sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | eigensoft 8.0.0+dfsg-2 (amd64) Sun, 15 Sep 2024 03:53:03 +0000 | +==============================================================================+ Package: eigensoft Version: 8.0.0+dfsg-2 Source Version: 8.0.0+dfsg-2 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-c810bbee-9552-43f0-b26a-760fb4fa43eb' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup eigensoft_8.0.0+dfsg-2 perl-5.40-throwaway amd64 ----------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup eigensoft_8.0.0+dfsg-2 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/eigensoft-f4OJr5/resolver-irqJeI' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:3 http://localhost:3142/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/eigensoft_8.0.0+dfsg-2.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/eigensoft-f4OJr5/eigensoft-8.0.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/eigensoft-f4OJr5' 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 [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [683 B] Get:5 copy:/<>/apt_archive ./ Packages [715 B] Fetched 2007 B in 0s (118 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 dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base gfortran gfortran-14 gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu groff-base intltool-debian libarchive-zip-perl libblas-dev libblas3 libdebhelper-perl libelf1t64 libfakeroot libfile-stripnondeterminism-perl libgfortran-14-dev libgfortran5 libgsl-dev libgsl28 libgslcblas0 libicu72 liblapack-dev liblapack3 liblapacke liblapacke-dev libmagic-mgc libmagic1t64 libpipeline1 libtmglib-dev libtmglib3 libtool libuchardet0 libxml2 m4 man-db po-debconf sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-multilib gfortran-doc gfortran-14-multilib gfortran-14-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 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 dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base gfortran gfortran-14 gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu groff-base intltool-debian libarchive-zip-perl libblas-dev libblas3 libdebhelper-perl libelf1t64 libfakeroot libfile-stripnondeterminism-perl libgfortran-14-dev libgfortran5 libgsl-dev libgsl28 libgslcblas0 libicu72 liblapack-dev liblapack3 liblapacke liblapacke-dev libmagic-mgc libmagic1t64 libpipeline1 libtmglib-dev libtmglib3 libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 49 newly installed, 0 to remove and 0 not upgraded. Need to get 44.2 MB of archives. After this operation, 181 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [912 B] Get:2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.36-1 [29.1 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.36-1 [75.1 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-4 [837 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libgfortran-14-dev amd64 14.2.0-4 [880 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-4 [11.7 MB] Get:36 http://deb.debian.org/debian unstable/main amd64 gfortran-14 amd64 14.2.0-4 [11.8 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.1.0-2 [1284 B] Get:38 http://deb.debian.org/debian unstable/main amd64 gfortran amd64 4:14.1.0-2 [1436 B] Get:39 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.0-3 [159 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-3 [116 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-3 [994 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-3 [1223 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.0-3 [4880 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libtmglib3 amd64 3.12.0-3 [127 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 liblapacke amd64 3.12.0-3 [379 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libtmglib-dev amd64 3.12.0-3 [130 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 liblapacke-dev amd64 3.12.0-3 [348 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 44.2 MB in 0s (94.2 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 22986 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... 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Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up autopoint (0.22.5-2) ... Setting up libgfortran5:amd64 (14.2.0-4) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libgsl28:amd64 (2.8+dfsg-3) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up libblas-dev:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) 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 libgfortran-14-dev:amd64 (14.2.0-4) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libgsl-dev (2.8+dfsg-3) ... Setting up libtool (2.4.7-7) ... Setting up gfortran-14-x86-64-linux-gnu (14.2.0-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libtmglib3:amd64 (3.12.0-3) ... Setting up liblapack-dev:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up liblapacke:amd64 (3.12.0-3) ... Setting up libtmglib-dev:amd64 (3.12.0-3) ... Setting up gfortran-14 (14.2.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up liblapacke-dev:amd64 (3.12.0-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran-x86-64-linux-gnu (4:14.1.0-2) ... Setting up gfortran (4:14.1.0-2) ... 