clonalframe →
1.2-9 →
armhf → 2018-12-06 12:06:29
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| clonalframe 1.2-9 (armhf) Thu, 06 Dec 2018 12:03:48 +0000 |
+==============================================================================+
Package: clonalframe
Version: 1.2-9
Source Version: 1.2-9
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-007603a7-0507-4492-8e69-ab45f134b4ac' 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 [11.2 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.0 MB]
Fetched 24.2 MB in 9s (2787 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://salsa.debian.org/med-team/clonalframe.git
Please use:
git clone https://salsa.debian.org/med-team/clonalframe.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 52.6 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main clonalframe 1.2-9 (dsc) [1991 B]
Get:2 http://172.17.0.1/private buster-staging/main clonalframe 1.2-9 (tar) [45.5 kB]
Get:3 http://172.17.0.1/private buster-staging/main clonalframe 1.2-9 (diff) [5156 B]
Fetched 52.6 kB in 0s (420 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/clonalframe-4girpC/clonalframe-1.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/clonalframe-4girpC' 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-pBVwaq/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-pBVwaq/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-pBVwaq/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-pBVwaq/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-pBVwaq/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-pBVwaq/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-pBVwaq/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-pBVwaq/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (11.0 kB/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 dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libgpg-error-l10n libnss-systemd libpam-systemd libssl1.1 openssl
systemd-sysv
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 1 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-pBVwaq/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15783 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 (>= 11~), qt5-qmake, libgsl-dev
Filtered Build-Depends: debhelper (>= 11~), qt5-qmake, libgsl-dev
dpkg-deb: building package 'sbuild-build-depends-clonalframe-dummy' in '/<<BUILDDIR>>/resolver-pBVwaq/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-pBVwaq/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-pBVwaq/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-pBVwaq/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-pBVwaq/apt_archive ./ Sources [508 B]
Get:5 copy:/<<BUILDDIR>>/resolver-pBVwaq/apt_archive ./ Packages [586 B]
Fetched 2427 B in 0s (12.6 kB/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 dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libgpg-error-l10n libnss-systemd libpam-systemd libssl1.1 openssl
systemd-sysv
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 dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl23
libgslcblas0 libicu63 libmagic-mgc libmagic1 libpipeline1 libsigsegv2
libtool libxml2 m4 man-db po-debconf qt5-qmake qt5-qmake-bin 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 apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl23
libgslcblas0 libicu63 libmagic-mgc libmagic1 libpipeline1 libsigsegv2
libtool libxml2 m4 man-db po-debconf qt5-qmake qt5-qmake-bin qtchooser
sbuild-build-depends-clonalframe-dummy
0 upgraded, 37 newly installed, 0 to remove and 1 not upgraded.
Need to get 20.6 MB/20.7 MB of archives.
After this operation, 76.7 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-pBVwaq/apt_archive ./ sbuild-build-depends-clonalframe-dummy 0.invalid.0 [872 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-2 [25.1 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-3 [1160 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-6 [547 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.45.0-1 [20.5 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.45.0-1 [12.4 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.1-2 [1051 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-4 [7974 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 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 1.0.21 [248 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.5.3 [1002 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libgslcblas0 armhf 2.5+dfsg-5 [78.8 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libgsl23 armhf 2.5+dfsg-5 [703 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libgsl-dev armhf 2.5+dfsg-5 [894 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf qt5-qmake-bin armhf 5.11.2+dfsg-7+rpi1 [779 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf qtchooser armhf 66-1 [23.0 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf qt5-qmake armhf 5.11.2+dfsg-7+rpi1 [221 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libarchive-zip-perl (1.64-1) ...
Setting up libicu63:armhf (63.1-4) ...
Setting up qt5-qmake-bin (5.11.2+dfsg-7+rpi1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libelf1:armhf (0.170-0.5) ...
Setting up groff-base (1.22.3-10) ...
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No schema files found: removed existing output file.
Setting up qtchooser (66-1) ...
Setting up gettext-base (0.19.8.1-9) ...
Setting up libpipeline1:armhf (1.5.0-2) ...
Setting up m4 (1.4.18-1) ...
Setting up libbsd0:armhf (0.9.1-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+b1) ...
Setting up libmagic-mgc (1:5.34-2) ...
Setting up libmagic1:armhf (1:5.34-2) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up qt5-qmake:armhf (5.11.2+dfsg-7+rpi1) ...
Processing triggers for libc-bin (2.27-8+rpi1) ...
Setting up dwz (0.12-2) ...
Setting up autotools-dev (20180224.1) ...
Setting up bsdmainutils (11.1.2) ...
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 (2.5+dfsg-5) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up libfile-stripnondeterminism-perl (0.45.0-1) ...
Setting up libgsl23:armhf (2.5+dfsg-5) ...
