spaced →
1.0.2+dfsg-1 →
armhf → 2016-04-05 07:26:11
sbuild (Debian sbuild) 0.68.0 (15 Jan 2016) on bm-wb-01
+==============================================================================+
| spaced 1.0.2+dfsg-1 (armhf) 05 Apr 2016 07:18 |
+==============================================================================+
Package: spaced
Version: 1.0.2+dfsg-1
Source Version: 1.0.2+dfsg-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/spaced-b2IfUU/spaced-1.0.2+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/spaced-b2IfUU' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/stretch-staging-armhf-sbuild-f5872478-10f7-4a1f-abab-531ec2c56e1d' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [8879 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [10.9 MB]
Fetched 19.8 MB in 21s (911 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'spaced' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/spaced.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/spaced.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 37.6 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main spaced 1.0.2+dfsg-1 (dsc) [1932 B]
Get:2 http://172.17.0.1/private stretch-staging/main spaced 1.0.2+dfsg-1 (tar) [28.3 kB]
Get:3 http://172.17.0.1/private stretch-staging/main spaced 1.0.2+dfsg-1 (diff) [7336 B]
Fetched 37.6 kB in 0s (1438 kB/s)
Download complete and in download only mode
+------------------------------------------------------------------------------+
| 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-3DU6Gg/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-3DU6Gg/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-3DU6Gg/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-3DU6Gg/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-3DU6Gg/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-3DU6Gg/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-3DU6Gg/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-3DU6Gg/apt_archive ./ Sources [214 B]
Get:5 file:/<<BUILDDIR>>/resolver-3DU6Gg/apt_archive ./ Packages [528 B]
Ign:4 file:/<<BUILDDIR>>/resolver-3DU6Gg/apt_archive ./ Sources
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Get:5 file:/<<BUILDDIR>>/resolver-3DU6Gg/apt_archive ./ Packages [528 B]
Reading package lists...
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
manpages
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 45 not upgraded.
Need to get 0 B/768 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-3DU6Gg/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
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+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 9), dh-autoreconf
Filtered Build-Depends: debhelper (>= 9), dh-autoreconf
dpkg-deb: building package 'sbuild-build-depends-spaced-dummy' in '/<<BUILDDIR>>/resolver-7D1m8a/apt_archive/sbuild-build-depends-spaced-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-7D1m8a/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-7D1m8a/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-7D1m8a/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-7D1m8a/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-7D1m8a/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-7D1m8a/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-7D1m8a/apt_archive ./ Sources [216 B]
Get:5 file:/<<BUILDDIR>>/resolver-7D1m8a/apt_archive ./ Packages [534 B]
Ign:4 file:/<<BUILDDIR>>/resolver-7D1m8a/apt_archive ./ Sources
Ign:5 file:/<<BUILDDIR>>/resolver-7D1m8a/apt_archive ./ Packages
Get:4 file:/<<BUILDDIR>>/resolver-7D1m8a/apt_archive ./ Sources [216 B]
Get:5 file:/<<BUILDDIR>>/resolver-7D1m8a/apt_archive ./ Packages [534 B]
Reading package lists...
Reading package lists...
Install spaced build dependencies (apt-based resolver)
------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
manpages
Use 'apt autoremove' to remove it.
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 libffi6
libfile-stripnondeterminism-perl libglib2.0-0 libicu55 libmagic1
libpipeline1 libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4
man-db po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libtool-doc gfortran | fortran95-compiler gcj-jdk less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
libltdl-dev xml-core 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 libffi6
libfile-stripnondeterminism-perl libglib2.0-0 libicu55 libmagic1
libpipeline1 libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4
man-db po-debconf sbuild-build-depends-spaced-dummy
0 upgraded, 31 newly installed, 0 to remove and 45 not upgraded.
Need to get 18.6 MB/18.6 MB of archives.
After this operation, 63.5 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-7D1m8a/apt_archive ./ sbuild-build-depends-spaced-dummy 0.invalid.0 [776 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.2-1 [88.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.9 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libicu55 armhf 55.1-7 [7380 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.3+dfsg1-1 [800 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-9 [338 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20150820.1 [71.7 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.7-2 [424 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.0-1 [2540 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.56-2 [94.9 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.016-1 [6998 B]
Get:29 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160313 [808 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-0.1 [200 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 11 [15.7 kB]
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Processing triggers for libc-bin (2.22-3) ...
