clonalframe →
1.2-7 →
armhf → 2017-10-02 05:32:27
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| clonalframe 1.2-7 (armhf) Mon, 02 Oct 2017 05:27:21 +0000 |
+==============================================================================+
Package: clonalframe
Version: 1.2-7
Source Version: 1.2-7
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-96605832-643a-42e5-b82c-a2bab6e2838c' 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 [10.2 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.1 MB]
Fetched 22.4 MB in 9s (2244 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: 'clonalframe' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/clonalframe.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/clonalframe.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 52.1 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main clonalframe 1.2-7 (dsc) [2011 B]
Get:2 http://172.17.0.1/private buster-staging/main clonalframe 1.2-7 (tar) [45.5 kB]
Get:3 http://172.17.0.1/private buster-staging/main clonalframe 1.2-7 (diff) [4592 B]
Fetched 52.1 kB in 0s (982 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/clonalframe-NdgDgK/clonalframe-1.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/clonalframe-NdgDgK' 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-IuGsxY/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-IuGsxY/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-IuGsxY/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-IuGsxY/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-IuGsxY/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-IuGsxY/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-IuGsxY/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-IuGsxY/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (8226 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 libreadline5 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 15 not upgraded.
Need to get 776 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-IuGsxY/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 776 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15082 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), qt5-qmake, libgsl-dev
Filtered Build-Depends: debhelper (>= 10), qt5-qmake, libgsl-dev
dpkg-deb: building package 'sbuild-build-depends-clonalframe-dummy' in '/<<BUILDDIR>>/resolver-IuGsxY/apt_archive/sbuild-build-depends-clonalframe-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-clonalframe-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-IuGsxY/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-IuGsxY/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-IuGsxY/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-IuGsxY/apt_archive ./ Sources [506 B]
Get:5 copy:/<<BUILDDIR>>/resolver-IuGsxY/apt_archive ./ Packages [586 B]
Fetched 2425 B in 0s (9503 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install clonalframe 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 libreadline5 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 qt5-qmake qtchooser
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation 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 less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev 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 qt5-qmake qtchooser
sbuild-build-depends-clonalframe-dummy
0 upgraded, 35 newly installed, 0 to remove and 15 not upgraded.
Need to get 21.2 MB of archives.
After this operation, 74.4 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-IuGsxY/apt_archive ./ sbuild-build-depends-clonalframe-dummy 0.invalid.0 [796 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 0.8.6-2 [95.8 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-1 [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 57.1-6 [7427 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-4 [609 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 [73.4 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 14 [15.9 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.038-1 [17.6 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.038-1 [11.1 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.0-1 [2650 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 10.8 [973 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 qtchooser armhf 63-g13a3d08-1 [21.9 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf qt5-qmake armhf 5.9.1+dfsg-9+rpi1 [919 kB]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 15082 files and directories currently installed.)
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Unpacking libbsd0:armhf (0.8.6-2) ...
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Preparing to unpack .../03-libpipeline1_1.4.2-1_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 groff-base (1.22.3-9) ...
Setting up libglib2.0-0:armhf (2.54.0-1) ...
No schema files found: doing nothing.
Setting up qtchooser (63-g13a3d08-1) ...
Setting up gettext-base (0.19.8.1-4) ...
Setting up libpipeline1:armhf (1.4.2-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-6) ...
Setting up libbsd0:armhf (0.8.6-2) ...
Setting up libxml2:armhf (2.9.4+dfsg1-4) ...
Setting up libmagic-mgc (1:5.32-1) ...
Setting up libmagic1:armhf (1:5.32-1) ...
Setting up libcroco3:armhf (0.6.12-1) ...
Setting up qt5-qmake:armhf (5.9.1+dfsg-9+rpi1) ...
Processing triggers for libc-bin (2.24-14) ...
Setting up autotools-dev (20161112.1) ...
Setting up bsdmainutils (9.0.12+nmu1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgslcblas0:armhf (2.4+dfsg-6) ...
Setting up autopoint (0.19.8.1-4) ...
Setting up libfile-stripnondeterminism-perl (0.038-1) ...
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 (2.7.6.1-2) ...
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 (14) ...
Setting up dh-strip-nondeterminism (0.038-1) ...
Setting up debhelper (10.8) ...
