eigensoft →
7.2.1+dfsg-2 →
armhf → 2020-07-25 11:28:30
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| eigensoft 7.2.1+dfsg-2 (armhf) Sat, 25 Jul 2020 11:18:03 +0000 |
+==============================================================================+
Package: eigensoft
Version: 7.2.1+dfsg-2
Source Version: 7.2.1+dfsg-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-0ca5254f-d6d0-4b37-b3c9-fc0d5b897d9c' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.8 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.7 MB in 27s (924 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://salsa.debian.org/med-team/eigensoft.git
Please use:
git clone https://salsa.debian.org/med-team/eigensoft.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 178 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main eigensoft 7.2.1+dfsg-2 (dsc) [2132 B]
Get:2 http://172.17.0.1/private bullseye-staging/main eigensoft 7.2.1+dfsg-2 (tar) [170 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main eigensoft 7.2.1+dfsg-2 (diff) [6020 B]
Fetched 178 kB in 1s (280 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/eigensoft-OrsYfR/eigensoft-7.2.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/eigensoft-OrsYfR' 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-nyXPQb/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-nyXPQb/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-nyXPQb/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-nyXPQb/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-nyXPQb/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-nyXPQb/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-nyXPQb/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-nyXPQb/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2816 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:
bsdextrautils libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 28 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-nyXPQb/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (19.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12307 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-compat (= 13), gfortran, libblas-dev, liblapack-dev, liblapacke-dev, libgsl-dev
Filtered Build-Depends: debhelper-compat (= 13), gfortran, libblas-dev, liblapack-dev, liblapacke-dev, libgsl-dev
dpkg-deb: building package 'sbuild-build-depends-eigensoft-dummy' in '/<<BUILDDIR>>/resolver-nyXPQb/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-nyXPQb/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-nyXPQb/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-nyXPQb/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-nyXPQb/apt_archive ./ Sources [525 B]
Get:5 copy:/<<BUILDDIR>>/resolver-nyXPQb/apt_archive ./ Packages [603 B]
Fetched 2461 B in 1s (3280 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:
dmsetup libargon2-1 libcryptsetup12 libdevmapper1.02.1 libjson-c4 libpam-cap
libssl1.1 netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-9
groff-base intltool-debian libarchive-zip-perl libblas-dev libblas3
libcroco3 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl
libgfortran-9-dev libgfortran5 libglib2.0-0 libgsl-dev libgsl25 libgslcblas0
libicu67 liblapack-dev liblapack3 liblapacke liblapacke-dev libmagic-mgc
libmagic1 libmount1 libpipeline1 libsigsegv2 libsub-override-perl
libtmglib-dev libtmglib3 libtool libuchardet0 libxml2 m4 man-db po-debconf
sensible-utils
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev gfortran-doc gfortran-9-doc libcoarrays-dev
groff liblapack-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info
| gsl-ref-html libtool-doc gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-9
groff-base intltool-debian libarchive-zip-perl libblas-dev libblas3
libcroco3 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl
libgfortran-9-dev libgfortran5 libglib2.0-0 libgsl-dev libgsl25 libgslcblas0
libicu67 liblapack-dev liblapack3 liblapacke liblapacke-dev libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtmglib-dev
libtmglib3 libtool libuchardet0 libxml2 m4 man-db po-debconf
sbuild-build-depends-eigensoft-dummy sensible-utils
The following packages will be upgraded:
libmount1
1 upgraded, 48 newly installed, 0 to remove and 27 not upgraded.
Need to get 34.6 MB of archives.
After this operation, 134 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-nyXPQb/apt_archive ./ sbuild-build-depends-eigensoft-dummy 0.invalid.0 [888 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libmount1 armhf 2.35.2-7 [190 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-3 [801 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2 [187 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.4-1 [1159 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-3 [8287 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5+b1 [593 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2 [1007 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.1.0-4+rpi1 [231 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-9-dev armhf 9.3.0-14+rpi1 [278 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf gfortran-9 armhf 9.3.0-14+rpi1 [8112 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:9.2.1-3.1+rpi1 [1440 B]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-2 [108 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-2 [113 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libgslcblas0 armhf 2.6+dfsg-2 [79.5 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libgsl25 armhf 2.6+dfsg-2 [753 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libgsl-dev armhf 2.6+dfsg-2 [950 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-2 [1602 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-2 [2981 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libtmglib3 armhf 3.9.0-2 [96.7 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf liblapacke armhf 3.9.0-2 [290 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libtmglib-dev armhf 3.9.0-2 [96.8 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf liblapacke-dev armhf 3.9.0-2 [260 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking liblapack3:armhf (3.9.0-2) ...