Setting up gettext (0.19.8.1-9) ...
Setting up libgsl-dev (2.5+dfsg-5) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.34-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.4-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-6) ...
Setting up po-debconf (1.0.21) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (0.45.0-1) ...
Setting up debhelper (11.5.3) ...
Setting up sbuild-build-depends-clonalframe-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-8+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.31.1-10+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-9+rpi1 gcc-8_8.2.0-9+rpi1 libc6-dev_2.27-8+rpi1 libstdc++-8-dev_8.2.0-9+rpi1 libstdc++6_8.2.0-9+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~alpha2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-10+rpi1 binutils-arm-linux-gnueabihf_2.31.1-10+rpi1 binutils-common_2.31.1-10+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-9+rpi1 dash_0.5.10.2-1 dbus_1.12.10-1 dbus-user-session_1.12.10-1 debconf_1.5.69 debhelper_11.5.3 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.45.0-1 diffutils_1:3.6-1 dirmngr_2.2.11-1 dmsetup_2:1.02.145-4.1+b5 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-2 e2fslibs_1.44.4-2 e2fsprogs_1.44.4-2 e2fsprogs-l10n_1.44.4-2 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20181018-1 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-9+rpi1 gcc_4:8.2.0-2+rpi1 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_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-9+rpi1 gcc-8-base_8.2.0-9+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.11-1 gnupg-agent_2.2.11-1 gnupg-l10n_2.2.11-1 gnupg-utils_2.2.11-1 gpg_2.2.11-1 gpg-agent_2.2.11-1 gpg-wks-client_2.2.11-1 gpg-wks-server_2.2.11-1 gpgconf_2.2.11-1 gpgsm_2.2.11-1 gpgv_2.2.11-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2.1 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-2 krb5-locales_1.16.1-1 libacl1_2.2.52-3 libapparmor1_2.13.1-3+b1 libapt-pkg5.0_1.8.0~alpha2 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-9+rpi1 libassuan0_2.5.1-2 libatomic1_8.2.0-9+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libbinutils_2.31.1-10+rpi1 libblkid1_2.32.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.27-8+rpi1 libc-dev-bin_2.27-8+rpi1 libc6_2.27-8+rpi1 libc6-dev_2.27-8+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-9+rpi1 libcom-err2_1.44.4-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.5-2 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.10-1 libdebconfclient0_0.245 libdevmapper1.02.1_2:1.02.145-4.1+b5 libdpkg-perl_1.19.2 libdrm-common_2.4.95-1+rpi1 libdrm2_2.4.95-1+rpi1 libelf1_0.170-0.5 libexpat1_2.2.6-1 libext2fs2_1.44.4-2 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_0.45.0-1 libgcc-8-dev_8.2.0-9+rpi1 libgcc1_1:8.2.0-9+rpi1 libgcrypt20_1.8.4-3 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.19-1+b1 libgomp1_8.2.0-9+rpi1 libgpg-error-l10n_1.32-3 libgpg-error0_1.32-3 libgsl-dev_2.5+dfsg-5 libgsl23_2.5+dfsg-5 libgslcblas0_2.5+dfsg-5 libgssapi-krb5-2_1.16.1-1 libhogweed4_3.4-1 libicu63_63.1-4 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-2 libisl19_0.20-2 libjson-c3_0.12.1-1.3 libk5crypto3_1.16.1-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkmod2_25-2 libkrb5-3_1.16.1-1 libkrb5support0_1.16.1-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1+b1 libldap-common_2.4.46+dfsg-5+rpi1 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1+20181013-1 libncurses6_6.1+20181013-1 libncursesw5_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4-1 libnpth0_1.6-1 libnss-systemd_239-13+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.8 libpam-modules-bin_1.1.8-3.8 libpam-runtime_1.1.8-3.8 libpam-systemd_239-13+rpi1 libpam0g_1.1.8-3.8 libpcre3_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.28_5.28.1-1 libpipeline1_1.5.0-2 libplymouth4_0.9.4-1 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libreadline7_7.0-5 libsasl2-2_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32.1-0.1 libsqlite3-0_3.25.3-2 libss2_1.44.4-2 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-9+rpi1 libstdc++6_8.2.0-9+rpi1 libsystemd0_239-13+rpi1 libtasn1-6_4.13-3 libtinfo5_6.1+20181013-1 libtinfo6_6.1+20181013-1 libtool_2.4.6-6 libubsan1_8.2.0-9+rpi1 libudev1_239-13+rpi1 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32.1-0.1 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.5+dfsg-1+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.4-3 mawk_1.3.3-17 mount_2.32.1-0.1 multiarch-support_2.27-8+rpi1 nano_3.2-1 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 netbase_5.5 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-1 perl-base_5.28.1-1 perl-modules-5.24_5.24.1-7 perl-modules-5.28_5.28.1-1 pinentry-curses_1.1.0-1 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 qt5-qmake_5.11.2+dfsg-7+rpi1 qt5-qmake-bin_5.11.2+dfsg-7+rpi1 qtchooser_66-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-clonalframe-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.5-2 sensible-utils_0.0.12 systemd_239-13+rpi1 systemd-sysv_239-13+rpi1 sysvinit-utils_2.92~beta-2 tar_1.30+dfsg-3+rpi1 tzdata_2018g-1 udev_239-13+rpi1 util-linux_2.32.1-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Dec 1 06:09:28 2018 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_1.2-9.dsc
dpkg-source: info: extracting clonalframe in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking clonalframe_1.2.orig.tar.gz
dpkg-source: info: unpacking clonalframe_1.2-9.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 01_gcc-4.6.patch
dpkg-source: info: applying no_qtlibs.patch
dpkg-source: info: applying glibc2.27.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-007603a7-0507-4492-8e69-ab45f134b4ac
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package clonalframe
dpkg-buildpackage: info: source version 1.2-9
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_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