Setting up sbuild-build-depends-clonalframe-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-14) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.29.1-3+rpi1 dpkg-dev_1.18.24 g++-7_7.2.0-5 gcc-7_7.2.0-5 libc6-dev_2.24-14 libstdc++-7-dev_7.2.0-5 libstdc++6_7.2.0-5 linux-libc-dev_4.9.30-2+deb9u2+rpi1+stretch
Package versions: adduser_3.116 apt_1.5 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1 base-files_10+rpi1 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-3+rpi1 binutils-arm-linux-gnueabihf_2.29.1-3+rpi1 binutils-common_2.29.1-3+rpi1 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-5 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-5 dash_0.5.8-2.5 debconf_1.5.63 debhelper_10.8 debianutils_4.8.2 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.6-1 dirmngr_2.2.1-1 dmsetup_2:1.02.142-1 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.6-1 e2fsprogs_1.43.6-1 fakeroot_1.22-1 fdisk_2.29.2-5 file_1:5.32-1 findutils_4.6.0+git+20170729-2 g++_4:7.2.0-1d1 g++-7_7.2.0-5 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_7.2.0-5 gcc-7-base_7.2.0-5 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.1-1 gnupg-agent_2.2.1-1 gnupg-l10n_2.2.1-1 gnupg-utils_2.2.1-1 gpg_2.2.1-1 gpg-agent_2.2.1-1 gpg-wks-client_2.2.1-1 gpg-wks-server_2.2.1-1 gpgconf_2.2.1-1 gpgsm_2.2.1-1 gpgv_2.2.1-1 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init-system-helpers_1.49 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.0-11 libapt-pkg5.0_1.5 libarchive-zip-perl_1.59-1 libasan4_7.2.0-5 libassuan0_2.4.3-3 libatomic1_7.2.0-5 libattr1_1:2.4.47-2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1+b1 libbinutils_2.29.1-3+rpi1 libblkid1_2.29.2-5 libbsd0_0.8.6-2 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-14 libc-dev-bin_2.24-14 libc6_2.24-14 libc6-dev_2.24-14 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.2.0-5 libcilkrts5_7.2.0-5 libcomerr2_1.43.6-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.11.16+really1.10.22-1 libdebconfclient0_0.230 libdevmapper1.02.1_2:1.02.142-1 libdpkg-perl_1.18.24 libdrm-common_2.4.82-1+rpi1 libdrm2_2.4.82-1+rpi1 libfakeroot_1.22-1 libfdisk1_2.29.2-5 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgcc-7-dev_7.2.0-5 libgcc1_1:7.2.0-5 libgcrypt20_1.7.9-1 libgdbm3_1.8.3-14 libglib2.0-0_2.54.0-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.15-2 libgomp1_7.2.0-5 libgpg-error0_1.27-3 libgsl-dev_2.4+dfsg-6 libgsl23_2.4+dfsg-6 libgslcblas0_2.4+dfsg-6 libhogweed4_3.3-2 libicu57_57.1-6 libidn11_1.33-2 libidn2-0_2.0.2-5 libip4tc0_1.6.1-2 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_2.29.2-5 libmpc3_1.0.3-2 libmpfr4_3.1.6-1 libncurses5_6.0+20170902-1 libncursesw5_6.0+20170902-1 libnettle6_3.3-2 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-4 libperl5.24_5.24.1-7 libperl5.26_5.26.0-8 libpipeline1_1.4.2-1 libplymouth4_0.9.3-1 libpng16-16_1.6.32-3 libprocps6_2:3.3.12-3 libreadline5_5.2+dfsg-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_2.29.2-5 libsqlite3-0_3.20.1-1 libss2_1.43.6-1 libssl1.1_1.1.0f-5 libstdc++-7-dev_7.2.0-5 libstdc++6_7.2.0-5 libsystemd0_234-3 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170902-1 libtool_2.4.6-2 libubsan0_7.2.0-5 libudev1_234-3 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-5 libxml2_2.9.4+dfsg1-4 linux-base_4.5 linux-libc-dev_4.9.30-2+deb9u2+rpi1+stretch login_1:4.4-4.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mount_2.29.2-5 mountall_2.54 multiarch-support_2.24-14 ncurses-base_6.0+20170902-1 ncurses-bin_6.0+20170902-1 openssl_1.1.0f-5 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.26.0-8 perl-base_5.26.0-8 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.0-8 pinentry-curses_1.0.0-2 plymouth_0.9.3-1 po-debconf_1.0.20 procps_2:3.3.12-3 qt5-qmake_5.9.1+dfsg-9+rpi1 qtchooser_63-g13a3d08-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-clonalframe-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 systemd_234-3 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2017b-2 udev_234-3 util-linux_2.29.2-5 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 Tue Sep 26 20:37:30 2017 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./clonalframe_1.2-7.dsc
dpkg-source: info: extracting clonalframe in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking clonalframe_1.2.orig.tar.gz