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 debhelper (13.20) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.40-2) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) amd64 (x86_64) Toolchain package versions: binutils_2.43.1-4 dpkg-dev_1.22.11 g++-13_13.3.0-6 g++-14_14.2.0-4 gcc-13_13.3.0-6 gcc-14_14.2.0-4 libc6-dev_2.40-2 libstdc++-13-dev_13.3.0-6 libstdc++-14-dev_14.2.0-4 libstdc++6_14.2.0-4 linux-libc-dev_6.10.9-1 Package versions: adduser_3.137 apt_2.9.8 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.4 bash_5.2.32-1+b1 binutils_2.43.1-4 binutils-common_2.43.1-4 binutils-x86-64-linux-gnu_2.43.1-4 bsdextrautils_2.40.2-8 bsdutils_1:2.40.2-8 build-essential_12.10 bzip2_1.0.8-6 coreutils_9.4-3.1 cpp_4:14.1.0-2 cpp-13_13.3.0-6 cpp-13-x86-64-linux-gnu_13.3.0-6 cpp-14_14.2.0-4 cpp-14-x86-64-linux-gnu_14.2.0-4 cpp-x86-64-linux-gnu_4:14.1.0-2 dash_0.5.12-9 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-8+b1 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.36-1 file_1:5.45-3 findutils_4.10.0-3 g++_4:14.1.0-2 g++-13_13.3.0-6 g++-13-x86-64-linux-gnu_13.3.0-6 g++-14_14.2.0-4 g++-14-x86-64-linux-gnu_14.2.0-4 g++-x86-64-linux-gnu_4:14.1.0-2 gcc_4:14.1.0-2 gcc-13_13.3.0-6 gcc-13-base_13.3.0-6 gcc-13-x86-64-linux-gnu_13.3.0-6 gcc-14_14.2.0-4 gcc-14-base_14.2.0-4 gcc-14-x86-64-linux-gnu_14.2.0-4 gcc-x86-64-linux-gnu_4:14.1.0-2 gettext_0.22.5-2 gettext-base_0.22.5-2 gfortran_4:14.1.0-2 gfortran-14_14.2.0-4 gfortran-14-x86-64-linux-gnu_14.2.0-4 gfortran-x86-64-linux-gnu_4:14.1.0-2 gnupg_2.2.43-8 gnupg-l10n_2.2.43-8 gnupg-utils_2.2.43-8+b1 gpg_2.2.43-8+b1 gpg-agent_2.2.43-8+b1 gpg-wks-client_2.2.43-8+b1 gpgconf_2.2.43-8+b1 gpgsm_2.2.43-8+b1 gpgv_2.2.43-8+b1 grep_3.11-4 groff-base_1.23.0-5 gzip_1.12-1.1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libapt-pkg6.0t64_2.9.8 libarchive-zip-perl_1.68-1 libasan8_14.2.0-4 libassuan0_2.5.6-1+b1 libassuan9_3.0.1-2 libatomic1_14.2.0-4 libattr1_1:2.5.2-1 libaudit-common_1:4.0.1-1 libaudit1_1:4.0.1-1 libbinutils_2.43.1-4 libblas-dev_3.12.0-3 libblas3_3.12.0-3 libblkid1_2.40.2-8 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-6 libc-bin_2.40-2 libc-dev-bin_2.40-2 libc-l10n_2.40-2 libc6_2.40-2 libc6-dev_2.40-2 libcap-ng0_0.8.5-2 libcap2_1:2.66-5 libcc1-0_14.2.0-4 libcrypt-dev_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.1-4 libctf0_2.43.1-4 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.20 libdpkg-perl_1.22.11 libeatmydata1_131-2 libelf1t64_0.191-2 libfakeroot_1.36-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.3.0-6 libgcc-14-dev_14.2.0-4 libgcc-s1_14.2.0-4 libgcrypt20_1.11.0-6 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgfortran-14-dev_14.2.0-4 libgfortran5_14.2.0-4 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-4 libgpg-error0_1.50-3 libgprofng0_2.43.1-4 libgsl-dev_2.8+dfsg-3 libgsl28_2.8+dfsg-3 libgslcblas0_2.8+dfsg-3 libhogweed6t64_3.10-1 libhwasan0_14.2.0-4 libicu72_72.1-5 libidn2-0_2.3.7-2 libisl23_0.27-1 libitm1_14.2.0-4 libjansson4_2.14-2+b2 libksba8_1.6.7-2 liblapack-dev_3.12.0-3 liblapack3_3.12.0-3 liblapacke_3.12.0-3 liblapacke-dev_3.12.0-3 libldap-2.5-0_2.5.18+dfsg-3+b1 liblsan0_14.2.0-4 liblz4-1_1.9.4-3 liblzma5_5.6.2-2 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.2-8 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncursesw6_6.5-2 libnettle8t64_3.10-1 libnpth0t64_1.6-3.1 libp11-kit0_0.25.5-2 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpcre2-8-0_10.42-4+b1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.0-5 libpipeline1_1.5.8-1 libquadmath0_14.2.0-4 libreadline8t64_8.2-5 libsasl2-2_2.1.28+dfsg1-8 libsasl2-modules-db_2.1.28+dfsg1-8 libseccomp2_2.5.5-1+b1 libselinux1_3.7-3 libsemanage-common_3.7-2 libsemanage2_3.7-2 libsepol2_3.7-1 libsframe1_2.43.1-4 libsmartcols1_2.40.2-8 libsqlite3-0_3.46.1-1 libssl3t64_3.3.2-1 libstdc++-13-dev_13.3.0-6 libstdc++-14-dev_14.2.0-4 libstdc++6_14.2.0-4 libsystemd0_256.6-1 libtasn1-6_4.19.0-3+b2 libtinfo6_6.5-2 libtmglib-dev_3.12.0-3 libtmglib3_3.12.0-3 libtool_2.4.7-7 libtsan2_14.2.0-4 libubsan1_14.2.0-4 libuchardet0_0.0.8-1+b1 libudev1_256.6-1 libunistring5_1.2-1 libuuid1_2.40.2-8 libxml2_2.12.7+dfsg-3+b1 libxxhash0_0.8.2-2+b1 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.10.9-1 locales-all_2.40-2 login_1:4.16.0-2+really2.40.2-8 login.defs_1:4.16.0-4 m4_1.4.19-4 make_4.3-4.1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 ncurses-base_6.5-2 ncurses-bin_6.5-2 openssl-provider-legacy_3.3.2-1 passwd_1:4.16.0-4 patch_2.7.6-7 perl_5.40.0-5 perl-base_5.40.0-5 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-5 pinentry-curses_1.2.1-4+b1 po-debconf_1.0.21+nmu1 readline-common_8.2-5 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sysvinit-utils_3.10-2 tar_1.35+dfsg-3 usr-is-merged_39 util-linux_2.40.2-8 xz-utils_5.6.2-2 zlib1g_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: eigensoft Binary: eigensoft Architecture: any Version: 8.0.0+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Homepage: http://www.hsph.harvard.edu/faculty/alkes-price/software/ Standards-Version: 4.6.2 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: 4dbd0c7d2ec075bc5629202db818578c1a96315b 231064 eigensoft_8.0.0+dfsg.orig.tar.xz 1956f229583dfd3cab5744b06ebfd3fe511350eb 6240 eigensoft_8.0.0+dfsg-2.debian.tar.xz Checksums-Sha256: 5a9576af6d30564391f5892713e9d434c4d0b5baeb75aa720ff1dad7cf556baf 231064 eigensoft_8.0.0+dfsg.orig.tar.xz a7cb4d5a066dbee75101e94b072c46fa40c187d4265a242f678e27215942edd7 6240 eigensoft_8.0.0+dfsg-2.debian.tar.xz Files: 6cc8676fe6f4fe95517ef7d2d2df6606 231064 eigensoft_8.0.0+dfsg.orig.tar.xz b66fd65eb720935b1b676360f8bcd74b 6240 eigensoft_8.0.0+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmW6jykRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtH0bw//Ueg3uVzVJCCFsvsgUVjzWvuEnuBEjDO4 