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
QT_SELECT=5 CXXFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive" dh_auto_configure
qmake -makefile "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 -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -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
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a
make V=1 -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/alignment_xmfa.o src/alignment_xmfa.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/alignment_structure.o src/alignment_structure.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/alignment.o src/alignment.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/boot.o src/boot.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 of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
for (unsigned int i=0;i<getB();i++) {
~^~~~~~~
src/alignment.cpp:243:36: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
for (unsigned int j=0;j<getN();j++) {
~^~~~~~~
src/alignment.cpp:244:42: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
for (unsigned int k=beg;k<end;k++)
~^~~~
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')
~~^~~~~
src/alignment.cpp:246:37: 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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/burst.o src/burst.cpp
src/alignment_xmfa.cpp: In constructor 'wb::Alignment_xmfa::Alignment_xmfa(char*, bool, int)':
src/alignment_xmfa.cpp:129:31: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
for (j=0;j<strlen(bufin[i]);j++) {
~^~~~~~~~~~~~~~~~~
src/alignment_xmfa.cpp: In member function 'void wb::Alignment_xmfa::Fgets(char*, int, FILE*)':
src/alignment_xmfa.cpp:187:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(buf,l,f);
~~~~~^~~~~~~~~
src/alignment_xmfa.cpp:189:18: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(buf,l,f);
~~~~~^~~~~~~~~
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/genes.o src/genes.cpp
src/genes.cpp: In constructor 'wb::Genes::Genes(wb::Alignment*, char*, char*)':
src/genes.cpp:34:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
fscanf(mapf,"%d",&buf);
~~~~~~^~~~~~~~~~~~~~~~
src/genes.cpp:53:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
fscanf(genes,"%d %d",&f1,&f2);
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/hashcell.o src/hashcell.cpp
src/burst.cpp: In member function 'void wb::Burst::burst(wb::Param*)':
src/burst.cpp:188:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (k=1;k<rid->size();k++)
~^~~~~~~~~~~~
src/burst.cpp:190:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'unsigned int'} and 'int' [-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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_ages.o src/move_ages.cpp
src/consensus.cpp: In member function 'char* wb::Consensus::retConsensus(double)':
src/consensus.cpp:148:14: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
bool all[n];
^~~
src/consensus.cpp:148:14: note: in a call to built-in allocation function 'void* __builtin_alloca_with_align(unsigned int, unsigned int)'
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_delta.o src/move_delta.cpp
src/hashcell.cpp: In member function 'void wb::HashCell::addNode(wb::Tree*)':
src/hashcell.cpp:51:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if (l>=t->recMap->size) break;
~^~~~~~~~~~~~~~~~~
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_gap.o src/move_gap.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");
^
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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_hidden.o src/move_hidden.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_mu.o src/move_mu.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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_nu.o src/move_nu.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 of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
for (unsigned int i=0;i<L;i++)
~^~
src/move_hidden.cpp:133:40: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-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 of integer expressions of different signedness: 'unsigned int' and 'int' [-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);
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_rho.o src/move_rho.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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/move_wb.o src/move_wb.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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/param.o src/param.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)
~~~~~~~~^
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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/tree.o src/tree.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/util.o src/util.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/arm-linux-gnueabihf/qt5/mkspecs/linux-g++ -o build/ClonalFrame.o src/ClonalFrame.cpp
src/util.cpp: In static member function 'static void wb::Util::normalize(double*, int)':
src/util.cpp:83:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
for (unsigned int i=0;i<size;i++) sum+=v[i];
~^~~~~
src/util.cpp:85:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
for (unsigned int i=0;i<size;i++) v[i]/=sum;
~^~~~~
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++;}
~~~^~~~~~~~~
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:341:12: 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);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~
src/ClonalFrame.cpp: In function 'gsl_rng* makerng()':
src/ClonalFrame.cpp:96:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&seed,sizeof(seed),1,devrandom);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -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[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' in '../clonalframe_1.2-9_armhf.deb'.
