phylonium →
1.3-1 →
armhf → 2020-11-08 05:45:16
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| phylonium 1.3-1 (armhf) Sun, 08 Nov 2020 05:39:26 +0000 |
+==============================================================================+
Package: phylonium
Version: 1.3-1
Source Version: 1.3-1
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-edf8678a-3dee-4b4d-b467-7e23904ce429' 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 [12.8 MB]
Fetched 24.7 MB in 11s (2195 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: 'phylonium' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/phylonium.git
Please use:
git clone https://salsa.debian.org/med-team/phylonium.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 44.5 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main phylonium 1.3-1 (dsc) [2304 B]
Get:2 http://172.17.0.1/private bullseye-staging/main phylonium 1.3-1 (tar) [44.1 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main phylonium 1.3-1 (tar) [409 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main phylonium 1.3-1 (diff) [4804 B]
Fetched 44.5 MB in 8s (5742 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/phylonium-1YsICI/phylonium-1.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/phylonium-1YsICI' 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-yGIQin/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-yGIQin/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-yGIQin/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-yGIQin/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-yGIQin/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-yGIQin/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-yGIQin/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-yGIQin/apt_archive ./ Packages [430 B]
Fetched 2106 B in 1s (3746 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 sensible-utils
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 60 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-yGIQin/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 (53.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12498 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), libdivsufsort-dev, libgsl-dev
Filtered Build-Depends: debhelper-compat (= 13), libdivsufsort-dev, libgsl-dev
dpkg-deb: building package 'sbuild-build-depends-phylonium-dummy' in '/<<BUILDDIR>>/resolver-yGIQin/apt_archive/sbuild-build-depends-phylonium-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-phylonium-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-yGIQin/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-yGIQin/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-yGIQin/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-yGIQin/apt_archive ./ Sources [510 B]
Get:5 copy:/<<BUILDDIR>>/resolver-yGIQin/apt_archive ./ Packages [592 B]
Fetched 2435 B in 1s (3807 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install phylonium 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:
libpam-cap 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 groff-base
intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl
libdivsufsort-dev libdivsufsort3 libelf1 libfile-stripnondeterminism-perl
libglib2.0-0 libgsl-dev libgsl25 libgslcblas0 libicu67 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc | gsl-doc-pdf
| gsl-doc-info | gsl-ref-html libtool-doc gfortran | fortran95-compiler
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 groff-base
intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl
libdivsufsort-dev libdivsufsort3 libelf1 libfile-stripnondeterminism-perl
libglib2.0-0 libgsl-dev libgsl25 libgslcblas0 libicu67 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db po-debconf sbuild-build-depends-phylonium-dummy
0 upgraded, 37 newly installed, 0 to remove and 60 not upgraded.
Need to get 20.3 MB of archives.
After this operation, 76.5 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-yGIQin/apt_archive ./ sbuild-build-depends-phylonium-dummy 0.invalid.0 [880 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 1.5.3-1 [29.9 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 libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2.1 [188 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.181-1 [161 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.2-1 [1176 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.1 [578 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libdivsufsort3 armhf 2.0.1-4 [44.5 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libdivsufsort-dev armhf 2.0.1-4 [27.4 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libgslcblas0 armhf 2.6+dfsg-2 [79.5 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libgsl25 armhf 2.6+dfsg-2 [753 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libgsl-dev armhf 2.6+dfsg-2 [950 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 20.3 MB in 5s (3966 kB/s)
Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 12498 files and directories currently installed.)
Preparing to unpack .../00-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../01-groff-base_1.22.4-5_armhf.deb ...
Unpacking groff-base (1.22.4-5) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../02-libpipeline1_1.5.3-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.3-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../03-man-db_2.9.3-2_armhf.deb ...
Unpacking man-db (2.9.3-2) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../04-libmagic-mgc_1%3a5.38-5_armhf.deb ...
Unpacking libmagic-mgc (1:5.38-5) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../05-libmagic1_1%3a5.38-5_armhf.deb ...