PkKwk6irxdPInqfuxYoeguzyP3X8suN5ZTzZvbpDazzG26Bo1EXrtxCVRliP19o+ yaB1sPbMe00xIu6ouTkRcDDfrx05ixkK6BmU0WPbQXo22m8FkEHTkP21usBPAsmQ nttlSUvShpNPPjsiSrWGG90dJ0HAK1pOafbUUVU+XAv4Ocl37DMUwUiw3hTmkHnU KkHB7UT6uOWY7ICVBT+p1bveyczJmi+vVLsvfbONQg6zZN7eHonsYo256oM8rte2 HCnc2uBcC7y/UtY4nKwrDvXKltid3QkzuBQhMCFMcojrY6CsGLKjsPbOk837g1s4 Rm8uNL9dchaCGuHQNtJ3RjrFgb3sIXMqKvNzxtALEKlc9WnyZKPU0gNsWOpuyU2+ wcY9nfNUQLXnbeqmSFftMxTHLy5ged7d/g4KSH4i6gliBZItZxJ7+2rk6096m1Cu PABDNTn8s1m0ilOBNEM6x4xpjfXBPre7rSNtYYergd8QVGUNPpfQEsy8QPY/1TvN g7V47kfO6YvcwjTlXZYvj/y7EqVbykO886m5BIvJiqOmNunnMhBVzRU8hmznG/31 sS5e179GaUSIcgFTp/RfUqYC+2rqWGINV4QHyLd74baFMWJaBqV3vQTIYCr+1c7c nGXl+q05XPc= =FR3v -----END PGP SIGNATURE----- gpgv: Signature made Wed Jan 31 18:19:21 2024 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./eigensoft_8.0.0+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting eigensoft in /<> dpkg-source: info: unpacking eigensoft_8.0.0+dfsg.orig.tar.xz dpkg-source: info: unpacking eigensoft_8.0.0+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying blas.patch dpkg-source: info: applying lapacke.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network eigensoft_8.0.0+dfsg-2 perl-5.40-throwaway amd64 ----------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network eigensoft_8.0.0+dfsg-2 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-c810bbee-9552-43f0-b26a-760fb4fa43eb SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package eigensoft dpkg-buildpackage: info: source version 8.0.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/eigensoft.substvars debian/files rm -fr -- debian/eigensoft/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) /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 eigensrc/pcatoy eigensrc/smartrel eigensrc/smarteigenstrat eigensrc/twstats eigensrc/eigenstrat eigensrc/eigenstratQTL eigensrc/smartpca cd ../bin/ ; rm -f baseprog convertf mergeit pca pcatoy smartrel smarteigenstrat twstats eigenstrat eigenstratQTL smartpca ; cd ../src make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building eigensoft using existing ./eigensoft_8.0.0+dfsg.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building eigensoft in eigensoft_8.0.0+dfsg-2.debian.tar.xz dpkg-source: info: building eigensoft in eigensoft_8.0.0+dfsg-2.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf 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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o baseprog.o baseprog.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcio.o mcio.c mcio.c: In function ‘snpsortit’: mcio.c:119:16: warning: result of ‘10^8’ is 2; did you mean ‘1e8’? [-Wxor-used-as-pow] 119 | base[1] = 10 ^ 8; | ^ | -- | 1 e mcio.c:119:13: note: you can silence this warning by using a hexadecimal constant (0xa rather than 10) 119 | base[1] = 10 ^ 8; | ^~ | 0xa mcio.c:120:16: warning: result of ‘10^9’ is 3; did you mean ‘1e9’? [-Wxor-used-as-pow] 120 | base[2] = 10 ^ 9; | ^ | -- | 1 e mcio.c:120:13: note: you can silence this warning by using a hexadecimal constant (0xa rather than 10) 120 | base[2] = 10 ^ 9; | ^~ | 0xa mcio.c: In function ‘getgenos’: mcio.c:1383:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1383 | system (cmd); | ^~~~~~~~~~~~ mcio.c: In function ‘outfiles’: mcio.c:3218:23: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 3218 | printf ("snpname: %s %d\n", snpname, numsnps); | ^~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o egsubs.o egsubs.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o h2d.o h2d.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -c -O3 -g -p -Wimplicit -I../../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o strsubs.o strsubs.c strsubs.c: In function ‘printslurmenv’: strsubs.c:2007:2: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2007 | system(sss) ; | ^~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -c -O3 -g -p -Wimplicit -I../../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sortit.o sortit.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -c -O3 -g -p -Wimplicit -I../../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vsubs.o vsubs.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -c -O3 -g -p -Wimplicit -I../../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o statsubs.o statsubs.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -c -O3 -g -p -Wimplicit -I../../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o linsubs.o linsubs.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -c -O3 -g -p -Wimplicit -I../../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o getpars.o getpars.