eigensoft →
6.1.4+dfsg-1 →
armhf → 2016-10-22 11:39:52
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd.raspbian.org
+==============================================================================+
| eigensoft 6.1.4+dfsg-1 (armhf) Sat, 22 Oct 2016 11:27:37 +0000 |
+==============================================================================+
Package: eigensoft
Version: 6.1.4+dfsg-1
Source Version: 6.1.4+dfsg-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-a1503b6d-c661-4980-b405-4ac5a34dde19' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9375 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.3 MB]
Fetched 20.7 MB in 25s (818 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 stretch-staging/main eigensoft 6.1.4+dfsg-1 (dsc) [2113 B]
Get:2 http://172.17.0.1/private stretch-staging/main eigensoft 6.1.4+dfsg-1 (tar) [158 kB]
Get:3 http://172.17.0.1/private stretch-staging/main eigensoft 6.1.4+dfsg-1 (diff) [5916 B]
Fetched 166 kB in 0s (850 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/eigensoft-kzqb8C/eigensoft-6.1.4+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/eigensoft-kzqb8C' 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-CtRFJC/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-CtRFJC/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-CtRFJC/gpg/trustdb.gpg: trustdb created
gpg: key 5FBC947B34E39F26: 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 5FBC947B34E39F26: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 5FBC947B34E39F26: 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-CtRFJC/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-CtRFJC/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-CtRFJC/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-CtRFJC/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-CtRFJC/apt_archive ./ Packages [432 B]
Fetched 2080 B in 0s (3482 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:
dirmngr fuse2fs gnupg-l10n libffi6 libfuse2 libgnutls30 libhogweed4
libldap-2.4-2 libnettle6 libp11-kit0 libsasl2-2 libsasl2-modules
libsasl2-modules-db libssl1.0.2 libtasn1-6 manpages
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 19 not upgraded.
Need to get 768 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-CtRFJC/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 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 ... 13148 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-CtRFJC/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-CtRFJC/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-CtRFJC/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-CtRFJC/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-CtRFJC/apt_archive ./ Sources [518 B]
Get:5 copy:/<<BUILDDIR>>/resolver-CtRFJC/apt_archive ./ Packages [599 B]
Fetched 2422 B in 0s (3994 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:
dirmngr fuse2fs gnupg-l10n libfuse2 libgnutls30 libhogweed4 libldap-2.4-2
libnettle6 libp11-kit0 libsasl2-2 libsasl2-modules libsasl2-modules-db
libssl1.0.2 libtasn1-6 manpages
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 libgsl2 libicu57
liblapack-dev liblapack3 liblapacke liblapacke-dev libmagic-mgc libmagic1
libpipeline1 libsigsegv2 libtimedate-perl libtmglib-dev libtmglib3 libtool
libunistring0 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-man
liblapack-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html
libtool-doc gcj-jdk less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur 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 libgsl2 libicu57
liblapack-dev liblapack3 liblapacke liblapacke-dev libmagic-mgc libmagic1
libpipeline1 libsigsegv2 libtimedate-perl libtmglib-dev libtmglib3 libtool
libunistring0 libxml2 m4 man-db po-debconf
sbuild-build-depends-eigensoft-dummy
0 upgraded, 46 newly installed, 0 to remove and 19 not upgraded.
Need to get 30.0 MB of archives.
After this operation, 111 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-CtRFJC/apt_archive ./ sbuild-build-depends-eigensoft-dummy 0.invalid.0 [800 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.11 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.28-4 [210 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-4 [104 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-4 [62.7 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-4 [7407 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2 [805 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.0-2+rpi1 [2523 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.2 [826 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.2.0-6+rpi1 [165 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libgfortran-6-dev armhf 6.2.0-6+rpi1 [199 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf gfortran-6 armhf 6.2.0-6+rpi1 [5405 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf gfortran armhf 4:6.1.1-1 [1370 B]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libblas-common armhf 3.6.1-2 [13.9 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.6.1-2 [112 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libblas-dev armhf 3.6.1-2 [18.9 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libgsl2 armhf 2.2.1+dfsg-1 [717 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libgsl-dev armhf 2.2.1+dfsg-1 [843 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf liblapack3 armhf 3.6.1-2 [1392 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf liblapack-dev armhf 3.6.1-2 [1379 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libtmglib3 armhf 3.6.1-2 [90.3 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf liblapacke armhf 3.6.1-2 [261 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libtmglib-dev armhf 3.6.1-2 [91.7 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf liblapacke-dev armhf 3.6.1-2 [235 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking liblapacke-dev (3.6.1-2) ...
