clonalorigin →
1.0-2 →
armhf → 2017-12-18 14:00:50
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| clonalorigin 1.0-2 (armhf) Mon, 18 Dec 2017 11:49:44 +0000 |
+==============================================================================+
Package: clonalorigin
Version: 1.0-2
Source Version: 1.0-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-ea9bc238-5b95-4bc3-b825-73284cef77bd' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.2 MB]
Fetched 22.7 MB in 28s (800 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: 'clonalorigin' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/clonalorigin.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/clonalorigin.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 196 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main clonalorigin 1.0-2 (dsc) [2008 B]
Get:2 http://172.17.0.1/private buster-staging/main clonalorigin 1.0-2 (tar) [186 kB]
Get:3 http://172.17.0.1/private buster-staging/main clonalorigin 1.0-2 (diff) [8000 B]
Fetched 196 kB in 0s (978 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/clonalorigin-639ZUw/clonalorigin-1.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/clonalorigin-639ZUw' 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-MhuTW3/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-MhuTW3/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-MhuTW3/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-MhuTW3/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-MhuTW3/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-MhuTW3/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-MhuTW3/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-MhuTW3/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (2861 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates e2fsprogs-l10n libsasl2-modules libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 56 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-MhuTW3/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 (20.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15166 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 (>= 10), libgsl-dev, rename
Filtered Build-Depends: debhelper (>= 10), libgsl-dev, rename
dpkg-deb: building package 'sbuild-build-depends-clonalorigin-dummy' in '/<<BUILDDIR>>/resolver-MhuTW3/apt_archive/sbuild-build-depends-clonalorigin-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-clonalorigin-dummy sbuild-build-depends-core-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-MhuTW3/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-MhuTW3/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-MhuTW3/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-MhuTW3/apt_archive ./ Sources [503 B]
Get:5 copy:/<<BUILDDIR>>/resolver-MhuTW3/apt_archive ./ Packages [582 B]
Fetched 2418 B in 0s (3265 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install clonalorigin build dependencies (apt-based resolver)
------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates e2fsprogs-l10n libsasl2-modules libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libcroco3
libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl23
libgslcblas0 libicu57 libmagic-mgc libmagic1 libpipeline1 libsigsegv2
libtimedate-perl libtool libxml2 m4 man-db po-debconf rename
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make dwz 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 less www-browser apparmor
libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libcroco3
libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl23
libgslcblas0 libicu57 libmagic-mgc libmagic1 libpipeline1 libsigsegv2
libtimedate-perl libtool libxml2 m4 man-db po-debconf rename
sbuild-build-depends-clonalorigin-dummy
0 upgraded, 34 newly installed, 0 to remove and 56 not upgraded.
Need to get 20.3 MB of archives.
After this operation, 70.6 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-MhuTW3/apt_archive ./ sbuild-build-depends-clonalorigin-dummy 0.invalid.0 [872 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-3 [95.9 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.14 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-4 [1012 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-1 [225 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.32-1 [105 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.32-1 [63.7 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-8 [7411 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-5.1 [608 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1+nmu1 [74.2 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 15 [16.2 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.040-1 [11.8 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.1-1 [2653 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.10.9 [975 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libgslcblas0 armhf 2.4+dfsg-6 [75.1 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libgsl23 armhf 2.4+dfsg-6 [681 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libgsl-dev armhf 2.4+dfsg-6 [863 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf rename all 0.20-6 [12.8 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 20.3 MB in 5s (3587 kB/s)
Selecting previously unselected package groff-base.
(Reading database ... 15166 files and directories currently installed.)
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Unpacking bsdmainutils (9.0.14) ...
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Preparing to unpack .../03-libpipeline1_1.5.0-1_armhf.deb ...
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Unpacking libmagic-mgc (1:5.32-1) ...
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Preparing to unpack .../11-libsigsegv2_2.11-1_armhf.deb ...
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Setting up libarchive-zip-perl (1.59-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.11-1) ...
Setting up rename (0.20-6) ...
update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode
Setting up groff-base (1.22.3-9) ...
Setting up libglib2.0-0:armhf (2.54.1-1) ...
No schema files found: doing nothing.
Setting up gettext-base (0.19.8.1-4) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-8) ...
Setting up libbsd0:armhf (0.8.6-3) ...
Setting up libxml2:armhf (2.9.4+dfsg1-5.1) ...
Setting up libmagic-mgc (1:5.32-1) ...