dpkg-source: info: unpacking clonalframe_1.2-7.debian.tar.xz
dpkg-source: info: applying 01_gcc-4.6.patch
dpkg-source: info: applying no_qtlibs.patch
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=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-96605832-643a-42e5-b82c-a2bab6e2838c
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package clonalframe
dpkg-buildpackage: info: source version 1.2-7
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build clonalframe-1.2
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
dh_autoreconf_clean
debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_clean
rm -rf bin build Makefile
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
qmake -makefile -nocache "QMAKE_CFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_LFLAGS_RELEASE=-Wl,-z,relro -Wl,-z,now" "QMAKE_LFLAGS_DEBUG=-Wl,-z,relro -Wl,-z,now" QMAKE_STRIP=: PREFIX=/usr
Info: creating stash file /<<PKGBUILDDIR>>/.qmake.stash
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
qmake
# did not found a better way to push hardening flags into Makefile
sed -i -e "s:CFLAGS *= .*:& -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security:" \
-e "s:CXXFLAGS *= .*:& -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security:" \
-e "s:LFLAGS *= .*:& -Wl,-z,relro -Wl,-z,now:" Makefile
/usr/bin/make
make[2]: Entering directory '/<<PKGBUILDDIR>>'
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/alignment_xmfa.o src/alignment_xmfa.cpp
src/alignment_xmfa.cpp: In constructor 'wb::Alignment_xmfa::Alignment_xmfa(char*, bool, int)':
src/alignment_xmfa.cpp:129:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j=0;j<strlen(bufin[i]);j++) {
~^~~~~~~~~~~~~~~~~
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/alignment_structure.o src/alignment_structure.cpp
src/alignment_structure.cpp: In constructor 'wb::Alignment_structure::Alignment_structure(char*, int)':
src/alignment_structure.cpp:45:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if (ch>='0' & ch<='9')
~~^~~~~
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/alignment.o src/alignment.cpp
src/alignment.cpp: In member function 'void wb::Alignment::writeToFile(char*)':
src/alignment.cpp:236:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
char * lets="ATCG";
^~~~~~
src/alignment.cpp:241:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int i=0;i<getB();i++) {
~^~~~~~~
src/alignment.cpp:243:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int j=0;j<getN();j++) {
~^~~~~~~
src/alignment.cpp:244:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int k=beg;k<end;k++)
~^~~~
src/alignment.cpp:246:41: warning: embedded '\0' in format [-Wformat-contains-nul]
sprintf(buf+end-beg,"\0");
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/boot.o src/boot.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/burst.o src/burst.cpp
src/burst.cpp: In member function 'void wb::Burst::burst(wb::Param*)':
src/burst.cpp:188:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (k=1;k<rid->size();k++)
~^~~~~~~~~~~~
src/burst.cpp:190:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (k>=rid->size()) continue;
~^~~~~~~~~~~~~
src/burst.cpp: In member function 'void wb::Burst::optimiseFathers(gsl_vector_int*, std::vector<std::vector<int> >*, int)':
src/burst.cpp:259:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (slvs->at(prop).size()>current && !descended(prop,i,fathers)) {
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
src/burst.cpp:252:89: warning: unused parameter 'f' [-Wunused-parameter]
void Burst::optimiseFathers(gsl_vector_int * fathers,vector<vector<int> > *slvs,int f) {
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/consensus.o src/consensus.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/genes.o src/genes.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/hashcell.o src/hashcell.cpp
src/hashcell.cpp: In member function 'void wb::HashCell::addNode(wb::Tree*)':
src/hashcell.cpp:51:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (l>=t->recMap->size) break;
~^~~~~~~~~~~~~~~~~
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_ages.o src/move_ages.cpp
src/move_ages.cpp: In member function 'virtual void wb::Move_ages::move(wb::Param*)':
src/move_ages.cpp:60:21: warning: suggest braces around empty body in an 'else' statement [-Wempty-body]
