last-align →
621-1 →
armhf → 2015-09-29 11:37:59
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-03
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║ last-align 621-1 (armhf) 29 Sep 2015 11:18 ║
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Package: last-align
Version: 621-1
Source Version: 621-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/last-align-9U4YQS/last-align-621' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/last-align-9U4YQS' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-46857af3-5e8f-4e2d-a153-494fec9359e6' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
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Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [8333 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [10.2 MB]
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NOTICE: 'last-align' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/last-align/trunk/
Need to get 551 kB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main last-align 621-1 (dsc) [1992 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main last-align 621-1 (tar) [542 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main last-align 621-1 (diff) [6924 B]
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Merged Build-Depends: build-essential, fakeroot
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dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-E9p249/apt_archive/sbuild-build-depends-core-dummy.deb'.
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│ Install core build dependencies (apt-based resolver) │
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The following NEW packages will be installed:
sbuild-build-depends-core-dummy
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Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), help2man, python-imaging
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), help2man, python-imaging
dpkg-deb: building package 'sbuild-build-depends-last-align-dummy' in '/«BUILDDIR»/resolver-jRqYkJ/apt_archive/sbuild-build-depends-last-align-dummy.deb'.
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install last-align build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
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The following extra packages will be installed:
bsdmainutils debhelper file gettext gettext-base groff-base help2man
intltool-debian libcroco3 libexpat1 libffi6 libfreetype6 libglib2.0-0
libicu55 libjbig0 libjpeg62-turbo liblcms2-2 libmagic1 libpipeline1
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsqlite3-0
libssl1.0.0 libtiff5 libunistring0 libwebp5 libwebpdemux1 libwebpmux1
libxml2 man-db mime-support po-debconf python python-imaging python-minimal
python-pil python2.7 python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc autopoint
libasprintf-dev libgettextpo-dev groff liblcms2-utils less www-browser
libmail-box-perl python-doc python-tk python-pil-doc python-pil-dbg
python2.7-doc binfmt-support
Recommended packages:
curl wget lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils debhelper file gettext gettext-base groff-base help2man
intltool-debian libcroco3 libexpat1 libffi6 libfreetype6 libglib2.0-0
libicu55 libjbig0 libjpeg62-turbo liblcms2-2 libmagic1 libpipeline1
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsqlite3-0
libssl1.0.0 libtiff5 libunistring0 libwebp5 libwebpdemux1 libwebpmux1
libxml2 man-db mime-support po-debconf python python-imaging python-minimal
python-pil python2.7 python2.7-minimal sbuild-build-depends-last-align-dummy
0 upgraded, 40 newly installed, 0 to remove and 41 not upgraded.
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Get:1 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-1 [1085 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.1-1 [23.9 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.3-1 [975 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libpython2.7-minimal armhf 2.7.10-4 [379 kB]
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Get:9 http://172.17.0.1/private/ stretch-staging/main libexpat1 armhf 2.1.0-7 [59.8 kB]
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Get:11 http://172.17.0.1/private/ stretch-staging/main libsqlite3-0 armhf 3.8.11.1-1 [391 kB]
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Get:13 http://172.17.0.1/private/ stretch-staging/main libpython2.7-stdlib armhf 2.7.10-4 [1736 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main python2.7 armhf 2.7.10-4 [258 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main libpython-stdlib armhf 2.7.9-1 [19.6 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main python armhf 2.7.9-1 [151 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.44.1-1.1 [2312 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main libicu55 armhf 55.1-5 [7378 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.2+zdfsg1-4 [797 kB]
Get:20 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main liblcms2-2 armhf 2.6-3 [113 kB]
