eigensoft →
6.1.4+dfsg-1+b1 →
armhf → 2017-08-17 22:20:35
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| eigensoft 6.1.4+dfsg-1+b1 (armhf) Thu, 17 Aug 2017 22:17:25 +0000 |
+==============================================================================+
Package: eigensoft
Version: 6.1.4+dfsg-1+b1
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-a3a231f0-ff24-4fef-a727-6e9c863fb470' 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 [10.1 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.0 MB]
Fetched 22.0 MB in 8s (2693 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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 (529 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/eigensoft-pxOoAs/eigensoft-6.1.4+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/eigensoft-pxOoAs' 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-uRjzKB/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-uRjzKB/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-uRjzKB/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-uRjzKB/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-uRjzKB/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-uRjzKB/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-uRjzKB/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-uRjzKB/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (5663 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
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 libssl1.1 openssl
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 35 not upgraded.
Need to get 776 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-uRjzKB/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 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 ... 14837 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
+------------------------------------------------------------------------------+
| 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-uRjzKB/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-uRjzKB/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-uRjzKB/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-uRjzKB/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-uRjzKB/apt_archive ./ Sources [518 B]
Get:5 copy:/<<BUILDDIR>>/resolver-uRjzKB/apt_archive ./ Packages [599 B]
Fetched 2450 B in 0s (5711 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
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 libssl1.1 openssl
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-6 groff-base intltool-debian libarchive-zip-perl libblas-common
libblas-dev libblas3 libbsd0 libcroco3 libfile-stripnondeterminism-perl
libgfortran-6-dev libgfortran3 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 gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc
gfortran-6-doc libgfortran3-dbg libcoarrays-dev groff liblapack-doc
gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libtool-doc
gcj-jdk m4-doc less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev xml-core 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-6 groff-base intltool-debian libarchive-zip-perl libblas-common
libblas-dev libblas3 libbsd0 libcroco3 libfile-stripnondeterminism-perl
libgfortran-6-dev libgfortran3 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, 46 newly installed, 0 to remove and 35 not upgraded.
Need to get 30.0 MB of archives.
After this operation, 113 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-uRjzKB/apt_archive ./ sbuild-build-depends-eigensoft-dummy 0.invalid.0 [808 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-1 [95.7 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.31-1 [223 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.31-1 [105 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.31-1 [63.5 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-2+b1 [117 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-3 [601 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-2 [736 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-2 [433 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.038-1 [17.6 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.038-1 [11.1 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.53.4-3 [2628 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-2+b1 [1220 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.7.2 [975 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libgfortran3 armhf 6.4.0-1+rpi1 [166 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libgfortran-6-dev armhf 6.4.0-1+rpi1 [199 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf gfortran-6 armhf 6.4.0-1+rpi1 [5420 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:6.3.0-4d1 [1358 B]
Get:35 http://172.17.0.1/private buster-staging/main armhf libblas-common armhf 3.7.1-1 [14.6 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.7.1-1 [108 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.7.1-1 [118 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libgslcblas0 armhf 2.4+dfsg-6 [75.1 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libgsl23 armhf 2.4+dfsg-6 [681 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libgsl-dev armhf 2.4+dfsg-6 [863 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.7.1-1 [1503 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.7.1-1 [1561 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libtmglib3 armhf 3.7.1-1 [89.6 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf liblapacke armhf 3.7.1-1 [275 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libtmglib-dev armhf 3.7.1-1 [93.0 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf liblapacke-dev armhf 3.7.1-1 [258 kB]
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Unpacking sbuild-build-depends-eigensoft-dummy (0.invalid.0) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.11-1) ...
Setting up libblas-common (3.7.1-1) ...
Setting up libgfortran3:armhf (6.4.0-1+rpi1) ...
Setting up groff-base (1.22.3-9) ...
Setting up libglib2.0-0:armhf (2.53.4-3) ...
No schema files found: doing nothing.
Setting up libgfortran-6-dev:armhf (6.4.0-1+rpi1) ...
Setting up gettext-base (0.19.8.1-2+b1) ...
Setting up libpipeline1:armhf (1.4.2-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-6) ...
Setting up libbsd0:armhf (0.8.6-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-3) ...