Unpacking libmagic1:armhf (1:5.38-5) ...
Selecting previously unselected package file.
Preparing to unpack .../06-file_1%3a5.38-5_armhf.deb ...
Unpacking file (1:5.38-5) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../07-gettext-base_0.19.8.1-10_armhf.deb ...
Unpacking gettext-base (0.19.8.1-10) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../08-libsigsegv2_2.12-2_armhf.deb ...
Unpacking libsigsegv2:armhf (2.12-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../09-m4_1.4.18-4_armhf.deb ...
Unpacking m4 (1.4.18-4) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../10-autoconf_2.69-11.1_all.deb ...
Unpacking autoconf (2.69-11.1) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../11-autotools-dev_20180224.1_all.deb ...
Unpacking autotools-dev (20180224.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../12-automake_1%3a1.16.2-4_all.deb ...
Unpacking automake (1:1.16.2-4) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../13-autopoint_0.19.8.1-10_all.deb ...
Unpacking autopoint (0.19.8.1-10) ...
Selecting previously unselected package libtool.
Preparing to unpack .../14-libtool_2.4.6-14_all.deb ...
Unpacking libtool (2.4.6-14) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../15-dh-autoreconf_19_all.deb ...
Unpacking dh-autoreconf (19) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../16-libdebhelper-perl_13.2.1_all.deb ...
Unpacking libdebhelper-perl (13.2.1) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../17-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../18-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.9.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.9.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../20-dh-strip-nondeterminism_1.9.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.9.0-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../21-libelf1_0.181-1_armhf.deb ...
Unpacking libelf1:armhf (0.181-1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../22-dwz_0.13-5_armhf.deb ...
Unpacking dwz (0.13-5) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../23-libglib2.0-0_2.66.2-1_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.66.2-1) ...
Selecting previously unselected package libicu67:armhf.
Preparing to unpack .../24-libicu67_67.1-4_armhf.deb ...
Unpacking libicu67:armhf (67.1-4) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../25-libxml2_2.9.10+dfsg-6.1_armhf.deb ...
Unpacking libxml2:armhf (2.9.10+dfsg-6.1) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../26-libcroco3_0.6.13-1_armhf.deb ...
Unpacking libcroco3:armhf (0.6.13-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../27-gettext_0.19.8.1-10_armhf.deb ...
Unpacking gettext (0.19.8.1-10) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../28-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../29-po-debconf_1.0.21_all.deb ...
Unpacking po-debconf (1.0.21) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../30-debhelper_13.2.1_all.deb ...
Unpacking debhelper (13.2.1) ...
Selecting previously unselected package libdivsufsort3:armhf.
Preparing to unpack .../31-libdivsufsort3_2.0.1-4_armhf.deb ...
Unpacking libdivsufsort3:armhf (2.0.1-4) ...
Selecting previously unselected package libdivsufsort-dev:armhf.
Preparing to unpack .../32-libdivsufsort-dev_2.0.1-4_armhf.deb ...
Unpacking libdivsufsort-dev:armhf (2.0.1-4) ...
Selecting previously unselected package libgslcblas0:armhf.
Preparing to unpack .../33-libgslcblas0_2.6+dfsg-2_armhf.deb ...
Unpacking libgslcblas0:armhf (2.6+dfsg-2) ...
Selecting previously unselected package libgsl25:armhf.
Preparing to unpack .../34-libgsl25_2.6+dfsg-2_armhf.deb ...
Unpacking libgsl25:armhf (2.6+dfsg-2) ...
Selecting previously unselected package libgsl-dev.
Preparing to unpack .../35-libgsl-dev_2.6+dfsg-2_armhf.deb ...
Unpacking libgsl-dev (2.6+dfsg-2) ...
Selecting previously unselected package sbuild-build-depends-phylonium-dummy.
Preparing to unpack .../36-sbuild-build-depends-phylonium-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-phylonium-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libicu67:armhf (67.1-4) ...