Get:23 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:24 http://172.17.0.1/private/ stretch-staging/main libwebp5 armhf 0.4.3-1.3 [174 kB]
Get:25 http://172.17.0.1/private/ stretch-staging/main libwebpdemux1 armhf 0.4.3-1.3 [52.3 kB]
Get:26 http://172.17.0.1/private/ stretch-staging/main libwebpmux1 armhf 0.4.3-1.3 [57.7 kB]
Get:27 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.25-2 [250 kB]
Get:28 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.25-2 [61.2 kB]
Get:29 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.6-1 [119 kB]
Get:30 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.6-1 [1393 kB]
Get:31 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:32 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:33 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20150811 [817 kB]
Get:34 http://172.17.0.1/private/ stretch-staging/main help2man armhf 1.47.2 [154 kB]
Get:35 http://172.17.0.1/private/ stretch-staging/main libfreetype6 armhf 2.6-2 [397 kB]
Get:36 http://172.17.0.1/private/ stretch-staging/main libjpeg62-turbo armhf 1:1.4.1-2 [103 kB]
Get:37 http://172.17.0.1/private/ stretch-staging/main libtiff5 armhf 4.0.5-1 [200 kB]
Get:38 http://172.17.0.1/private/ stretch-staging/main python-pil armhf 2.9.0-1 [287 kB]
Get:39 http://172.17.0.1/private/ stretch-staging/main python-imaging all 2.9.0-1 [9652 B]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25.1-1 dpkg-dev_1.18.2 g++-4.9_4.9.3-4 g++-5_5.2.1-16+rpi1 gcc-4.9_4.9.3-4 gcc-5_5.2.1-16+rpi1 libc6-dev_2.19-19 libstdc++-4.9-dev_4.9.3-4 libstdc++-5-dev_5.2.1-16+rpi1 libstdc++6_5.2.1-16+rpi1 linux-libc-dev_3.16.7-ckt4-1+rpi1+b2
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4+rpi1 base-passwd_3.5.38 bash_4.3-14 binutils_2.25.1-1 bsdmainutils_9.0.6 bsdutils_1:2.26.2-9 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.2.1-4+rpi2 cpp-4.9_4.9.3-4 cpp-5_5.2.1-16+rpi1 dash_0.5.7-4 debconf_1.5.57 debfoster_2.7-2 debhelper_9.20150811 debianutils_4.5.1 diffutils_1:3.3-1 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.4.2-9 g++_4:5.2.1-4+rpi2 g++-4.9_4.9.3-4 g++-5_5.2.1-16+rpi1 gcc_4:5.2.1-4+rpi2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.4-4 gcc-4.9_4.9.3-4 gcc-4.9-base_4.9.3-4 gcc-5_5.2.1-16+rpi1 gcc-5-base_5.2.1-16+rpi1 gettext_0.19.6-1 gettext-base_0.19.6-1 gnupg_1.4.19-5 gpgv_1.4.19-5 grep_2.21-2 groff-base_1.22.3-1 gzip_1.6-4 help2man_1.47.2 hostname_3.16 init_1.23 init-system-helpers_1.23 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-2+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.9.2-3 libapt-pkg4.12_1.0.9.10 libapt-pkg4.16_1.0.10.2 libasan1_4.9.3-4 libasan2_5.2.1-16+rpi1 libatomic1_5.2.1-16+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-1 libaudit1_1:2.4.4-1 libblkid1_2.26.2-9 libbz2-1.0_1.0.6-8 libc-bin_2.19-19 libc-dev-bin_2.19-19 libc6_2.19-19 libc6-dev_2.19-19 libcap2_1:2.24-11 libcap2-bin_1:2.24-11 libcc1-0_5.2.1-16+rpi1 libcloog-isl4_0.18.3-1 libcomerr2_1.42.13-1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-11 libdbus-1-3_1.8.20-1 libdebconfclient0_0.195 libdevmapper1.02.1_2:1.02.104-1 libdpkg-perl_1.18.2 libdrm2_2.4.64-1 libexpat1_2.1.0-7 libfakeroot_1.20.2-1 libfdisk1_2.26.2-9 libffi6_3.2.1-3 libfreetype6_2.6-2 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.3-4 libgcc-5-dev_5.2.1-16+rpi1 libgcc1_1:5.2.1-16+rpi1 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.44.1-1.1 libgmp10_2:6.0.0+dfsg-7+rpi1 libgomp1_5.2.1-16+rpi1 libgpg-error0_1.19-2 libicu55_55.1-5 libisl13_0.14-2 libjbig0_2.1-3.1 libjpeg62-turbo_1:1.4.1-2 libklibc_2.0.4-2+rpi1 libkmod2_21-1 liblcms2-2_2.6-3 liblocale-gettext-perl_1.05-9 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.26.2-9 libmpc3_1.0.3-1 libmpfr4_3.1.3-1 libncurses5_6.0+20150810-1 libncursesw5_6.0+20150810-1 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-7.1 libpipeline1_1.4.1-1 libpng12-0_1.2.50-2+b2 libprocps3_2:3.3.9-9 libprocps4_2:3.3.10-2 libpython-stdlib_2.7.9-1 libpython2.7-minimal_2.7.10-4 libpython2.7-stdlib_2.7.10-4 libreadline6_6.3-8+b3 libseccomp2_2.2.3-2 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-2+b1 libsmartcols1_2.26.2-9 libsqlite3-0_3.8.11.1-1 libss2_1.42.13-1 libssl1.0.0_1.0.2d-1 libstdc++-4.9-dev_4.9.3-4 libstdc++-5-dev_5.2.1-16+rpi1 libstdc++6_5.2.1-16+rpi1 libsystemd0_225-1 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7.1 libtiff5_4.0.5-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20150810-1 libubsan0_5.2.1-16+rpi1 libudev1_225-1 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.26.2-9 libwebp5_0.4.3-1.3 libwebpdemux1_0.4.3-1.3 libwebpmux1_0.4.3-1.3 libxml2_2.9.2+zdfsg1-4 linux-libc-dev_3.16.7-ckt4-1+rpi1+b2 login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.2 makedev_2.3.1-93 man-db_2.7.3-1 mawk_1.3.3-17 mime-support_3.59 mount_2.26.2-9 mountall_2.54 multiarch-support_2.19-19 ncurses-base_6.0+20150810-1 ncurses-bin_6.0+20150810-1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 plymouth_0.9.0-9 po-debconf_1.0.18 procps_2:3.3.10-2 python_2.7.9-1 python-imaging_2.9.0-1 python-minimal_2.7.9-1 python-pil_2.9.0-1 python2.7_2.7.10-4 python2.7-minimal_2.7.10-4 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-last-align-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_225-1 systemd-sysv_225-1 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-1 tzdata_2015f-1 udev_225-1 util-linux_2.26.2-9 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 Thu Sep 24 06:55:27 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./last-align_621-1.dsc