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -c -O3 -g -p -Wimplicit -I../../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o xsearch.o xsearch.c xsearch.c: In function ‘xloadsearchx’: xsearch.c:256:19: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 256 | sprintf (xx, "%d", i); | ^~ xsearch.c:256:18: note: directive argument in the range [0, 2147483646] 256 | sprintf (xx, "%d", i); | ^~~~ In file included from /usr/include/stdio.h:970, from xsearch.c:1: In function ‘sprintf’, inlined from ‘xloadsearchx’ at xsearch.c:256:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 8 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ xsearch.c: In function ‘xloadsearchx’: xsearch.c:256:19: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 256 | sprintf (xx, "%d", i); | ^~ xsearch.c:256:18: note: directive argument in the range [0, 2147483646] 256 | sprintf (xx, "%d", i); | ^~~~ In function ‘sprintf’, inlined from ‘xloadsearchx’ at xsearch.c:256:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 8 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ xsearch.c: In function ‘xloadsearch’: xsearch.c:278:19: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 278 | sprintf (xx, "%d", i); | ^~ xsearch.c:278:18: note: directive argument in the range [0, 2147483646] 278 | sprintf (xx, "%d", i); | ^~~~ In function ‘sprintf’, inlined from ‘xloadsearch’ at xsearch.c:278:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 8 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ xsearch.c: In function ‘xloadsearch’: xsearch.c:278:19: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 278 | sprintf (xx, "%d", i); | ^~ xsearch.c:278:18: note: directive argument in the range [0, 2147483646] 278 | sprintf (xx, "%d", i); | ^~~~ In function ‘sprintf’, inlined from ‘xloadsearch’ at xsearch.c:278:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 8 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -c -O3 -g -p -Wimplicit -I../../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gauss.o gauss.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -c -O3 -g -p -Wimplicit -I../../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gds.o gds.c ar -r libnick.a strsubs.o sortit.o vsubs.o statsubs.o linsubs.o getpars.o xsearch.o gauss.o gds.o ar: creating libnick.a ranlib libnick.a make[3]: Leaving directory '/<>/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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convertf.o convertf.c 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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/eigsubs.o eigensrc/eigsubs.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/smartrel.o eigensrc/smartrel.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o twsubs.o twsubs.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o qpsubs.o qpsubs.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regsubs.o regsubs.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/smartsubs.o eigensrc/smartsubs.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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/smarteigenstrat.o eigensrc/smarteigenstrat.c eigensrc/smarteigenstrat.c: In function ‘readpcafile’: eigensrc/smarteigenstrat.c:332:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 332 | fscanf (fppca, "%d", &K); | ^~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/smarteigenstrat.c:339:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 339 | fscanf (fppca, "%lf", &tempdouble); /* eigenvalues */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/smarteigenstrat.c:342:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 342 | fscanf (fppca, "%lf", &V[NSAMPLES * n + k]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/smarteigenstrat.c:360:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 360 | fscanf (fppca, "%lf", &tempdouble); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -Wl,-z,relro -Wl,-z,now eigensrc/smarteigenstrat.o mcio.o admutils.o nicksrc/libnick.a -lgsl -lblas -lm -llapacke -llapack -lpthread -o eigensrc/smarteigenstrat cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now eigensrc/eigenstrat.c -lgsl -lblas -lm -llapacke -llapack -lpthread -o eigensrc/eigenstrat eigensrc/eigenstrat.c: In function ‘main’: eigensrc/eigenstrat.c:86:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 86 | fscanf (fp, "%c", &Xchar); | ^~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstrat.c:123:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 123 | fscanf (fppca, "%d", &K); | ^~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstrat.c:130:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 130 | fscanf (fppca, "%lf", &tempdouble); /* eigenvalues */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstrat.c:133:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 133 | fscanf (fppca, "%lf", &V[NSAMPLES * n + k]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstrat.c:151:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 151 | fscanf (fppca, "%lf", &tempdouble); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstrat.c:165:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 165 | fscanf (fppheno, "%c", &Xchar); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstrat.c:188:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 188 | fscanf (fppheno, "%c", &Xchar); /* should be end of file */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstrat.c:244:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 244 | fscanf (fp, "%c", &Xchar); | ^~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstrat.c:267:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 267 | fscanf (fp, "%c", &Xchar); /* should be \n character */ | ^~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now eigensrc/eigenstratQTL.c -lgsl -lblas -lm -llapacke -llapack -lpthread -o eigensrc/eigenstratQTL eigensrc/eigenstratQTL.c: In function ‘main’: eigensrc/eigenstratQTL.c:86:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 86 | fscanf (fp, "%c", &Xchar); | ^~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstratQTL.c:123:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 123 | fscanf (fppca, "%d", &K); | ^~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstratQTL.c:130:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 