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 (2.66.2-1) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.2.1) ...
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 libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libdivsufsort3:armhf (2.0.1-4) ...
Setting up libelf1:armhf (0.181-1) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.1) ...
Setting up libdivsufsort-dev:armhf (2.0.1-4) ...
Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
Setting up libgsl-dev (2.6+dfsg-2) ...
Setting up libtool (2.4.6-14) ...
Setting up m4 (1.4.18-4) ...
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 automake (1:1.16.2-4) ...
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 man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up po-debconf (1.0.21) ...
Setting up debhelper (13.2.1) ...
Setting up sbuild-build-depends-phylonium-dummy (0.invalid.0) ...
Setting up dh-autoreconf (19) ...
Processing triggers for libc-bin (2.31-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.35-2+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-5+rpi1 gcc-10_10.2.0-5+rpi1 libc6-dev_2.31-3+rpi1 libstdc++-10-dev_10.2.0-5+rpi1 libstdc++6_10.2.0-5+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.10 aptitude_0.8.13-2 aptitude-common_0.8.13-2 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-7 binutils_2.35-2+rpi1 binutils-arm-linux-gnueabihf_2.35-2+rpi1 binutils-common_2.35-2+rpi1 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.30-3 cpp_4:10.1.0-1+rpi1 cpp-10_10.2.0-5+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.36-3 file_1:5.38-5 findutils_4.7.0-1 g++_4:10.1.0-1+rpi1 g++-10_10.2.0-5+rpi1 gcc_4:10.1.0-1+rpi1 gcc-10_10.2.0-5+rpi1 gcc-10-base_10.2.0-5+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 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_3:20200821-2 libacl1_2.2.53-8 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libasan6_10.2.0-5+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-5+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.35-2+rpi1 libblkid1_2.36-3 libboost-iostreams1.71.0_1.71.0-6+b1 libbz2-1.0_1.0.8-4 libc-bin_2.31-3+rpi1 libc-dev-bin_2.31-3+rpi1 libc6_2.31-3+rpi1 libc6-dev_2.31-3+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.43-1 libcap2-bin_1:2.43-1 libcc1-0_10.2.0-5+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35-2+rpi1 libctf0_2.35-2+rpi1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.253 libdebhelper-perl_13.2.1 libdivsufsort-dev_2.0.1-4 libdivsufsort3_2.0.1-4 libdpkg-perl_1.20.5+rpi1 libelf1_0.181-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.36-3 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-5+rpi1 libgcc-s1_10.2.0-5+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.2-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2+b1 libgomp1_10.2.0-5+rpi1 libgpg-error0_1.38-2 libgsl-dev_2.6+dfsg-2 libgsl25_2.6+dfsg-2 libgslcblas0_2.6+dfsg-2 libhogweed6_3.6-2 libicu67_67.1-4 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libksba8_1.4.0-2 libldap-2.4-2_2.4.51+dfsg-1 libldap-common_2.4.51+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_2.36-3 libmpc3_1.2.0~rc1-1 libmpfr6_4.1.0-3 libncursesw6_6.2-1 libnettle8_3.6-2 libnpth0_1.6-2 libp11-kit0_0.23.21-2 libpam-cap_1:2.43-1 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_1.5.3-1 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_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.2-1 libsigsegv2_2.12-2 libsmartcols1_2.36-3 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libstdc++-10-dev_10.2.0-5+rpi1 libstdc++6_10.2.0-5+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.2-1+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.2.0-5+rpi1 libuchardet0_0.0.7-1 libudev1_246.2-1+rpi1 libunistring2_0.9.10-4 libuuid1_2.36-3 libxapian30_1.4.17-1 libxml2_2.9.10+dfsg-6.1 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36-3 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-phylonium-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-4 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.36-3 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 '/tmp/dpkg-verify-sig.DG8ejPNn/trustedkeys.kbx': General error
gpgv: Signature made Fri Nov 6 10:29:05 2020 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "npatra974@gmail.com"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./phylonium_1.3-1.dsc
dpkg-source: info: extracting phylonium in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking phylonium_1.3.orig.tar.gz
dpkg-source: info: unpacking phylonium_1.3.orig-debian-tests-data.tar.gz
dpkg-source: info: unpacking phylonium_1.3-1.debian.tar.xz
Check disk 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=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-edf8678a-3dee-4b4d-b467-7e23904ce429
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package phylonium
dpkg-buildpackage: info: source version 1.3-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
configure.ac:11: installing './ar-lib'
configure.ac:6: installing './compile'
configure.ac:3: installing './install-sh'
configure.ac:3: installing './missing'
parallel-tests: installing './test-driver'
libs/Makefile.am: installing './depcomp'
test/Makefile.am:7: warning: source file '$(top_srcdir)/src/esa.cxx' is in a subdirectory,
test/Makefile.am:7: but option 'subdir-objects' is disabled
automake: warning: possible forward-incompatibility.
