eigensoft →
6.1.4+dfsg-1+b2 →
armhf → 2018-04-24 11:12:28
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| eigensoft 6.1.4+dfsg-1+b2 (armhf) Tue, 24 Apr 2018 11:03:51 +0000 |
+==============================================================================+
Package: eigensoft
Version: 6.1.4+dfsg-1+b2
Source Version: 6.1.4+dfsg-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-edd180f9-728f-4e83-8d8e-3d04796937bd' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.7 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.5 MB]
Fetched 23.2 MB in 29s (805 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http: aptMethod::Configuration: could not load seccomp policy: Invalid argument
W: store: aptMethod::Configuration: could not load seccomp policy: Invalid argument
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'eigensoft' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/eigensoft.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/eigensoft.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 166 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main eigensoft 6.1.4+dfsg-1 (dsc) [2113 B]
Get:2 http://172.17.0.1/private buster-staging/main eigensoft 6.1.4+dfsg-1 (tar) [158 kB]
Get:3 http://172.17.0.1/private buster-staging/main eigensoft 6.1.4+dfsg-1 (diff) [5916 B]
Fetched 166 kB in 0s (1562 kB/s)
Download complete and in download only mode
W: http: aptMethod::Configuration: could not load seccomp policy: Invalid argument
I: NOTICE: Log filtering will replace 'build/eigensoft-AVjCQ5/eigensoft-6.1.4+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/eigensoft-AVjCQ5' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-CiQqnF/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-CiQqnF/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-CiQqnF/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-CiQqnF/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-CiQqnF/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-CiQqnF/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-CiQqnF/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-CiQqnF/apt_archive ./ Packages [430 B]
Fetched 2106 B in 1s (3129 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: copy: aptMethod::Configuration: could not load seccomp policy: Invalid argument
W: store: aptMethod::Configuration: could not load seccomp policy: Invalid argument
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 28 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-CiQqnF/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15677 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
W: copy: aptMethod::Configuration: could not load seccomp policy: Invalid argument
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 9), gfortran, libblas-dev, liblapack-dev, liblapacke-dev, libgsl-dev
Filtered Build-Depends: debhelper (>= 9), gfortran, libblas-dev, liblapack-dev, liblapacke-dev, libgsl-dev
dpkg-deb: building package 'sbuild-build-depends-eigensoft-dummy' in '/<<BUILDDIR>>/resolver-CiQqnF/apt_archive/sbuild-build-depends-eigensoft-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-eigensoft-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-CiQqnF/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-CiQqnF/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-CiQqnF/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-CiQqnF/apt_archive ./ Sources [518 B]
Get:5 copy:/<<BUILDDIR>>/resolver-CiQqnF/apt_archive ./ Packages [597 B]
Fetched 2448 B in 1s (2785 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: copy: aptMethod::Configuration: could not load seccomp policy: Invalid argument
W: store: aptMethod::Configuration: could not load seccomp policy: Invalid argument
Reading package lists...
Install eigensoft build dependencies (apt-based resolver)
---------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base gfortran
gfortran-7 groff-base intltool-debian libarchive-zip-perl libblas-dev
libblas3 libbsd0 libcroco3 libfile-stripnondeterminism-perl
libgfortran-7-dev libgfortran4 libglib2.0-0 libgsl-dev libgsl23 libgslcblas0
libicu57 liblapack-dev liblapack3 liblapacke liblapacke-dev libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtmglib-dev libtmglib3
libtool libxml2 m4 man-db po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev
gfortran-doc gfortran-7-doc libgfortran4-dbg 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 libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base gfortran
gfortran-7 groff-base intltool-debian libarchive-zip-perl libblas-dev
libblas3 libbsd0 libcroco3 libfile-stripnondeterminism-perl
libgfortran-7-dev libgfortran4 libglib2.0-0 libgsl-dev libgsl23 libgslcblas0
libicu57 liblapack-dev liblapack3 liblapacke liblapacke-dev libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtmglib-dev libtmglib3
libtool libxml2 m4 man-db po-debconf sbuild-build-depends-eigensoft-dummy
0 upgraded, 45 newly installed, 0 to remove and 28 not upgraded.
Need to get 20.2 MB/30.4 MB of archives.