Setting up libmagic1:armhf (1:5.32-1) ...
Setting up libcroco3:armhf (0.6.12-1) ...
Processing triggers for libc-bin (2.25-2+rpi1) ...
Setting up autotools-dev (20161112.1+nmu1) ...
Setting up bsdmainutils (9.0.14) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgslcblas0:armhf (2.4+dfsg-6) ...
Setting up autopoint (0.19.8.1-4) ...
Setting up libfile-stripnondeterminism-perl (0.040-1) ...
Setting up libgsl23:armhf (2.4+dfsg-6) ...
Setting up gettext (0.19.8.1-4) ...
Setting up libgsl-dev (2.4+dfsg-6) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.32-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.15.1-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.6.1-4) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2) ...
Setting up po-debconf (1.0.20) ...
Setting up dh-autoreconf (15) ...
Setting up dh-strip-nondeterminism (0.040-1) ...
Setting up debhelper (10.10.9) ...
Setting up sbuild-build-depends-clonalorigin-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.25-2+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.8.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.29.1-8+rpi1 dpkg-dev_1.19.0.4 g++-7_7.2.0-14 gcc-7_7.2.0-14 libc6-dev_2.25-2+rpi1 libstdc++-7-dev_7.2.0-14 libstdc++6_7.2.0-14 linux-libc-dev_4.9.51-1+rpi3+b1
Package versions: adduser_3.116 apt_1.6~alpha5 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1+nmu1 base-files_10+rpi1 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-8+rpi1 binutils-arm-linux-gnueabihf_2.29.1-8+rpi1 binutils-common_2.29.1-8+rpi1 bsdmainutils_9.0.14 bsdutils_1:2.30.2-0.1 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.11+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-14 dash_0.5.8-2.5 debconf_1.5.65 debhelper_10.10.9 debianutils_4.8.3 dh-autoreconf_15 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.2-1+rpi1 dmsetup_2:1.02.145-4 dpkg_1.19.0.4 dpkg-dev_1.19.0.4 e2fslibs_1.43.7-1 e2fsprogs_1.43.7-1 e2fsprogs-l10n_1.43.7-1 fakeroot_1.22-2 fdisk_2.30.2-0.1 file_1:5.32-1 findutils_4.6.0+git+20170828-2 g++_4:7.2.0-1d1 g++-7_7.2.0-14 gcc_4:7.2.0-1d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-7_7.2.0-14 gcc-7-base_7.2.0-14 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.2-1+rpi1 gnupg-agent_2.2.2-1+rpi1 gnupg-l10n_2.2.2-1+rpi1 gnupg-utils_2.2.2-1+rpi1 gpg_2.2.2-1+rpi1 gpg-agent_2.2.2-1+rpi1 gpg-wks-client_2.2.2-1+rpi1 gpg-wks-server_2.2.2-1+rpi1 gpgconf_2.2.2-1+rpi1 gpgsm_2.2.2-1+rpi1 gpgv_2.2.2-1+rpi1 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.1-3 libapt-pkg5.0_1.6~alpha5 libarchive-zip-perl_1.59-1 libasan4_7.2.0-14 libassuan0_2.4.4-1 libatomic1_7.2.0-14 libattr1_1:2.4.47-2 libaudit-common_1:2.8.1-2 libaudit1_1:2.8.1-2 libbinutils_2.29.1-8+rpi1 libblkid1_2.30.2-0.1 libbsd0_0.8.6-3 libbz2-1.0_1.0.6-8.1 libc-bin_2.25-2+rpi1 libc-dev-bin_2.25-2+rpi1 libc6_2.25-2+rpi1 libc6-dev_2.25-2+rpi1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.1 libcc1-0_7.2.0-14 libcilkrts5_7.2.0-14 libcomerr2_1.43.7-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.2-1 libdebconfclient0_0.232 libdevmapper1.02.1_2:1.02.145-4 libdpkg-perl_1.19.0.4 libdrm-common_2.4.88-1+rpi1 libdrm2_2.4.88-1+rpi1 libfakeroot_1.22-2 libfdisk1_2.30.2-0.1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.2.0-14 libgcc1_1:7.2.0-14 libgcrypt20_1.8.1-4 libgdbm3_1.8.3-14 libglib2.0-0_2.54.1-1 libgmp10_2:6.1.2+dfsg-1.1 libgnutls30_3.5.16-1 libgomp1_7.2.0-14 libgpg-error0_1.27-5 libgsl-dev_2.4+dfsg-6 libgsl23_2.4+dfsg-6 libgslcblas0_2.4+dfsg-6 libhogweed4_3.3-2 libicu57_57.1-8 libidn11_1.33-2 libidn2-0_2.0.4-1.1 libip4tc0_1.6.1-2+b1 libisl15_0.18-1 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.30.2-0.1 libmpc3_1.0.3-2 libmpfr4_3.1.6-1 libncurses5_6.0+20170902-1 libncursesw5_6.0+20170902-1 libnettle6_3.3-2 libnpth0_1.5-3 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-4 libperl5.24_5.24.1-7 libperl5.26_5.26.1-2 libpipeline1_1.5.0-1 libplymouth4_0.9.3-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3 libreadline7_7.0-3 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libsmartcols1_2.30.2-0.1 libsqlite3-0_3.21.0-1 libss2_1.43.7-1 libssl1.1_1.1.0g-2 libstdc++-7-dev_7.2.0-14 libstdc++6_7.2.0-14 libsystemd0_235-3 libtasn1-6_4.12-2.1 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170902-1 libtool_2.4.6-2 libubsan0_7.2.0-14 libudev1_235-3 