automake: At least a source file is in a subdirectory, but the 'subdir-objects'
automake: automake option hasn't been enabled. For now, the corresponding output
automake: object file(s) will be placed in the top-level directory. However,
automake: this behaviour will change in future Automake versions: they will
automake: unconditionally cause object files to be placed in the same subdirectory
automake: of the corresponding sources.
automake: You are advised to start using 'subdir-objects' option throughout your
automake: project, to avoid future incompatibilities.
test/Makefile.am:7: warning: source file '$(top_srcdir)/src/evo_model.cxx' is in a subdirectory,
test/Makefile.am:7: but option 'subdir-objects' is disabled
test/Makefile.am:7: warning: source file '$(top_srcdir)/src/process.cxx' is in a subdirectory,
test/Makefile.am:7: but option 'subdir-objects' is disabled
test/Makefile.am:7: warning: source file '$(top_srcdir)/src/sequence.cxx' is in a subdirectory,
test/Makefile.am:7: but option 'subdir-objects' is disabled
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- --disable-x86simd
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --disable-x86simd
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... none
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking whether make sets $(MAKE)... (cached) yes
checking how to run the C preprocessor... gcc -E
checking for ranlib... ranlib
checking for ar... ar
checking the archiver (ar) interface... ar
checking for g++ option to support OpenMP... -fopenmp
checking whether g++ supports C++14 features with -std=gnu++14... yes
checking for gcc option to support OpenMP... -fopenmp
checking for __attribute__((ifunc))... yes
checking for cos in -lm... yes
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking divsufsort.h usability... yes
checking divsufsort.h presence... yes
checking for divsufsort.h... yes
checking for divsufsort in -ldivsufsort... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stdint.h... (cached) yes
checking for inttypes.h... (cached) yes
checking err.h usability... yes
checking err.h presence... yes
checking for err.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for inline... inline
checking for size_t... yes
checking for ssize_t... yes
checking for int32_t... yes
checking for uint8_t... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for floor... yes
checking for pow... yes
checking for sqrt... yes
checking for strdup... yes
checking for strerror... yes
checking for strtoul... yes
checking for strtod... yes
checking for reallocarray... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating libs/Makefile
config.status: creating Makefile
config.status: creating man/phylonium.1
config.status: creating src/Makefile
config.status: creating test/Makefile
config.status: creating config.h
config.status: executing depfiles commands
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make all-recursive
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making all in libs
make[3]: Entering directory '/<<PKGBUILDDIR>>/libs'
rm -f libcompat.a
gcc -DHAVE_CONFIG_H -I. -I.. -I../opt -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libpfasta_a-pfasta.o `test -f 'pfasta.c' || echo './'`pfasta.c
ar cru libcompat.a
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o revseqcmp.o revseqcmp.c
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libcompat.a
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o seqcmp.o seqcmp.c
rm -f libseqcmp.a
ar cru libseqcmp.a seqcmp.o
ar: `u' modifier ignored since `D' is the default (see `U')
rm -f librevseqcmp.a
ranlib libseqcmp.a
ar cru librevseqcmp.a revseqcmp.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib librevseqcmp.a
rm -f libpfasta.a
ar cru libpfasta.a libpfasta_a-pfasta.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libpfasta.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/libs'
Making all in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-phylonium.o `test -f 'phylonium.cxx' || echo './'`phylonium.cxx
g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-io.o `test -f 'io.cxx' || echo './'`io.cxx
g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-sequence.o `test -f 'sequence.cxx' || echo './'`sequence.cxx
g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-esa.o `test -f 'esa.cxx' || echo './'`esa.cxx
esa.cxx: In constructor 'esa::esa(const sequence&)':
esa.cxx:63:55: warning: narrowing conversion of '(((& seq)->sequence::size() * 2) + 1)' from 'unsigned int' to 'int' [-Wnarrowing]