After this operation, 113 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-CiQqnF/apt_archive ./ sbuild-build-depends-eigensoft-dummy 0.invalid.0 [884 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 17 [16.5 kB]
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Get:16 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.041-1 [19.9 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.041-1 [12.0 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.2.1 [1013 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-12 [191 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libgfortran-7-dev armhf 7.3.0-12 [232 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf gfortran-7 armhf 7.3.0-12 [5454 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:7.2.0-1d1 [1352 B]
Get:28 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.7.1-4 [112 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libgslcblas0 armhf 2.4+dfsg-6 [75.1 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libgsl23 armhf 2.4+dfsg-6 [681 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libgsl-dev armhf 2.4+dfsg-6 [863 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.7.1-4 [1564 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libtmglib3 armhf 3.7.1-4 [91.8 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf liblapacke armhf 3.7.1-4 [275 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libtmglib-dev armhf 3.7.1-4 [95.0 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf liblapacke-dev armhf 3.7.1-4 [259 kB]
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Setting up libicu57:armhf (57.1-9) ...
Setting up libbsd0:armhf (0.8.7-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-6.1) ...
Setting up libmagic-mgc (1:5.32-2) ...
Setting up libmagic1:armhf (1:5.32-2) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up libblas3:armhf (3.7.1-4) ...
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
Processing triggers for libc-bin (2.27-3+rpi1) ...
Setting up autotools-dev (20180224.1) ...
Setting up libgfortran-7-dev:armhf (7.3.0-12) ...
Setting up gfortran-7 (7.3.0-12) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgslcblas0:armhf (2.4+dfsg-6) ...
Setting up autopoint (0.19.8.1-6) ...
Setting up libfile-stripnondeterminism-perl (0.041-1) ...
Setting up gfortran (4:7.2.0-1d1) ...
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 libgsl23:armhf (2.4+dfsg-6) ...
Setting up gettext (0.19.8.1-6) ...
Setting up libblas-dev:armhf (3.7.1-4) ...
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 libgsl-dev (2.4+dfsg-6) ...
Setting up liblapack3:armhf (3.7.1-4) ...
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 autoconf (2.69-11) ...
Setting up file (1:5.32-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.15.1-3.1) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up liblapack-dev:armhf (3.7.1-4) ...
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 libtool (2.4.6-2.1) ...
Setting up libtmglib3:armhf (3.7.1-4) ...
Setting up po-debconf (1.0.20) ...
Setting up liblapacke:armhf (3.7.1-4) ...
Setting up libtmglib-dev:armhf (3.7.1-4) ...
Setting up liblapacke-dev:armhf (3.7.1-4) ...
Setting up dh-autoreconf (17) ...
Setting up dh-strip-nondeterminism (0.041-1) ...
Setting up debhelper (11.2.1) ...
Setting up sbuild-build-depends-eigensoft-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
W: copy: aptMethod::Configuration: could not load seccomp policy: Invalid argument
W: http: aptMethod::Configuration: could not load seccomp policy: Invalid argument
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.30-8+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-12 gcc-7_7.3.0-12 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180402-1+rpi1 linux-libc-dev_4.15.11-1+rpi1
Package versions: adduser_3.117 apt_1.6~beta1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.44 bash_4.4.18-2 binutils_2.30-8+rpi1 binutils-arm-linux-gnueabihf_2.30-8+rpi1 binutils-common_2.30-8+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.5 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.3.0-12 dash_0.5.8-2.10 dbus_1.12.6-2 dbus-user-session_1.12.6-2 debconf_1.5.66 debhelper_11.2.1 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.041-1 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.44.1-1 e2fsprogs_1.44.1-1 e2fsprogs-l10n_1.44.1-1 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.32-2 findutils_4.6.0+git+20171230-2 g++_4:7.2.0-1d1 g++-7_7.3.0-12 gcc_4:7.2.0-1d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1 gcc-5-base_5.5.0-8 gcc-7_7.3.0-12 gcc-7-base_7.3.0-12 gcc-8-base_8-20180402-1+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gfortran_4:7.2.0-1d1 gfortran-7_7.3.0-12 gnupg_2.2.5-1 gnupg-agent_2.2.5-1 gnupg-l10n_2.2.5-1 gnupg-utils_2.2.5-1 gpg_2.2.5-1 gpg-agent_2.2.5-1 gpg-wks-client_2.2.5-1 gpg-wks-server_2.2.5-1 gpgconf_2.2.5-1 