dpkg-source: info: extracting last-align in last-align-621
dpkg-source: info: unpacking last-align_621.orig.tar.gz
dpkg-source: info: unpacking last-align_621-1.debian.tar.xz
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
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-46857af3-5e8f-4e2d-a153-494fec9359e6
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package last-align
dpkg-buildpackage: source version 621-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build last-align-621
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j1 clean
make[1]: Entering directory '/«PKGBUILDDIR»'
make[2]: Entering directory '/«PKGBUILDDIR»/src'
rm -f lastdb lastal last-split last-merge-batches last-pair-probs *.o */*.o
make[2]: Leaving directory '/«PKGBUILDDIR»/src'
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_clean
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/«PKGBUILDDIR»'
make all CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic" CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
make[2]: Entering directory '/«PKGBUILDDIR»'
make[3]: Entering directory '/«PKGBUILDDIR»/src'
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o Alphabet.o Alphabet.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o MultiSequence.o MultiSequence.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc
if test -e ../.hg ; \
then echo \"`hg id -n`\" | cmp -s version.hh - || echo \"`hg id -n`\" > version.hh ; \
elif test -e ../.hg_archival.txt ; \
then echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" | cmp -s version.hh - || echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" > version.hh ; \
else test -e version.hh || echo \"UNKNOWN\" > version.hh ; \
fi
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o LastdbArguments.o LastdbArguments.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o io.o io.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o fileMap.o fileMap.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o TantanMasker.o TantanMasker.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o ScoreMatrix.o ScoreMatrix.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o LambdaCalculator.o LambdaCalculator.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o tantan.o tantan.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc
SubsetSuffixArraySort.cc: In member function 'void cbrc::SubsetSuffixArray::sortIndex(const uchar*, cbrc::SubsetSuffixArray::indexT, int)':
SubsetSuffixArraySort.cc:334:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if( end - beg <= maxUnsortedInterval && depth >= minLength ) continue;
^
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o lastdb.o lastdb.cc
g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Wl,-z,relro -o lastdb Alphabet.o MultiSequence.o CyclicSubsetSeed.o SubsetSuffixArray.o LastdbArguments.o io.o fileMap.o TantanMasker.o ScoreMatrix.o LambdaCalculator.o tantan.o SubsetSuffixArraySort.o MultiSequenceQual.o lastdb.o
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o LastalArguments.o LastalArguments.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o DiagonalTable.o DiagonalTable.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o SegmentPair.o SegmentPair.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o Alignment.o Alignment.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o SegmentPairPot.o SegmentPairPot.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o AlignmentPot.o AlignmentPot.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o GeneralizedAffineGapCosts.o GeneralizedAffineGapCosts.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o Centroid.o Centroid.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o GeneticCode.o GeneticCode.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o LastEvaluer.o LastEvaluer.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o gaplessXdrop.o gaplessXdrop.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o gaplessPssmXdrop.o gaplessPssmXdrop.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o gaplessTwoQualityXdrop.o gaplessTwoQualityXdrop.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o AlignmentWrite.o AlignmentWrite.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o lastal.o lastal.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/sls_alp.o alp/sls_alp.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/sls_basic.o alp/sls_basic.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/njn_random.o alp/njn_random.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp
