minimap →
0.2-3 →
armhf → 2016-08-06 11:20:40
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on bm-wb-03
+==============================================================================+
| minimap 0.2-3 (armhf) 06 Aug 2016 11:14 |
+==============================================================================+
Package: minimap
Version: 0.2-3
Source Version: 0.2-3
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/minimap-IC_zGA/minimap-0.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/minimap-IC_zGA' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-eef9b2b7-fa67-41cc-9e5f-a50487b60d88' 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 [9204 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.1 MB]
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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: 'minimap' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/minimap.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/minimap.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 112 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main minimap 0.2-3 (dsc) [2064 B]
Get:2 http://172.17.0.1/private stretch-staging/main minimap 0.2-3 (tar) [31.2 kB]
Get:3 http://172.17.0.1/private stretch-staging/main minimap 0.2-3 (diff) [78.5 kB]
Fetched 112 kB in 0s (1571 kB/s)
Download complete and in download only mode
Check architectures
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Check dependencies
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-tU8IEJ/apt_archive/sbuild-build-depends-core-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Get:1 file:/<<BUILDDIR>>/resolver-tU8IEJ/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-tU8IEJ/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-tU8IEJ/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-tU8IEJ/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-tU8IEJ/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-tU8IEJ/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-tU8IEJ/apt_archive ./ Sources [214 B]
Get:5 file:/<<BUILDDIR>>/resolver-tU8IEJ/apt_archive ./ Packages [526 B]
Reading package lists...
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W: file:///<<BUILDDIR>>/resolver-tU8IEJ/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
Reading package lists...
+------------------------------------------------------------------------------+
| Install core build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 57 not upgraded.
Need to get 0 B/762 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-tU8IEJ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [762 B]
debconf: delaying package configuration, since apt-utils is not installed
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Merged Build-Depends: debhelper (>= 9), d-shlibs, zlib1g-dev
Filtered Build-Depends: debhelper (>= 9), d-shlibs, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-minimap-dummy' in '/<<BUILDDIR>>/resolver-yNd75B/apt_archive/sbuild-build-depends-minimap-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Get:1 file:/<<BUILDDIR>>/resolver-yNd75B/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-yNd75B/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-yNd75B/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-yNd75B/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-yNd75B/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-yNd75B/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-yNd75B/apt_archive ./ Sources [226 B]
Get:5 file:/<<BUILDDIR>>/resolver-yNd75B/apt_archive ./ Packages [541 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-yNd75B/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
Reading package lists...
+------------------------------------------------------------------------------+
| Install minimap build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils d-shlibs 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 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libunistring0
libxml2 m4 man-db po-debconf zlib1g-dev
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 d-shlibs 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 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libunistring0
libxml2 m4 man-db po-debconf sbuild-build-depends-minimap-dummy zlib1g-dev
0 upgraded, 34 newly installed, 0 to remove and 57 not upgraded.
Need to get 11.5 MB/18.9 MB of archives.
After this operation, 64.5 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-yNd75B/apt_archive ./ sbuild-build-depends-minimap-dummy 0.invalid.0 [784 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [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 libmagic-mgc armhf 1:5.28-4 [210 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-4 [104 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-4 [62.7 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-1 [804 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf d-shlibs all 0.75 [18.0 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.1-2 [2546 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 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 1.57-1 [95.1 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.022-1 [13.1 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 0.022-1 [7902 B]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-0.1 [200 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160709 [799 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
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Processing triggers for libc-bin (2.23-1+rpi1) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libarchive-zip-perl (1.57-1) ...
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Setting up libsigsegv2:armhf (2.10-5) ...
Setting up groff-base (1.22.3-8) ...
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Setting up gettext-base (0.19.8.1-1) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up m4 (1.4.17-5) ...
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Setting up libffi6:armhf (3.2.1-4) ...
Setting up bsdmainutils (9.0.10) ...
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 autopoint (0.19.8.1-1) ...