130 | fscanf (fppca, "%lf", &tempdouble); /* eigenvalues */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstratQTL.c:133:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 133 | fscanf (fppca, "%lf", &V[NSAMPLES * n + k]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstratQTL.c:151:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 151 | fscanf (fppca, "%lf", &tempdouble); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstratQTL.c:172:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 172 | fscanf (fppheno, "%lf", &iscase[n]); /* QTL phenotype */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstratQTL.c:174:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 174 | fscanf (fppheno, "%lf", &tempdouble); /* to check # entries */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstratQTL.c:227:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 227 | fscanf (fp, "%c", &Xchar); | ^~~~~~~~~~~~~~~~~~~~~~~~~ eigensrc/eigenstratQTL.c:250:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 250 | fscanf (fp, "%c", &Xchar); /* should be \n character */ | ^~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:1292:23: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘char *’ [-Wformat=] 1292 | printf("elllist: %3d %20s\n", indx -> ID) ; fflush(stdout) ; | ~~^ ~~~~~~~~~~ | | | | int char * | %3s eigensrc/smartpca.c:1292:28: warning: format ‘%s’ expects a matching ‘char *’ argument [-Wformat=] 1292 | printf("elllist: %3d %20s\n", indx -> ID) ; fflush(stdout) ; | ~~~^ | | | char * eigensrc/smartpca.c:1675:43: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘double’ [-Wformat=] 1675 | printf("coeff multiplier (eigenvector %d): %9.3f\n", y, j) ; | ~^ ~ | | | | int double | %f eigensrc/smartpca.c:1675:51: warning: format ‘%f’ expects argument of type ‘double’, but argument 3 has type ‘int’ [-Wformat=] 1675 | printf("coeff multiplier (eigenvector %d): %9.3f\n", y, j) ; | ~~~~^ ~ | | | | double int | %9.3d eigensrc/smartpca.c:700:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 700 | system (buff); | ^~~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gval.o gval.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ksrc/kjg_fpca.o ksrc/kjg_fpca.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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,-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 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 rm -f -- debian/eigensoft.substvars rm -fr -- debian/.debhelper/generated/eigensoft/ debian/eigensoft/ debian/tmp/ dh_auto_install --destdir=debian/eigensoft/ install -m0755 -d /<>/eigensoft-8.0.0\+dfsg/debian/eigensoft debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install install -m0755 -d debian/eigensoft/usr/bin cp --reflink=auto -a ./bin/baseprog ./bin/convertf ./bin/eigenstrat ./bin/eigenstratQTL ./bin/evec2pca-ped.perl ./bin/evec2pca.perl ./bin/gc.perl ./bin/mergeit ./bin/pca ./bin/pcatoy ./bin/ploteig ./bin/rescale_ell ./bin/smarteigenstrat ./bin/smarteigenstrat.perl ./bin/smartpca ./bin/smartpca.perl ./bin/smartrel ./bin/twstats debian/eigensoft/usr/bin/ install -m0755 -d debian/eigensoft/usr/lib/debian-med/bin cp --reflink=auto -a ./bin/gc.perl debian/eigensoft/usr/lib/debian-med/bin/ install -m0755 -d debian/eigensoft/usr/lib/eigensoft cp --reflink=auto -a ./bin/smarteigenstrat ./bin/smartpca debian/eigensoft/usr/lib/eigensoft/ install -m0755 -d debian/eigensoft/usr/share/eigensoft cp --reflink=auto -a ./CONVERTF ./EIGENSTRAT ./POPGEN debian/eigensoft/usr/share/eigensoft/ 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 -f 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 cd debian && for pl in `grep -lR '/usr/.*/bin/perl' | grep -v debian/rules` ; do \ sed -i -e "s?/usr/.*/bin/perl?/usr/bin/perl?" ${pl} ; \ done rm debian/eigensoft/usr/bin/gc.perl make[1]: Leaving directory '/<>' dh_installdocs install -m0755 -d debian/eigensoft/usr/share/doc/eigensoft install -m0755 -d debian/eigensoft/usr/share/doc/eigensoft cp --reflink=auto -a ./README debian/eigensoft/usr/share/doc/eigensoft chmod -R u\+rw,go=rX debian/eigensoft/usr/share/doc install -p -m0644 debian/README.Debian debian/eigensoft/usr/share/doc/eigensoft/README.Debian install -p -m0644 debian/copyright debian/eigensoft/usr/share/doc/eigensoft/copyright dh_installchangelogs install -m0755 -d debian/eigensoft/usr/share/doc/eigensoft install -p -m0644 debian/.debhelper/generated/eigensoft/dh_installchangelogs.dch.trimmed debian/eigensoft/usr/share/doc/eigensoft/changelog.Debian dh_installexamples install -m0755 -d debian/eigensoft/usr/share/doc/eigensoft/examples cp --reflink=auto -a ./CONVERTF debian/eigensoft/usr/share/doc/eigensoft/examples cp --reflink=auto -a ./EIGENSTRAT debian/eigensoft/usr/share/doc/eigensoft/examples cp --reflink=auto -a ./POPGEN debian/eigensoft/usr/share/doc/eigensoft/examples dh_installman install -m0755 -d debian/eigensoft/usr/share/man/man1/ install -p -m0644 ./debian/mans/smarteigenstrat.1 debian/eigensoft/usr/share/man/man1/smarteigenstrat.1 man-recode --to-code UTF-8 --suffix .dh-new debian/eigensoft/usr/share/man/man1/smarteigenstrat.1 mv debian/eigensoft/usr/share/man/man1/smarteigenstrat.1.dh-new debian/eigensoft/usr/share/man/man1/smarteigenstrat.1 chmod 0644 -- debian/eigensoft/usr/share/man/man1/smarteigenstrat.1 dh_perl mv debian/eigensoft.substvars.new debian/eigensoft.substvars dh_link install -m0755 -d debian/eigensoft/usr/bin rm -f