Selecting previously unselected package sbuild-build-depends-eigensoft-dummy.
Preparing to unpack .../45-sbuild-build-depends-eigensoft-dummy_0.invalid.0_armhf.deb ...
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 (2.10-5) ...
Setting up libblas-common (3.6.1-2) ...
Setting up libgfortran3:armhf (6.2.0-6+rpi1) ...
Setting up groff-base (1.22.3-8) ...
Setting up libglib2.0-0:armhf (2.50.0-2+rpi1) ...
No schema files found: doing nothing.
Setting up libgfortran-6-dev:armhf (6.2.0-6+rpi1) ...
Setting up gettext-base (0.19.8.1-1) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up libgsl2:armhf (2.2.1+dfsg-1) ...
Setting up m4 (1.4.17-5) ...
Setting up libicu57:armhf (57.1-4) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2) ...
Setting up libmagic-mgc (1:5.28-4) ...
Setting up libmagic1:armhf (1:5.28-4) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Setting up libblas3 (3.6.1-2) ...
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 (2.24-3) ...
Setting up autotools-dev (20160430.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up bsdmainutils (9.0.11) ...
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 autopoint (0.19.8.1-1) ...
Setting up libfile-stripnondeterminism-perl (0.028-1) ...
Setting up gfortran-6 (6.2.0-6+rpi1) ...
Setting up gettext (0.19.8.1-1) ...
Setting up libgsl-dev (2.2.1+dfsg-1) ...
Setting up liblapack3 (3.6.1-2) ...
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 (1:5.28-4) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2) ...
Setting up gfortran (4:6.1.1-1) ...
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 (3.6.1-2) ...
Setting up po-debconf (1.0.20) ...
Setting up libblas-dev (3.6.1-2) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
Setting up liblapacke (3.6.1-2) ...
Setting up liblapack-dev (3.6.1-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up libtmglib-dev (3.6.1-2) ...
Setting up liblapacke-dev (3.6.1-2) ...
Setting up dh-autoreconf (12) ...
Setting up dh-strip-nondeterminism (0.028-1) ...
Setting up debhelper (10.2.2) ...
Setting up sbuild-build-depends-eigensoft-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-3) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.27-8 dpkg-dev_1.18.10 g++-6_6.2.0-6+rpi1 gcc-6_6.2.0-6+rpi1 libc6-dev_2.24-3 libstdc++-6-dev_6.2.0-6+rpi1 libstdc++6_6.2.0-6+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3.1 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.40 bash_4.4-1 binutils_2.27-8 bsdmainutils_9.0.11 bsdutils_1:2.28.2-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.2.0-6+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.2 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dirmngr_2.1.15-3 dmsetup_2:1.02.133-1 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.28-4 findutils_4.6.0+git+20160703-2 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.2.0-6+rpi1 gcc_4:6.1.1-1 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-6_6.2.0-6+rpi1 gcc-6-base_6.2.0-6+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gfortran_4:6.1.1-1 gfortran-6_6.2.0-6+rpi1 gnupg_2.1.15-3 gnupg-agent_2.1.15-3 gnupg-l10n_2.1.15-3 gpgv_2.1.15-3 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 hostname_3.18 init_1.45 init-system-helpers_1.45 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10.95-4+b1 libapt-pkg5.0_1.3.1 libarchive-zip-perl_1.59-1 libasan3_6.2.0-6+rpi1 libassuan0_2.4.3-1 libatomic1_6.2.0-6+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblas-common_3.6.1-2 libblas-dev_3.6.1-2 libblas3_3.6.1-2 libblkid1_2.28.2-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-3 libc-dev-bin_2.24-3 libc6_2.24-3 libc6-dev_2.24-3 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.2.0-6+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-12 libdbus-1-3_1.10.10-1 libdebconfclient0_0.217 libdevmapper1.02.1_2:1.02.133-1 libdpkg-perl_1.18.10 libdrm2_2.4.71-1 libfakeroot_1.21-2 libfdisk1_2.28.