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.30.2-0.1 libxml2_2.9.4+dfsg1-5.1 linux-base_4.5 linux-libc-dev_4.9.51-1+rpi3+b1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-4 mawk_1.3.3-17 mount_2.30.2-0.1 multiarch-support_2.25-2+rpi1 ncurses-base_6.0+20170902-1 ncurses-bin_6.0+20170902-1 openssl_1.1.0g-2 passwd_1:4.5-1 patch_2.7.5-1 perl_5.26.1-2 perl-base_5.26.1-2 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.1-2 pinentry-curses_1.0.0-3 plymouth_0.9.3-1 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 rename_0.20-6 sbuild-build-depends-clonalorigin-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.11 systemd_235-3 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2017c-1 udev_235-3 util-linux_2.30.2-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Dec 13 07:27:30 2017 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./clonalorigin_1.0-2.dsc
dpkg-source: info: extracting clonalorigin in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking clonalorigin_1.0.orig.tar.gz
dpkg-source: info: unpacking clonalorigin_1.0-2.debian.tar.xz
dpkg-source: info: applying portability.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=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-ea9bc238-5b95-4bc3-b825-73284cef77bd
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package clonalorigin
dpkg-buildpackage: info: source version 1.0-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build clonalorigin-1.0
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --sourcedirectory=warg
dh_auto_clean -O--sourcedirectory=warg
dh_clean -O--sourcedirectory=warg
debian/rules build-arch
dh build-arch --sourcedirectory=warg
dh_update_autotools_config -a -O--sourcedirectory=warg
dh_autoreconf -a -O--sourcedirectory=warg
configure.ac:41: installing 'config/compile'
configure.ac:9: installing 'config/install-sh'
configure.ac:9: installing 'config/missing'
Makefile.am: installing './INSTALL'
src/Makefile.am: installing 'config/depcomp'
parallel-tests: installing 'config/test-driver'
dh_auto_configure -a -O--sourcedirectory=warg
cd warg && ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking
configure: WARNING: unrecognized options: --disable-maintainer-mode
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 g++... g++
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 g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... none
checking for gcc... gcc
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 dependency style of gcc... none
checking for gsl-config... /usr/bin/gsl-config
checking for GSL - version >= 0.2.5... yes
checking how to run the C preprocessor... gcc -E
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 for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for floor... no
checking for pow... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating scripts/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
dh_auto_build -a -O--sourcedirectory=warg
cd warg && make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>/warg'
Making all in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/warg/src'
make all-am
make[3]: Entering directory '/<<PKGBUILDDIR>>/warg/src'
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-data.o `test -f 'data.cpp' || echo './'`data.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-rng.o `test -f 'rng.cpp' || echo './'`rng.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-wargxml.o `test -f 'wargxml.cpp' || echo './'`wargxml.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-move.o `test -f 'move.cpp' || echo './'`move.cpp
rng.cpp: In function 'long unsigned int weakarg::makerng(bool)':
rng.cpp:16:14: warning: variable 'rng_seed' set but not used [-Wunused-but-set-variable]
long int rng_seed;
^~~~~~~~
rng.cpp: In function 'int weakarg::loadrng(std::__cxx11::string)':
rng.cpp:66:14: warning: variable 'rng_seed' set but not used [-Wunused-but-set-variable]
long int rng_seed;
^~~~~~~~
data.cpp: In constructor 'weakarg::Data::Data(std::__cxx11::string)':
data.cpp:50:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
}else if(getNumber(tmpname)!=which){
~~~~~~~~~~~~~~~~~~^~~~~~~
data.cpp: In member function 'void weakarg::Data::subset(std::vector<int>, int)':
data.cpp:169:14: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (num<=0 &&seed>=0 || num<0) return;
