg6.0 libasan6 libassuan0 libatomic1 libbinutils libblkid1 libcap-ng0 libcc1-0 libcom-err2 libctf-nobfd0 libctf0 libdb5.3 libdpkg-perl libext2fs2 libfakeroot libgcc-11-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libip4tc2 libkeyutils1 liblzma5 libmount1 libncurses6 libncursesw6 libpng16-16 libreadline8 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++-11-dev libstdc++6 libsystemd0 libtinfo6 libubsan1 libudev1 libuuid1 libzstd1 login logsave lto-disabled-list mawk mount ncurses-base ncurses-bin openssl passwd pinentry-curses policyrcd-script-zg2 readline-common systemd systemd-sysv util-linux xz-utils 81 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 64.8 MB of archives. After this operation, 8109 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu kinetic/main armhf base-files armhf 12.2ubuntu1 [62.4 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic/main armhf bsdutils armhf 1:2.38-4ubuntu1 [86.3 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic/main armhf libzstd1 armhf 1.5.2+dfsg-1 [243 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic/main armhf libgpg-error0 armhf 1.45-2 [61.2 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main armhf libgcrypt20 armhf 1.10.1-2ubuntu1 [450 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main armhf libatomic1 armhf 12.1.0-5ubuntu1 [7662 B] Get:7 http://ftpmaster.internal/ubuntu kinetic/main armhf libubsan1 armhf 12.1.0-5ubuntu1 [950 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic/main armhf libgomp1 armhf 12.1.0-5ubuntu1 [109 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic/main armhf gcc-12-base armhf 12.1.0-5ubuntu1 [19.3 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic/main armhf libgcc-s1 armhf 12.1.0-5ubuntu1 [41.1 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic/main armhf libcc1-0 armhf 12.1.0-5ubuntu1 [38.9 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic/main armhf libstdc++6 armhf 12.1.0-5ubuntu1 [602 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic/main armhf liblzma5 armhf 5.2.5-2.1 [86.4 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic/main armhf libblkid1 armhf 2.38-4ubuntu1 [137 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic/main armhf libuuid1 armhf 2.38-4ubuntu1 [22.8 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic/main armhf libfdisk1 armhf 2.38-4ubuntu1 [186 kB] Get:17 http://ftpmaster.internal/ubuntu kinetic/main armhf systemd-sysv armhf 251.2-2ubuntu1 [11.2 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic/main armhf libapparmor1 armhf 3.0.4-2ubuntu3 [32.9 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic/main armhf libip4tc2 armhf 1.8.7-1ubuntu6 [17.5 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic/main armhf libselinux1 armhf 3.4-1 [69.3 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic/main armhf libmount1 armhf 2.38-4ubuntu1 [153 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic/main armhf libssl3 armhf 3.0.4-1ubuntu1 [1569 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic/main armhf mount armhf 2.38-4ubuntu1 [126 kB] Get:24 http://ftpmaster.internal/ubuntu kinetic/main armhf libsemanage-common all 3.4-1 [9828 B] Get:25 http://ftpmaster.internal/ubuntu kinetic/main armhf libsepol2 armhf 3.4-2 [263 kB] Get:26 http://ftpmaster.internal/ubuntu kinetic/main armhf libsemanage2 armhf 3.4-1 [84.8 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic/main armhf passwd armhf 1:4.11.1+dfsg1-2ubuntu1 [743 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic/main armhf adduser all 3.121ubuntu1 [150 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic/main armhf systemd armhf 251.2-2ubuntu1 [4625 kB] Get:30 http://ftpmaster.internal/ubuntu kinetic/main armhf libsystemd0 armhf 251.2-2ubuntu1 [304 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic/main armhf libudev1 armhf 251.2-2ubuntu1 [74.9 kB] Get:32 http://ftpmaster.internal/ubuntu kinetic/main armhf libapt-pkg6.0 armhf 2.5.1 [897 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic/main armhf dpkg armhf 1.21.8ubuntu1 [1296 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic/main armhf dash armhf 0.5.11+git20210903+057cd650a4ed-8ubuntu1 [79.6 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main armhf login armhf 1:4.11.1+dfsg1-2ubuntu1 [182 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic/main armhf ncurses-bin armhf 6.3+20220423-2 [174 kB] Get:37 http://ftpmaster.internal/ubuntu kinetic/main armhf libsmartcols1 armhf 2.38-4ubuntu1 [94.9 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic/main armhf util-linux-extra armhf 2.38-4ubuntu1 [98.7 kB] Get:39 http://ftpmaster.internal/ubuntu kinetic/main armhf util-linux armhf 2.38-4ubuntu1 [1157 kB] Get:40 http://ftpmaster.internal/ubuntu kinetic/main armhf init-system-helpers all 1.63 [38.7 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic/main armhf ncurses-base all 6.3+20220423-2 [21.2 kB] Get:42 http://ftpmaster.internal/ubuntu kinetic/main armhf libgnutls30 armhf 3.7.6-2ubuntu1 [941 kB] Get:43 http://ftpmaster.internal/ubuntu kinetic/main armhf apt armhf 2.5.1 [1363 kB] Get:44 http://ftpmaster.internal/ubuntu kinetic/main