gpgsm_2.2.5-1 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hostname_3.20 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-4 libapt-pkg5.0_1.6~beta1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-1.1 libasan4_7.3.0-12 libassuan0_2.5.1-2 libatomic1_8-20180402-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libbinutils_2.30-8+rpi1 libblas-dev_3.7.1-4 libblas3_3.7.1-4 libblkid1_2.31.1-0.5 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3+rpi1 libc-dev-bin_2.27-3+rpi1 libc6_2.27-3+rpi1 libc6-dev_2.27-3+rpi1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_8-20180402-1+rpi1 libcilkrts5_7.3.0-12 libcom-err2_1.44.1-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.6-2 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.91-2+rpi1 libdrm2_2.4.91-2+rpi1 libexpat1_2.2.5-3 libext2fs2_1.44.1-1 libfakeroot_1.22-2 libfdisk1_2.31.1-0.5 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.041-1 libgcc-7-dev_7.3.0-12 libgcc1_1:8-20180402-1+rpi1 libgcrypt20_1.8.2-2 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgfortran-7-dev_7.3.0-12 libgfortran4_7.3.0-12 libglib2.0-0_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180402-1+rpi1 libgpg-error0_1.28-2 libgsl-dev_2.4+dfsg-6 libgsl23_2.4+dfsg-6 libgslcblas0_2.4+dfsg-6 libhogweed4_3.4-1 libicu57_57.1-9 libidn11_1.33-2.1 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl15_0.18-4 libjson-c3_0.12.1-1.3 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libksba8_1.3.5-2 liblapack-dev_3.7.1-4 liblapack3_3.7.1-4 liblapacke_3.7.1-4 liblapacke-dev_3.7.1-4 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-2 libmagic1_1:5.32-2 libmount1_2.31.1-0.5 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1-1 libncursesw5_6.1-1 libnettle6_3.4-1 libnpth0_1.5-3 libnss-systemd_238-4 libp11-kit0_0.23.10-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-4 libpam0g_1.1.8-3.7 libpcre3_2:8.39-9 libperl5.24_5.24.1-7 libperl5.26_5.26.1-5 libpipeline1_1.5.0-1 libplymouth4_0.9.3-2 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-4 libreadline7_7.0-3 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-2 libsmartcols1_2.31.1-0.5 libsqlite3-0_3.23.0-1 libss2_1.44.1-1 libssl1.1_1.1.0h-2 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180402-1+rpi1 libsystemd0_238-4 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.1-1 libtmglib-dev_3.7.1-4 libtmglib3_3.7.1-4 libtool_2.4.6-2.1 libubsan0_7.3.0-12 libudev1_238-4 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.5 libxml2_2.9.4+dfsg1-6.1 linux-base_4.5 linux-libc-dev_4.15.11-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.3-2 mawk_1.3.3-17 mount_2.31.1-0.5 multiarch-support_2.27-3+rpi1 nano_2.9.5-1 ncurses-base_6.1-1 ncurses-bin_6.1-1 netbase_5.4 openssl_1.1.0h-2 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.1-5 perl-base_5.26.1-5 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.1-5 pinentry-curses_1.1.0-1 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.12-4 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-eigensoft-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-4 systemd-sysv_238-4 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018d-1 udev_238-4 util-linux_2.31.1-0.5 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun Oct 16 13:17:49 2016 UTC
gpgv: using RSA key 578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./eigensoft_6.1.4+dfsg-1.dsc
dpkg-source: info: extracting eigensoft in /<<BUILDDIR>>/eigensoft-6.1.4+dfsg
dpkg-source: info: unpacking eigensoft_6.1.4+dfsg.orig.tar.xz
dpkg-source: info: unpacking eigensoft_6.1.4+dfsg-1.debian.tar.xz
dpkg-source: info: applying blas.patch
dpkg-source: info: applying libm.patch
dpkg-source: info: applying lapacke.patch
dpkg-source: info: applying fixing_headers.patch
dpkg-source: info: applying fix_perl_interpreter.patch
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 6.1.4+dfsg-1+b2
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-edd180f9-728f-4e83-8d8e-3d04796937bd
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package eigensoft
dpkg-buildpackage: info: source version 6.1.4+dfsg-1+b2
dpkg-buildpackage: info: source distribution buster-staging
dpkg-source --before-build eigensoft-6.1.4+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/<<BUILDDIR>>/eigensoft-6.1.4+dfsg'
dh_clean
/usr/bin/make -C src clobber
make[2]: Entering directory '/<<BUILDDIR>>/eigensoft-6.1.4+dfsg/src'
rm -f *.o */*.o */*.a
rm -f baseprog convertf mergeit pca pcaselection eigensrc/pcatoy eigensrc/smartrel eigensrc/smarteigenstrat eigensrc/twstats eigensrc/eigenstrat eigensrc/eigenstratQTL eigensrc/smartpca
cd ../bin/ ; rm -f baseprog convertf mergeit pca pcaselection pcatoy smartrel smarteigenstrat twstats eigenstrat eigenstratQTL smartpca ; cd ../src
make[2]: Leaving directory '/<<BUILDDIR>>/eigensoft-6.1.4+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/eigensoft-6.1.4+dfsg'