Selecting previously unselected package liblapack-dev:armhf.
Preparing to unpack .../38-liblapack-dev_3.9.0-2_armhf.deb ...
Unpacking liblapack-dev:armhf (3.9.0-2) ...
Selecting previously unselected package libtmglib3:armhf.
Preparing to unpack .../39-libtmglib3_3.9.0-2_armhf.deb ...
Unpacking libtmglib3:armhf (3.9.0-2) ...
Selecting previously unselected package liblapacke:armhf.
Preparing to unpack .../40-liblapacke_3.9.0-2_armhf.deb ...
Unpacking liblapacke:armhf (3.9.0-2) ...
Selecting previously unselected package libtmglib-dev:armhf.
Preparing to unpack .../41-libtmglib-dev_3.9.0-2_armhf.deb ...
Unpacking libtmglib-dev:armhf (3.9.0-2) ...
Selecting previously unselected package liblapacke-dev:armhf.
Preparing to unpack .../42-liblapacke-dev_3.9.0-2_armhf.deb ...
Unpacking liblapacke-dev:armhf (3.9.0-2) ...
Selecting previously unselected package sbuild-build-depends-eigensoft-dummy.
Preparing to unpack .../43-sbuild-build-depends-eigensoft-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-eigensoft-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.2-2) ...
Setting up libicu67:armhf (67.1-3) ...
Setting up libgslcblas0:armhf (2.6+dfsg-2) ...
Setting up libmagic-mgc (1:5.38-5) ...
Setting up libgsl25:armhf (2.6+dfsg-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.64.4-1) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.2) ...
Setting up libmagic1:armhf (1:5.38-5) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-5) ...
Setting up autotools-dev (20180224.1) ...
Setting up libblas3:armhf (3.9.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up libgfortran5:armhf (10.1.0-4+rpi1) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.10+dfsg-5+b1) ...
Setting up libblas-dev:armhf (3.9.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
Setting up liblapack3:armhf (3.9.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libgsl-dev (2.6+dfsg-2) ...
Setting up libtool (2.4.6-14) ...
Setting up libgfortran-9-dev:armhf (9.3.0-14+rpi1) ...
Setting up m4 (1.4.18-4) ...
Setting up libtmglib3:armhf (3.9.0-2) ...
Setting up liblapack-dev:armhf (3.9.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-5) ...
Setting up liblapacke:armhf (3.9.0-2) ...
Setting up libtmglib-dev:armhf (3.9.0-2) ...
Setting up automake (1:1.16.2-3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up gfortran-9 (9.3.0-14+rpi1) ...
Setting up liblapacke-dev:armhf (3.9.0-2) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gfortran (4:9.2.1-3.1+rpi1) ...
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 intltool-debian (0.35.0+20060710.5) ...
Setting up po-debconf (1.0.21) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.2) ...
Setting up sbuild-build-depends-eigensoft-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.30-8+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.34-8+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-14+rpi1 gcc-9_9.3.0-14+rpi1 libc6-dev_2.30-8+rpi1 libstdc++-9-dev_9.3.0-14+rpi1 libstdc++6_10.1.0-4+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.1.6 autoconf_2.69-11.1 automake_1:1.16.2-3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-8+rpi1 binutils-arm-linux-gnueabihf_2.34-8+rpi1 binutils-common_2.34-8+rpi1 bsdextrautils_2.35.2-6 bsdutils_1:2.35.2-6 build-essential_12.8 bzip2_1.0.8-3 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-14+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dmsetup_2:1.02.167-1+b2 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.2-6 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-14+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-4+rpi1 gcc-9_9.3.0-14+rpi1 gcc-9-base_9.3.0-14+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gfortran_4:9.2.1-3.1+rpi1 gfortran-9_9.3.0-14+rpi1 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-8 libapt-pkg6.0_2.1.6 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2 libasan5_9.3.0-14+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.1.0-4+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-8+rpi1 libblas-dev_3.9.0-2 libblas3_3.9.0-2 libblkid1_2.35.2-6 libbz2-1.0_1.0.8-3 libc-bin_2.30-8+rpi1 libc-dev-bin_2.30-8+rpi1 libc6_2.30-8+rpi1 libc6-dev_2.30-8+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.36-1 libcap2-bin_1:2.36-1 libcc1-0_10.1.0-4+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libcryptsetup12_2:2.3.3-1 libctf-nobfd0_2.34-8+rpi1 libctf0_2.34-8+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.252 