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.2.0-6+rpi1 libgcc1_1:6.2.0-6+rpi1 libgcrypt20_1.7.3-1 libgdbm3_1.8.3-14 libgfortran-6-dev_6.2.0-6+rpi1 libgfortran3_6.2.0-6+rpi1 libglib2.0-0_2.50.0-2+rpi1 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.4-2 libgomp1_6.2.0-6+rpi1 libgpg-error0_1.24-1 libgsl-dev_2.2.1+dfsg-1 libgsl2_2.2.1+dfsg-1 libhogweed4_3.2-1 libicu57_57.1-4 libidn11_1.33-1 libip4tc0_1.6.0-3 libisl15_0.17.1-1 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 libksba8_1.3.5-2 liblapack-dev_3.6.1-2 liblapack3_3.6.1-2 liblapacke_3.6.1-2 liblapacke-dev_3.6.1-2 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b3 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmount1_2.28.2-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnettle6_3.2-1 libnpth0_1.2-3 libp11-kit0_0.23.2-5 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpcre3_2:8.39-2 libperl5.24_5.24.1~rc3-3 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libprocps6_2:3.3.12-2 libreadline6_6.3-9 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28.2-1 libsqlite3-0_3.14.2-1 libss2_1.43.3-1 libssl1.0.2_1.0.2j-1 libstdc++-6-dev_6.2.0-6+rpi1 libstdc++6_6.2.0-6+rpi1 libsystemd0_231-9 libtasn1-6_4.9-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtmglib-dev_3.6.1-2 libtmglib3_3.6.1-2 libtool_2.4.6-2 libubsan0_6.2.0-6+rpi1 libudev1_231-9 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28.2-1 libxml2_2.9.4+dfsg1-2 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.2 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.07-1 mawk_1.3.3-17 mount_2.28.2-1 multiarch-support_2.24-3 nano_2.7.0-1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 passwd_1:4.2-3.2 patch_2.7.5-1 perl_5.24.1~rc3-3 perl-base_5.24.1~rc3-3 perl-modules-5.24_5.24.1~rc3-3 pinentry-curses_0.9.7-5 po-debconf_1.0.20 procps_2:3.3.12-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-eigensoft-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_231-9 systemd-sysv_231-9 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016g-1 udev_231-9 util-linux_2.28.2-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| 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
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=111
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-a1503b6d-c661-4980-b405-4ac5a34dde19
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package eigensoft
dpkg-buildpackage: info: source version 6.1.4+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build eigensoft-6.1.4+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
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_testdir -a
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_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/eigensoft/usr/bin/pca debian/eigensoft/usr/bin/pcatoy debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/mergeit debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/bin/pcaselection debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/eigenstratQTL 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/pca debian/eigensoft/usr/bin/pcatoy debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/mergeit debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/bin/pcaselection debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/eigenstratQTL 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/pca debian/eigensoft/usr/bin/pcatoy debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/mergeit debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/bin/pcaselection debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/eigenstratQTL 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/bin/pca debian/eigensoft/usr/bin/pcatoy debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/mergeit debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/bin/pcaselection debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/eigenstratQTL 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/pca debian/eigensoft/usr/bin/pcatoy debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/mergeit debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/bin/pcaselection debian/eigensoft/usr/bin/baseprog debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/bin/eigenstratQTL were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'eigensoft-dbgsym' in '../eigensoft-dbgsym_6.1.4+dfsg-1_armhf.deb'.
dpkg-deb: building package 'eigensoft' in '../eigensoft_6.1.4+dfsg-1_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian nitrogen6x test autobuilder <root@raspbian.org> >../eigensoft_6.1.4+dfsg-1_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 2016-10-22T11:35:34Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
eigensoft_6.1.4+dfsg-1_armhf.changes:
-------------------------------------
Format: 1.8
Date: Sun, 16 Oct 2016 15:16:45 +0200
Source: eigensoft
Binary: eigensoft
Architecture: armhf
Version: 6.1.4+dfsg-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian nitrogen6x test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
eigensoft - reduction of population bias for genetic analyses
Changes:
eigensoft (6.1.4+dfsg-1) unstable; urgency=medium
.