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Setting up libglib2.0-0:armhf (2.48.1-2) ...
No schema files found: doing nothing.
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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 man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-0.1) ...
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Processing triggers for libc-bin (2.23-1+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26.1-1 dpkg-dev_1.18.7 g++-5_5.4.0-4 gcc-5_5.4.0-4 libc6-dev_2.23-1+rpi1 libstdc++-5-dev_5.4.0-4 libstdc++6_6.1.1-1+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3~pre2 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-15 binutils_2.26.1-1 bsdmainutils_9.0.10 bsdutils_1:2.28-5 build-essential_11.7 bzip2_1.0.6-8 console-setup_1.146 console-setup-linux_1.146 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-3 cpp-5_5.4.0-4 d-shlibs_0.75 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160709 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.022-1 diffutils_1:3.3-3 dmsetup_2:1.02.127-1 dpkg_1.18.7 dpkg-dev_1.18.7 e2fslibs_1.43.1-1 e2fsprogs_1.43.1-1 fakeroot_1.21-1 file_1:5.28-4 findutils_4.6.0+git+20160517-5 fuse2fs_1.43.1-1 g++_4:5.3.1-3 g++-5_5.4.0-4 gcc_4:5.3.1-3 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_5.4.0-4 gcc-5-base_5.4.0-4 gcc-6-base_6.1.1-1+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_1.4.20-6 gpgv_1.4.20-6 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 hostname_3.18 ifupdown_0.8.13 init_1.36 init-system-helpers_1.36 initscripts_2.88dsf-59.7 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 iproute2_4.3.0-1 kbd_2.0.3-2 keyboard-configuration_1.146 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10.95-4 libapt-pkg5.0_1.3~pre2 libarchive-zip-perl_1.57-1 libasan2_5.4.0-4 libatm1_1:2.5.1-1.6 libatomic1_6.1.1-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.5.2-1+rpi1 libaudit1_1:2.5.2-1+rpi1 libblkid1_2.28-5 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.23-1+rpi1 libc-dev-bin_2.23-1+rpi1 libc6_2.23-1+rpi1 libc6-dev_2.23-1+rpi1 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-1+rpi1 libcomerr2_1.43.1-1 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_0.213 libdevmapper1.02.1_2:1.02.127-1 libdpkg-perl_1.18.7 libdrm2_2.4.68-1 libfakeroot_1.21-1 libfdisk1_2.28-5 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.022-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-5-dev_5.4.0-4 libgcc1_1:6.1.1-1+rpi1 libgcrypt20_1.7.1-2 libgdbm3_1.8.3-14 libglib2.0-0_2.48.1-2 libgmp10_2:6.1.1+dfsg-1 libgomp1_6.1.1-1+rpi1 libgpg-error0_1.23-1 libicu55_55.1-7 libidn11_1.32-3.1 libisl15_0.17.1-1 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 liblocale-gettext-perl_1.07-3 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmount1_2.28-5 libmpc3_1.0.3-1 libmpfr4_3.1.4-2 libncurses5_6.0+20160319-2 libncursesw5_6.0+20160319-2 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpcre3_2:8.38-3.1 libperl5.22_5.22.2-2 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng12-0_1.2.54-6 libprocps5_2:3.3.11-3 libreadline6_6.3-8+b3 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28-5 libss2_1.43.1-1 libstdc++-5-dev_5.4.0-4 libstdc++6_6.1.1-1+rpi1 libsystemd0_230-5 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160319-2 libtool_2.4.6-0.1 libubsan0_6.1.1-1+rpi1 libudev1_230-5 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28-5 libxml2_2.9.4+dfsg1-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.06-1 mawk_1.3.3-17 mount_2.28-5 multiarch-support_2.23-1+rpi1 ncurses-base_6.0+20160319-2 ncurses-bin_6.0+20160319-2 netbase_5.3 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-2 perl-base_5.22.2-2 perl-modules-5.22_5.22.2-2 po-debconf_1.0.19 procps_2:3.3.11-3 psmisc_22.21-2.1 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-minimap-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_230-5 systemd-sysv_230-5 sysv-rc_2.88dsf-59.7 sysvinit-utils_2.88dsf-59.7 tar_1.29-1+rpi1 tzdata_2016f-1 udev_230-5 util-linux_2.28-5 xkb-data_2.17-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sun Jul 31 17:35:46 2016 UTC using RSA key ID F09F4872
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./minimap_0.2-3.dsc
dpkg-source: info: extracting minimap in minimap-0.2
dpkg-source: info: unpacking minimap_0.2.orig.tar.gz
dpkg-source: info: unpacking minimap_0.2-3.debian.tar.xz
dpkg-source: info: applying make_shared_lib
dpkg-source: info: applying hardening
dpkg-source: info: applying ensure_64bit_value
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
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-eef9b2b7-fa67-41cc-9e5f-a50487b60d88