dpkg-deb: building package 'clonalframe-dbgsym' in '../clonalframe-dbgsym_1.2-9_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../clonalframe_1.2-9_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-12-06T12:06:27Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
clonalframe_1.2-9_armhf.changes:
--------------------------------
Format: 1.8
Date: Sat, 01 Dec 2018 07:06:11 +0100
Source: clonalframe
Binary: clonalframe
Architecture: armhf
Version: 1.2-9
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
Closes: 915009
Changes:
clonalframe (1.2-9) unstable; urgency=medium
.
* More easy way to propagate Debian build flags (thanks to Jonas Smedegaard
for the hint)
Closes: #915009
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
Checksums-Sha1:
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40ae0d93188596edf40377addddd8014a3bf98c7 4643 clonalframe_1.2-9_armhf.buildinfo
fe54ef505e65a8e3352d927e8de654c4b7e2f1d0 41488 clonalframe_1.2-9_armhf.deb
Checksums-Sha256:
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Files:
e48da3e9865901e8368d145e287c4612 458624 debug optional clonalframe-dbgsym_1.2-9_armhf.deb
7cbce0cb8f8eccbe5c3b5c198ec85a3d 4643 science optional clonalframe_1.2-9_armhf.buildinfo
c6fc95751d6115d5adce529722880a25 41488 science optional clonalframe_1.2-9_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
clonalframe-dbgsym_1.2-9_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 458624 bytes: control archive=536 bytes.
382 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: clonalframe-dbgsym
Source: clonalframe
Version: 1.2-9
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 495
Depends: clonalframe (= 1.2-9)
Section: debug
Priority: optional
Description: debug symbols for clonalframe
Build-Ids: b7f380e8e0315a7cea0079613d67224c10c3fe85
drwxr-xr-x root/root 0 2018-12-01 06:06 ./
drwxr-xr-x root/root 0 2018-12-01 06:06 ./usr/
drwxr-xr-x root/root 0 2018-12-01 06:06 ./usr/lib/
drwxr-xr-x root/root 0 2018-12-01 06:06 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-12-01 06:06 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-12-01 06:06 ./usr/lib/debug/.build-id/b7/
-rw-r--r-- root/root 496232 2018-12-01 06:06 ./usr/lib/debug/.build-id/b7/f380e8e0315a7cea0079613d67224c10c3fe85.debug
drwxr-xr-x root/root 0 2018-12-01 06:06 ./usr/share/
drwxr-xr-x root/root 0 2018-12-01 06:06 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-12-01 06:06 ./usr/share/doc/clonalframe-dbgsym -> clonalframe
clonalframe_1.2-9_armhf.deb
---------------------------
new Debian package, version 2.0.
size 41488 bytes: control archive=1140 bytes.
1250 bytes, 23 lines control
348 bytes, 5 lines md5sums
Package: clonalframe
Version: 1.2-9
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 102
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgsl23 (>= 2.5), libgslcblas0 (>= 2.4), 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 2018-12-01 06:06 ./
drwxr-xr-x root/root 0 2018-12-01 06:06 ./usr/
drwxr-xr-x root/root 0 2018-12-01 06:06 ./usr/bin/
-rwxr-xr-x root/root 87560 2018-12-01 06:06 ./usr/bin/ClonalFrame
drwxr-xr-x root/root 0 2018-12-01 06:06 ./usr/share/
drwxr-xr-x root/root 0 2018-12-01 06:06 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-12-01 06:06 ./usr/share/doc/clonalframe/
-rw-r--r-- root/root 412 2018-12-01 06:06 ./usr/share/doc/clonalframe/README.Debian
-rw-r--r-- root/root 1173 2018-12-01 06:06 ./usr/share/doc/clonalframe/changelog.Debian.gz
-rw-r--r-- root/root 1300 2018-12-01 06:06 ./usr/share/doc/clonalframe/copyright
drwxr-xr-x root/root 0 2018-12-01 06:06 ./usr/share/man/
drwxr-xr-x root/root 0 2018-12-01 06:06 ./usr/share/man/man1/
-rw-r--r-- root/root 1055 2018-12-01 06:06 ./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: 5280
Build-Time: 22
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 122
Job: clonalframe_1.2-9
Machine Architecture: armhf
Package: clonalframe
Package-Time: 159
Source-Version: 1.2-9
Space: 5280
Status: successful
Version: 1.2-9
--------------------------------------------------------------------------------
Finished at 2018-12-06T12:06:27Z
Build needed 00:02:39, 5280k disk space