libdebhelper-perl_13.2 libdevmapper1.02.1_2:1.02.167-1+b2 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.35.2-6 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-9-dev_9.3.0-14+rpi1 libgcc-s1_10.1.0-4+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran-9-dev_9.3.0-14+rpi1 libgfortran5_10.1.0-4+rpi1 libglib2.0-0_2.64.4-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2 libgomp1_10.1.0-4+rpi1 libgpg-error0_1.38-2 libgsl-dev_2.6+dfsg-2 libgsl25_2.6+dfsg-2 libgslcblas0_2.6+dfsg-2 libhogweed5_3.5.1+really3.5.1-2 libicu67_67.1-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libjson-c4_0.13.1+dfsg-9 libksba8_1.4.0-2 liblapack-dev_3.9.0-2 liblapack3_3.9.0-2 liblapacke_3.9.0-2 liblapacke-dev_3.9.0-2 libldap-2.4-2_2.4.50+dfsg-1 libldap-common_2.4.50+dfsg-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.2-7 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-2 libp11-kit0_0.23.20-1 libpam-cap_1:2.36-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2 libreadline7_7.0-5 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.2-6 libsqlite3-0_3.32.3-1 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-14+rpi1 libstdc++6_10.1.0-4+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.6-2+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtmglib-dev_3.9.0-2 libtmglib3_3.9.0-2 libtool_2.4.6-14 libubsan1_10.1.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_245.6-2+rpi1 libunistring2_0.9.10-4 libuuid1_2.35.2-6 libxml2_2.9.10+dfsg-5+b1 libzstd1_1.4.5+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.35.2-6 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-eigensoft-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.35.2-6 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Jul 23 06:55:26 2020 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./eigensoft_7.2.1+dfsg-2.dsc
dpkg-source: info: extracting eigensoft in /<<BUILDDIR>>/eigensoft-7.2.1+dfsg
dpkg-source: info: unpacking eigensoft_7.2.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking eigensoft_7.2.1+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying blas.patch
dpkg-source: info: applying lapacke.patch
Check 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=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-0ca5254f-d6d0-4b37-b3c9-fc0d5b897d9c
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package eigensoft
dpkg-buildpackage: info: source version 7.2.1+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/<<BUILDDIR>>/eigensoft-7.2.1+dfsg'
dh_clean
/usr/bin/make -C src clobber
make[2]: Entering directory '/<<BUILDDIR>>/eigensoft-7.2.1+dfsg/src'
rm -f *.o */*.o */*.a nicksrc/*.o eigensrc/*.o ksrc/*.o
rm -f baseprog convertf mergeit pca smshrink eigensrc/pcatoy eigensrc/smartrel eigensrc/smarteigenstrat eigensrc/twstats eigensrc/eigenstrat eigensrc/eigenstratQTL eigensrc/smartpca
cd ../bin/ ; rm -f baseprog convertf mergeit pca smshrink pcatoy smartrel smarteigenstrat twstats eigenstrat eigenstratQTL smartpca ; cd ../src
make[2]: Leaving directory '/<<BUILDDIR>>/eigensoft-7.2.1+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/eigensoft-7.2.1+dfsg'
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/eigensoft-7.2.1+dfsg'
/usr/bin/make DEBUG_OPTIONS=-g -C src all
make[2]: Entering directory '/<<BUILDDIR>>/eigensoft-7.2.1+dfsg/src'
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o baseprog.o baseprog.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcio.o mcio.c
mcio.c: In function 'getgenos':
mcio.c:1368:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
1368 | system (cmd);
| ^~~~~~~~~~~~
In file included from ../include/statsubs.h:6,
from ../include/nicklib.h:4,
from ../include/admutils.h:2,
from ../include/mcio.h:11,
from mcio.c:3:
mcio.c: In function 'getindivs':
../include/strsubs.h:83:54: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
83 | #define ZALLOC(item,n,type) if ((item = (type *)calloc((n),sizeof(type))) == NULL) \
| ^~~~~~~~~~~~~~~~~~~~~~~~
mcio.c:952:3: note: in expansion of macro 'ZALLOC'
952 | ZALLOC (indivmarkers, nindiv, Indiv *);
| ^~~~~~
In file included from ../include/strsubs.h:1,
from ../include/vsubs.h:5,
from ../include/mcio.h:10,
from mcio.c:3:
/usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here
542 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
In file included from /usr/include/stdio.h:867,
from ../include/mcio.h:4,
from mcio.c:3:
In function 'printf',