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package minimap
dpkg-buildpackage: info: source version 0.2-3
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build minimap-0.2
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j1 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -fr gmon.out *.o a.out minimap sdust minimap-lite *~ *.a *.dSYM session*
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_update_autotools_config -a
dh_auto_configure -a
dh_auto_build -a
make -j1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
gcc -c -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wno-unused-function -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -I. main.c -o main.o
gcc -c -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wno-unused-function -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -I. kthread.c -o kthread.o
gcc -c -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wno-unused-function -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -I. misc.c -o misc.o
gcc -c -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wno-unused-function -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -I. bseq.c -o bseq.o
gcc -c -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wno-unused-function -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -I. sketch.c -o sketch.o
gcc -c -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wno-unused-function -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -I. sdust.c -o sdust.o
gcc -c -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wno-unused-function -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -I. index.c -o index.o
index.c: In function 'mm_idx_load':
index.c:317:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&mi->freq_thres, sizeof(float), 1, fp);
^
index.c:319:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(mi->len, 4, mi->n, fp);
^
index.c:324:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&l, 1, 1, fp);
^
index.c:326:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(mi->name[i], 1, l, fp);
^
index.c:335:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&b->n, 4, 1, fp);
^
index.c:337:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(b->p, 8, b->n, fp);
^
index.c:338:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&size, 4, 1, fp);
^
index.c:345:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(x, 8, 2, fp);
^
gcc -c -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wno-unused-function -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -I. map.c -o map.o
ar -csru libminimap.a kthread.o misc.o bseq.o sketch.o sdust.o index.o map.o
ar: `u' modifier ignored since `D' is the default (see `U')
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wno-unused-function -fPIC -Wl,-z,relro -Wl,-z,now main.o -o minimap -L. -lminimap -lm -lz -lpthread
gcc -shared -o libminimap.so.0 kthread.o misc.o bseq.o sketch.o sdust.o index.o map.o -fPIC -Wl,-soname,libminimap.so.0 -lm -lz -lpthread -Wl,-z,relro -Wl,-z,now
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
ln -s libminimap.so.* libminimap.so
d-shlibmove --commit \
--multiarch \
--devunversioned \
--movedev "*.h" /usr/include/minimap \
libminimap.so
Library package automatic movement utility
--> zlib1g-dev package exists.
set -e
install -d -m 755 debian/libminimap-dev/usr/lib/arm-linux-gnueabihf
install -d -m 755 debian/libminimap0/usr/lib/arm-linux-gnueabihf
mv ./libminimap.a debian/libminimap-dev/usr/lib/arm-linux-gnueabihf
mv ./libminimap.la debian/libminimap-dev/usr/lib/arm-linux-gnueabihf || true
mv ./libminimap.so debian/libminimap-dev/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/libminimap.so.0 debian/libminimap0/usr/lib/arm-linux-gnueabihf
PKGDEV=libminimap-dev
PKGSHL=libminimap0
install -d -m 755 debian/libminimap-dev//usr/include/minimap
mv *.h debian/libminimap-dev//usr/include/minimap
mv: cannot stat './libminimap.la': No such file or directory
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/minimap/usr/bin/minimap was not linked against libm.so.6 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libminimap0/usr/lib/arm-linux-gnueabihf/libminimap.so.0 was not linked against libm.so.6 (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
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
dpkg-gencontrol: warning: Depends field of package libminimap-dev: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package libminimap-dev: unused substitution variable ${devlibs:Depends}
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'libminimap0-dbgsym' in '../libminimap0-dbgsym_0.2-3_armhf.deb'.