Setting up libmagic-mgc (1:5.31-1) ...
Setting up libmagic1:armhf (1:5.31-1) ...
Setting up libcroco3:armhf (0.6.12-1) ...
Setting up libblas3 (3.7.1-1) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Processing triggers for libc-bin (2.24-12) ...
Setting up autotools-dev (20161112.1) ...
Setting up bsdmainutils (9.0.12+nmu1) ...
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 (0.19.8.1-2) ...
Setting up libfile-stripnondeterminism-perl (0.038-1) ...
Setting up gfortran-6 (6.4.0-1+rpi1) ...
Setting up libgsl23:armhf (2.4+dfsg-6) ...
Setting up gettext (0.19.8.1-2+b1) ...
Setting up libgsl-dev (2.4+dfsg-6) ...
Setting up liblapack3 (3.7.1-1) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up autoconf (2.69-10) ...
Setting up file (1:5.31-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.15.1-2) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2) ...
Setting up gfortran (4:6.3.0-4d1) ...
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 libtmglib3 (3.7.1-1) ...
Setting up po-debconf (1.0.20) ...
Setting up libblas-dev (3.7.1-1) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
Setting up liblapacke (3.7.1-1) ...
Setting up liblapack-dev (3.7.1-1) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up libtmglib-dev (3.7.1-1) ...
Setting up liblapacke-dev (3.7.1-1) ...
Setting up dh-autoreconf (14) ...
Setting up dh-strip-nondeterminism (0.038-1) ...
Setting up debhelper (10.7.2) ...
Setting up sbuild-build-depends-eigensoft-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-12) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.28-6 dpkg-dev_1.18.24 g++-6_6.4.0-1+rpi1 gcc-6_6.4.0-1+rpi1 libc6-dev_2.24-12 libstdc++-6-dev_6.4.0-1+rpi1 libstdc++6_7.1.0-9+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.5~beta1+b3 autoconf_2.69-10 automake_1:1.15.1-2 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_10+rpi1 base-passwd_3.5.43 bash_4.4-5 binutils_2.28-6 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-2+rpi1 build-essential_12.3 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:6.3.0-4d1 cpp-6_6.4.0-1+rpi1 dash_0.5.8-2.5 debconf_1.5.63 debhelper_10.7.2 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-3.1 file_1:5.31-1 findutils_4.6.0+git+20170606-3 g++_4:6.3.0-4d1 g++-6_6.4.0-1+rpi1 gcc_4:6.3.0-4d1 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_4.9.3-14 gcc-5-base_5.4.1-4 gcc-6_6.4.0-1+rpi1 gcc-6-base_6.4.0-1+rpi1 gcc-7-base_7.1.0-9+rpi1 gettext_0.19.8.1-2+b1 gettext-base_0.19.8.1-2+b1 gfortran_4:6.3.0-4d1 gfortran-6_6.4.0-1+rpi1 gnupg_2.1.18-8 gnupg-agent_2.1.18-8 gpgv_2.1.18-8 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init-system-helpers_1.49 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.0-6 libapt-pkg5.0_1.5~beta1+b3 libarchive-zip-perl_1.59-1 libasan3_6.4.0-1+rpi1 libassuan0_2.4.3-2 libatomic1_7.1.0-9+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1 libblas-common_3.7.1-1 libblas-dev_3.7.1-1 libblas3_3.7.1-1 libblkid1_2.29.2-2+rpi1 libbsd0_0.8.6-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12 libc-dev-bin_2.24-12 libc6_2.24-12 libc6-dev_2.24-12 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.1.0-9+rpi1 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.3-4 libdb5.3_5.3.28-12 libdbus-1-3_1.10.20-1 libdebconfclient0_0.229 libdevmapper1.02.1_2:1.02.137-2 libdpkg-perl_1.18.24 libdrm2_2.4.81-2+rpi1 libfakeroot_1.21-3.1 libfdisk1_2.29.2-2+rpi1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgcc-6-dev_6.4.0-1+rpi1 libgcc1_1:7.1.0-9+rpi1 libgcrypt20_1.7.8-2 libgdbm3_1.8.3-14 libgfortran-6-dev_6.4.0-1+rpi1 libgfortran3_6.4.0-1+rpi1 libglib2.0-0_2.53.4-3 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.14-2 libgomp1_7.1.0-9+rpi1 libgpg-error0_1.27-3 libgsl-dev_2.4+dfsg-6 libgsl23_2.4+dfsg-6 libgslcblas0_2.4+dfsg-6 libhogweed4_3.3-1 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_2.0.2-1 libip4tc0_1.6.1-2 libisl15_0.18-1 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libksba8_1.3.5-2 liblapack-dev_3.7.1-1 liblapack3_3.7.1-1 liblapacke_3.7.1-1 liblapacke-dev_3.7.1-1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.31-1 libmagic1_1:5.31-1 libmount1_2.29.2-2+rpi1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20170715-2 libncursesw5_6.0+20170715-2 libnettle6_3.3-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-3 