inlined from 'outfiles' at mcio.c:3159:5:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:107:10: warning: '%s' directive argument is null [-Wformat-overflow=]
107 | return __printf_chk (__USE_FORTIFY_LEVEL - 1, __fmt, __va_arg_pack ());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o egsubs.o egsubs.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o admutils.o admutils.c
admutils.c: In function 'setid2pops':
admutils.c:1256:31: warning: format '%s' expects a matching 'char *' argument [-Wformat=]
1256 | printf ("(setid2pops): %s not found\n");
| ~^
| |
| char *
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o h2d.o h2d.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/exclude.o eigensrc/exclude.c
/usr/bin/make -C nicksrc
make[3]: Entering directory '/<<BUILDDIR>>/eigensoft-7.2.1+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
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-7.2.1+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 -lgsl -lblas -lm -llapacke -llapack -lpthread -o baseprog
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convertf.o convertf.c
convertf.c: In function 'main':
convertf.c:257:5: warning: implicit declaration of function 'setfamilypopnames' [-Wimplicit-function-declaration]
257 | setfamilypopnames (YES);
| ^~~~~~~~~~~~~~~~~
cc -Wl,-z,relro -Wl,-z,now convertf.o mcio.o egsubs.o admutils.o h2d.o eigensrc/exclude.o nicksrc/libnick.a -lgsl -lblas -lm -llapacke -llapack -lpthread -o convertf
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mergeit.o mergeit.c
cc -Wl,-z,relro -Wl,-z,now mergeit.o mcio.o admutils.o nicksrc/libnick.a -lgsl -lblas -lm -llapacke -llapack -lpthread -o mergeit
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o pca.o pca.c
pca.c: In function 'main':
pca.c:102:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
102 | fscanf (fp, "%c", &Xchar);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
pca.c:167:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
167 | fscanf (fp, "%c", &Xchar);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
pca.c:190:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
190 | fscanf (fp, "%c", &Xchar); /* should be \n character */
| ^~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/eigsubs.o eigensrc/eigsubs.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/eigx.o eigensrc/eigx.c
cc -Wl,-z,relro -Wl,-z,now pca.o eigensrc/eigsubs.o eigensrc/eigx.o nicksrc/libnick.a -lgsl -lblas -lm -llapacke -llapack -lpthread -o pca
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smshrink.o smshrink.c
smshrink.c: In function 'main':
smshrink.c:624:5: warning: implicit declaration of function 'setid2pops'; did you mean 'setsdpos'? [-Wimplicit-function-declaration]
624 | setid2pops (id2pops, indivmarkers, numindivs);
| ^~~~~~~~~~
| setsdpos
smshrink.c:774:5: warning: implicit declaration of function 'kjg_fpca' [-Wimplicit-function-declaration]
774 | kjg_fpca (numeigs, fastdim, fastiter, evals, evecs);
| ^~~~~~~~
smshrink.c:578:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
578 | system (buff);
| ^~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/smartsubs.o eigensrc/smartsubs.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o twsubs.o twsubs.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o qpsubs.o qpsubs.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regsubs.o regsubs.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gval.o gval.c
gval.c: In function 'setgval':
gval.c:67:5: warning: implicit declaration of function 'getcolxz' [-Wimplicit-function-declaration]
67 | getcolxz (cc, cupt, xindex, xtypes, nrows, i, xmean, xfancy, &n0, &n1);
| ^~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ksrc/kjg_fpca.o ksrc/kjg_fpca.c
ksrc/kjg_fpca.c: In function 'kjg_fpca':
ksrc/kjg_fpca.c:31:14: warning: implicit declaration of function 'get_ncols' [-Wimplicit-function-declaration]
31 | size_t m = get_ncols ();
| ^~~~~~~~~
ksrc/kjg_fpca.c:32:14: warning: implicit declaration of function 'get_nrows' [-Wimplicit-function-declaration]
32 | size_t n = get_nrows ();
| ^~~~~~~~~
ksrc/kjg_fpca.c: In function 'kjg_fpca_XTXA':
ksrc/kjg_fpca.c:118:11: warning: implicit declaration of function 'kjg_geno_get_normalized_rows' [-Wimplicit-function-declaration]
118 | r = kjg_geno_get_normalized_rows (i, KJG_FPCA_ROWS, Y);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ksrc/kjg_gsl.o ksrc/kjg_gsl.c
ksrc/kjg_gsl.c: In function 'kjg_gsl_matrix_fscanf':