dpkg-deb: building package 'minimap-dbgsym' in '../minimap-dbgsym_0.2-3_armhf.deb'.
dpkg-deb: building package 'libminimap-dev' in '../libminimap-dev_0.2-3_armhf.deb'.
dpkg-deb: building package 'minimap' in '../minimap_0.2-3_armhf.deb'.
dpkg-deb: building package 'libminimap0' in '../libminimap0_0.2-3_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../minimap_0.2-3_armhf.changes
dpkg-genchanges: warning: package libminimap0-dbgsym listed in files list but not in control info
dpkg-genchanges: warning: package minimap-dbgsym listed in files list but not in control info
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build minimap-0.2
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160806-1119
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
minimap_0.2-3_armhf.changes:
----------------------------
Format: 1.8
Date: Sun, 31 Jul 2016 17:06:30 +0000
Source: minimap
Binary: minimap libminimap0 libminimap-dev
Architecture: armhf
Version: 0.2-3
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
libminimap-dev - development headers for libminimap
libminimap0 - library for approximate mapping of long biosequences
minimap - tool for approximate mapping of long biosequences such as DNA rea
Changes:
minimap (0.2-3) unstable; urgency=medium
.
* Add missing header files.
* Adjust autopkgtest to build example outside of upstream source.
* Update uploader email.
* Bump Standards-Version with no changes.
* Use secure Vcs-Git.
* Enable full hardening.
Checksums-Sha1:
3fb55231666ad6e25fd4f2e6f123e572e59d6cec 31684 libminimap-dev_0.2-3_armhf.deb
b67a403eb5ed46429fad68157eab0811f1b272f1 41338 libminimap0-dbgsym_0.2-3_armhf.deb
c6d74519c700e17ef4395135d9152d6b65f09703 20662 libminimap0_0.2-3_armhf.deb
5b537925f965425b28bdab3a028a675902997a9b 45982 minimap-dbgsym_0.2-3_armhf.deb
412950c0f07cbb594431f8954debcb7afe42dd2c 24922 minimap_0.2-3_armhf.deb
Checksums-Sha256:
702d53280d4f2cea6c03c4a0439737a700c746cae5831f610bf96986d5f18f7f 31684 libminimap-dev_0.2-3_armhf.deb
728dfaef20c0800a07d3e9e4588131a4e958f74b5e827a7521b3a164798c4728 41338 libminimap0-dbgsym_0.2-3_armhf.deb
9a508a84913943d36db93f0d7372cf5caa1d570ea3499a0650c28750e9fe1ce1 20662 libminimap0_0.2-3_armhf.deb
8cc0f9c803c0fd14934f177891d8fe462e4086dc87ce4bc58e8ddd1cc90e8493 45982 minimap-dbgsym_0.2-3_armhf.deb
a2323b20dba90d51ff6563882653730ef81edd34ac75c739571dc627451bd8dd 24922 minimap_0.2-3_armhf.deb
Files:
1e019e9d785f7b37c5e26f1044d88d37 31684 libdevel optional libminimap-dev_0.2-3_armhf.deb
ce893fc38bcc294e531bc48368f6052b 41338 debug extra libminimap0-dbgsym_0.2-3_armhf.deb
937d007cf63171f31988a083b5faaac5 20662 libs optional libminimap0_0.2-3_armhf.deb
0c0ca07236ff20a0cf7a1258b07751fd 45982 debug extra minimap-dbgsym_0.2-3_armhf.deb
75e729a4b020bd363f1aad51a42b510d 24922 science optional minimap_0.2-3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libminimap-dev_0.2-3_armhf.deb
------------------------------
new debian package, version 2.0.
size 31684 bytes: control archive=943 bytes.