} else ;//printf("Age change rejected because out of range\n");
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_delta.o src/move_delta.cpp
src/move_delta.cpp: In constructor 'wb::Move_delta::Move_delta(gsl_rng*, wb::Param*)':
src/move_delta.cpp:24:50: warning: unused parameter 'p' [-Wunused-parameter]
Move_delta::Move_delta(gsl_rng * rng,Param * p):Move(rng) {
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_gap.o src/move_gap.cpp
src/move_gap.cpp: In constructor 'wb::Move_gap::Move_gap(gsl_rng*, wb::Param*)':
src/move_gap.cpp:24:46: warning: unused parameter 'p' [-Wunused-parameter]
Move_gap::Move_gap(gsl_rng * rng,Param * p) : Move(rng) {}
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_hidden.o src/move_hidden.cpp
src/move_hidden.cpp: In constructor 'wb::Move_hidden::Move_hidden(gsl_rng*, wb::Param*)':
src/move_hidden.cpp:25:52: warning: unused parameter 'p' [-Wunused-parameter]
Move_hidden::Move_hidden(gsl_rng * rng,Param * p) : Move(rng)
^
src/move_hidden.cpp: In member function 'void wb::Move_hidden::forwardfast(wb::Param*, wb::Tree*)':
src/move_hidden.cpp:127:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int i=0;i<L;i++)
~^~
src/move_hidden.cpp:133:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int j=0;j<nbstates;j++) gsl_vector_set(probas,j,gsl_vector_get(pbeg,j));
~^~~~~~~~~
src/move_hidden.cpp:137:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int j=0;j<nbstates;j++) gsl_vector_set(probas,j,gsl_vector_get(probas,j)*gsl_matrix_get(a,j,j)*gsl_matrix_get(e,j,msgs[k]));
~^~~~~~~~~
src/move_hidden.cpp:132:21: warning: unused variable 'top' [-Wunused-variable]
int top=0,left=0,right=0;
^~~
src/move_hidden.cpp:132:27: warning: unused variable 'left' [-Wunused-variable]
int top=0,left=0,right=0;
^~~~
src/move_hidden.cpp:132:34: warning: unused variable 'right' [-Wunused-variable]
int top=0,left=0,right=0;
^~~~~
src/move_hidden.cpp: In member function 'void wb::Move_hidden::backward(wb::Param*, gsl_matrix*, wb::Tree*)':
src/move_hidden.cpp:203:17: warning: unused variable 'd' [-Wunused-variable]
int d=gsl_vector_int_get(p->a->polySites,old)- gsl_vector_int_get(p->a->polySites,old-1);
^
src/move_hidden.cpp: In member function 'int wb::Move_hidden::setState(wb::Tree*, wb::Param*, int, gsl_vector*)':
src/move_hidden.cpp:263:19: warning: 'r' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf("error here r=%f calcMode=%d site=%d j=%d msg=%d recmapabove=%d recmapleft=%d recmapright=%d recmapfather=%d ancseq=%d ancseqleft=%d ancseqfather=%d\n",
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
r,calculMode,site,j,msgs[site],
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gsl_vector_char_get(t->recMap,site),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gsl_vector_char_get(t->left->recMap,site),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gsl_vector_char_get(t->right->recMap,site),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gsl_vector_char_get(t->father->recMap,site),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gsl_vector_char_get(t->ancSeq,site),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gsl_vector_char_get(t->left->ancSeq,site),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gsl_vector_char_get(t->father->ancSeq,site));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_hidden2.o src/move_hidden2.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_mu.o src/move_mu.cpp
src/move_mu.cpp: In constructor 'wb::Move_mu::Move_mu(gsl_rng*, wb::Param*)':
src/move_mu.cpp:24:44: warning: unused parameter 'p' [-Wunused-parameter]
Move_mu::Move_mu(gsl_rng * rng,Param * p):Move(rng) {}
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_nu.o src/move_nu.cpp
src/move_nu.cpp: In constructor 'wb::Move_nu::Move_nu(gsl_rng*, wb::Param*)':
src/move_nu.cpp:24:44: warning: unused parameter 'p' [-Wunused-parameter]
Move_nu::Move_nu(gsl_rng * rng,Param * p):Move(rng) {}
^
src/move_nu.cpp: In member function 'virtual void wb::Move_nu::move(wb::Param*)':
src/move_nu.cpp:56:16: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (gsl_vector_char_get(t->recMap,j)==1)
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_rho.o src/move_rho.cpp
src/move_rho.cpp: In constructor 'wb::Move_rho::Move_rho(gsl_rng*, wb::Param*)':
src/move_rho.cpp:24:46: warning: unused parameter 'p' [-Wunused-parameter]