Setting up groff-base (1.22.3-7) ...
Setting up libbsd0:armhf (0.8.2-1) ...
Setting up bsdmainutils (9.0.9) ...
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 libpipeline1:armhf (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up m4 (1.4.17-5) ...
Setting up autoconf (2.69-9) ...
Setting up autotools-dev (20150820.1) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up autopoint (0.19.7-2) ...
Setting up libffi6:armhf (3.2.1-4) ...
Setting up libglib2.0-0:armhf (2.48.0-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.19) ...
Setting up libarchive-zip-perl (1.56-2) ...
Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libtool (2.4.6-0.1) ...
Setting up dh-strip-nondeterminism (0.016-1) ...
Setting up debhelper (9.20160313) ...
Setting up dh-autoreconf (11) ...
Setting up sbuild-build-depends-spaced-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.22-3) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-5 dpkg-dev_1.18.4 g++-5_5.3.1-11 gcc-5_5.3.1-11 libc6-dev_2.22-3 libstdc++-5-dev_5.3.1-11 libstdc++6_5.3.1-11 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.114 apt_1.2.6 autoconf_2.69-9 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.5+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.26-5 bsdmainutils_9.0.9 bsdutils_1:2.27.1-6 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-11 dash_0.5.8-2.1 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160313 debianutils_4.7 dh-autoreconf_11 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.116-1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0+git+20160126-2 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-11 gcc_4:5.3.1-1+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_4.9.3-12 gcc-5_5.3.1-11 gcc-5-base_5.3.1-11 gettext_0.19.7-2 gettext-base_0.19.7-2 gnupg_1.4.20-4 gpgv_1.4.20-4 grep_2.22-1 groff-base_1.22.3-7 gzip_1.6-4 hostname_3.17 init_1.29 init-system-helpers_1.29 initscripts_2.88dsf-59.3 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-8+rpi1 kmod_22-1 libacl1_2.2.52-3 libapparmor1_2.10-3 libapt-pkg5.0_1.2.6 libarchive-zip-perl_1.56-2 libasan2_5.3.1-11 libatomic1_5.3.1-11 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libblkid1_2.27.1-6 libbsd0_0.8.2-1 libbz2-1.0_1.0.6-8 libc-bin_2.22-3 libc-dev-bin_2.22-3 libc6_2.22-3 libc6-dev_2.22-3 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-11 libcomerr2_1.42.13-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.8-1 libdebconfclient0_0.207 libdevmapper1.02.1_2:1.02.116-1 libdpkg-perl_1.18.4 libdrm2_2.4.67-1 libfakeroot_1.20.2-1 libfdisk1_2.27.1-6 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libgc1c2_1:7.4.2-7.3 libgcc-5-dev_5.3.1-11 libgcc1_1:5.3.1-11 libgcrypt20_1.6.5-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.48.0-1 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-11 libgpg-error0_1.21-2 libicu55_55.1-7 libisl15_0.16.1-1 libklibc_2.0.4-8+rpi1 libkmod2_22-1 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-6 libmpc3_1.0.3-1 libmpfr4_3.1.4-1 libncurses5_6.0+20160213-1 libncursesw5_6.0+20160213-1 libpam-modules_1.1.8-3.2 libpam-modules-bin_1.1.8-3.2 libpam-runtime_1.1.8-3.2 libpam0g_1.1.8-3.2 libpcre3_2:8.38-3 libperl5.22_5.22.1-9 libpipeline1_1.4.1-2 libpng12-0_1.2.54-4 libprocps5_2:3.3.11-3 libreadline6_6.3-8+b3 libseccomp2_2.2.3-3 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsigsegv2_2.10-5 libsmartcols1_2.27.1-6 libss2_1.42.13-1 libstdc++-5-dev_5.3.1-11 libstdc++6_5.3.1-11 libsystemd0_229-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160213-1 libtool_2.4.6-0.1 libubsan0_5.3.1-11 libudev1_229-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-6 libxml2_2.9.3+dfsg1-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160110+rpi1 m4_1.4.17-5 make_4.1-6 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.04-2 mawk_1.3.3-17 mount_2.27.1-6 multiarch-support_2.22-3 nano_2.5.3-2 ncurses-base_6.0+20160213-1 ncurses-bin_6.0+20160213-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-9 perl-base_5.22.1-9 perl-modules-5.22_5.22.1-9 po-debconf_1.0.19 procps_2:3.3.11-3 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-spaced-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_229-2 systemd-sysv_229-2 sysv-rc_2.88dsf-59.3 sysvinit-utils_2.88dsf-59.3 tar_1.28-2.1 tzdata_2016a-1 udev_229-2 util-linux_2.27.1-6 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Tue Mar 29 04:41:30 2016 UTC using RSA key ID AFE826FB