~~~~~~~^~~~~~~~~
data.cpp:177:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<numv.size();i++) if(numv[i]<tried.size()&&numv[i]>=0) {if(!tried[numv[i]]) {regions.push_back(numv[i]);tried[numv[i]]=true;}else{cerr<<"Warning: Duplicate blocks of "<<numv[i]<<" were specified and have been removed from the analysis."<<endl;}}else{cerr<<"Warning: Invalid blocks were specified and have been removed from the analysis."<<endl;}
~^~~~~~~~~~~~
data.cpp:177:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<numv.size();i++) if(numv[i]<tried.size()&&numv[i]>=0) {if(!tried[numv[i]]) {regions.push_back(numv[i]);tried[numv[i]]=true;}else{cerr<<"Warning: Duplicate blocks of "<<numv[i]<<" were specified and have been removed from the analysis."<<endl;}}else{cerr<<"Warning: Invalid blocks were specified and have been removed from the analysis."<<endl;}
rng.cpp: In function 'long unsigned int weakarg::seedrng(long unsigned int)':
rng.cpp:40:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&tseed,sizeof(tseed),1,devrandom);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-metropolis.o `test -f 'metropolis.cpp' || echo './'`metropolis.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-moveaddedge.o `test -f 'moveaddedge.cpp' || echo './'`moveaddedge.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-moveageclonal.o `test -f 'moveageclonal.cpp' || echo './'`moveageclonal.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-movedelta.o `test -f 'movedelta.cpp' || echo './'`movedelta.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-moveedgechange.o `test -f 'moveedgechange.cpp' || echo './'`moveedgechange.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-moveregraftclonal.o `test -f 'moveregraftclonal.cpp' || echo './'`moveregraftclonal.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-moveremedge.o `test -f 'moveremedge.cpp' || echo './'`moveremedge.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-moverho.o `test -f 'moverho.cpp' || echo './'`moverho.cpp
moveregraftclonal.cpp: In member function 'virtual int weakarg::MoveRegraftClonal::move()':
moveregraftclonal.cpp:43:9: warning: unused variable 'notmovednode' [-Wunused-variable]
int notmovednode=rectree->otherChild(origfather,which);
^~~~~~~~~~~~
moveregraftclonal.cpp: In member function 'void weakarg::MoveRegraftClonal::regraft(int, int)':
moveregraftclonal.cpp:157:54: warning: unused variable 'wnode' [-Wunused-variable]
Node *fanode=rectree->getNode(which)->getFather(), *wnode=rectree->getNode(which), *wtonode=rectree->getNode(whichto);
^~~~~
moveregraftclonal.cpp:157:86: warning: unused variable 'wtonode' [-Wunused-variable]
Node *fanode=rectree->getNode(which)->getFather(), *wnode=rectree->getNode(which), *wtonode=rectree->getNode(whichto);
^~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-movescaletree.o `test -f 'movescaletree.cpp' || echo './'`movescaletree.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-movegreedytree.o `test -f 'movegreedytree.cpp' || echo './'`movegreedytree.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-movesitechange.o `test -f 'movesitechange.cpp' || echo './'`movesitechange.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-movetheta.o `test -f 'movetheta.cpp' || echo './'`movetheta.cpp
movegreedytree.cpp: In member function 'void weakarg::MoveGreedyTree::applyChanges(std::vector<double>)':
movegreedytree.cpp:230:19: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
int whichto=-1,tmp;
^~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-movetimechange.o `test -f 'movetimechange.cpp' || echo './'`movetimechange.cpp
In file included from /usr/include/c++/7/vector:69:0,
from data.h:3,
from param.h:3,
from move.h:4,
from movesitechange.h:4,
from movesitechange.cpp:1:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-mpiutils.o `test -f 'mpiutils.cpp' || echo './'`mpiutils.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-node.o `test -f 'node.cpp' || echo './'`node.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-param.o `test -f 'param.cpp' || echo './'`param.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-recedge.o `test -f 'recedge.cpp' || echo './'`recedge.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-rectree.o `test -f 'rectree.cpp' || echo './'`rectree.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-tree.o `test -f 'tree.cpp' || echo './'`tree.cpp