ksrc/kjg_gsl.c:38:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
38 | fscanf (stream, "%lg", &x);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
cc -Wl,-z,relro -Wl,-z,now smshrink.o eigensrc/eigsubs.o eigensrc/exclude.o eigensrc/smartsubs.o eigensrc/eigx.o twsubs.o mcio.o qpsubs.o admutils.o egsubs.o regsubs.o gval.o nicksrc/libnick.a ksrc/kjg_fpca.o ksrc/kjg_gsl.o -lgsl -lblas -lm -llapacke -llapack -lpthread -o smshrink
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/pcatoy.o eigensrc/pcatoy.c
cc -Wl,-z,relro -Wl,-z,now eigensrc/pcatoy.o eigensrc/eigsubs.o eigensrc/eigx.o nicksrc/libnick.a -lgsl -lblas -lm -llapacke -llapack -lpthread -o eigensrc/pcatoy
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/smartrel.o eigensrc/smartrel.c
cc -Wl,-z,relro -Wl,-z,now eigensrc/smartrel.o twsubs.o mcio.o qpsubs.o admutils.o egsubs.o regsubs.o eigensrc/eigsubs.o eigensrc/eigx.o eigensrc/smartsubs.o nicksrc/libnick.a -lgsl -lblas -lm -llapacke -llapack -lpthread -o eigensrc/smartrel
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/smarteigenstrat.o eigensrc/smarteigenstrat.c
eigensrc/smarteigenstrat.c: In function 'readpcafile':
eigensrc/smarteigenstrat.c:332:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
332 | fscanf (fppca, "%d", &K);
| ^~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/smarteigenstrat.c:339:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
339 | fscanf (fppca, "%lf", &tempdouble); /* eigenvalues */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/smarteigenstrat.c:342:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
342 | fscanf (fppca, "%lf", &V[NSAMPLES * n + k]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/smarteigenstrat.c:360:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
360 | fscanf (fppca, "%lf", &tempdouble);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -Wl,-z,relro -Wl,-z,now eigensrc/smarteigenstrat.o mcio.o admutils.o nicksrc/libnick.a -lgsl -lblas -lm -llapacke -llapack -lpthread -o eigensrc/smarteigenstrat
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/twstats.o eigensrc/twstats.c
cc -Wl,-z,relro -Wl,-z,now eigensrc/twstats.o nicksrc/libnick.a -lgsl -lblas -lm -llapacke -llapack -lpthread -o eigensrc/twstats
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now eigensrc/eigenstrat.c -lgsl -lblas -lm -llapacke -llapack -lpthread -o eigensrc/eigenstrat
eigensrc/eigenstrat.c: In function 'main':
eigensrc/eigenstrat.c:86:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
86 | fscanf (fp, "%c", &Xchar);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:123:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
123 | fscanf (fppca, "%d", &K);
| ^~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:130:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
130 | fscanf (fppca, "%lf", &tempdouble); /* eigenvalues */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:133:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
133 | fscanf (fppca, "%lf", &V[NSAMPLES * n + k]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:151:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
151 | fscanf (fppca, "%lf", &tempdouble);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:165:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
165 | fscanf (fppheno, "%c", &Xchar);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:188:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
188 | fscanf (fppheno, "%c", &Xchar); /* should be end of file */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:244:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
244 | fscanf (fp, "%c", &Xchar);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstrat.c:267:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
267 | fscanf (fp, "%c", &Xchar); /* should be \n character */
| ^~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now eigensrc/eigenstratQTL.c -lgsl -lblas -lm -llapacke -llapack -lpthread -o eigensrc/eigenstratQTL
eigensrc/eigenstratQTL.c: In function 'main':
eigensrc/eigenstratQTL.c:86:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
86 | fscanf (fp, "%c", &Xchar);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:123:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
123 | fscanf (fppca, "%d", &K);
| ^~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:130:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