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/eigensoft-6.1.4+dfsg'
/usr/bin/make DEBUG_OPTIONS=-g -C src all
make[2]: Entering directory '/<<BUILDDIR>>/eigensoft-6.1.4+dfsg/src'
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o baseprog.o baseprog.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcio.o mcio.c
mcio.c: In function 'getgenos':
mcio.c:1391:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmd);
^~~~~~~~~~~~
In file included from ../include/statsubs.h:6:0,
from ../include/nicklib.h:4,
from ../include/admutils.h:2,
from ../include/mcio.h:11,
from mcio.c:3:
mcio.c: In function 'getindivs':
../include/strsubs.h:83:54: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
#define ZALLOC(item,n,type) if ((item = (type *)calloc((n),sizeof(type))) == NULL) \
^~~~~~~~~~~~~~~~~~~~~~~~
mcio.c:955:3: note: in expansion of macro 'ZALLOC'
ZALLOC(indivmarkers, nindiv, Indiv *);
^~~~~~
In file included from ../include/strsubs.h:1:0,
from ../include/vsubs.h:5,
from ../include/mcio.h:10,
from mcio.c:3:
/usr/include/stdlib.h:541:14: note: in a call to allocation function 'calloc' declared here
extern void *calloc (size_t __nmemb, size_t __size)
^~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o egsubs.o egsubs.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o admutils.o admutils.c
admutils.c: In function 'setid2pops':
admutils.c:1288:35: warning: format '%s' expects a matching 'char *' argument [-Wformat=]
printf ("(setid2pops): %s not found\n");
~^
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o h2d.o h2d.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/exclude.o eigensrc/exclude.c
/usr/bin/make -C nicksrc
make[3]: Entering directory '/<<BUILDDIR>>/eigensoft-6.1.4+dfsg/src/nicksrc'
cc -I../../include -D_GNU_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gauss.o gauss.c
cc -I../../include -D_GNU_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gds.o gds.c
gds.c: In function 'ewens':
gds.c:412:5: warning: 'return' with no value, in function returning non-void
return;
^~~~~~
gds.c:403:1: note: declared here
ewens (int *a, int n, double theta)
^~~~~
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 '/<<BUILDDIR>>/eigensoft-6.1.4+dfsg/src/nicksrc'
cc -Wl,-z,relro -Wl,-z,now baseprog.o mcio.o egsubs.o admutils.o h2d.o eigensrc/exclude.o nicksrc/libnick.a -lgfortran -lrt -lgsl -lblas -fopenmp -lm -llapacke -llapack -pthread -o baseprog
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -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 -lgfortran -lrt -lgsl -lblas -fopenmp -lm -llapacke -llapack -pthread -o convertf
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -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 -lgfortran -lrt -lgsl -lblas -fopenmp -lm -llapacke -llapack -pthread -o mergeit
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o pca.o pca.c
pca.c: In function 'main':
pca.c:110:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fp, "%c", &Xchar);
^~~~~~~~~~~~~~~~~~~~~~~~~
pca.c:186:15: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fp, "%c", &Xchar);
^~~~~~~~~~~~~~~~~~~~~~~~~
pca.c:216:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fp, "%c", &Xchar); /* should be \n character */
^~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/eigsubs.o eigensrc/eigsubs.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigx.o eigx.c
cc -Wl,-z,relro -Wl,-z,now pca.o eigensrc/eigsubs.o eigx.o nicksrc/libnick.a -lgfortran -lrt -lgsl -lblas -fopenmp -lm -llapacke -llapack -pthread -o pca
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o pcaselection.o pcaselection.c
pcaselection.c: In function 'read_evec':
pcaselection.c:256:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fp, "%s", buffer);
^~~~~~~~~~~~~~~~~~~~~~~~~
pcaselection.c:325:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fp, "%s", buffer);
^~~~~~~~~~~~~~~~~~~~~~~~~
cc -Wl,-z,relro -Wl,-z,now pcaselection.o mcio.o admutils.o nicksrc/libnick.a -lgfortran -lrt -lgsl -lblas -fopenmp -lm -llapacke -llapack -pthread -o pcaselection
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/pcatoy.o eigensrc/pcatoy.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/eigx.o eigensrc/eigx.c
cc -Wl,-z,relro -Wl,-z,now eigensrc/pcatoy.o eigensrc/eigsubs.o eigensrc/eigx.o nicksrc/libnick.a -lgfortran -lrt -lgsl -lblas -fopenmp -lm -llapacke -llapack -pthread -o eigensrc/pcatoy
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/smartrel.o eigensrc/smartrel.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o twsubs.o twsubs.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o qpsubs.o qpsubs.c
qpsubs.c: In function 'doinbreed':
qpsubs.c:2507:3: warning: 'return' with no value, in function returning non-void
return;
^~~~~~
qpsubs.c:2343:1: note: declared here
doinbreed (double *inb, double *inbest, double *inbsig, SNP **xsnplist,