rectree.cpp: In member function 'int weakarg::RecTree::moveNodeTime(int, int*, double, int, std::vector<int>*, std::vector<int>*)':
rectree.cpp:1112:7: warning: variable 'newfather' set but not used [-Wunused-but-set-variable]
int newfather,notnewfather;
^~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-weakarg.o `test -f 'weakarg.cpp' || echo './'`weakarg.cpp
weakarg.cpp:40:13: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
ret.append(__DATE__);
^~~~~~~~
weakarg.cpp:42:13: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
ret.append(__TIME__);
^~~~~~~~
weakarg.cpp: In function 'int main(int, char**)':
weakarg.cpp:127:10: warning: variable 'setregions' set but not used [-Wunused-but-set-variable]
bool setregions=false;
^~~~~~~~~~
weakarg.cpp: In function 'std::vector<double> weakarg::readInputFiles(weakarg::Data*&, weakarg::RecTree*&, std::vector<double>&, std::vector<int>&, std::vector<int>&, std::vector<std::__cxx11::basic_string<char> >, std::__cxx11::string, int)':
weakarg.cpp:342:7: warning: variable 'setregions' set but not used [-Wunused-but-set-variable]
bool setregions=false;
^~~~~~~~~~
weakarg.cpp: In function 'bool weakarg::initializeTree(weakarg::Data*&, weakarg::RecTree*&, std::vector<std::__cxx11::basic_string<char> >, std::__cxx11::string)':
weakarg.cpp:404:2: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(readparams) p->setTheta(pars[2]);p->setRho(pars[0]);p->setDelta(pars[2]);
^~
weakarg.cpp:404:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(readparams) p->setTheta(pars[2]);p->setRho(pars[0]);p->setDelta(pars[2]);
^
In file included from /usr/include/c++/7/vector:69:0,
from node.h:4,
from tree.h:3,
from tree.cpp:1:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from node.h:4,
from tree.h:3,
from rectree.h:3,
from weakarg.cpp:6:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from node.h:4,
from tree.h:3,
from rectree.h:3,
from weakarg.cpp:6:
/usr/include/c++/7/bits/stl_vector.h: In function 'weakarg::ProgramOptions& weakarg::opt()':
/usr/include/c++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wl,-z,relro -Wl,-z,now -o warg warg-data.o warg-rng.o warg-wargxml.o warg-move.o warg-metropolis.o warg-moveaddedge.o warg-moveageclonal.o warg-movedelta.o warg-moveedgechange.o warg-moveregraftclonal.o warg-moveremedge.o warg-moverho.o warg-movescaletree.o warg-movegreedytree.o warg-movesitechange.o warg-movetheta.o warg-movetimechange.o warg-mpiutils.o warg-node.o warg-param.o warg-recedge.o warg-rectree.o warg-tree.o warg-weakarg.o -L/usr/lib/arm-linux-gnueabihf -lgsl -lgslcblas -lm
make[3]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
Making all in scripts
make[2]: Entering directory '/<<PKGBUILDDIR>>/warg/scripts'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg/scripts'
make[2]: Entering directory '/<<PKGBUILDDIR>>/warg'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/warg'
dh_auto_test -a -O--sourcedirectory=warg
cd warg && make -j4 check VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>/warg'
Making check in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/warg/src'
make profilerun.sh
make[3]: Entering directory '/<<PKGBUILDDIR>>/warg/src'
make[3]: 'profilerun.sh' is up to date.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
make check-TESTS
make[3]: Entering directory '/<<PKGBUILDDIR>>/warg/src'
make[4]: Entering directory '/<<PKGBUILDDIR>>/warg/src'
PASS: profilerun.sh
============================================================================
Testsuite summary for clonalorigin 0.0.1
============================================================================
# TOTAL: 1
# PASS: 1
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[4]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
Making check in scripts
make[2]: Entering directory '/<<PKGBUILDDIR>>/warg/scripts'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg/scripts'
make[2]: Entering directory '/<<PKGBUILDDIR>>/warg'
make[2]: Nothing to be done for 'check-am'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/warg'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --sourcedirectory=warg
dh_testroot -a -O--sourcedirectory=warg
dh_prep -a -O--sourcedirectory=warg
dh_auto_install -a -O--sourcedirectory=warg