libperl5.24_5.24.1-7 libperl5.26_5.26.0-4 libpipeline1_1.4.2-1 libplymouth4_0.9.2-4 libpng16-16_1.6.30-2 libprocps6_2:3.3.12-3 libreadline5_5.2+dfsg-3 libreadline7_7.0-3 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.11-1 libsmartcols1_2.29.2-2+rpi1 libsqlite3-0_3.19.3-3 libss2_1.43.4-2 libssl1.1_1.1.0f-3 libstdc++-6-dev_6.4.0-1+rpi1 libstdc++6_7.1.0-9+rpi1 libsystemd0_233-10 libtasn1-6_4.12-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170715-2 libtmglib-dev_3.7.1-1 libtmglib3_3.7.1-1 libtool_2.4.6-2 libubsan0_7.1.0-9+rpi1 libudev1_233-10 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-2+rpi1 libxml2_2.9.4+dfsg1-3 linux-base_4.5 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-4.1 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mount_2.29.2-2+rpi1 mountall_2.54 multiarch-support_2.24-12 ncurses-base_6.0+20170715-2 ncurses-bin_6.0+20170715-2 openssl_1.1.0f-3 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.26.0-4 perl-base_5.26.0-4 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.0-4 pinentry-curses_1.0.0-2 plymouth_0.9.2-4 po-debconf_1.0.20 procps_2:3.3.12-3 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_4.4-1 sensible-utils_0.0.9+nmu1 systemd_233-10 sysvinit-utils_2.88dsf-59.9 tar_1.29b-2 tzdata_2017b-2 udev_233-10 util-linux_2.29.2-2+rpi1 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 disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 6.1.4+dfsg-1+b1
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=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-a3a231f0-ff24-4fef-a727-6e9c863fb470
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package eigensoft
dpkg-buildpackage: info: source version 6.1.4+dfsg-1+b1
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
dh_auto_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
dh_auto_configure -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);
^~~~~~~~~~~~
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' [-Wimplicit-function-declaration]
setid2pops (id2pops, indivmarkers, numindivs);
^~~~~~~~~~
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' [-Wimplicit-function-declaration]
getcolxz (cc, cupt, xindex, xtypes, nrows, i, xmean, xfancy, &n0, &n1);
^~~~~~~~
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'
dh_auto_test -a
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -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/bin/eigenstratQTL debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/bin/pca debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/pcatoy debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/bin/pcaselection debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/mergeit 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/bin/eigenstratQTL debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/bin/pca debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/pcatoy debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/bin/pcaselection debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/mergeit were not linked against libblas.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/eigensoft/usr/bin/eigenstratQTL debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/bin/pca debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/pcatoy debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/bin/pcaselection debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/mergeit were not linked against libgfortran.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/eigensoft/usr/bin/eigenstratQTL debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/bin/pca debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/pcatoy debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/bin/pcaselection debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/mergeit 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/bin/eigenstratQTL debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/bin/pca debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/pcatoy debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/bin/pcaselection debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/mergeit were not linked against librt.so.1 (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-dbgsym' in '../eigensoft-dbgsym_6.1.4+dfsg-1+b1_armhf.deb'.