armhf logsave armhf 1.46.5-2ubuntu2 [9340 B] Get:45 http://ftpmaster.internal/ubuntu kinetic/main armhf libext2fs2 armhf 1.46.5-2ubuntu2 [188 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic/main armhf e2fsprogs armhf 1.46.5-2ubuntu2 [562 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/main armhf init armhf 1.63 [5674 B] Get:48 http://ftpmaster.internal/ubuntu kinetic/main armhf libcap-ng0 armhf 0.8.3-1 [13.8 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/main armhf libdb5.3 armhf 5.3.28+dfsg1-0.9 [641 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic/main armhf libncurses6 armhf 6.3+20220423-2 [88.3 kB] Get:51 http://ftpmaster.internal/ubuntu kinetic/main armhf libncursesw6 armhf 6.3+20220423-2 [116 kB] Get:52 http://ftpmaster.internal/ubuntu kinetic/main armhf libtinfo6 armhf 6.3+20220423-2 [83.6 kB] Get:53 http://ftpmaster.internal/ubuntu kinetic/main armhf libcom-err2 armhf 1.46.5-2ubuntu2 [8210 B] Get:54 http://ftpmaster.internal/ubuntu kinetic/main armhf libss2 armhf 1.46.5-2ubuntu2 [10.1 kB] Get:55 http://ftpmaster.internal/ubuntu kinetic/main armhf mawk armhf 1.3.4.20200120-3.1 [97.1 kB] Get:56 http://ftpmaster.internal/ubuntu kinetic/main armhf libkeyutils1 armhf 1.6.1-3ubuntu1 [8722 B] Get:57 http://ftpmaster.internal/ubuntu kinetic/main armhf readline-common all 8.1.2-1.2 [53.6 kB] Get:58 http://ftpmaster.internal/ubuntu kinetic/main armhf libreadline8 armhf 8.1.2-1.2 [128 kB] Get:59 http://ftpmaster.internal/ubuntu kinetic/main armhf libsqlite3-0 armhf 3.39.0-1 [551 kB] Get:60 http://ftpmaster.internal/ubuntu kinetic/main armhf openssl armhf 3.0.4-1ubuntu1 [1146 kB] Get:61 http://ftpmaster.internal/ubuntu kinetic/main armhf libpng16-16 armhf 1.6.37-5 [167 kB] Get:62 http://ftpmaster.internal/ubuntu kinetic/main armhf xz-utils armhf 5.2.5-2.1 [83.6 kB] Get:63 http://ftpmaster.internal/ubuntu kinetic/main armhf libctf0 armhf 2.38.50.20220629-4ubuntu1 [95.2 kB] Get:64 http://ftpmaster.internal/ubuntu kinetic/main armhf libctf-nobfd0 armhf 2.38.50.20220629-4ubuntu1 [94.9 kB] Get:65 http://ftpmaster.internal/ubuntu kinetic/main armhf libbinutils armhf 2.38.50.20220629-4ubuntu1 [498 kB] Get:66 http://ftpmaster.internal/ubuntu kinetic/main armhf binutils armhf 2.38.50.20220629-4ubuntu1 [3174 B] Get:67 http://ftpmaster.internal/ubuntu kinetic/main armhf binutils-common armhf 2.38.50.20220629-4ubuntu1 [223 kB] Get:68 http://ftpmaster.internal/ubuntu kinetic/main armhf binutils-arm-linux-gnueabihf armhf 2.38.50.20220629-4ubuntu1 [3050 kB] Get:69 http://ftpmaster.internal/ubuntu kinetic/main armhf libasan6 armhf 11.3.0-3ubuntu1 [2246 kB] Get:70 http://ftpmaster.internal/ubuntu kinetic/main armhf g++-11 armhf 11.3.0-3ubuntu1 [8980 kB] Get:71 http://ftpmaster.internal/ubuntu kinetic/main armhf gcc-11 armhf 11.3.0-3ubuntu1 [15.7 MB] Get:72 http://ftpmaster.internal/ubuntu kinetic/main armhf libstdc++-11-dev armhf 11.3.0-3ubuntu1 [2125 kB] Get:73 http://ftpmaster.internal/ubuntu kinetic/main armhf libgcc-11-dev armhf 11.3.0-3ubuntu1 [822 kB] Get:74 http://ftpmaster.internal/ubuntu kinetic/main armhf cpp-11 armhf 11.3.0-3ubuntu1 [7796 kB] Get:75 http://ftpmaster.internal/ubuntu kinetic/main armhf gcc-11-base armhf 11.3.0-3ubuntu1 [20.8 kB] Get:76 http://ftpmaster.internal/ubuntu kinetic/main armhf dpkg-dev all 1.21.8ubuntu1 [1069 kB] Get:77 http://ftpmaster.internal/ubuntu kinetic/main armhf libdpkg-perl all 1.21.8ubuntu1 [237 kB] Get:78 http://ftpmaster.internal/ubuntu kinetic/main armhf lto-disabled-list all 28 [12.3 kB] Get:79 http://ftpmaster.internal/ubuntu kinetic/main armhf libfakeroot armhf 1.29-1ubuntu1 [25.6 kB] Get:80 http://ftpmaster.internal/ubuntu kinetic/main armhf fakeroot armhf 1.29-1ubuntu1 [61.8 kB] Get:81 http://ftpmaster.internal/ubuntu kinetic/main armhf libassuan0 armhf 2.5.5-4 [30.4 kB] Get:82 http://ftpmaster.internal/ubuntu kinetic/main armhf pinentry-curses armhf 1.2.0-2ubuntu1 [36.2 kB] Get:83 http://ftpmaster.internal/ubuntu kinetic/main armhf policyrcd-script-zg2 all 0.1-3.1 [5730 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 64.8 MB in 4s (16.5 MB/s) (Reading database ... 13176 files and directories currently installed.) 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Kernel reported to sbuild: 5.4.0-121-generic #137-Ubuntu SMP Wed Jun 15 13:35:38 UTC 2022 armv7l sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-039.buildd +==============================================================================+ | eigensoft 7.2.1+dfsg-3build1 (armhf) Mon, 04 Jul 2022 14:01:29 +0000 | +==============================================================================+ Package: eigensoft Version: 7.2.1+dfsg-3build1 Source Version: 7.2.1+dfsg-3build1 Distribution: kinetic Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-23990306/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/eigensoft-8wJBpX/resolver-gqwzHo' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- eigensoft_7.2.1+dfsg-3build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/eigensoft-8wJBpX/eigensoft-7.2.