63 | esa::esa(const sequence &seq) : m_size{seq.size() * 2 + 1}
| ~~~~~~~~~~~~~~~^~~
g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-process.o `test -f 'process.cxx' || echo './'`process.cxx
g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-evo_model.o `test -f 'evo_model.cxx' || echo './'`evo_model.cxx
g++ -std=gnu++14 -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o phylonium phylonium-phylonium.o phylonium-io.o phylonium-sequence.o phylonium-esa.o phylonium-process.o phylonium-evo_model.o ../libs/libcompat.a ../libs/libpfasta.a ../libs/librevseqcmp.a ../libs/libseqcmp.a -ldivsufsort -lm
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making all in test
make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
Making all in .
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 check VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making check in libs
make[2]: Entering directory '/<<PKGBUILDDIR>>/libs'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/libs'
Making check in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making check in test
make[2]: Entering directory '/<<PKGBUILDDIR>>/test'
make simf unittests
make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o simf-simf.o `test -f 'simf.cxx' || echo './'`simf.cxx
g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-esa.o `test -f '../src/esa.cxx' || echo './'`../src/esa.cxx
g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-evo_model.o `test -f '../src/evo_model.cxx' || echo './'`../src/evo_model.cxx
g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-process.o `test -f '../src/process.cxx' || echo './'`../src/process.cxx
../src/process.cxx:420: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
420 | #pragma omp parallel for num_threads(THREADS)
|
../src/process.cxx:432: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas]
432 | #pragma omp critical
|
../src/process.cxx:435: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas]
435 | #pragma omp atomic
|
../src/process.cxx:441: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas]
441 | #pragma omp critical
|
../src/process.cxx:511: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
511 | #pragma omp parallel for num_threads(THREADS)
|
../src/process.cxx:518: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas]
518 | #pragma omp atomic
|
../src/process.cxx:526: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas]
526 | #pragma omp atomic read
|
../src/process.cxx:532: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas]
532 | #pragma omp critical
|
../src/esa.cxx: In constructor 'esa::esa(const sequence&)':
../src/esa.cxx:63:55: warning: narrowing conversion of '(((& seq)->sequence::size() * 2) + 1)' from 'unsigned int' to 'int' [-Wnarrowing]
63 | esa::esa(const sequence &seq) : m_size{seq.size() * 2 + 1}
| ~~~~~~~~~~~~~~~^~~
g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-sequence.o `test -f '../src/sequence.cxx' || echo './'`../src/sequence.cxx
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from simf.cxx:13:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-Tmain.o `test -f 'Tmain.cxx' || echo './'`Tmain.cxx
/usr/include/c++/10/bits/vector.tcc: In function 'int main(int, char**)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-Tprocess.o `test -f 'Tprocess.cxx' || echo './'`Tprocess.cxx
g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-Tsequence.o `test -f 'Tsequence.cxx' || echo './'`Tsequence.cxx
g++ -std=gnu++14 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o simf simf-simf.o -ldivsufsort -lm
In file included from /usr/include/c++/10/vector:72,
from catch.hpp:521,
from Tmain.cxx:3:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator<Catch::SectionEndInfo>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Catch::SectionEndInfo>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from catch.hpp:521,
from Tmain.cxx:3:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Catch::SectionEndInfo*, std::vector<Catch::SectionEndInfo> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -std=gnu++14 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o unittests unittests-esa.o unittests-evo_model.o unittests-process.o unittests-sequence.o unittests-Tmain.o unittests-Tprocess.o unittests-Tsequence.o ../libs/libcompat.a ../libs/libpfasta.a ../libs/librevseqcmp.a ../libs/libseqcmp.a -ldivsufsort -lm
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
Making check in .