dpkg-deb: building package 'eigensoft' in '../eigensoft_6.1.4+dfsg-1+b1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../eigensoft_6.1.4+dfsg-1+b1_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 2017-08-17T22:20:32Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
eigensoft_6.1.4+dfsg-1+b1_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+b1
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
eigensoft - reduction of population bias for genetic analyses
Changes:
eigensoft (6.1.4+dfsg-1+b1) 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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c61303d597b1a4524c8a5ec9711f46c87342d8c6 251146 eigensoft_6.1.4+dfsg-1+b1_armhf.deb
fd49dac23259b15f03ee23b5956671806a89c31b 5227 eigensoft_6.1.4+dfsg-1_armhf.buildinfo
Checksums-Sha256:
711aea889ef91180dce2315ec34509f68fbfb05f884ef5bd81c0dbb651cafeb0 933100 eigensoft-dbgsym_6.1.4+dfsg-1+b1_armhf.deb
c274fd1321879dd44c0061dca03c05d0043d4408c221c0d356ee7ceda73288be 251146 eigensoft_6.1.4+dfsg-1+b1_armhf.deb
d8a66be33f17d70436dae21777d19a8b59611715e7aefb38e77a5d5779490433 5227 eigensoft_6.1.4+dfsg-1_armhf.buildinfo
Files:
faec7feb89a1e379fb379d0240b4a53e 933100 debug extra eigensoft-dbgsym_6.1.4+dfsg-1+b1_armhf.deb
b8c1298d228a0d187e51d2444be62530 251146 science optional eigensoft_6.1.4+dfsg-1+b1_armhf.deb
734e642f21deb6a3e1fc3900e78a22c6 5227 science optional eigensoft_6.1.4+dfsg-1_armhf.buildinfo
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
eigensoft-dbgsym_6.1.4+dfsg-1+b1_armhf.deb
------------------------------------------
new debian package, version 2.0.
size 933100 bytes: control archive=1067 bytes.
858 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+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1252
Depends: eigensoft (= 6.1.4+dfsg-1+b1)
Section: debug
Priority: extra
Description: Debug symbols for eigensoft
Build-Ids: 25189dc1d75c189e9a0c4dd589a793e6fc1965b5 2a0228773fca55e34b89a51704c5c77d503b1237 31cb952adf66e5069b5998ca3e208be81e5fc023 44defe67c3879ec5dcb2e652ee08d3e40ee97d1e 608fc9a09b5b5fc9ee173b83bfda657d556af16c 6f1bf75ccd9f9c859c8b1405ab8138613d14fc56 864d0ce46277b499f7c837680913d72c66d1f1dc 9db16e8bef894fad0cee79501eca54e57d455612 aa8b6fcb24457c05f0f226b45dd77356010b6c6a cc1702ce4ac3dc5f60bf61c572d6928f8dd713ec dffaf0ec443fe8efd25347fb658333344587f091 e16285b7df033eb4d2a4f9bf059d6d6d7285148e
drwxr-xr-x root/root 0 2016-10-16 13:16 ./
drwxr-xr-x root/root 0 2016-10-16 13:16 ./usr/
drwxr-xr-x root/root 0 2016-10-16 13:16 ./usr/lib/
drwxr-xr-x root/root 0 2016-10-16 13:16 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-10-16 13:16 ./usr/lib/debug/.build-id/
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eigensoft_6.1.4+dfsg-1+b1_armhf.deb
-----------------------------------
new debian package, version 2.0.
size 251146 bytes: control archive=3782 bytes.
1209 bytes, 21 lines control
13692 bytes, 167 lines md5sums
Package: eigensoft
Source: eigensoft (6.1.4+dfsg-1)
Version: 6.1.4+dfsg-1+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2041
Depends: libblas3 | libblas.so.3, libc6 (>= 2.23), libgfortran3 (>= 4.3), 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: 12976
Build-Time: 60
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 111
Job: eigensoft_6.1.4+dfsg-1
Machine Architecture: armhf
Package: eigensoft
Package-Time: 187
Source-Version: 6.1.4+dfsg-1
Space: 12976
Status: successful
Version: 6.1.4+dfsg-1+b1
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Finished at 2017-08-17T22:20:32Z
Build needed 00:03:07, 12976k disk space