g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Wl,-z,relro -o lastal Alphabet.o MultiSequence.o CyclicSubsetSeed.o SubsetSuffixArray.o LastalArguments.o io.o fileMap.o TantanMasker.o ScoreMatrix.o tantan.o DiagonalTable.o SegmentPair.o Alignment.o GappedXdropAligner.o SegmentPairPot.o AlignmentPot.o GeneralizedAffineGapCosts.o Centroid.o LambdaCalculator.o TwoQualityScoreMatrix.o OneQualityScoreMatrix.o QualityPssmMaker.o GeneticCode.o LastEvaluer.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o SubsetSuffixArraySearch.o AlignmentWrite.o MultiSequenceQual.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o lastal.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o split/cbrc_linalg.o split/cbrc_linalg.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o split/last-split.o split/last-split.cc
split/last-split.cc: In function 'void doOneQuery(std::vector<cbrc::UnsplitAlignment>::const_iterator, std::vector<cbrc::UnsplitAlignment>::const_iterator, cbrc::SplitAligner&, const LastSplitOptions&, bool)':
split/last-split.cc:151:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned i = 0; i < end - beg; ++i) {
^
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o split/last-split-main.o split/last-split-main.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc
g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Wl,-z,relro -o last-split Alphabet.o MultiSequence.o fileMap.o split/cbrc_linalg.o split/last-split.o split/cbrc_split_aligner.o split/last-split-main.o split/cbrc_unsplit_alignment.o
gcc -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o last-merge-batches.o last-merge-batches.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o last-merge-batches last-merge-batches.o
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o last-pair-probs.o last-pair-probs.cc
last-pair-probs.cc: In function 'Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set<std::__cxx11::basic_string<char> >&)':
last-pair-probs.cc:430:74: warning: 'qStrand' may be used uninitialized in this function [-Wmaybe-uninitialized]
linesBeg, linesEnd, strand, scale, circularChroms);
^
last-pair-probs.cc:430:74: warning: 'rName' may be used uninitialized in this function [-Wmaybe-uninitialized]
last-pair-probs.cc:430:74: warning: 'qName' may be used uninitialized in this function [-Wmaybe-uninitialized]
last-pair-probs.cc: In function 'bool readBatch(std::istream&, char, double, const std::set<std::__cxx11::basic_string<char> >&, std::vector<char>&, std::vector<const char*>&, std::vector<Alignment>&)':
last-pair-probs.cc:453:74: warning: 'rName' may be used uninitialized in this function [-Wmaybe-uninitialized]
linesBeg, linesEnd, strand, scale, circularChroms);
^
last-pair-probs.cc:437:10: note: 'rName' was declared here
String rName, qName;
^
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc
g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Wl,-z,relro -o last-pair-probs last-pair-probs.o last-pair-probs-main.o io.o
make[3]: Leaving directory '/«PKGBUILDDIR»/src'
make[2]: Leaving directory '/«PKGBUILDDIR»'
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»'
make install prefix=/«PKGBUILDDIR»/debian/last-align/usr
make[2]: Entering directory '/«PKGBUILDDIR»'
make[3]: Entering directory '/«PKGBUILDDIR»/src'
if test -e ../.hg ; \
then echo \"`hg id -n`\" | cmp -s version.hh - || echo \"`hg id -n`\" > version.hh ; \
elif test -e ../.hg_archival.txt ; \
then echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" | cmp -s version.hh - || echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" > version.hh ; \
else test -e version.hh || echo \"UNKNOWN\" > version.hh ; \
fi
make[3]: Leaving directory '/«PKGBUILDDIR»/src'
mkdir -p /«PKGBUILDDIR»/debian/last-align/usr/bin
cp src/last?? src/last-split src/last-merge-batches src/last-pair-probs scripts/* /«PKGBUILDDIR»/debian/last-align/usr/bin
make[2]: Leaving directory '/«PKGBUILDDIR»'
mkdir -p /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1/
help2man --no-info --version-string="621" \
--name='make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format' \
/«PKGBUILDDIR»/scripts/last-dotplot > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//last-dotplot.1
help2man --no-info --version-string="621" \
--name="genome-scale comparison of biological sequences" \
--help-option="-h" \
/«PKGBUILDDIR»/src/lastal > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//lastal.1
help2man --no-info --version-string="621" \
--name="genome-scale comparison of biological sequences" \
--help-option="-h" \
/«PKGBUILDDIR»/src/lastdb > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//lastdb.1
help2man --no-info --version-string="621" \
--name="Sort MAF-format alignments by sequence name" \
/«PKGBUILDDIR»/scripts/maf-sort > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//maf-sort.1
help2man --no-info --version-string="621" \
--name="changes the order of the sequences in MAF-format alignments" \
/«PKGBUILDDIR»/scripts/maf-swap > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//maf-swap.1
help2man --no-info --version-string="621" \
--name="Add extra column with mapping probabilities" \
/«PKGBUILDDIR»/scripts/last-map-probs > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//last-map-probs.1