^~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regsubs.o regsubs.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -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 -lgfortran -lrt -lgsl -lblas -fopenmp -lm -llapacke -llapack -pthread -o eigensrc/smartrel
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/smarteigenstrat.o eigensrc/smarteigenstrat.c
eigensrc/smarteigenstrat.c: In function 'readpcafile':
eigensrc/smarteigenstrat.c:355:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fppca, "%d", &K);
^~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/smarteigenstrat.c:363:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fppca, "%lf", &tempdouble); /* eigenvalues */
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/smarteigenstrat.c:367:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fppca, "%lf", &V[NSAMPLES * n + k]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/smarteigenstrat.c:386:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fppca, "%lf", &tempdouble);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -Wl,-z,relro -Wl,-z,now eigensrc/smarteigenstrat.o mcio.o admutils.o nicksrc/libnick.a -lgfortran -lrt -lgsl -lblas -fopenmp -lm -llapacke -llapack -pthread -o eigensrc/smarteigenstrat
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -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 -lgfortran -lrt -lgsl -lblas -fopenmp -lm -llapacke -llapack -pthread -o eigensrc/twstats
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/eigenstrat.o eigensrc/eigenstrat.c
eigensrc/eigenstrat.c: In function 'main':
eigensrc/eigenstrat.c:94:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fp, "%c", &Xchar);
^~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:136:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fppca, "%d", &K);
^~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:144:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fppca, "%lf", &tempdouble); /* eigenvalues */
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:148:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fppca, "%lf", &V[NSAMPLES * n + k]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:167:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fppca, "%lf", &tempdouble);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:184:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fppheno, "%c", &Xchar);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:212:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fppheno, "%c", &Xchar); /* should be end of file */
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:278:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fp, "%c", &Xchar);
^~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:306:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fp, "%c", &Xchar); /* should be \n character */
^~~~~~~~~~~~~~~~~~~~~~~~~
cc -Wl,-z,relro -Wl,-z,now eigensrc/eigenstrat.o -lgfortran -lrt -lgsl -lblas -fopenmp -lm -llapacke -llapack -pthread -o eigensrc/eigenstrat
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/eigenstratQTL.o eigensrc/eigenstratQTL.c
eigensrc/eigenstratQTL.c: In function 'main':
eigensrc/eigenstratQTL.c:94:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fp, "%c", &Xchar);
^~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:136:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fppca, "%d", &K);
^~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:144:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fppca, "%lf", &tempdouble); /* eigenvalues */
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:148:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fppca, "%lf", &V[NSAMPLES * n + k]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:167:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fppca, "%lf", &tempdouble);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:192:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fppheno, "%lf", &iscase[n]); /* QTL phenotype */
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:194:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fppheno, "%lf", &tempdouble); /* to check # entries */
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:257:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fp, "%c", &Xchar);
^~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:285:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf (fp, "%c", &Xchar); /* should be \n character */
^~~~~~~~~~~~~~~~~~~~~~~~~
cc -Wl,-z,relro -Wl,-z,now eigensrc/eigenstratQTL.o -lgfortran -lrt -lgsl -lblas -fopenmp -lm -llapacke -llapack -pthread -o eigensrc/eigenstratQTL
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/smartpca.o eigensrc/smartpca.c
eigensrc/smartpca.c: In function 'main':
eigensrc/smartpca.c:664:7: warning: implicit declaration of function 'setid2pops'; did you mean 'setsdpos'? [-Wimplicit-function-declaration]