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/eigensoft-8wJBpX' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), gfortran, libblas-dev, liblapack-dev, liblapacke-dev, libgsl-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), gfortran, libblas-dev, liblapack-dev, liblapacke-dev, libgsl-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [396 B] Get:5 copy:/<>/apt_archive ./ Packages [480 B] Fetched 1833 B in 0s (58.6 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-11 groff-base intltool-debian libarchive-zip-perl libblas-dev libblas3 libdebhelper-perl libdw1 libelf1 libfile-stripnondeterminism-perl libgfortran-11-dev libgfortran5 libgsl-dev libgsl27 libgslcblas0 libicu71 liblapack-dev liblapack3 liblapacke liblapacke-dev libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtmglib-dev libtmglib3 libtool libuchardet0 libxml2 m4 man-db po-debconf sgml-base Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc gfortran-11-doc libcoarrays-dev groff liblapack-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libtool-doc gcj-jdk m4-doc apparmor less www-browser libmail-box-perl sgml-base-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-11 groff-base intltool-debian libarchive-zip-perl libblas-dev libblas3 libdebhelper-perl libdw1 libelf1 libfile-stripnondeterminism-perl libgfortran-11-dev libgfortran5 libgsl-dev libgsl27 libgslcblas0 libicu71 liblapack-dev liblapack3 liblapacke liblapacke-dev libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtmglib-dev libtmglib3 libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy sgml-base 0 upgraded, 49 newly installed, 0 to remove and 0 not upgraded. Need to get 33.9 MB of archives. After this operation, 115 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [700 B] Get:2 http://ftpmaster.internal/ubuntu kinetic/main armhf sgml-base all 1.30 [12.5 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic/main armhf libelf1 armhf 0.187-1 [43.1 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic/main armhf libicu71 armhf 71.1-3 [10.3 MB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main armhf libxml2 armhf 2.9.14+dfsg-1 [592 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main armhf bsdextrautils armhf 2.38-4ubuntu1 [76.6 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/main armhf libmagic-mgc armhf 1:5.41-4 [257 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic/main armhf libmagic1 armhf 1:5.41-4 [80.1 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic/main armhf file armhf 1:5.41-4 [20.6 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic/main armhf gettext-base armhf 0.21-6 [37.8 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic/main armhf libuchardet0 armhf 0.0.7-1build2 [75.7 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic/main armhf groff-base armhf 1.22.4-8build1 [870 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic/main armhf libpipeline1 armhf 1.5.6-1 [25.5 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic/main armhf man-db armhf 2.10.2-1 [1151 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic/main armhf libsigsegv2 armhf 2.13-1ubuntu3 [13.7 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic/main armhf m4 armhf 1.4.18-5ubuntu2 [191 kB] Get:17 http://ftpmaster.internal/ubuntu kinetic/main armhf autoconf all 2.71-2 [338 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic/main armhf autotools-dev all 20220109.1 [44.9 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic/main armhf automake all 1:1.16.5-1.3 [558 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic/main armhf autopoint all 0.21-6 [421 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic/main armhf libdebhelper-perl all 13.7.1ubuntu1 [66.9 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic/main armhf libtool all 2.4.7-4 [166 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic/main armhf dh-autoreconf all 20 [16.1 kB] Get:24 http://ftpmaster.internal/ubuntu kinetic/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] Get:25 http://ftpmaster.internal/ubuntu kinetic/main armhf libsub-override-perl all 0.09-3 [9756 B] Get:26 http://ftpmaster.internal/ubuntu kinetic/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [18.1 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic/main armhf dh-strip-nondeterminism all 1.13.0-1 [5344 B] Get:28 http://ftpmaster.internal/ubuntu kinetic/main armhf libdw1 armhf 0.187-1 [223 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic/main armhf debugedit armhf 1:5.0-4build1 [43.3 kB] Get:30 http://ftpmaster.internal/ubuntu kinetic/main armhf dwz armhf 0.14-1build2 [99.2 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic/main armhf gettext armhf 0.21-6 [800 kB] Get:32 http://ftpmaster.internal/ubuntu kinetic/main armhf intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic/main armhf po-debconf all 1.0.21+nmu1 [233 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic/main armhf debhelper all 13.7.1ubuntu1 [940 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main armhf libgfortran5 armhf 12.1.0-5ubuntu1 [295 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic/main armhf libgfortran-11-dev armhf 11.3.0-3ubuntu1 [342 kB] Get:37 http://ftpmaster.internal/ubuntu kinetic/main armhf gfortran-11 armhf 11.3.0-3ubuntu1 [8368 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic/main armhf gfortran armhf 4:11.2.0-1ubuntu1 [1172 B] Get:39 http://ftpmaster.internal/ubuntu kinetic/main armhf libblas3 armhf 3.10.1-2 [115 kB] Get:40 http://ftpmaster.internal/ubuntu kinetic/main armhf libblas-dev armhf 3.10.1-2 [125 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic/universe armhf libgslcblas0 armhf 2.7.1+dfsg-3 [73.7 kB] Get:42 http://ftpmaster.internal/ubuntu kinetic/universe armhf libgsl27 armhf 2.7.1+dfsg-3 [842 kB] Get:43 http://ftpmaster.internal/ubuntu kinetic/universe armhf libgsl-dev armhf 2.7.1+dfsg-3 [1080 kB] Get:44 http://ftpmaster.internal/ubuntu kinetic/main armhf liblapack3 armhf 3.10.1-2 [1941 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic/main armhf liblapack-dev armhf 3.10.1-2 [1999 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic/main armhf libtmglib3 armhf 3.10.1-2 [97.8 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/main armhf liblapacke armhf 3.10.1-2 [364 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic/main armhf libtmglib-dev armhf 3.10.1-2 [101 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/main armhf liblapacke-dev armhf 3.10.1-2 [318 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 33.9 MB in 2s (17.6 MB/s) Selecting previously unselected package sgml-base. 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Setting up libelf1:armhf (0.187-1) ... Setting up libxml2:armhf (2.9.14+dfsg-1) ... Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up libdw1:armhf (0.187-1) ... Setting up gettext (0.21-6) ... Setting up libgsl-dev (2.7.1+dfsg-3) ... Setting up libtool (2.4.7-4) ... Setting up libgfortran-11-dev:armhf (11.3.0-3ubuntu1) ... Setting up m4 (1.4.18-5ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libblas3:armhf (3.10.1-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up gfortran-11 (11.3.0-3ubuntu1) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1build2) ... Setting up groff-base (1.22.4-8build1) ... Setting up debugedit (1:5.0-4build1) ... Setting up libblas-dev:armhf (3.10.1-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up liblapack3:armhf (3.10.1-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.10.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up gfortran (4:11.2.0-1ubuntu1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up dh-autoreconf (20) ... Setting up libtmglib3:armhf (3.10.1-2) ... Setting up liblapack-dev:armhf (3.10.1-2) ... 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 (3.10.1-2) ... Setting up libtmglib-dev:armhf (3.10.1-2) ... Setting up debhelper (13.7.1ubuntu1) ... Setting up liblapacke-dev:armhf (3.10.1-2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-121-generic #137-Ubuntu SMP Wed Jun 15 13:35:38 UTC 2022 arm64 (armv7l) Toolchain package versions: binutils_2.38.50.20220629-4ubuntu1 dpkg-dev_1.21.8ubuntu1 g++-11_11.3.0-3ubuntu1 gcc-11_11.3.0-3ubuntu1 libc6-dev_2.35-0ubuntu3 libstdc++-11-dev_11.3.0-3ubuntu1 libstdc++6_12.1.0-5ubuntu1 linux-libc-dev_5.15.0-27.28 Package versions: adduser_3.121ubuntu1 advancecomp_2.1-2.1ubuntu2 apt_2.5.1 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2ubuntu1 base-passwd_3.5.52build1 bash_5.1-6ubuntu1 binutils_2.38.50.20220629-4ubuntu1 binutils-arm-linux-gnueabihf_2.38.50.20220629-4ubuntu1 binutils-common_2.38.50.20220629-4ubuntu1 bsdextrautils_2.38-4ubuntu1 bsdutils_1:2.38-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016 coreutils_8.32-4.1ubuntu1 cpp_4:11.2.0-1ubuntu1 cpp-11_11.3.0-3ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-8ubuntu1 debconf_1.5.79ubuntu1 debhelper_13.7.1ubuntu1 debianutils_5.7-0.2 debugedit_1:5.0-4build1 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-0ubuntu2 dpkg_1.21.8ubuntu1 dpkg-dev_1.21.8ubuntu1 dwz_0.14-1build2 e2fsprogs_1.46.5-2ubuntu2 fakeroot_1.29-1ubuntu1 file_1:5.41-4 findutils_4.8.0-1ubuntu3 g++_4:11.2.0-1ubuntu1 g++-11_11.3.0-3ubuntu1 gcc_4:11.2.0-1ubuntu1 gcc-11_11.3.0-3ubuntu1 gcc-11-base_11.3.0-3ubuntu1 gcc-12-base_12.1.0-5ubuntu1 gettext_0.21-6 gettext-base_0.21-6 gfortran_4:11.2.0-1ubuntu1 gfortran-11_11.3.0-3ubuntu1 gpg_2.2.27-3ubuntu2 gpg-agent_2.2.27-3ubuntu2 gpgconf_2.2.27-3ubuntu2 gpgv_2.2.27-3ubuntu2 grep_3.7-1build1 groff-base_1.22.4-8build1 gzip_1.10-4ubuntu4 hostname_3.23ubuntu2 init_1.63 init-system-helpers_1.63 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapparmor1_3.0.4-2ubuntu3 libapt-pkg6.0_2.5.1 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan6_11.3.0-3ubuntu1 libassuan0_2.5.5-4 libatomic1_12.1.0-5ubuntu1 libattr1_1:2.5.1-1build1 libaudit-common_1:3.0.7-1build1 libaudit1_1:3.0.7-1build1 libbinutils_2.38.50.20220629-4ubuntu1 libblas-dev_3.10.1-2 libblas3_3.10.1-2 libblkid1_2.38-4ubuntu1 libbz2-1.0_1.0.8-5build1 libc-bin_2.35-0ubuntu3 libc-dev-bin_2.35-0ubuntu3 libc6_2.35-0ubuntu3 libc6-dev_2.35-0ubuntu3 libcap-ng0_0.8.3-1 libcap2_1:2.44-1build3 libcc1-0_12.1.0-5ubuntu1 libcom-err2_1.46.5-2ubuntu2 libcrypt-dev_1:4.4.27-1 libcrypt1_1:4.4.27-1 libcryptsetup12_2:2.4.3-1ubuntu1 libctf-nobfd0_2.38.50.20220629-4ubuntu1 libctf0_2.38.50.20220629-4ubuntu1 libdb5.3_5.3.28+dfsg1-0.9 libdebconfclient0_0.261ubuntu1 