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make check-TESTS
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Entering directory '/<<PKGBUILDDIR>>'
PASS: test/unittests
PASS: test/simple.sh
============================================================================
Testsuite summary for phylonium 1.3
============================================================================
# TOTAL: 2
# PASS: 2
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_testroot -a
dh_prep -a
dh_auto_install -a
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/phylonium AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making install in libs
make[2]: Entering directory '/<<PKGBUILDDIR>>/libs'
make[3]: Entering directory '/<<PKGBUILDDIR>>/libs'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/libs'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/libs'
Making install in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/phylonium/usr/bin'
/usr/bin/install -c phylonium '/<<PKGBUILDDIR>>/debian/phylonium/usr/bin'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making install in test
make[2]: Entering directory '/<<PKGBUILDDIR>>/test'
make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
Making install in .
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/phylonium/usr/share/doc/phylonium'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/phylonium/usr/share/man/man1'
/usr/bin/install -c -m 644 documentation/manual.pdf '/<<PKGBUILDDIR>>/debian/phylonium/usr/share/doc/phylonium'
/usr/bin/install -c -m 644 man/phylonium.1 '/<<PKGBUILDDIR>>/debian/phylonium/usr/share/man/man1'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installdocs: warning: Could not parse doc-base for doc-base Document id; skipping
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a -a
dh_strip -a -a
dh_makeshlibs -a -a
dh_shlibdeps -a -a
dpkg-shlibdeps: warning: debian/phylonium/usr/bin/phylonium contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phylonium/usr/bin/phylonium was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'phylonium' in '../phylonium_1.3-1_armhf.deb'.
dpkg-deb: building package 'phylonium-dbgsym' in '../phylonium-dbgsym_1.3-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../phylonium_1.3-1_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 2020-11-08T05:45:13Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
phylonium_1.3-1_armhf.changes:
------------------------------
Format: 1.8
Date: Fri, 06 Nov 2020 14:27:37 +0530
Source: phylonium
Binary: phylonium phylonium-dbgsym
Architecture: armhf
Version: 1.3-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Nilesh Patra <npatra974@gmail.com>
Description:
phylonium - Fast and Accurate Estimation of Evolutionary Distances
Changes:
phylonium (1.3-1) unstable; urgency=medium
.
* Team Upload.
* Multi-orig tarball for testing data
* New upstream version 1.3
* Add autopkgtests
* Standards-Version: 4.5.0 (routine-update)
* debhelper-compat 13 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)\
Checksums-Sha1:
d969fe189589ce53782dcd0ff257bac0fe1cc9ed 520972 phylonium-dbgsym_1.3-1_armhf.deb
b83bb8a3da1289da2aa9b395f03ce9180216a0f1 4644 phylonium_1.3-1_armhf.buildinfo
0d659784e11cd75a63824edc96955b551e07441d 279296 phylonium_1.3-1_armhf.deb
Checksums-Sha256:
6e014a9a713ea7687f79095338b810f6891e2be893a9caedc99310b2dc816caf 520972 phylonium-dbgsym_1.3-1_armhf.deb
7c4bc5477e33a49adc56f20e20b1f1fd27744d66e3ba15258fc51b22e9cbed64 4644 phylonium_1.3-1_armhf.buildinfo
e142dd4446f71808b3f905cd867e255d071e69c5de751f97da6ebbda21fee632 279296 phylonium_1.3-1_armhf.deb
Files:
6869934f7918680b9b79daf1928f72d2 520972 debug optional phylonium-dbgsym_1.3-1_armhf.deb
c0e7c71c346adcea8405735b764677ac 4644 science optional phylonium_1.3-1_armhf.buildinfo
b134fa79866c15f4909089e633dbdd13 279296 science optional phylonium_1.3-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
phylonium-dbgsym_1.3-1_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 520972 bytes: control archive=536 bytes.