setid2pops (id2pops, indivmarkers, numindivs);
^~~~~~~~~~
setsdpos
eigensrc/smartpca.c:825:7: warning: implicit declaration of function 'kjg_fpca' [-Wimplicit-function-declaration]
kjg_fpca (numeigs, fastdim, fastiter, evals, evecs);
^~~~~~~~
eigensrc/smartpca.c:624:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (buff);
^~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gval.o gval.c
gval.c: In function 'setgval':
gval.c:69:7: warning: implicit declaration of function 'getcolxz'; did you mean 'get_ncols'? [-Wimplicit-function-declaration]
getcolxz (cc, cupt, xindex, xtypes, nrows, i, xmean, xfancy, &n0, &n1);
^~~~~~~~
get_ncols
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ksrc/kjg_fpca.o ksrc/kjg_fpca.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-6.1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -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]
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 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 -lgfortran -lrt -lgsl -lblas -fopenmp -lm -llapacke -llapack -pthread -o eigensrc/smartpca
make[2]: Leaving directory '/<<BUILDDIR>>/eigensoft-6.1.4+dfsg/src'
cd src && make install
make[2]: Entering directory '/<<BUILDDIR>>/eigensoft-6.1.4+dfsg/src'
mv baseprog convertf mergeit pca pcaselection eigensrc/pcatoy eigensrc/smartrel eigensrc/smarteigenstrat eigensrc/twstats eigensrc/eigenstrat eigensrc/eigenstratQTL eigensrc/smartpca ../bin
make[2]: Leaving directory '/<<BUILDDIR>>/eigensoft-6.1.4+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/eigensoft-6.1.4+dfsg'
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/eigensoft-6.1.4+dfsg'
dh_install
find debian/eigensoft/usr/share/ -type f -empty -delete
# file consists only from single line with wrong interpreter
find debian/eigensoft/usr/share/ -type f -name HGDP.X.perl -delete
# Fix wrappers and drop *.perl extension in /usr/bin while keeping
# the original name in /usr/lib/debian-med/bin
mkdir -p debian/eigensoft/usr/lib/debian-med/bin
for pl in evec2pca-ped evec2pca smarteigenstrat smartpca ; do \
rm debian/eigensoft/usr/bin/${pl} ; \
sed -i \
-e "s?\(command[[:space:]]*=[[:space:]]*\"\)\(${pl}\)?\1/usr/lib/eigensoft/\2?" \
-e "s?\(cmd[[:space:]]*=[[:space:]]*\"\)\(${pl}\)?\1/usr/lib/eigensoft/\2?" \
-e "s?\(cmd[[:space:]]*=[[:space:]]*\"\)\(evec2pca.*\)\.perl?\1?" \
-e "s?\(${pl}\)\.perl?\1?" \
debian/eigensoft/usr/bin/${pl}.perl ; \
cp -a debian/eigensoft/usr/bin/${pl}.perl debian/eigensoft/usr/bin/${pl} ; \
mv debian/eigensoft/usr/bin/${pl}.perl debian/eigensoft/usr/lib/debian-med/bin ; \
done
rm: cannot remove 'debian/eigensoft/usr/bin/evec2pca-ped': No such file or directory
rm: cannot remove 'debian/eigensoft/usr/bin/evec2pca': No such file or directory
rm debian/eigensoft/usr/bin/gc.perl
make[1]: Leaving directory '/<<BUILDDIR>>/eigensoft-6.1.4+dfsg'
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 '/<<BUILDDIR>>/eigensoft-6.1.4+dfsg'
dh_fixperms
find debian/*/usr/share/eigensoft -type f -name "*.perl" -exec chmod +x \{\} \;
make[1]: Leaving directory '/<<BUILDDIR>>/eigensoft-6.1.4+dfsg'
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/bin/pca debian/eigensoft/usr/bin/pcaselection debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/bin/mergeit debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/eigenstratQTL debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/pcatoy were not linked against libgomp.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/bin/pca debian/eigensoft/usr/bin/pcaselection debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/bin/mergeit debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/eigenstratQTL debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/pcatoy were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/bin/pca debian/eigensoft/usr/bin/pcaselection debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/bin/mergeit debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/eigenstratQTL debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/pcatoy were not linked against librt.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/bin/pca debian/eigensoft/usr/bin/pcaselection debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/bin/mergeit debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/eigenstratQTL debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/pcatoy were not linked against libgfortran.so.4 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/bin/pca debian/eigensoft/usr/bin/pcaselection debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/bin/mergeit debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/eigenstratQTL debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/pcatoy 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
dpkg-deb: building package 'eigensoft' in '../eigensoft_6.1.4+dfsg-1+b2_armhf.deb'.