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./spaced_1.0.2+dfsg-1.dsc
dpkg-source: info: extracting spaced in spaced-1.0.2+dfsg
dpkg-source: info: unpacking spaced_1.0.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking spaced_1.0.2+dfsg-1.debian.tar.xz
dpkg-source: info: applying 0001-Add-man-page.patch
dpkg-source: info: applying 0002-Fix-FTBFS-without-OpenMP.patch
dpkg-source: info: applying 0003-Add-autotools-buildsystem.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-f5872478-10f7-4a1f-abab-531ec2c56e1d
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: source package spaced
dpkg-buildpackage: source version 1.0.2+dfsg-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build spaced-1.0.2+dfsg
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean --with autoreconf
dh_testdir
dh_auto_clean
dh_autoreconf_clean
dh_clean
debian/rules build-arch
dh build-arch --with autoreconf
dh_testdir -a
dh_update_autotools_config -a
dh_autoreconf -a
configure.ac:3: installing './install-sh'
configure.ac:3: installing './missing'
Makefile.am: installing './depcomp'
dh_auto_configure -a
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... none
checking for g++ option to support OpenMP... -fopenmp
checking whether g++ supports C++11 features by default... no
checking whether g++ supports C++11 features with -std=gnu++11... yes
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for inttypes.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for size_t... yes
checking for uint64_t... yes
checking for pow... yes
checking for sqrt... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
dh_auto_build -a
make -j1
make[1]: Entering directory '/<<BUILDDIR>>/spaced-1.0.2+dfsg'
make all-am
make[2]: Entering directory '/<<BUILDDIR>>/spaced-1.0.2+dfsg'
g++ -DHAVE_CONFIG_H -I. -Wall -Wextra -std=c++11 -Wno-char-subscripts -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o spaced-extkey.o `test -f 'extkey.cpp' || echo './'`extkey.cpp
g++ -DHAVE_CONFIG_H -I. -Wall -Wextra -std=c++11 -Wno-char-subscripts -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o spaced-patternset.o `test -f 'patternset.cpp' || echo './'`patternset.cpp
patternset.cpp:846:44: warning: unused parameter 'errmsg' [-Wunused-parameter]
void patternset::SecureMessage(std::string errmsg, int pos) {
^
patternset.cpp:846:56: warning: unused parameter 'pos' [-Wunused-parameter]
void patternset::SecureMessage(std::string errmsg, int pos) {
^
g++ -DHAVE_CONFIG_H -I. -Wall -Wextra -std=c++11 -Wno-char-subscripts -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o spaced-spaced.o `test -f 'spaced.cc' || echo './'`spaced.cc
In file included from spaced.cc:15:0:
sort.h: In function 'void getFirstBits(std::vector<unsigned char>&, unsigned char*, long long unsigned int, long unsigned int, unsigned char*, int)':
sort.h:83:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i<length;i++){
^
sort.h:96:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i<length;i++){
^
sort.h:108:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i<length;i++){
^
sort.h:120:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i<length;i++){
^
sort.h: In instantiation of 'void spacedDNA(std::vector<std::__cxx11::basic_string<char> >&, unsigned char*, uint, int, int, int, int, bool, std::__cxx11::string) [with uint = long long unsigned int; std::__cxx11::string = std::__cxx11::basic_string<char>]':
spaced.cc:223:112: required from here
sort.h:220:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(uint i=0; i<seqNum;i++){
^