374 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: phylonium-dbgsym
Source: phylonium
Version: 1.3-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 538
Depends: phylonium (= 1.3-1)
Section: debug
Priority: optional
Description: debug symbols for phylonium
Build-Ids: d5850cb32ce080d80e56fda738e2089b3b01f835
drwxr-xr-x root/root 0 2020-11-06 08:57 ./
drwxr-xr-x root/root 0 2020-11-06 08:57 ./usr/
drwxr-xr-x root/root 0 2020-11-06 08:57 ./usr/lib/
drwxr-xr-x root/root 0 2020-11-06 08:57 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-11-06 08:57 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-11-06 08:57 ./usr/lib/debug/.build-id/d5/
-rw-r--r-- root/root 540392 2020-11-06 08:57 ./usr/lib/debug/.build-id/d5/850cb32ce080d80e56fda738e2089b3b01f835.debug
drwxr-xr-x root/root 0 2020-11-06 08:57 ./usr/share/
drwxr-xr-x root/root 0 2020-11-06 08:57 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-11-06 08:57 ./usr/share/doc/phylonium-dbgsym -> phylonium
phylonium_1.3-1_armhf.deb
-------------------------
new Debian package, version 2.0.
size 279296 bytes: control archive=856 bytes.
678 bytes, 14 lines control
338 bytes, 5 lines md5sums
Package: phylonium
Version: 1.3-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 329
Depends: libc6 (>= 2.29), libdivsufsort3 (>= 2.0.1), libgcc-s1 (>= 3.5), libgomp1 (>= 4.9), libstdc++6 (>= 5.2)
Section: science
Priority: optional
Homepage: https://github.com/EvolBioInf/phylonium
Description: Fast and Accurate Estimation of Evolutionary Distances
This is the phylonium program for estimating the evolutionary distances
between closely related genomes. It is much faster than alignment based
approaches for phylogeny reconstruction and usually more accurate than
competing alignment-free methods.
drwxr-xr-x root/root 0 2020-11-06 08:57 ./
drwxr-xr-x root/root 0 2020-11-06 08:57 ./usr/
drwxr-xr-x root/root 0 2020-11-06 08:57 ./usr/bin/
-rwxr-xr-x root/root 79576 2020-11-06 08:57 ./usr/bin/phylonium
drwxr-xr-x root/root 0 2020-11-06 08:57 ./usr/share/
drwxr-xr-x root/root 0 2020-11-06 08:57 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-11-06 08:57 ./usr/share/doc/phylonium/
-rw-r--r-- root/root 468 2020-11-06 08:57 ./usr/share/doc/phylonium/changelog.Debian.gz
-rw-r--r-- root/root 3983 2020-11-06 08:57 ./usr/share/doc/phylonium/copyright
-rw-r--r-- root/root 239700 2020-11-06 08:57 ./usr/share/doc/phylonium/manual.pdf.gz
drwxr-xr-x root/root 0 2020-11-06 08:57 ./usr/share/man/
drwxr-xr-x root/root 0 2020-11-06 08:57 ./usr/share/man/man1/
-rw-r--r-- root/root 1512 2020-11-06 08:57 ./usr/share/man/man1/phylonium.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 82808
Build-Time: 190
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 125
Job: phylonium_1.3-1
Machine Architecture: armhf
Package: phylonium
Package-Time: 347
Source-Version: 1.3-1
Space: 82808
Status: successful
Version: 1.3-1
--------------------------------------------------------------------------------
Finished at 2020-11-08T05:45:13Z
Build needed 00:05:47, 82808k disk space