# This script has not enough to put in a manual page.
#help2man --no-info --version-string="621" \
# --name="Read files of lastal output, merge corresponding batches, and write them." \
# /«PKGBUILDDIR»/scripts/last-merge-batches > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//last-merge-batches.1
#help2man --no-info --version-string="621" \
# --name="Clean up MAF-format alignments" \
# /«PKGBUILDDIR»/scripts/last-reduce-alignments > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//last-reduce-alignments.1
#help2man --no-info --version-string="621" \
# --name='Remove MAF-format alignments which are "dominated" by others' \
# /«PKGBUILDDIR»/scripts/last-remove-dominated > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//last-remove-dominated.1
help2man --no-info --version-string="621" \
--name='Estimates "split" or "spliced" alignments.' \
/«PKGBUILDDIR»/src/last-split > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//last-split.1
help2man --no-info --version-string="621" \
--name="Join two or more sets of MAF-format multiple alignments" \
/«PKGBUILDDIR»/scripts/maf-join > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//maf-join.1
help2man --no-info --version-string="621" \
--name="Convert MAF-format alignments to tabular format" \
/«PKGBUILDDIR»/scripts/maf-convert > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//maf-convert.1
help2man --no-info --version-string="621" \
--name="Cull alignments whose top\-sequence coordinates are contained in LIMIT or more" \
/«PKGBUILDDIR»/scripts/maf-cull > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//maf-cull.1
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_installchangelogs ChangeLog.txt
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_installexamples -a
dh_installman -a
dh_perl -a
dh_link -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastdb contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/last-align/usr/bin/last-pair-probs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/last-align/usr/bin/last-split contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastal contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'last-align' in '../last-align_621-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../last-align_621-1_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build last-align-621
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20150929-1134
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
last-align_621-1_armhf.changes:
───────────────────────────────
Format: 1.8
Date: Thu, 24 Sep 2015 08:53:43 +0200
Source: last-align
Binary: last-align
Architecture: armhf
Version: 621-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
last-align - genome-scale comparison of biological sequences
Changes:
last-align (621-1) unstable; urgency=medium
.
* New upstream version
Checksums-Sha1:
994c32433732f309cd04801ef8a987d8a8ec08f8 532324 last-align_621-1_armhf.deb
Checksums-Sha256:
ef206c7792d54f6099af68692d83d96fc419678ba864c5c6bf83d3fbacf67de1 532324 last-align_621-1_armhf.deb
Files:
65851c9485e1e8e36625de92a4c4b5a0 532324 science optional last-align_621-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
last-align_621-1_armhf.deb
──────────────────────────
new debian package, version 2.0.
size 532324 bytes: control archive=3355 bytes.
1176 bytes, 25 lines control
6269 bytes, 88 lines md5sums
Package: last-align
Version: 621-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1576
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 5.2)
Recommends: python, python-imaging
Suggests: parallel
Section: science
Priority: optional
Homepage: http://last.cbrc.jp/
Description: genome-scale comparison of biological sequences
LAST is software for comparing and aligning sequences, typically DNA or
protein sequences. LAST is similar to BLAST, but it copes better with very
large amounts of sequence data. Here are two things LAST is good at:
.
* Comparing large (e.g. mammalian) genomes.
* Mapping lots of sequence tags onto a genome.
.
The main technical innovation is that LAST finds initial matches based on
their multiplicity, instead of using a fixed size (e.g. BLAST uses 10-mers).