cd warg && make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/clonalorigin AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<PKGBUILDDIR>>/warg'
Making install in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/warg/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>/warg/src'
make[3]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/clonalorigin/usr/bin'
/usr/bin/install -c warg '/<<PKGBUILDDIR>>/debian/clonalorigin/usr/bin'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
Making install in scripts
make[2]: Entering directory '/<<PKGBUILDDIR>>/warg/scripts'
make[3]: Entering directory '/<<PKGBUILDDIR>>/warg/scripts'
make[3]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/clonalorigin/usr/bin'
/usr/bin/install -c blocksplit.pl computeMedians.pl makeMauveWargFile.pl '/<<PKGBUILDDIR>>/debian/clonalorigin/usr/bin'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/warg/scripts'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg/scripts'
make[2]: Entering directory '/<<PKGBUILDDIR>>/warg'
make[3]: Entering directory '/<<PKGBUILDDIR>>/warg'
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>>/warg'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/warg'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
rename 's/\.pl//' debian/clonalorigin/usr/bin/*.pl
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a -O--sourcedirectory=warg
dh_installchangelogs -a -O--sourcedirectory=warg
dh_installman -a -O--sourcedirectory=warg
dh_perl -a -O--sourcedirectory=warg
dh_link -a -O--sourcedirectory=warg
dh_strip_nondeterminism -a -O--sourcedirectory=warg
dh_compress -a -O--sourcedirectory=warg
dh_fixperms -a -O--sourcedirectory=warg
dh_missing -a -O--sourcedirectory=warg
dh_strip -a -O--sourcedirectory=warg
dh_makeshlibs -a -O--sourcedirectory=warg
dh_shlibdeps -a -O--sourcedirectory=warg
dpkg-shlibdeps: warning: debian/clonalorigin/usr/bin/warg 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/clonalorigin/usr/bin/warg was not linked against libgslcblas.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/clonalorigin/usr/bin/warg was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a -O--sourcedirectory=warg
dh_gencontrol -a -O--sourcedirectory=warg
dpkg-gencontrol: warning: package clonalorigin: unused substitution variable ${perl:Depends}
dpkg-gencontrol: warning: package clonalorigin: unused substitution variable ${perl:Depends}
dh_md5sums -a -O--sourcedirectory=warg
dh_builddeb -a -O--sourcedirectory=warg
dpkg-deb: building package 'clonalorigin' in '../clonalorigin_1.0-2_armhf.deb'.
dpkg-deb: building package 'clonalorigin-dbgsym' in '../clonalorigin-dbgsym_1.0-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../clonalorigin_1.0-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build clonalorigin-1.0
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-12-18T14:00:43Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
clonalorigin_1.0-2_armhf.changes:
---------------------------------
Format: 1.8
Date: Wed, 13 Dec 2017 08:26:41 +0100
Source: clonalorigin
Binary: clonalorigin
Architecture: armhf
Version: 1.0-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
clonalorigin - inference of homologous recombination in bacteria using whole gen
Closes: 884206
Changes:
clonalorigin (1.0-2) unstable; urgency=medium
.
* Drop -msse for portability reasons
Closes: #884206
* Standards-Version: 4.1.2
Checksums-Sha1:
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0304be1690dd812cc457325ca417fefeb26d0e5f 4493 clonalorigin_1.0-2_armhf.buildinfo
b52f58bd7a7a3ac3c8008bf3f4788706165b0dde 128100 clonalorigin_1.0-2_armhf.deb
Checksums-Sha256:
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228160a01613c217d2503994fb4299ccfd6c154f793568463d55dc1f905bf787 4493 clonalorigin_1.0-2_armhf.buildinfo
681f4fedb9155fe55c0390e60403e10fab1fa796d90aa171b7fec06d313968de 128100 clonalorigin_1.0-2_armhf.deb
Files:
035fe174db47e8904d45a7748f2bd3d5 1479176 debug optional clonalorigin-dbgsym_1.0-2_armhf.deb
4a573e12ffca96c70256bf71d131f357 4493 science optional clonalorigin_1.0-2_armhf.buildinfo
5ed03a0b329f9210515ce59ea9e13b9d 128100 science optional clonalorigin_1.0-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
clonalorigin-dbgsym_1.0-2_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 1479176 bytes: control archive=536 bytes.