687 bytes, 17 lines control
724 bytes, 11 lines md5sums
Package: libminimap-dev
Source: minimap
Version: 0.2-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 112
Depends: libminimap0 (= 0.2-3), zlib1g-dev
Section: libdevel
Priority: optional
Homepage: https://github.com/lh3/minimap
Description: development headers for libminimap
Minimap is an experimental tool to efficiently find multiple approximate
mapping positions between two sets of long sequences, such as between
DNA reads and reference genomes, between genomes and between long noisy reads.
.
This package contains the C library headers for using minimap in custom tools,
along with a static library.
drwxr-xr-x root/root 0 2016-08-06 11:19 ./
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/include/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/include/minimap/
-rw-r--r-- root/root 359 2015-12-07 02:29 ./usr/include/minimap/bseq.h
-rw-r--r-- root/root 4294 2016-08-06 11:18 ./usr/include/minimap/kdq.h
-rw-r--r-- root/root 21313 2015-12-07 02:29 ./usr/include/minimap/khash.h
-rw-r--r-- root/root 8741 2015-12-07 02:29 ./usr/include/minimap/kseq.h
-rw-r--r-- root/root 5390 2015-12-07 02:29 ./usr/include/minimap/ksort.h
-rw-r--r-- root/root 3289 2015-12-07 02:29 ./usr/include/minimap/kvec.h
-rw-r--r-- root/root 3053 2015-12-07 02:29 ./usr/include/minimap/minimap.h
-rw-r--r-- root/root 539 2015-12-07 02:29 ./usr/include/minimap/sdust.h
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/lib/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 47336 2016-08-06 11:19 ./usr/lib/arm-linux-gnueabihf/libminimap.a
lrwxrwxrwx root/root 0 2016-08-06 11:19 ./usr/lib/arm-linux-gnueabihf/libminimap.so -> libminimap.so.0
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/share/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/share/doc/libminimap-dev/
-rw-r--r-- root/root 373 2016-07-31 17:32 ./usr/share/doc/libminimap-dev/changelog.Debian.gz
-rw-r--r-- root/root 2185 2016-01-11 22:02 ./usr/share/doc/libminimap-dev/copyright
libminimap0-dbgsym_0.2-3_armhf.deb
----------------------------------
new debian package, version 2.0.
size 41338 bytes: control archive=489 bytes.
415 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libminimap0-dbgsym
Source: minimap
Version: 0.2-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 56
Depends: libminimap0 (= 0.2-3)
Section: debug
Priority: extra
Homepage: https://github.com/lh3/minimap
Description: Debug symbols for libminimap0
Auto-Built-Package: debug-symbols
Build-Ids: 2f372bfabd5b58372ecc9e3f63ec73174551f96a
drwxr-xr-x root/root 0 2016-08-06 11:19 ./
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/lib/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/lib/debug/.build-id/2f/
-rw-r--r-- root/root 46252 2016-08-06 11:19 ./usr/lib/debug/.build-id/2f/372bfabd5b58372ecc9e3f63ec73174551f96a.debug
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/share/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-08-06 11:19 ./usr/share/doc/libminimap0-dbgsym -> libminimap0
libminimap0_0.2-3_armhf.deb
---------------------------
new debian package, version 2.0.
size 20662 bytes: control archive=813 bytes.