sort.h:241:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i< sequences.size();i++){
^
sort.h:255:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int p = 0; p < patternSet.size(); p++ ){
^
sort.h:256:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int k = 0; k < patternSet[p].length(); k++){
^
sort.h:286:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int o=0; o<matchPos.size();o++){
^
sort.h:307:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int o=0; o<matchPos.size();o++){
^
sort.h: In instantiation of 'void spacedDNA(std::vector<std::__cxx11::basic_string<char> >&, unsigned char*, uint, int, int, int, int, bool, std::__cxx11::string) [with uint = unsigned int; std::__cxx11::string = std::__cxx11::basic_string<char>]':
spaced.cc:225:105: required from here
sort.h:220:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(uint i=0; i<seqNum;i++){
^
sort.h:241:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i< sequences.size();i++){
^
sort.h:255:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int p = 0; p < patternSet.size(); p++ ){
^
sort.h:256:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int k = 0; k < patternSet[p].length(); k++){
^
sort.h:286:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int o=0; o<matchPos.size();o++){
^
sort.h:307:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int o=0; o<matchPos.size();o++){
^
sort.h: In instantiation of 'void spacedProt(std::vector<std::__cxx11::basic_string<char> >&, unsigned char*, uint, int, int, int, int, std::__cxx11::string) [with uint = long long unsigned int; std::__cxx11::string = std::__cxx11::basic_string<char>]':
spaced.cc:242:110: required from here
sort.h:554:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int p = 0; p < patternSet.size(); p++ ){
^
sort.h:555:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int k = 0; k < patternSet[p].length(); k++){
^
sort.h:579:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int o=0; o<matchPos.size();o++){
^
sort.h:509:6: warning: unused variable 'ell' [-Wunused-variable]
int ell=dontCare+weight-1;
^
sort.h: In instantiation of 'void spacedProt(std::vector<std::__cxx11::basic_string<char> >&, unsigned char*, uint, int, int, int, int, std::__cxx11::string) [with uint = unsigned int; std::__cxx11::string = std::__cxx11::basic_string<char>]':
spaced.cc:244:104: required from here
sort.h:554:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int p = 0; p < patternSet.size(); p++ ){
^
sort.h:555:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int k = 0; k < patternSet[p].length(); k++){
^
sort.h:579:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int o=0; o<matchPos.size();o++){
^
sort.h:509:6: warning: unused variable 'ell' [-Wunused-variable]
int ell=dontCare+weight-1;
^
sort.h: In instantiation of 'void writeDmat(std::vector<std::vector<double> >, std::vector<sequence<uint> >&, std::__cxx11::string, unsigned char*) [with uint = long long unsigned int; std::__cxx11::string = std::__cxx11::basic_string<char>]':
sort.h:502:17: required from 'void spacedDNA(std::vector<std::__cxx11::basic_string<char> >&, unsigned char*, uint, int, int, int, int, bool, std::__cxx11::string) [with uint = long long unsigned int; std::__cxx11::string = std::__cxx11::basic_string<char>]'
spaced.cc:223:112: required from here
sort.h:133:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < sequences.size(); i++) {
^
sort.h:141:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < sequences.size(); j++) {
^
sort.h: In instantiation of 'void writeDmat(std::vector<std::vector<double> >, std::vector<sequence<uint> >&, std::__cxx11::string, unsigned char*) [with uint = unsigned int; std::__cxx11::string = std::__cxx11::basic_string<char>]':
sort.h:502:17: required from 'void spacedDNA(std::vector<std::__cxx11::basic_string<char> >&, unsigned char*, uint, int, int, int, int, bool, std::__cxx11::string) [with uint = unsigned int; std::__cxx11::string = std::__cxx11::basic_string<char>]'
spaced.cc:225:105: required from here