130 | fscanf (fppca, "%lf", &tempdouble); /* eigenvalues */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:133:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
133 | fscanf (fppca, "%lf", &V[NSAMPLES * n + k]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:151:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
151 | fscanf (fppca, "%lf", &tempdouble);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:172:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
172 | fscanf (fppheno, "%lf", &iscase[n]); /* QTL phenotype */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:174:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
174 | fscanf (fppheno, "%lf", &tempdouble); /* to check # entries */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:227:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
227 | fscanf (fp, "%c", &Xchar);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
eigensrc/eigenstratQTL.c:250:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
250 | fscanf (fp, "%c", &Xchar); /* should be \n character */
| ^~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/eigensoft-7.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/openblas -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigensrc/smartpca.o eigensrc/smartpca.c
eigensrc/smartpca.c: In function 'main':
eigensrc/smartpca.c:644:5: warning: implicit declaration of function 'setid2pops'; did you mean 'setsdpos'? [-Wimplicit-function-declaration]
644 | setid2pops (id2pops, indivmarkers, numindivs);
| ^~~~~~~~~~
| setsdpos
eigensrc/smartpca.c:809:5: warning: implicit declaration of function 'kjg_fpca' [-Wimplicit-function-declaration]
809 | kjg_fpca (numeigs, fastdim, fastiter, evals, evecs);
| ^~~~~~~~
eigensrc/smartpca.c:597:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
597 | system (buff);
| ^~~~~~~~~~~~~
cc -Wl,-z,relro -Wl,-z,now eigensrc/smartpca.o eigensrc/eigsubs.o eigensrc/exclude.o eigensrc/smartsubs.o eigensrc/eigx.o mcio.o qpsubs.o admutils.o egsubs.o regsubs.o gval.o nicksrc/libnick.a ksrc/kjg_fpca.o ksrc/kjg_gsl.o -lgsl -lblas -lm -llapacke -llapack -lpthread -o eigensrc/smartpca
make[2]: Leaving directory '/<<BUILDDIR>>/eigensoft-7.2.1+dfsg/src'
cd src && make install
make[2]: Entering directory '/<<BUILDDIR>>/eigensoft-7.2.1+dfsg/src'
mv baseprog convertf mergeit pca smshrink eigensrc/pcatoy eigensrc/smartrel eigensrc/smarteigenstrat eigensrc/twstats eigensrc/eigenstrat eigensrc/eigenstratQTL eigensrc/smartpca ../bin
make[2]: Leaving directory '/<<BUILDDIR>>/eigensoft-7.2.1+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/eigensoft-7.2.1+dfsg'
create-stamp debian/debhelper-build-stamp
dh_testroot -a
dh_prep -a
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/eigensoft-7.2.1+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-7.2.1+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-7.2.1+dfsg'
dh_fixperms
find debian/*/usr/share/eigensoft -type f -name "*.perl" -exec chmod +x \{\} \;
make[1]: Leaving directory '/<<BUILDDIR>>/eigensoft-7.2.1+dfsg'
dh_missing -a
dh_dwz -a -a
dh_strip -a -a
dh_makeshlibs -a -a
dh_shlibdeps -a -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/eigensoft/usr/bin/eigenstratQTL debian/eigensoft/usr/bin/eigenstrat debian/eigensoft/usr/bin/pcatoy debian/eigensoft/usr/bin/smartrel debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/bin/mergeit debian/eigensoft/usr/bin/smshrink debian/eigensoft/usr/bin/convertf debian/eigensoft/usr/bin/twstats debian/eigensoft/usr/bin/pca debian/eigensoft/usr/lib/eigensoft/smarteigenstrat debian/eigensoft/usr/bin/baseprog were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/eigensoft/usr/lib/eigensoft/smartpca debian/eigensoft/usr/bin/smshrink were not linked against libblas.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'eigensoft-dbgsym' in '../eigensoft-dbgsym_7.2.1+dfsg-2_armhf.deb'.
dpkg-deb: building package 'eigensoft' in '../eigensoft_7.2.1+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../eigensoft_7.2.1+dfsg-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-07-25T11:28:22Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
eigensoft_7.2.1+dfsg-2_armhf.changes:
-------------------------------------
Format: 1.8
Date: Thu, 23 Jul 2020 08:53:03 +0200
Source: eigensoft
Binary: eigensoft eigensoft-dbgsym
Architecture: armhf
Version: 7.2.1+dfsg-2
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
eigensoft - reduction of population bias for genetic analyses
Changes:
eigensoft (7.2.1+dfsg-2) unstable; urgency=medium
.