677 bytes, 17 lines control
228 bytes, 3 lines md5sums
25 bytes, 1 lines shlibs
60 bytes, 2 lines triggers
Package: libminimap0
Source: minimap
Version: 0.2-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 56
Depends: libc6 (>= 2.4), zlib1g (>= 1:1.1.4)
Section: libs
Priority: optional
Homepage: https://github.com/lh3/minimap
Description: library for approximate mapping of long biosequences
Minimap is an experimental tool to efficiently find multiple approximate
mapping positions between two sets of long sequences, such as between DNA
reads and reference genomes, between genomes and between long noisy reads.
.
This package contains a shared library offering the minimap API to custom C
programs.
drwxr-xr-x root/root 0 2016-08-06 11:19 ./
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/lib/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 42544 2016-08-06 11:19 ./usr/lib/arm-linux-gnueabihf/libminimap.so.0
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/share/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/share/doc/libminimap0/
-rw-r--r-- root/root 373 2016-07-31 17:32 ./usr/share/doc/libminimap0/changelog.Debian.gz
-rw-r--r-- root/root 2185 2016-01-11 22:02 ./usr/share/doc/libminimap0/copyright
minimap-dbgsym_0.2-3_armhf.deb
------------------------------
new debian package, version 2.0.
size 45982 bytes: control archive=482 bytes.
403 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: minimap-dbgsym
Source: minimap
Version: 0.2-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 61
Depends: minimap (= 0.2-3)
Section: debug
Priority: extra
Homepage: https://github.com/lh3/minimap
Description: Debug symbols for minimap
Auto-Built-Package: debug-symbols
Build-Ids: 9f65d22d30ef2235ccbfae7abebeb34248dd1239
drwxr-xr-x root/root 0 2016-08-06 11:19 ./
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/lib/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/lib/debug/.build-id/9f/
-rw-r--r-- root/root 52144 2016-08-06 11:19 ./usr/lib/debug/.build-id/9f/65d22d30ef2235ccbfae7abebeb34248dd1239.debug
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/share/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-08-06 11:19 ./usr/share/doc/minimap-dbgsym -> minimap
minimap_0.2-3_armhf.deb
-----------------------
new debian package, version 2.0.
size 24922 bytes: control archive=873 bytes.
972 bytes, 20 lines control
258 bytes, 4 lines md5sums
Package: minimap
Version: 0.2-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 62
Depends: libc6 (>= 2.4), zlib1g (>= 1:1.1.4)
Section: science
Priority: optional
Homepage: https://github.com/lh3/minimap
Description: tool for approximate mapping of long biosequences such as DNA reads
Minimap is an experimental tool to efficiently find multiple approximate
mapping positions between two sets of long biological sequences, such as
between DNA reads and reference genomes, between genomes and between long
noisy reads.
Minimap does not generate alignments as of now and because of this, it is
usually tens of times faster than mainstream aligners.
It does not replace mainstream aligners, but it can be useful when you
want to quickly identify long approximate matches at moderate divergence among
a huge collection of sequences. For this task, it is much faster than most
existing tools.
drwxr-xr-x root/root 0 2016-08-06 11:19 ./
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/bin/
-rwxr-xr-x root/root 46800 2016-08-06 11:19 ./usr/bin/minimap
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/share/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/share/doc/minimap/
-rw-r--r-- root/root 373 2016-07-31 17:32 ./usr/share/doc/minimap/changelog.Debian.gz
-rw-r--r-- root/root 2185 2016-01-11 22:02 ./usr/share/doc/minimap/copyright
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/share/man/
drwxr-xr-x root/root 0 2016-08-06 11:19 ./usr/share/man/man1/
-rw-r--r-- root/root 2365 2016-08-06 11:19 ./usr/share/man/man1/minimap.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 1536
Build-Time: 53
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 180
Job: minimap_0.2-3
Machine Architecture: armhf
Package: minimap
Package-Time: 276
Source-Version: 0.2-3
Space: 1536
Status: successful
Version: 0.2-3
--------------------------------------------------------------------------------
Finished at 20160806-1119
Build needed 00:04:36, 1536k disc space