Move_rho::Move_rho(gsl_rng * rng,Param * p):Move(rng)
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_wb.o src/move_wb.cpp
src/move_wb.cpp: In member function 'virtual void wb::Move_wb::move(wb::Param*)':
src/move_wb.cpp:127:17: warning: unused variable 'sizeys2' [-Wunused-variable]
int sizeys2=propLocs(ys,probys,x,p);
^~~~~~~
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move.o src/move.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/param.o src/param.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/recorder.o src/recorder.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/tree_coal.o src/tree_coal.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/tree_simple.o src/tree_simple.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/tree_upgma.o src/tree_upgma.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/tree_newick.o src/tree_newick.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/tree.o src/tree.cpp
src/tree.cpp: In static member function 'static wb::Tree* wb::Tree::move(wb::Tree*, wb::Tree*, double, gsl_vector_char*, gsl_vector_char*, wb::Param*)':
src/tree.cpp:99:12: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (z!=NULL)
^
src/tree.cpp: In member function 'double wb::Tree::llhoodb(wb::Param*)':
src/tree.cpp:229:87: warning: 'vals[9]' may be used uninitialized in this function [-Wmaybe-uninitialized]
} else if (gsl_vector_char_get(recMap,i)==0) {ret+=vals[8];} else {ret+=vals[9];p->rec++;}
~~~^~~~~~~~~
src/tree.cpp:223:29: warning: 'vals[5]' may be used uninitialized in this function [-Wmaybe-uninitialized]
{ret+=vals[5];p->rec++;}
~~~^~~~~~~~~
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/util.o src/util.cpp
src/util.cpp: In static member function 'static void wb::Util::normalize(double*, int)':
src/util.cpp:83:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int i=0;i<size;i++) sum+=v[i];
~^~~~~
src/util.cpp:85:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int i=0;i<size;i++) v[i]/=sum;
~^~~~~
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/ClonalFrame.o src/ClonalFrame.cpp
src/ClonalFrame.cpp: In function 'gsl_rng* makerng()':
src/ClonalFrame.cpp:83:14: warning: variable 'rng_seed' set but not used [-Wunused-but-set-variable]
long int rng_seed;
^~~~~~~~
src/ClonalFrame.cpp: In function 'int main(int, char**)':
src/ClonalFrame.cpp:263:68: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
if (cleanup==true) {a->cleanUp();a->writeToFile("/tmp/out.xmfa");}
^
src/ClonalFrame.cpp:341:51: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
printf("Time spent in MH in seconds:%d\n",t2-t);
~~~~^
g++ -Wl,-O1 -Wl,-z,relro -Wl,-z,now -o bin/ClonalFrame build/alignment_xmfa.o build/alignment_structure.o build/alignment.o build/boot.o build/burst.o build/consensus.o build/genes.o build/hashcell.o build/move_ages.o build/move_delta.o build/move_gap.o build/move_hidden.o build/move_hidden2.o build/move_mu.o build/move_nu.o build/move_rho.o build/move_wb.o build/move.o build/param.o build/recorder.o build/tree_coal.o build/tree_simple.o build/tree_upgma.o build/tree_newick.o build/tree.o build/util.o build/ClonalFrame.o -lgsl -lgslcblas
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
dh_install -a
dh_installdocs -a
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_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/clonalframe/usr/bin/ClonalFrame 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/clonalframe/usr/bin/ClonalFrame was not linked against libgslcblas.so.0 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'clonalframe-dbgsym' in '../clonalframe-dbgsym_1.2-7_armhf.deb'.
dpkg-deb: building package 'clonalframe' in '../clonalframe_1.2-7_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../clonalframe_1.2-7_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build clonalframe-1.2
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-10-02T05:32:25Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
clonalframe_1.2-7_armhf.changes:
--------------------------------
Format: 1.8
Date: Tue, 26 Sep 2017 22:33:07 +0200
Source: clonalframe
Binary: clonalframe
Architecture: armhf
Version: 1.2-7
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
clonalframe - inference of bacterial microevolution using multilocus sequence d
Changes:
clonalframe (1.2-7) unstable; urgency=medium
.