* Standards-Version: 4.5.0 (routine-update)
* debhelper-compat 13 (routine-update)
* Remove trailing whitespace in debian/rules (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
Repository-Browse.
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Checksums-Sha256:
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Files:
a81acdf84f2410ce07aafa10b3e444a3 1198652 debug optional eigensoft-dbgsym_7.2.1+dfsg-2_armhf.deb
cf503bc59d95d2c1013e53e525832a4d 4962 science optional eigensoft_7.2.1+dfsg-2_armhf.buildinfo
ccc7a03f939d9e7db04117ee47dc2443 245204 science optional eigensoft_7.2.1+dfsg-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
eigensoft-dbgsym_7.2.1+dfsg-2_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 1198652 bytes: control archive=1152 bytes.
840 bytes, 12 lines control
1361 bytes, 13 lines md5sums
Package: eigensoft-dbgsym
Source: eigensoft
Version: 7.2.1+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1546
Depends: eigensoft (= 7.2.1+dfsg-2)
Section: debug
Priority: optional
Description: debug symbols for eigensoft
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drwxr-xr-x root/root 0 2020-07-23 06:53 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-07-23 06:53 ./usr/share/doc/eigensoft-dbgsym -> eigensoft
eigensoft_7.2.1+dfsg-2_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 245204 bytes: control archive=3280 bytes.
1149 bytes, 20 lines control
13143 bytes, 161 lines md5sums
Package: eigensoft
Version: 7.2.1+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2399
Depends: libblas3 | libblas.so.3, libc6 (>= 2.29), libgsl25 (>= 2.6), liblapack3 | liblapack.so.3, liblapacke (>= 3.9.0), perl:any
Recommends: gnuplot
Section: science
Priority: optional
Homepage: http://www.hsph.harvard.edu/faculty/alkes-price/software/
Description: reduction of population bias for genetic analyses
The EIGENSOFT package combines functionality from the group's population
genetics methods (Patterson et al. 2006) and their EIGENSTRAT stratification
method (Price et al. 2006). The EIGENSTRAT method uses principal components
analysis to explicitly model ancestry differences between cases and
controls along continuous axes of variation; the resulting correction is
specific to a candidate marker's variation in frequency across ancestral
populations, minimizing spurious associations while maximizing power to
detect true associations. The EIGENSOFT package has a built-in plotting
script and supports multiple file formats and quantitative phenotypes.
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lrwxrwxrwx root/root 0 2020-07-23 06:53 ./usr/bin/gc-eigensoft -> ../lib/debian-med/bin/gc.perl
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-rwxr-xr-x root/root 2112 2020-07-23 06:53 ./usr/bin/smarteigenstrat
-rwxr-xr-x root/root 4738 2020-07-23 06:53 ./usr/bin/smartpca
-rwxr-xr-x root/root 268384 2020-07-23 06:53 ./usr/bin/smartrel
-rwxr-xr-x root/root 309396 2020-07-23 06:53 ./usr/bin/smshrink
-rwxr-xr-x root/root 145068 2020-07-23 06:53 ./usr/bin/twstats
drwxr-xr-x root/root 0 2020-07-23 06:53 ./usr/lib/
drwxr-xr-x root/root 0 2020-07-23 06:53 ./usr/lib/debian-med/
drwxr-xr-x root/root 0 2020-07-23 06:53 ./usr/lib/debian-med/bin/
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-rwxr-xr-x root/root 2112 2020-07-23 06:53 ./usr/lib/debian-med/bin/smarteigenstrat.perl
-rwxr-xr-x root/root 4738 2020-07-23 06:53 ./usr/lib/debian-med/bin/smartpca.perl
drwxr-xr-x root/root 0 2020-07-23 06:53 ./usr/lib/eigensoft/
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-rw-r--r-- root/root 2553 2020-07-23 06:53 ./usr/share/doc/eigensoft/copyright
drwxr-xr-x root/root 0 2020-07-23 06:53 ./usr/share/doc/eigensoft/examples/
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 15340
Build-Time: 173
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 393
Job: eigensoft_7.2.1+dfsg-2
Machine Architecture: armhf
Package: eigensoft
Package-Time: 619
Source-Version: 7.2.1+dfsg-2
Space: 15340
Status: successful
Version: 7.2.1+dfsg-2
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Finished at 2020-07-25T11:28:22Z
Build needed 00:10:19, 15340k disc space