debian/eigensoft/usr/bin/gc-eigensoft ln -s ../lib/debian-med/bin/gc.perl debian/eigensoft/usr/bin/gc-eigensoft dh_strip_nondeterminism dh_compress cd debian/eigensoft chmod a-x usr/share/doc/eigensoft/README usr/share/doc/eigensoft/changelog.Debian usr/share/man/man1/smarteigenstrat.1 gzip -9nf usr/share/doc/eigensoft/README usr/share/doc/eigensoft/changelog.Debian usr/share/man/man1/smarteigenstrat.1 cd '/<>' rm -f debian/eigensoft.debhelper.log debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms find debian/eigensoft ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/eigensoft/usr/share/doc -type f -a -true -a ! -regex 'debian/eigensoft/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/eigensoft/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/eigensoft/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/eigensoft -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/eigensoft/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/eigensoft/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/*/usr/share/eigensoft -type f -name "*.perl" -exec chmod +x \{\} \; make[1]: Leaving directory '/<>' dh_missing dh_dwz -a install -m0755 -d debian/eigensoft/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/eigensoft/usr/lib/debug/.dwz/x86_64-linux-gnu/eigensoft.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/eigensoft.debug -- debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/eigenstratQTL debian/eigensoft/usr/bin/mergeit debian/eigensoft/usr/bin/pca debian/eigensoft/usr/bin/pcatoy debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/lib/eigensoft/smartpca objcopy --compress-debug-sections debian/eigensoft/usr/lib/debug/.dwz/x86_64-linux-gnu/eigensoft.debug chmod 0644 -- debian/eigensoft/usr/lib/debug/.dwz/x86_64-linux-gnu/eigensoft.debug dh_strip -a install -m0755 -d debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/c0 objcopy --only-keep-debug --compress-debug-sections debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/c0/2da3e35a804b2632a4a2d0a945c1ae97c09cc6.debug chmod 0644 -- debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/c0/2da3e35a804b2632a4a2d0a945c1ae97c09cc6.debug strip --remove-section=.comment --remove-section=.note debian/eigensoft/usr/lib/eigensoft/smarteigenstrat objcopy --add-gnu-debuglink debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/c0/2da3e35a804b2632a4a2d0a945c1ae97c09cc6.debug debian/eigensoft/usr/lib/eigensoft/smarteigenstrat install -m0755 -d debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/39 objcopy --only-keep-debug --compress-debug-sections debian/eigensoft/usr/lib/eigensoft/smartpca debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/39/b66e3ea20370e5ebd67907f9de2c3085dede76.debug chmod 0644 -- debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/39/b66e3ea20370e5ebd67907f9de2c3085dede76.debug strip --remove-section=.comment --remove-section=.note debian/eigensoft/usr/lib/eigensoft/smartpca objcopy --add-gnu-debuglink debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/39/b66e3ea20370e5ebd67907f9de2c3085dede76.debug debian/eigensoft/usr/lib/eigensoft/smartpca install -m0755 -d debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/04 objcopy --only-keep-debug --compress-debug-sections debian/eigensoft/usr/bin/baseprog debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/04/93334672b34a193bf3c96eee9270d7ae264f08.debug chmod 0644 -- debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/04/93334672b34a193bf3c96eee9270d7ae264f08.debug strip --remove-section=.comment --remove-section=.note debian/eigensoft/usr/bin/baseprog objcopy --add-gnu-debuglink debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/04/93334672b34a193bf3c96eee9270d7ae264f08.debug debian/eigensoft/usr/bin/baseprog install -m0755 -d debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/75 objcopy --only-keep-debug --compress-debug-sections debian/eigensoft/usr/bin/convertf debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/75/87c1138ba95d38609b9c6d81f03d3cbc099883.debug chmod 0644 -- debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/75/87c1138ba95d38609b9c6d81f03d3cbc099883.debug strip --remove-section=.comment --remove-section=.note debian/eigensoft/usr/bin/convertf objcopy --add-gnu-debuglink debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/75/87c1138ba95d38609b9c6d81f03d3cbc099883.debug debian/eigensoft/usr/bin/convertf install -m0755 -d debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/51 objcopy --only-keep-debug --compress-debug-sections debian/eigensoft/usr/bin/pca debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/51/76d7f2c4e31c5a11958887a8612bb1ea7792f9.debug chmod 0644 -- debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/51/76d7f2c4e31c5a11958887a8612bb1ea7792f9.debug strip --remove-section=.comment --remove-section=.note debian/eigensoft/usr/bin/pca objcopy --add-gnu-debuglink debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/51/76d7f2c4e31c5a11958887a8612bb1ea7792f9.debug debian/eigensoft/usr/bin/pca install -m0755 -d debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/7c objcopy --only-keep-debug --compress-debug-sections debian/eigensoft/usr/bin/eigenstratQTL debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/7c/4e2cc44814be43981987da0eba815af90bfab0.debug chmod 0644 -- debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/7c/4e2cc44814be43981987da0eba815af90bfab0.debug strip --remove-section=.comment --remove-section=.note debian/eigensoft/usr/bin/eigenstratQTL objcopy --add-gnu-debuglink debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/7c/4e2cc44814be43981987da0eba815af90bfab0.debug debian/eigensoft/usr/bin/eigenstratQTL install -m0755 -d debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/ca objcopy --only-keep-debug --compress-debug-sections debian/eigensoft/usr/bin/smartrel debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/ca/b980667b29847f1b7e0e330fcc28a7cacdf0d5.debug chmod 0644 -- debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/ca/b980667b29847f1b7e0e330fcc28a7cacdf0d5.debug strip --remove-section=.comment --remove-section=.note debian/eigensoft/usr/bin/smartrel objcopy --add-gnu-debuglink debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/ca/b980667b29847f1b7e0e330fcc28a7cacdf0d5.debug debian/eigensoft/usr/bin/smartrel install -m0755 -d debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/fe objcopy --only-keep-debug --compress-debug-sections debian/eigensoft/usr/bin/eigenstrat debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/fe/2b0163355ca4793e2252518f2706ad43ea6736.debug chmod 0644 -- debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/fe/2b0163355ca4793e2252518f2706ad43ea6736.debug strip --remove-section=.comment --remove-section=.note debian/eigensoft/usr/bin/eigenstrat objcopy --add-gnu-debuglink debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/fe/2b0163355ca4793e2252518f2706ad43ea6736.debug debian/eigensoft/usr/bin/eigenstrat install -m0755 -d debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/18 objcopy --only-keep-debug --compress-debug-sections debian/eigensoft/usr/bin/twstats debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/18/cc6dd4054bb522567f97f0fb3bf51d10a7a217.debug chmod 0644 -- debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/18/cc6dd4054bb522567f97f0fb3bf51d10a7a217.debug strip --remove-section=.comment --remove-section=.note debian/eigensoft/usr/bin/twstats objcopy --add-gnu-debuglink debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/18/cc6dd4054bb522567f97f0fb3bf51d10a7a217.debug debian/eigensoft/usr/bin/twstats install -m0755 -d debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/46 objcopy --only-keep-debug --compress-debug-sections debian/eigensoft/usr/bin/mergeit debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/46/e9db27ef695a01ae336962eeabf0bbc9ae5e96.debug chmod 0644 -- debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/46/e9db27ef695a01ae336962eeabf0bbc9ae5e96.debug strip --remove-section=.comment --remove-section=.note debian/eigensoft/usr/bin/mergeit objcopy --add-gnu-debuglink debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/46/e9db27ef695a01ae336962eeabf0bbc9ae5e96.debug debian/eigensoft/usr/bin/mergeit install -m0755 -d debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/c0 objcopy --only-keep-debug --compress-debug-sections debian/eigensoft/usr/bin/pcatoy debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/c0/c4a2396f68055627935a015e5c4fcdb7a5f6f3.debug chmod 0644 -- debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/c0/c4a2396f68055627935a015e5c4fcdb7a5f6f3.debug strip --remove-section=.comment --remove-section=.note debian/eigensoft/usr/bin/pcatoy objcopy --add-gnu-debuglink debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.build-id/c0/c4a2396f68055627935a015e5c4fcdb7a5f6f3.debug debian/eigensoft/usr/bin/pcatoy install -m0755 -d debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/eigensoft/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/eigensoft/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/eigensoft/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/eigensoft/usr/lib/debug install -m0755 -d debian/.debhelper/eigensoft/dbgsym-root/usr/share/doc ln -s eigensoft debian/.debhelper/eigensoft/dbgsym-root/usr/share/doc/eigensoft-dbgsym install -m0755 -d debian/.debhelper/eigensoft dh_makeshlibs -a rm -f debian/eigensoft/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/eigensoft/DEBIAN dpkg-shlibdeps -Tdebian/eigensoft.substvars debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/pca debian/eigensoft/usr/bin/eigenstratQTL debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/bin/mergeit debian/eigensoft/usr/bin/pcatoy dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/eigensoft/usr/lib/eigensoft/smartpca was not linked against libblas.so.3 (it uses none of the library's symbols) dh_installdeb install -m0755 -d debian/eigensoft/DEBIAN dh_gencontrol install -m0755 -d debian/eigensoft/DEBIAN echo misc:Depends= >> debian/eigensoft.substvars echo misc:Pre-Depends= >> debian/eigensoft.substvars install -m0755 -d debian/.debhelper/eigensoft/dbgsym-root/DEBIAN dpkg-gencontrol -peigensoft -ldebian/changelog -Tdebian/eigensoft.substvars -cdebian/control -Pdebian/.debhelper/eigensoft/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=eigensoft-dbgsym "-DDepends=eigensoft (= \${binary:Version})" "-DDescription=debug symbols for eigensoft" "-DBuild-Ids=0493334672b34a193bf3c96eee9270d7ae264f08 18cc6dd4054bb522567f97f0fb3bf51d10a7a217 39b66e3ea20370e5ebd67907f9de2c3085dede76 46e9db27ef695a01ae336962eeabf0bbc9ae5e96 5176d7f2c4e31c5a11958887a8612bb1ea7792f9 7587c1138ba95d38609b9c6d81f03d3cbc099883 7c4e2cc44814be43981987da0eba815af90bfab0 c02da3e35a804b2632a4a2d0a945c1ae97c09cc6 c0c4a2396f68055627935a015e5c4fcdb7a5f6f3 cab980667b29847f1b7e0e330fcc28a7cacdf0d5 