libdebhelper-perl_13.7.1ubuntu1 libdevmapper1.02.1_2:1.02.175-2.1ubuntu4 libdpkg-perl_1.21.8ubuntu1 libdw1_0.187-1 libelf1_0.187-1 libext2fs2_1.46.5-2ubuntu2 libfakeroot_1.29-1ubuntu1 libfdisk1_2.38-4ubuntu1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-11-dev_11.3.0-3ubuntu1 libgcc-s1_12.1.0-5ubuntu1 libgcrypt20_1.10.1-2ubuntu1 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgfortran-11-dev_11.3.0-3ubuntu1 libgfortran5_12.1.0-5ubuntu1 libgmp10_2:6.2.1+dfsg-3ubuntu1 libgnutls30_3.7.6-2ubuntu1 libgomp1_12.1.0-5ubuntu1 libgpg-error0_1.45-2 libgsl-dev_2.7.1+dfsg-3 libgsl27_2.7.1+dfsg-3 libgslcblas0_2.7.1+dfsg-3 libgssapi-krb5-2_1.19.2-2 libhogweed6_3.7.3-1build2 libicu71_71.1-3 libidn2-0_2.3.2-2build1 libip4tc2_1.8.7-1ubuntu6 libisl23_0.24-2build1 libjson-c5_0.16-1 libk5crypto3_1.19.2-2 libkeyutils1_1.6.1-3ubuntu1 libkmod2_29-1ubuntu1 libkrb5-3_1.19.2-2 libkrb5support0_1.19.2-2 liblapack-dev_3.10.1-2 liblapack3_3.10.1-2 liblapacke_3.10.1-2 liblapacke-dev_3.10.1-2 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblz4-1_1.9.3-2build2 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmount1_2.38-4ubuntu1 libmpc3_1.2.1-2build1 libmpfr6_4.1.0-3build3 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.7.3-1build2 libnpth0_1.6-3build2 libnsl-dev_1.3.0-2build2 libnsl2_1.3.0-2build2 libp11-kit0_0.24.1-1 libpam-modules_1.4.0-13ubuntu1 libpam-modules-bin_1.4.0-13ubuntu1 libpam-runtime_1.4.0-13ubuntu1 libpam0g_1.4.0-13ubuntu1 libpcre2-8-0_10.40-1 libpcre3_2:8.39-14 libperl5.34_5.34.0-3ubuntu1 libpipeline1_1.5.6-1 libpng16-16_1.6.37-5 libprocps8_2:3.3.17-6ubuntu2 libreadline8_8.1.2-1.2 libseccomp2_2.5.4-1ubuntu1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol2_3.4-2 libsigsegv2_2.13-1ubuntu3 libsmartcols1_2.38-4ubuntu1 libsqlite3-0_3.39.0-1 libss2_1.46.5-2ubuntu2 libssl3_3.0.4-1ubuntu1 libstdc++-11-dev_11.3.0-3ubuntu1 libstdc++6_12.1.0-5ubuntu1 libsub-override-perl_0.09-3 libsystemd0_251.2-2ubuntu1 libtasn1-6_4.18.0-4build1 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.2-2build1 libtirpc-dev_1.3.2-2build1 libtirpc3_1.3.2-2build1 libtmglib-dev_3.10.1-2 libtmglib3_3.10.1-2 libtool_2.4.7-4 libubsan1_12.1.0-5ubuntu1 libuchardet0_0.0.7-1build2 libudev1_251.2-2ubuntu1 libunistring2_1.0-1 libuuid1_2.38-4ubuntu1 libxml2_2.9.14+dfsg-1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.15.0-27.28 lockfile-progs_0.1.19build1 login_1:4.11.1+dfsg1-2ubuntu1 logsave_1.46.5-2ubuntu2 lsb-base_11.1.0ubuntu4 lto-disabled-list_28 m4_1.4.18-5ubuntu2 make_4.3-4.1build1 man-db_2.10.2-1 mawk_1.3.4.20200120-3.1 mount_2.38-4ubuntu1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 openssl_3.0.4-1ubuntu1 optipng_0.7.7-2build1 passwd_1:4.11.1+dfsg1-2ubuntu1 patch_2.7.6-7build2 perl_5.34.0-3ubuntu1 perl-base_5.34.0-3ubuntu1 perl-modules-5.34_5.34.0-3ubuntu1 pinentry-curses_1.2.0-2ubuntu1 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:3.3.17-6ubuntu2 readline-common_8.1.2-1.2 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1ubuntu2 sensible-utils_0.0.17 sgml-base_1.30 systemd_251.2-2ubuntu1 systemd-sysv_251.2-2ubuntu1 sysvinit-utils_3.01-1ubuntu1 tar_1.34+dfsg-1build3 tzdata_2022a-0ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_25ubuntu2 util-linux_2.38-4ubuntu1 util-linux-extra_2.38-4ubuntu1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-2ubuntu9 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: eigensoft Binary: eigensoft Architecture: any Version: 7.2.1+dfsg-3build1 Maintainer: Ubuntu Developers Uploaders: Steffen Moeller , Andreas Tille Homepage: http://www.hsph.harvard.edu/faculty/alkes-price/software/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/eigensoft Vcs-Git: https://salsa.debian.org/med-team/eigensoft.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), 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 deee4470683104e8ab3ac61a0af708ea1be3e23f 6204 eigensoft_7.2.1+dfsg-3build1.debian.tar.xz Checksums-Sha256: 182e2f030d08ea5350b3e7a2636dfcc1f23a174266de9f4c87134ad7f85fb008 170148 eigensoft_7.2.1+dfsg.orig.tar.xz 315ca6faa63d845877d8653bf41df089aa5c38b1613f5165ea86a2e3cfc4bab7 6204 eigensoft_7.2.1+dfsg-3build1.debian.tar.xz Files: a20c83aeb532f9689716c7a03bf1f3e5 170148 eigensoft_7.2.1+dfsg.orig.tar.xz 23d0c5d8c3433135ad74a1ba1789aba6 6204 eigensoft_7.2.1+dfsg-3build1.debian.tar.xz Original-Maintainer: Debian Med Packaging Team -----BEGIN PGP SIGNATURE----- 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Can't check signature: No public key dpkg-source: warning: cannot verify signature ./eigensoft_7.2.1+dfsg-3build1.dsc dpkg-source: info: extracting eigensoft in /<> dpkg-source: info: unpacking eigensoft_7.2.1+dfsg.orig.tar.xz dpkg-source: info: unpacking eigensoft_7.2.1+dfsg-3build1.