dpkg-deb: building package 'eigensoft-dbgsym' in '../eigensoft-dbgsym_6.1.4+dfsg-1+b2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../eigensoft_6.1.4+dfsg-1+b2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build eigensoft-6.1.4+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-04-24T11:12:19Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
eigensoft_6.1.4+dfsg-1+b2_armhf.changes:
----------------------------------------
Format: 1.8
Date: Sun, 16 Oct 2016 15:16:45 +0200
Source: eigensoft (6.1.4+dfsg-1)
Binary: eigensoft
Binary-Only: yes
Architecture: armhf
Version: 6.1.4+dfsg-1+b2
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
eigensoft - reduction of population bias for genetic analyses
Changes:
eigensoft (6.1.4+dfsg-1+b2) buster-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
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512efd5f8453d53f32569b7ac2bb24e5aadd6d75 5244 eigensoft_6.1.4+dfsg-1+b2_armhf.buildinfo
b1b31c25ef5ac09df8c482f27087d9b7bd5e82f7 250520 eigensoft_6.1.4+dfsg-1+b2_armhf.deb
Checksums-Sha256:
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dbdbf0d22e314d521831e0618e254235f73237eef36baeb7960823c22ade44b7 5244 eigensoft_6.1.4+dfsg-1+b2_armhf.buildinfo
99da2f9b8424713e3956a291055f15c9893cb7b9fa0c0b0db2ac6dea2d6fc5b7 250520 eigensoft_6.1.4+dfsg-1+b2_armhf.deb
Files:
00cdb1efa1cbc536399c34f7374638da 895472 debug optional eigensoft-dbgsym_6.1.4+dfsg-1+b2_armhf.deb
ffbfb619a448fcd829206d74a4965f06 5244 science optional eigensoft_6.1.4+dfsg-1+b2_armhf.buildinfo
a093c9d7c9c7963a220d27d3fecdc03c 250520 science optional eigensoft_6.1.4+dfsg-1+b2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
eigensoft-dbgsym_6.1.4+dfsg-1+b2_armhf.deb
------------------------------------------
new Debian package, version 2.0.
size 895472 bytes: control archive=1104 bytes.
861 bytes, 12 lines control
1272 bytes, 12 lines md5sums
Package: eigensoft-dbgsym
Source: eigensoft (6.1.4+dfsg-1)
Version: 6.1.4+dfsg-1+b2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1212
Depends: eigensoft (= 6.1.4+dfsg-1+b2)
Section: debug
Priority: optional
Description: debug symbols for eigensoft
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eigensoft_6.1.4+dfsg-1+b2_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 250520 bytes: control archive=3556 bytes.
1207 bytes, 21 lines control
13692 bytes, 167 lines md5sums
Package: eigensoft
Source: eigensoft (6.1.4+dfsg-1)
Version: 6.1.4+dfsg-1+b2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2028
Depends: libblas3 | libblas.so.3, libc6 (>= 2.23), libgfortran4 (>= 7), libgomp1 (>= 4.2.1), libgsl23, liblapack3 | liblapack.so.3, liblapacke, 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.
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 12468
Build-Time: 148
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 300
Job: eigensoft_6.1.4+dfsg-1
Machine Architecture: armhf
Package: eigensoft
Package-Time: 508
Source-Version: 6.1.4+dfsg-1
Space: 12468
Status: successful
Version: 6.1.4+dfsg-1+b2
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Finished at 2018-04-24T11:12:19Z
Build needed 00:08:28, 12468k disc space