sort.h:133:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < sequences.size(); i++) {
^
sort.h:141:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < sequences.size(); j++) {
^
g++ -DHAVE_CONFIG_H -I. -Wall -Wextra -std=c++11 -Wno-char-subscripts -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o spaced-variance.o `test -f 'variance.cpp' || echo './'`variance.cpp
variance.cpp:627:42: warning: unused parameter 'errmsg' [-Wunused-parameter]
void variance::SecureMessage(std::string errmsg) {
^
g++ -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -Wl,-z,relro -o spaced spaced-extkey.o spaced-patternset.o spaced-spaced.o spaced-variance.o
make[2]: Leaving directory '/<<BUILDDIR>>/spaced-1.0.2+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/spaced-1.0.2+dfsg'
dh_auto_test -a
make -j1 check VERBOSE=1
make[1]: Entering directory '/<<BUILDDIR>>/spaced-1.0.2+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/spaced-1.0.2+dfsg'
fakeroot debian/rules binary-arch
dh binary-arch --with autoreconf
dh_testroot -a
dh_prep -a
dh_auto_install -a
make -j1 install DESTDIR=/<<BUILDDIR>>/spaced-1.0.2\+dfsg/debian/spaced AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<BUILDDIR>>/spaced-1.0.2+dfsg'
make[2]: Entering directory '/<<BUILDDIR>>/spaced-1.0.2+dfsg'
/bin/mkdir -p '/<<BUILDDIR>>/spaced-1.0.2+dfsg/debian/spaced/usr/bin'
/usr/bin/install -c spaced '/<<BUILDDIR>>/spaced-1.0.2+dfsg/debian/spaced/usr/bin'
/bin/mkdir -p '/<<BUILDDIR>>/spaced-1.0.2+dfsg/debian/spaced/usr/share/man/man1'
/usr/bin/install -c -m 644 spaced.1 '/<<BUILDDIR>>/spaced-1.0.2+dfsg/debian/spaced/usr/share/man/man1'
make[2]: Leaving directory '/<<BUILDDIR>>/spaced-1.0.2+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/spaced-1.0.2+dfsg'
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_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/spaced/usr/bin/spaced 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/spaced/usr/bin/spaced was not linked against libpthread.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/spaced/usr/bin/spaced was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'spaced-dbgsym' in '../spaced-dbgsym_1.0.2+dfsg-1_armhf.deb'.
dpkg-deb: building package 'spaced' in '../spaced_1.0.2+dfsg-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../spaced_1.0.2+dfsg-1_armhf.changes
dpkg-genchanges: warning: package spaced-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build spaced-1.0.2+dfsg
dpkg-buildpackage: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160405-0725
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
spaced_1.0.2+dfsg-1_armhf.changes:
----------------------------------
Format: 1.8
Date: Mon, 28 Mar 2016 19:41:33 +0200
Source: spaced
Binary: spaced
Architecture: armhf
Version: 1.0.2+dfsg-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Fabian Klötzl <kloetzl@evolbio.mpg.de>
Description:
spaced - alignment-free sequence comparison using spaced words
Closes: 815672
Changes:
spaced (1.0.2+dfsg-1) unstable; urgency=medium
.
* Initial release (Closes: #815672)
* Remove the precompiled binary via get-orig-source script
* Add a manpage
* Fix a problem if the compiler does not support OpenMP
* Add autotools as proper build system
Checksums-Sha1:
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9e52f7ee5b1c6d338901bc96e53916482ddb5cfd 43300 spaced_1.0.2+dfsg-1_armhf.deb
Checksums-Sha256:
c1ea255edaf38ffcdf95a14a8139fc327969b0c9a29b9075343ec46268eb6064 377536 spaced-dbgsym_1.0.2+dfsg-1_armhf.deb
2aec6fa77658145bd695ec63f3de46df9da68788e2772879a8c1f9f177bf4c39 43300 spaced_1.0.2+dfsg-1_armhf.deb
Files:
dddc1f67c8c200520971650b358fe125 377536 debug extra spaced-dbgsym_1.0.2+dfsg-1_armhf.deb
1514b40c3f05eb777ef568c269f2111e 43300 science optional spaced_1.0.2+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
spaced-dbgsym_1.0.2+dfsg-1_armhf.deb
------------------------------------
new debian package, version 2.0.
size 377536 bytes: control archive=484 bytes.