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 Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-23990306 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-23990306 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-23990306 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package eigensoft dpkg-buildpackage: info: source version 7.2.1+dfsg-3build1 dpkg-buildpackage: info: source distribution jammy dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean /usr/bin/make -C src clobber make[2]: Entering directory '/<>/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 '/<>/src' make[1]: Leaving directory '/<>' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' /usr/bin/make DEBUG_OPTIONS=-g -C src all make[2]: Entering directory '/<>/src' cc -g -O2 -ffile-prefix-map=/<>=. -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=/<>=. -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:543:14: note: in a call to allocation function ‘calloc’ declared here 543 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ In file included from /usr/include/stdio.h:894, from ../include/mcio.h:4, from mcio.c:3: In function ‘printf’, inlined from ‘outfiles’ at mcio.c:3159:5: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:112:10: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 112 | return __printf_chk (__USE_FORTIFY_LEVEL - 1, __fmt, __va_arg_pack ()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -ffile-prefix-map=/<>=. -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=/<>=. -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 -ffile-prefix-map=/<>=. -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=/<>=. -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 '/<>/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 '/<>/src/nicksrc' cc -Wl,-Bsymbolic-functions -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=/<>=. -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,-Bsymbolic-functions -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=/<>=. -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,-Bsymbolic-functions -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=/<>=. -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 -ffile-prefix-map=/<>=. -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=/<>=. -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,-Bsymbolic-functions -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=/<>=. -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 -ffile-prefix-map=/<>=. -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=/<>=. -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=/<>=. -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=/<>=. -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=/<>=. -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 -ffile-prefix-map=/<>=. -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 -ffile-prefix-map=/<>=. -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:38:11: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 38 | fscanf (stream, "%lg", &x); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -Wl,-Bsymbolic-functions -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=/<>=. -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,-Bsymbolic-functions -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=/<>=. -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,-Bsymbolic-functions -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=/<>=. -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,-Bsymbolic-functions -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=/<>=. -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,-Bsymbolic-functions -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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 -ffile-prefix-map=/<>=. -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,-Bsymbolic-functions -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 '/<>/src' cd src && make install make[2]: Entering directory '/<>/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 '/<>/src' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/eigensoft/ -a debian/rules override_dh_install make[1]: Entering directory '/<>' 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 '/<>' dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms find debian/*/usr/share/eigensoft -type f -name "*.perl" -exec chmod +x \{\} \; make[1]: Leaving directory '/<>' dh_missing -a dh_dwz -a dh_strip -a debugedit: debian/eigensoft/usr/lib/eigensoft/smarteigenstrat: Unknown DWARF DW_FORM_0x1f21 41a93ee8b61889b4d628b7320f747dd3a084e186 debugedit: debian/eigensoft/usr/lib/eigensoft/smartpca: Unknown DWARF DW_FORM_0x1f20 df18469d677d9046fc2a88cb0a91c30f0beafec9 debugedit: debian/eigensoft/usr/bin/convertf: Unknown DWARF DW_FORM_0x1f21 f28f4a7d7a24ab4288f07d7a59539396ebf3fc84 debugedit: debian/eigensoft/usr/bin/smartrel: Unknown DWARF DW_FORM_0x1f21 35df239086029c1ecf4d67d188f7594595831dfd debugedit: debian/eigensoft/usr/bin/twstats: Unknown DWARF DW_FORM_0x1f21 b0563546c434ab58e66e76839b2748a19b73620c debugedit: debian/eigensoft/usr/bin/pca: Unknown DWARF DW_FORM_0x1f21 9b79355a8cd706ce58da834dc92b3f46dd3d4cdc debugedit: debian/eigensoft/usr/bin/eigenstrat: Unknown DWARF DW_FORM_0x1f21 597fc84e86ff3e157185e40d53c09a9df6050832 debugedit: debian/eigensoft/usr/bin/smshrink: Unknown DWARF DW_FORM_0x1f20 febaca5fa16e534862bdb2062edeb3b93fefd224 debugedit: debian/eigensoft/usr/bin/pcatoy: Unknown DWARF DW_FORM_0x1f20 1c83afbd57b03222ec340032393844ac83aabf7a debugedit: debian/eigensoft/usr/bin/baseprog: Unknown DWARF DW_FORM_0x1f21 9cdddcaee8d3a24025eb295d11b6e577818ddc3c debugedit: debian/eigensoft/usr/bin/mergeit: Unknown DWARF DW_FORM_0x1f21 914bde150b109346d78f8edf7282692293c2a339 debugedit: debian/eigensoft/usr/bin/eigenstratQTL: Unknown DWARF DW_FORM_0x1f21 52fd5a18303c54a285f351862531648517542a20 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 -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 149 pkgstriptranslations: processing eigensoft (in debian/eigensoft); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/eigensoft/DEBIAN/control, package eigensoft, directory debian/eigensoft pkgstripfiles: Running PNG optimization (using 4 cpus) for package eigensoft ... pkgstripfiles: No PNG files. dpkg-deb: building package 'eigensoft' in '../eigensoft_7.2.1+dfsg-3build1_armhf.deb'. dpkg-genbuildinfo --build=any -O../eigensoft_7.2.1+dfsg-3build1_armhf.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../eigensoft_7.2.1+dfsg-3build1_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-07-04T14:02:37Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ eigensoft_7.2.1+dfsg-3build1_armhf.changes: ------------------------------------------- Format: 1.8 Date: Tue, 07 Dec 2021 17:29:17 +0000 Source: eigensoft Binary: eigensoft Built-For-Profiles: noudeb Architecture: armhf Version: 7.2.1+dfsg-3build1 Distribution: kinetic Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Steve Langasek Description: eigensoft - reduction of population bias for genetic analyses Changes: eigensoft (7.2.1+dfsg-3build1) jammy; urgency=medium . * No-change rebuild against libgsl27 Checksums-Sha1: 682c11b3e0fa10890387dc3b0c0ec85444287f2a 5909 eigensoft_7.2.1+dfsg-3build1_armhf.buildinfo e87151b3cee598ad7ecff8f077ab825c9179995a 328464 eigensoft_7.2.1+dfsg-3build1_armhf.deb Checksums-Sha256: 192a30f9d5358471da655ba62ac8cd791d357268eb3d0414e81d9dd6270f2389 5909 eigensoft_7.2.1+dfsg-3build1_armhf.buildinfo bdba43fcfdb9cf17e04b9627c2aa1b1e01da221a2602b0db7c782b3e939c139e 328464 eigensoft_7.2.1+dfsg-3build1_armhf.deb Files: ecddbb51f924f9dba59e7b4671c2bfd7 5909 science optional eigensoft_7.2.1+dfsg-3build1_armhf.buildinfo fee6105ca35d618fb782848d8b2e2dda 328464 science optional eigensoft_7.2.1+dfsg-3build1_armhf.deb Original-Maintainer: Debian Med Packaging Team /<>/eigensoft_7.2.1+dfsg-3build1_armhf.changes.new could not be renamed to /<>/eigensoft_7.2.1+dfsg-3build1_armhf.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: eigensoft Binary: eigensoft Architecture: armhf Version: 7.2.1+dfsg-3build1 Checksums-Md5: fee6105ca35d618fb782848d8b2e2dda 328464 eigensoft_7.2.1+dfsg-3build1_armhf.deb Checksums-Sha1: e87151b3cee598ad7ecff8f077ab825c9179995a 328464 eigensoft_7.2.1+dfsg-3build1_armhf.deb Checksums-Sha256: bdba43fcfdb9cf17e04b9627c2aa1b1e01da221a2602b0db7c782b3e939c139e 328464 eigensoft_7.2.1+dfsg-3build1_armhf.deb Build-Origin: Ubuntu Build-Architecture: armhf Build-Date: Mon, 04 Jul 2022 14:02:36 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-6), autotools-dev (= 20220109.1), base-files (= 12.2ubuntu1), base-passwd (= 3.5.52build1), bash (= 5.1-6ubuntu1), binutils (= 2.38.50.20220629-4ubuntu1), binutils-arm-linux-gnueabihf (= 2.38.50.20220629-4ubuntu1), binutils-common (= 2.38.50.20220629-4ubuntu1), bsdextrautils (= 2.38-4ubuntu1), bsdutils (= 1:2.38-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.3.0-3ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-8ubuntu1), debconf (= 1.5.79ubuntu1), debhelper (= 13.7.1ubuntu1), debianutils (= 5.7-0.2), debugedit (= 1:5.0-4build1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-0ubuntu2), dpkg (= 1.21.8ubuntu1), dpkg-dev (= 1.21.8ubuntu1), dwz (= 0.14-1build2), file (= 1:5.41-4), findutils (= 4.8.0-1ubuntu3), g++ (= 4:11.2.0-1ubuntu1), g++-11 (= 11.3.0-3ubuntu1), gcc (= 4:11.2.0-1ubuntu1), gcc-11 (= 11.3.0-3ubuntu1), gcc-11-base (= 11.3.0-3ubuntu1), gcc-12-base (= 12.1.0-5ubuntu1), gettext (= 0.21-6), gettext-base (= 0.21-6), gfortran (= 4:11.2.0-1ubuntu1), gfortran-11 (= 11.3.0-3ubuntu1), grep (= 3.7-1build1), groff-base (= 1.22.4-8build1), gzip (= 1.10-4ubuntu4), hostname (= 3.23ubuntu2), init-system-helpers (= 1.63), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.3.0-3ubuntu1), libatomic1 (= 12.1.0-5ubuntu1), libattr1 (= 1:2.5.1-1build1), libaudit-common (= 1:3.0.7-1build1), libaudit1 (= 1:3.0.7-1build1), libbinutils (= 2.38.50.20220629-4ubuntu1), libblas-dev (= 3.10.1-2), libblas3 (= 3.10.1-2), libblkid1 (= 2.38-4ubuntu1), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.35-0ubuntu3), libc-dev-bin (= 2.35-0ubuntu3), libc6 (= 2.35-0ubuntu3), libc6-dev (= 2.35-0ubuntu3), libcap-ng0 (= 0.8.3-1), libcap2 (= 1:2.44-1build3), libcc1-0 (= 12.1.0-5ubuntu1), libcom-err2 (= 1.46.5-2ubuntu2), libcrypt-dev (= 1:4.4.27-1), libcrypt1 (= 1:4.4.27-1), libctf-nobfd0 (= 2.38.50.20220629-4ubuntu1), libctf0 (= 2.38.50.20220629-4ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.9), libdebconfclient0 (= 0.261ubuntu1), libdebhelper-perl (= 13.7.1ubuntu1), libdpkg-perl (= 1.21.8ubuntu1), libdw1 (= 0.187-1), libelf1 (= 0.187-1), libfile-stripnondeterminism-perl (= 1.13.0-1), libgcc-11-dev (= 11.3.0-3ubuntu1), libgcc-s1 (= 12.1.0-5ubuntu1), libgcrypt20 (= 1.10.1-2ubuntu1), libgdbm-compat4 (= 1.23-1), libgdbm6 (= 1.23-1), libgfortran-11-dev (= 11.3.0-3ubuntu1), libgfortran5 (= 12.1.0-5ubuntu1), libgmp10 (= 2:6.2.1+dfsg-3ubuntu1), libgomp1 (= 12.1.0-5ubuntu1), libgpg-error0 (= 1.45-2), libgsl-dev (= 2.7.1+dfsg-3), libgsl27 (= 2.7.1+dfsg-3), libgslcblas0 (= 2.7.1+dfsg-3), libgssapi-krb5-2 (= 1.19.2-2), libicu71 (= 71.1-3), libisl23 (= 0.24-2build1), libk5crypto3 (= 1.19.2-2), libkeyutils1 (= 1.6.1-3ubuntu1), libkrb5-3 (= 1.19.2-2), libkrb5support0 (= 1.19.2-2), liblapack-dev (= 3.10.1-2), liblapack3 (= 3.10.1-2), liblapacke (= 3.10.1-2), liblapacke-dev (= 3.10.1-2), liblz4-1 (= 1.9.3-2build2), liblzma5 (= 5.2.5-2.1), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmount1 (= 2.38-4ubuntu1), libmpc3 (= 1.2.1-2build1), libmpfr6 (= 4.1.0-3build3), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libpam-modules (= 1.4.0-13ubuntu1), libpam-modules-bin (= 1.4.0-13ubuntu1), libpam-runtime (= 1.4.0-13ubuntu1), libpam0g (= 1.4.0-13ubuntu1), libpcre2-8-0 (= 10.40-1), libpcre3 (= 2:8.39-14), libperl5.34 (= 5.34.0-3ubuntu1), libpipeline1 (= 1.5.6-1), libseccomp2 (= 2.5.4-1ubuntu1), libselinux1 (= 3.4-1), libsigsegv2 (= 2.13-1ubuntu3), libsmartcols1 (= 2.38-4ubuntu1), libssl3 (= 3.0.4-1ubuntu1), libstdc++-11-dev (= 11.3.0-3ubuntu1), libstdc++6 (= 12.1.0-5ubuntu1), libsub-override-perl (= 0.09-3), libsystemd0 (= 251.2-2ubuntu1), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.2-2build1), libtirpc-dev (= 1.3.2-2build1), libtirpc3 (= 1.3.2-2build1), libtmglib-dev (= 3.10.1-2), libtmglib3 (= 3.10.1-2), libtool (= 2.4.7-4), libubsan1 (= 12.1.0-5ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 251.2-2ubuntu1), libunistring2 (= 1.0-1), libuuid1 (= 2.38-4ubuntu1), libxml2 (= 2.9.14+dfsg-1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.15.0-27.28), login (= 1:4.11.1+dfsg1-2ubuntu1), lsb-base (= 11.1.0ubuntu4), lto-disabled-list (= 28), m4 (= 1.4.18-5ubuntu2), make (= 4.3-4.1build1), man-db (= 2.10.2-1), mawk (= 1.3.4.20200120-3.1), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), patch (= 2.7.6-7build2), perl (= 5.34.0-3ubuntu1), perl-base (= 5.34.0-3ubuntu1), perl-modules-5.34 (= 5.34.0-3ubuntu1), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), sgml-base (= 1.30), sysvinit-utils (= 3.01-1ubuntu1), tar (= 1.34+dfsg-1build3), util-linux (= 2.38-4ubuntu1), util-linux-extra (= 2.38-4ubuntu1), xz-utils (= 5.2.5-2.1), zlib1g (= 1:1.2.11.dfsg-2ubuntu9) Environment: DEB_BUILD_OPTIONS="noautodbgsym parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1638898157" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ eigensoft_7.2.1+dfsg-3build1_armhf.deb -------------------------------------- new Debian package, version 2.0. size 328464 bytes: control archive=3339 bytes. 1237 bytes, 21 lines control 13143 bytes, 161 lines md5sums Package: eigensoft Version: 7.2.1+dfsg-3build1 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 2362 Depends: libblas3 | libblas.so.3, libc6 (>= 2.34), libgsl27 (>= 2.7.1), liblapack3 | liblapack.so.3, liblapacke (>= 3.10.1), perl:any Recommends: gnuplot Section: science Priority: optional Homepage: http://www.hsph.harvard.edu/faculty/alkes-price/software/ Description: reduction of population bias for genetic analyses The EIGENSOFT package combines functionality from the group's population genetics methods (Patterson et al. 2006) and their EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker's variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2021-12-07 17:29 ./ drwxr-xr-x root/root 0 2021-12-07 17:29 ./usr/ drwxr-xr-x root/root 0 2021-12-07 17:29 ./usr/bin/ -rwxr-xr-x root/root 198520 2021-12-07 17:29 ./usr/bin/baseprog -rwxr-xr-x root/root 198656 2021-12-07 17:29 ./usr/bin/convertf -rwxr-xr-x root/root 67116 2021-12-07 17:29 ./usr/bin/eigenstrat -rwxr-xr-x root/root 67116 2021-12-07 17:29 ./usr/bin/eigenstratQTL -rwxr-xr-x root/root 1462 2021-12-07 17:29 ./usr/bin/evec2pca -rwxr-xr-x root/root 2311 2021-12-07 17:29 ./usr/bin/evec2pca-ped lrwxrwxrwx root/root 0 2021-12-07 17:29 ./usr/bin/gc-eigensoft -> ../lib/debian-med/bin/gc.perl -rwxr-xr-x root/root 198560 2021-12-07 17:29 ./usr/bin/mergeit -rwxr-xr-x root/root 67120 2021-12-07 17:29 ./usr/bin/pca -rwxr-xr-x root/root 67120 2021-12-07 17:29 ./usr/bin/pcatoy -rwxr-xr-x root/root 2112 2021-12-07 17:29 ./usr/bin/smarteigenstrat -rwxr-xr-x root/root 4738 2021-12-07 17:29 ./usr/bin/smartpca -rwxr-xr-x 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+------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: 11948 Build-Time: 50 Distribution: kinetic Host Architecture: armhf Install-Time: 16 Job: eigensoft_7.2.1+dfsg-3build1.dsc Machine Architecture: arm64 Package: eigensoft Package-Time: 68 Source-Version: 7.2.1+dfsg-3build1 Space: 11948 Status: successful Version: 7.2.1+dfsg-3build1 -------------------------------------------------------------------------------- Finished at 2022-07-04T14:02:37Z Build needed 00:01:08, 11948k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=kinetic --arch=armhf PACKAGEBUILD-23990306 Scanning for processes to kill in build PACKAGEBUILD-23990306