387 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: clonalorigin-dbgsym
Source: clonalorigin
Version: 1.0-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1503
Depends: clonalorigin (= 1.0-2)
Section: debug
Priority: optional
Description: debug symbols for clonalorigin
Build-Ids: 909d5a8204f2c0c7b714aa196e457e24303b0b35
drwxr-xr-x root/root 0 2017-12-13 07:26 ./
drwxr-xr-x root/root 0 2017-12-13 07:26 ./usr/
drwxr-xr-x root/root 0 2017-12-13 07:26 ./usr/lib/
drwxr-xr-x root/root 0 2017-12-13 07:26 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-12-13 07:26 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-12-13 07:26 ./usr/lib/debug/.build-id/90/
-rw-r--r-- root/root 1528360 2017-12-13 07:26 ./usr/lib/debug/.build-id/90/9d5a8204f2c0c7b714aa196e457e24303b0b35.debug
drwxr-xr-x root/root 0 2017-12-13 07:26 ./usr/share/
drwxr-xr-x root/root 0 2017-12-13 07:26 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-12-13 07:26 ./usr/share/doc/clonalorigin-dbgsym -> clonalorigin
clonalorigin_1.0-2_armhf.deb
----------------------------
new Debian package, version 2.0.
size 128100 bytes: control archive=1164 bytes.
1076 bytes, 20 lines control
507 bytes, 8 lines md5sums
Package: clonalorigin
Version: 1.0-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 337
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgsl23, libgslcblas0, libstdc++6 (>= 5.2)
Section: science
Priority: optional
Homepage: https://github.com/xavierdidelot/clonalorigin
Description: inference of homologous recombination in bacteria using whole genome sequences
Bacteria, unlike us, can reproduce on their own. They do however have
mechanisms that transfer DNA between organisms, a process more formally
known as recombination. The mechanisms by which recombination takes
place have been studied extensively in the laboratory but much remains
to be understood concerning how, when and where recombination takes
place within natural populations of bacteria and how it helps them to
adapt to new environments. ClonalOrigin performs a comparative analysis
of the sequences of a sample of bacterial genomes in order to
reconstruct the recombination events that have taken place in their
ancestry.
drwxr-xr-x root/root 0 2017-12-13 07:26 ./
drwxr-xr-x root/root 0 2017-12-13 07:26 ./usr/
drwxr-xr-x root/root 0 2017-12-13 07:26 ./usr/bin/
-rwxr-xr-x root/root 430 2017-12-13 07:26 ./usr/bin/blocksplit
lrwxrwxrwx root/root 0 2017-12-13 07:26 ./usr/bin/clonalorigin -> warg
-rwxr-xr-x root/root 3039 2017-12-13 07:26 ./usr/bin/computeMedians
-rwxr-xr-x root/root 1111 2017-12-13 07:26 ./usr/bin/makeMauveWargFile
-rwxr-xr-x root/root 322176 2017-12-13 07:26 ./usr/bin/warg
drwxr-xr-x root/root 0 2017-12-13 07:26 ./usr/share/
drwxr-xr-x root/root 0 2017-12-13 07:26 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-12-13 07:26 ./usr/share/doc/clonalorigin/
-rw-r--r-- root/root 504 2017-12-13 07:26 ./usr/share/doc/clonalorigin/README.Debian
-rw-r--r-- root/root 233 2017-12-13 07:26 ./usr/share/doc/clonalorigin/changelog.Debian.gz
-rw-r--r-- root/root 514 2017-12-13 07:26 ./usr/share/doc/clonalorigin/copyright
drwxr-xr-x root/root 0 2017-12-13 07:26 ./usr/share/man/
drwxr-xr-x root/root 0 2017-12-13 07:26 ./usr/share/man/man1/
lrwxrwxrwx root/root 0 2017-12-13 07:26 ./usr/share/man/man1/clonalorigin.1.gz -> warg.1.gz
-rw-r--r-- root/root 1604 2017-12-13 07:26 ./usr/share/man/man1/warg.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 20088
Build-Time: 7327
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 478
Job: clonalorigin_1.0-2
Machine Architecture: armhf
Package: clonalorigin
Package-Time: 7859
Source-Version: 1.0-2
Space: 20088
Status: successful
Version: 1.0-2
--------------------------------------------------------------------------------
Finished at 2017-12-18T14:00:43Z
Build needed 02:10:59, 20088k disc space