fe2b0163355ca4793e2252518f2706ad43ea6736" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/eigensoft/dbgsym-root/DEBIAN/control dpkg-gencontrol -peigensoft -ldebian/changelog -Tdebian/eigensoft.substvars -cdebian/control -Pdebian/eigensoft chmod 0644 -- debian/eigensoft/DEBIAN/control dh_md5sums install -m0755 -d debian/eigensoft/DEBIAN cd debian/eigensoft >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/eigensoft/DEBIAN/md5sums install -m0755 -d debian/.debhelper/eigensoft/dbgsym-root/DEBIAN cd debian/.debhelper/eigensoft/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/eigensoft/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/eigensoft .. dpkg-deb --root-owner-group --build debian/.debhelper/eigensoft/dbgsym-root .. dpkg-deb: building package 'eigensoft' in '../eigensoft_8.0.0+dfsg-2_amd64.deb'. dpkg-deb: building package 'eigensoft-dbgsym' in '../eigensoft-dbgsym_8.0.0+dfsg-2_amd64.deb'. dpkg-genbuildinfo -O../eigensoft_8.0.0+dfsg-2_amd64.buildinfo dpkg-genchanges -O../eigensoft_8.0.0+dfsg-2_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2024-09-15T03:54:11Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ eigensoft_8.0.0+dfsg-2_amd64.changes: ------------------------------------- Format: 1.8 Date: Wed, 31 Jan 2024 19:16:19 +0100 Source: eigensoft Binary: eigensoft eigensoft-dbgsym Architecture: source amd64 Version: 8.0.0+dfsg-2 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: eigensoft - reduction of population bias for genetic analyses Closes: 1045139 Changes: eigensoft (8.0.0+dfsg-2) unstable; urgency=medium . * Fix download filename in watch file * Standards-Version: 4.6.2 (routine-update) * Change interpreter PATH only in debian dir not in upstream source Closes: #1045139 Checksums-Sha1: 17921df07c03e24b21846847c66dbc4915019ff3 1224 eigensoft_8.0.0+dfsg-2.dsc 1956f229583dfd3cab5744b06ebfd3fe511350eb 6240 eigensoft_8.0.0+dfsg-2.debian.tar.xz c25d6ab7519dce8deeec803daab91f0d5d148af7 3209136 eigensoft-dbgsym_8.0.0+dfsg-2_amd64.deb 6847a5a976001277b4fa4ac16e4490b03cb7b39a 5830 eigensoft_8.0.0+dfsg-2_amd64.buildinfo 5c167ac322e3aea747d6b36ee076b373c35bffcc 518440 eigensoft_8.0.0+dfsg-2_amd64.deb Checksums-Sha256: 4cf7ca1b9d00e0a208132ed5b0ec2d8d42bf3a60b7c140afe51b417969d54bd2 1224 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eigensoft-dbgsym_8.0.0+dfsg-2_amd64.deb --------------------------------------- new Debian package, version 2.0. size 3209136 bytes: control archive=1104 bytes. 799 bytes, 12 lines control 1252 bytes, 12 lines md5sums Package: eigensoft-dbgsym Source: eigensoft Version: 8.0.0+dfsg-2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 3466 Depends: eigensoft (= 8.0.0+dfsg-2) Section: debug Priority: optional Description: debug symbols for eigensoft Build-Ids: 0493334672b34a193bf3c96eee9270d7ae264f08 18cc6dd4054bb522567f97f0fb3bf51d10a7a217 39b66e3ea20370e5ebd67907f9de2c3085dede76 46e9db27ef695a01ae336962eeabf0bbc9ae5e96 5176d7f2c4e31c5a11958887a8612bb1ea7792f9 7587c1138ba95d38609b9c6d81f03d3cbc099883 7c4e2cc44814be43981987da0eba815af90bfab0 c02da3e35a804b2632a4a2d0a945c1ae97c09cc6 c0c4a2396f68055627935a015e5c4fcdb7a5f6f3 cab980667b29847f1b7e0e330fcc28a7cacdf0d5 fe2b0163355ca4793e2252518f2706ad43ea6736 drwxr-xr-x root/root 0 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Team Installed-Size: 3921 Depends: libblas3 | libblas.so.3, libc6 (>= 2.34), libgsl28 (>= 2.8+dfsg), liblapack3 | liblapack.so.3, liblapacke (>= 3.12.0), 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. drwxr-xr-x root/root 0 2024-01-31 18:16 ./ drwxr-xr-x root/root 0 2024-01-31 18:16 ./usr/ drwxr-xr-x root/root 0 2024-01-31 18:16 ./usr/bin/ -rwxr-xr-x root/root 420400 2024-01-31 18:16 ./usr/bin/baseprog -rwxr-xr-x root/root 432824 2024-01-31 18:16 ./usr/bin/convertf -rwxr-xr-x root/root 18672 2024-01-31 18:16 ./usr/bin/eigenstrat -rwxr-xr-x root/root 18672 2024-01-31 18:16 ./usr/bin/eigenstratQTL -rwxr-xr-x root/root 1462 2024-01-31 18:16 ./usr/bin/evec2pca -rwxr-xr-x root/root 2311 2024-01-31 18:16 ./usr/bin/evec2pca-ped lrwxrwxrwx root/root 0 2024-01-31 18:16 ./usr/bin/gc-eigensoft -> ../lib/debian-med/bin/gc.perl -rwxr-xr-x root/root 412256 2024-01-31 18:16 ./usr/bin/mergeit -rwxr-xr-x root/root 145648 2024-01-31 18:16 ./usr/bin/pca -rwxr-xr-x root/root 137456 2024-01-31 18:16 ./usr/bin/pcatoy -rwxr-xr-x root/root 5702 2024-01-31 18:16 ./usr/bin/ploteig -rwxr-xr-x 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2024-01-31 18:16 ./usr/lib/eigensoft/smarteigenstrat -rwxr-xr-x root/root 572200 2024-01-31 18:16 ./usr/lib/eigensoft/smartpca drwxr-xr-x root/root 0 2024-01-31 18:16 ./usr/share/ drwxr-xr-x root/root 0 2024-01-31 18:16 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-31 18:16 ./usr/share/doc/eigensoft/ -rw-r--r-- root/root 726 2024-01-31 18:16 ./usr/share/doc/eigensoft/README.Debian -rw-r--r-- root/root 2631 2021-06-07 14:37 ./usr/share/doc/eigensoft/README.gz -rw-r--r-- root/root 597 2024-01-31 18:16 ./usr/share/doc/eigensoft/changelog.Debian.gz -rw-r--r-- root/root 2553 2024-01-31 18:16 ./usr/share/doc/eigensoft/copyright drwxr-xr-x root/root 0 2024-01-31 18:16 ./usr/share/doc/eigensoft/examples/ drwxr-xr-x root/root 0 2021-06-07 14:37 ./usr/share/doc/eigensoft/examples/CONVERTF/ -rw-r--r-- root/root 17865 2021-06-07 14:37 ./usr/share/doc/eigensoft/examples/CONVERTF/README -rw-r--r-- root/root 1610 2021-06-07 14:37 ./usr/share/doc/eigensoft/examples/CONVERTF/example.ancestrymapgeno 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