* Do not link against Qt5 libraries (Thanks for the hint to
Christian Seiler <christian@iwakd.de>)
Checksums-Sha1:
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ef3c0ca16ee240f7eb8a25f40a562b8666ff3b20 4473 clonalframe_1.2-7_armhf.buildinfo
d1e5c2b09da0fa543477d976ff472bcd45334096 41484 clonalframe_1.2-7_armhf.deb
Checksums-Sha256:
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60a2b15516da496baac82f2b53ee22de654b1ec5ce8927dbe4c497025a8c0707 41484 clonalframe_1.2-7_armhf.deb
Files:
62e036239f59ae2c7a1b5be4f0774618 310202 debug optional clonalframe-dbgsym_1.2-7_armhf.deb
9fdc570c08d8a3000a7e737b19901bad 4473 science optional clonalframe_1.2-7_armhf.buildinfo
5bbfc211084cbc8e0c4e9f41cae623c6 41484 science optional clonalframe_1.2-7_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
clonalframe-dbgsym_1.2-7_armhf.deb
----------------------------------
new debian package, version 2.0.
size 310202 bytes: control archive=454 bytes.
382 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: clonalframe-dbgsym
Source: clonalframe
Version: 1.2-7
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 344
Depends: clonalframe (= 1.2-7)
Section: debug
Priority: optional
Description: debug symbols for clonalframe
Build-Ids: a5381921e0c8645122ae5fb5608d0f32c3ea2761
drwxr-xr-x root/root 0 2017-09-26 20:33 ./
drwxr-xr-x root/root 0 2017-09-26 20:33 ./usr/
drwxr-xr-x root/root 0 2017-09-26 20:33 ./usr/lib/
drwxr-xr-x root/root 0 2017-09-26 20:33 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-09-26 20:33 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-09-26 20:33 ./usr/lib/debug/.build-id/a5/
-rw-r--r-- root/root 341784 2017-09-26 20:33 ./usr/lib/debug/.build-id/a5/381921e0c8645122ae5fb5608d0f32c3ea2761.debug
drwxr-xr-x root/root 0 2017-09-26 20:33 ./usr/share/
drwxr-xr-x root/root 0 2017-09-26 20:33 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-09-26 20:33 ./usr/share/doc/clonalframe-dbgsym -> clonalframe
clonalframe_1.2-7_armhf.deb
---------------------------
new debian package, version 2.0.
size 41484 bytes: control archive=1051 bytes.
1232 bytes, 23 lines control
348 bytes, 5 lines md5sums
Package: clonalframe
Version: 1.2-7
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 101
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgsl23, libgslcblas0, libstdc++6 (>= 5.2)
Suggests: clonalframeml
Section: science
Priority: optional
Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm
Description: inference of bacterial microevolution using multilocus sequence data
ClonalFrame identifies the clonal relationships between the members of
a sample, while also estimating the chromosomal position of homologous
recombination events that have disrupted the clonal inheritance.
.
ClonalFrame can be applied to any kind of sequence data, from a single
fragment of DNA to whole genomes. It is well suited for the analysis of
MLST data, where 7 gene fragments have been sequenced, but becomes
progressively more powerful as the sequenced regions increase in length
and number up to whole genomes. However, it requires the sequences to be
aligned. If you have genomic data that is not aligned, it is recommend to
use Mauve which produces alignment of whole bacterial genomes in
exactly the format required for analysis with ClonalFrame.
drwxr-xr-x root/root 0 2017-09-26 20:33 ./
drwxr-xr-x root/root 0 2017-09-26 20:33 ./usr/
drwxr-xr-x root/root 0 2017-09-26 20:33 ./usr/bin/
-rwxr-xr-x root/root 87560 2017-09-26 20:33 ./usr/bin/ClonalFrame
drwxr-xr-x root/root 0 2017-09-26 20:33 ./usr/share/
drwxr-xr-x root/root 0 2017-09-26 20:33 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-09-26 20:33 ./usr/share/doc/clonalframe/
-rw-r--r-- root/root 412 2017-09-26 20:33 ./usr/share/doc/clonalframe/README.Debian
-rw-r--r-- root/root 987 2017-09-26 20:33 ./usr/share/doc/clonalframe/changelog.Debian.gz
-rw-r--r-- root/root 1268 2017-09-26 20:33 ./usr/share/doc/clonalframe/copyright
drwxr-xr-x root/root 0 2017-09-26 20:33 ./usr/share/man/
drwxr-xr-x root/root 0 2017-09-26 20:33 ./usr/share/man/man1/
-rw-r--r-- root/root 1055 2017-09-26 20:33 ./usr/share/man/man1/ClonalFrame.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 3976
Build-Time: 60
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 227
Job: clonalframe_1.2-7
Machine Architecture: armhf
Package: clonalframe
Package-Time: 304
Source-Version: 1.2-7
Space: 3976
Status: successful
Version: 1.2-7
--------------------------------------------------------------------------------
Finished at 2017-10-02T05:32:25Z
Build needed 00:05:04, 3976k disk space