* New upstream version
* fix perl interpreter path
Checksums-Sha1:
322f8f1e85f1f11b2d8faa0f5f0955f9437764d4 925974 eigensoft-dbgsym_6.1.4+dfsg-1_armhf.deb
a01a1c0a1b6d97f50fd2ad223fc1fc6f2214c1e5 250608 eigensoft_6.1.4+dfsg-1_armhf.deb
Checksums-Sha256:
8191f32d6500026c4b39a1813a8d51ba659b953ab44f7dd8b278d9b1d045314c 925974 eigensoft-dbgsym_6.1.4+dfsg-1_armhf.deb
23b2b65592364dd7ac63bbcd28abfa4862a71fa62f254a738d6766ff3689bc74 250608 eigensoft_6.1.4+dfsg-1_armhf.deb
Files:
b008631db057358bbe2c98f6bcfad156 925974 debug extra eigensoft-dbgsym_6.1.4+dfsg-1_armhf.deb
f8983beb7fd26ce71a7cbd1b6b3349e4 250608 science optional eigensoft_6.1.4+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
eigensoft-dbgsym_6.1.4+dfsg-1_armhf.deb
---------------------------------------
new debian package, version 2.0.
size 925974 bytes: control archive=1110 bytes.
905 bytes, 13 lines control
1272 bytes, 12 lines md5sums
Package: eigensoft-dbgsym
Source: eigensoft
Version: 6.1.4+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1251
Depends: eigensoft (= 6.1.4+dfsg-1)
Section: debug
Priority: extra
Homepage: http://www.hsph.harvard.edu/faculty/alkes-price/software/
Description: Debug symbols for eigensoft
Auto-Built-Package: debug-symbols
Build-Ids: 01902ef5df296f183d8939cbef63e9a367359b49 10362dc79039f87edb94bec50bbe177390bcdc79 11df9831068144957b71eaedf0c484205b85632c 39292870de71f4c0ab0ce7f182cbf1bb57fadf45 3a0e1e718f67e843fd525e7dfa54fafa6d67aa7b 486ba31c8c2025cd9d477d313a75774d8c695da8 4e9ccc2fd1895dcc3fe81950e0b1331a5798ab1c 66e1dcde3d2c6827daf6d2769480a0b35b439f39 7d70622128251583032697cbeecf81dfec1637e6 99b0eff4f0db287ba8c9eb8d3107f3386c2ea91f e8f7aa4c3d89a494397b045ad761dfba27e79a17 f1119c49207994f2a4112f403c42ad03de298b46
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/
drwxr-xr-x root/root 0 2016-10-16 13:16 ./usr/lib/debug/.build-id/01/
-rw-r--r-- root/root 141408 2016-10-16 13:16 ./usr/lib/debug/.build-id/01/902ef5df296f183d8939cbef63e9a367359b49.debug
drwxr-xr-x root/root 0 2016-10-16 13:16 ./usr/lib/debug/.build-id/10/
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eigensoft_6.1.4+dfsg-1_armhf.deb
--------------------------------
new debian package, version 2.0.
size 250608 bytes: control archive=3739 bytes.
1172 bytes, 20 lines control
13608 bytes, 166 lines md5sums
Package: eigensoft
Version: 6.1.4+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2035
Depends: libblas3 | libblas.so.3, libc6 (>= 2.23), libgfortran3 (>= 4.3), libgomp1 (>= 4.2.1), libgsl2, 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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drwxr-xr-x root/root 0 2016-10-16 13:16 ./usr/share/man/
drwxr-xr-x root/root 0 2016-10-16 13:16 ./usr/share/man/man1/
-rw-r--r-- root/root 884 2016-10-16 13:16 ./usr/share/man/man1/smarteigenstrat.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 12656
Build-Time: 160
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 264
Job: eigensoft_6.1.4+dfsg-1
Machine Architecture: armhf
Package: eigensoft
Package-Time: 477
Source-Version: 6.1.4+dfsg-1
Space: 12656
Status: successful
Version: 6.1.4+dfsg-1
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Finished at 2016-10-22T11:35:34Z
Build needed 00:07:57, 12656k disc space