408 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: spaced-dbgsym
Source: spaced
Version: 1.0.2+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 401
Depends: spaced (= 1.0.2+dfsg-1)
Section: debug
Priority: extra
Homepage: http://spaced.gobics.de/
Description: Debug symbols for spaced
Auto-Built-Package: debug-symbols
Build-Ids: 42968fb1ef067209be54ddf5e6681f72ad2cc51f
drwxr-xr-x root/root 0 2016-04-05 07:25 ./
drwxr-xr-x root/root 0 2016-04-05 07:25 ./usr/
drwxr-xr-x root/root 0 2016-04-05 07:25 ./usr/lib/
drwxr-xr-x root/root 0 2016-04-05 07:25 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-04-05 07:25 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-04-05 07:25 ./usr/lib/debug/.build-id/42/
-rw-r--r-- root/root 399556 2016-04-05 07:25 ./usr/lib/debug/.build-id/42/968fb1ef067209be54ddf5e6681f72ad2cc51f.debug
drwxr-xr-x root/root 0 2016-04-05 07:25 ./usr/share/
drwxr-xr-x root/root 0 2016-04-05 07:25 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-04-05 07:25 ./usr/share/doc/spaced-dbgsym -> spaced
spaced_1.0.2+dfsg-1_armhf.deb
-----------------------------
new debian package, version 2.0.
size 43300 bytes: control archive=987 bytes.
1349 bytes, 24 lines control
254 bytes, 4 lines md5sums
Package: spaced
Version: 1.0.2+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 112
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgomp1 (>= 4.9), libstdc++6 (>= 5.2)
Section: science
Priority: optional
Homepage: http://spaced.gobics.de/
Description: alignment-free sequence comparison using spaced words
Spaced (Words) is a new approach to alignment-free sequence
comparison. While most alignment-free algorithms compare the
word-composition of sequences, spaced uses a pattern of care and
don't care positions. The occurrence of a spaced word in a sequence
is then defined by the characters at the match positions only, while
the characters at the don't care positions are ignored. Instead of
comparing the frequencies of contiguous words in the input sequences,
this new approach compares the frequencies of the spaced words according
to the pre-defined pattern. An information-theoretic distance measure
is then used to define pairwise distances on the set of input sequences
based on their spaced-word frequencies. Systematic test runs on real and
simulated sequence sets have shown that, for phylogeny reconstruction,
this multiple-spaced-words approach is far superior to the classical
alignment-free approach based on contiguous word frequencies.
drwxr-xr-x root/root 0 2016-04-05 07:25 ./
drwxr-xr-x root/root 0 2016-04-05 07:25 ./usr/
drwxr-xr-x root/root 0 2016-04-05 07:25 ./usr/bin/
-rwxr-xr-x root/root 100224 2016-04-05 07:25 ./usr/bin/spaced
drwxr-xr-x root/root 0 2016-04-05 07:25 ./usr/share/
drwxr-xr-x root/root 0 2016-04-05 07:25 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-04-05 07:25 ./usr/share/doc/spaced/
-rw-r--r-- root/root 278 2016-03-29 03:18 ./usr/share/doc/spaced/changelog.Debian.gz
-rw-r--r-- root/root 1846 2016-03-29 04:13 ./usr/share/doc/spaced/copyright
drwxr-xr-x root/root 0 2016-04-05 07:25 ./usr/share/man/
drwxr-xr-x root/root 0 2016-04-05 07:25 ./usr/share/man/man1/
-rw-r--r-- root/root 1674 2016-04-05 07:25 ./usr/share/man/man1/spaced.1.gz
+------------------------------------------------------------------------------+
| Post Build |
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+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 5556
Build-Time: 144
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 202
Job: spaced_1.0.2+dfsg-1
Machine Architecture: armhf
Package: spaced
Package-Time: 388
Source-Version: 1.0.2+dfsg-1
Space: 5556
Status: successful
Version: 1.0.2+dfsg-1
--------------------------------------------------------------------------------
Finished at 20160405-0725
Build needed 00:06:28, 5556k disc space