This allows one to map tags to genomes without repeat-masking, without becoming
overwhelmed by repetitive hits. To find these variable-sized matches, it uses
a suffix array (inspired by Vmatch). To achieve high sensitivity, it uses a
discontiguous suffix array, analogous to spaced seeds.
drwxr-xr-x root/root 0 2015-09-29 11:34 ./
drwxr-xr-x root/root 0 2015-09-29 11:34 ./usr/
drwxr-xr-x root/root 0 2015-09-29 11:34 ./usr/bin/
-rwxr-xr-x root/root 475 2015-09-29 11:34 ./usr/bin/fastq-interleave
-rwxr-xr-x root/root 11475 2015-09-29 11:34 ./usr/bin/last-dotplot
-rwxr-xr-x root/root 4703 2015-09-29 11:34 ./usr/bin/last-map-probs
-rwxr-xr-x root/root 5600 2015-09-29 11:34 ./usr/bin/last-merge-batches
-rwxr-xr-x root/root 51080 2015-09-29 11:34 ./usr/bin/last-pair-probs
-rwxr-xr-x root/root 3931 2015-09-29 11:34 ./usr/bin/last-postmask
-rwxr-xr-x root/root 112660 2015-09-29 11:34 ./usr/bin/last-split
-rwxr-xr-x root/root 12466 2015-09-29 11:34 ./usr/bin/last-train
-rwxr-xr-x root/root 722744 2015-09-29 11:34 ./usr/bin/lastal
-rwxr-xr-x root/root 141124 2015-09-29 11:34 ./usr/bin/lastdb
-rwxr-xr-x root/root 25453 2015-09-29 11:34 ./usr/bin/maf-convert
-rwxr-xr-x root/root 4266 2015-09-29 11:34 ./usr/bin/maf-cull
-rwxr-xr-x root/root 8992 2015-09-29 11:34 ./usr/bin/maf-join
-rwxr-xr-x root/root 2027 2015-09-29 11:34 ./usr/bin/maf-sort
-rwxr-xr-x root/root 4762 2015-09-29 11:34 ./usr/bin/maf-swap
-rwxr-xr-x root/root 234 2015-09-29 11:34 ./usr/bin/parallel-fasta
-rwxr-xr-x root/root 295 2015-09-29 11:34 ./usr/bin/parallel-fastq
drwxr-xr-x root/root 0 2015-09-29 11:34 ./usr/share/
drwxr-xr-x root/root 0 2015-09-29 11:34 ./usr/share/doc-base/
-rw-r--r-- root/root 281 2013-09-12 08:58 ./usr/share/doc-base/last-align-manual
-rw-r--r-- root/root 291 2014-01-28 17:31 ./usr/share/doc-base/last-align-scripts
-rw-r--r-- root/root 294 2013-09-12 08:58 ./usr/share/doc-base/last-align-seeds
drwxr-xr-x root/root 0 2015-09-29 11:34 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-09-29 11:34 ./usr/share/doc/last-align/
-rw-r--r-- root/root 11694 2015-09-18 16:29 ./usr/share/doc/last-align/FAQ.html
-rw-r--r-- root/root 2724 2015-08-31 16:57 ./usr/share/doc/last-align/FAQ.txt
-rw-r--r-- root/root 862 2015-09-18 16:28 ./usr/share/doc/last-align/Makefile
-rw-r--r-- root/root 201 2013-09-12 08:58 ./usr/share/doc/last-align/NEWS.Debian.gz
-rw-r--r-- root/root 9832 2015-09-18 16:29 ./usr/share/doc/last-align/bisulfite.html
-rw-r--r-- root/root 2585 2014-02-07 17:26 ./usr/share/doc/last-align/bisulfite.txt
-rw-r--r-- root/root 3874 2015-09-24 06:53 ./usr/share/doc/last-align/changelog.Debian.gz
-rw-r--r-- root/root 25722 2015-09-18 16:29 ./usr/share/doc/last-align/changelog.gz
-rw-r--r-- root/root 1016 2015-08-21 13:14 ./usr/share/doc/last-align/copyright
drwxr-xr-x root/root 0 2015-09-29 11:34 ./usr/share/doc/last-align/examples/
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 36024
Build-Time: 662
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 279
Job: last-align_621-1
Machine Architecture: armhf
Package: last-align
Package-Time: 999
Source-Version: 621-1
Space: 36024
Status: successful
Version: 621-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20150929-1134
Build needed 00:16:39, 36024k disc space