last-align →
588-1 →
armhf → 2015-07-12 12:00:52
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-02
╔══════════════════════════════════════════════════════════════════════════════╗
║ last-align 588-1 (armhf) 12 Jul 2015 11:43 ║
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Package: last-align
Version: 588-1
Source Version: 588-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/last-align-idAfqo/last-align-588' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/last-align-idAfqo' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-f6bdc5f8-b971-4510-aed6-c2bc18f504f4' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
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Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
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Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [9927 kB]
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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 355 kB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main last-align 588-1 (dsc) [1992 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main last-align 588-1 (tar) [346 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main last-align 588-1 (diff) [6948 B]
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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-Ra5d5L/apt_archive/sbuild-build-depends-core-dummy.deb'.
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│ Install core build dependencies (apt-based resolver) │
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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-hdbipw/apt_archive/sbuild-build-depends-last-align-dummy.deb'.
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install last-align build dependencies (apt-based resolver) │
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Installing build dependencies
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Reading state information...
The following extra packages will be installed:
bsdmainutils debhelper file gettext gettext-base groff-base help2man
intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi6 libfreetype6
libglib2.0-0 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 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 autopoint libasprintf-dev libgettextpo-dev
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 libasprintf0c2 libcroco3 libexpat1 libffi6 libfreetype6
libglib2.0-0 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 80 not upgraded.
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Get:2 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-1 [1085 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.0.2-5 [972 kB]
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Get:6 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.22+15-2 [244 kB]
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Get:8 http://172.17.0.1/private/ stretch-staging/main libpython2.7-minimal armhf 2.7.10-3 [380 kB]
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Get:14 http://172.17.0.1/private/ stretch-staging/main libsqlite3-0 armhf 3.8.10.2-1 [389 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main libssl1.0.0 armhf 1.0.2d-1 [882 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main libpython2.7-stdlib armhf 2.7.10-3 [1815 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main python2.7 armhf 2.7.10-3 [259 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main libpython-stdlib armhf 2.7.9-1 [19.6 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main python armhf 2.7.9-1 [151 kB]
Get:20 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.44.1-1.1 [2312 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main libfreetype6 armhf 2.5.2-4 [412 kB]
Get:23 http://172.17.0.1/private/ stretch-staging/main libjbig0 armhf 2.1-3.1 [27.5 kB]
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Get:25 http://172.17.0.1/private/ stretch-staging/main libjpeg62-turbo armhf 1:1.4.0-7 [102 kB]
Get:26 http://172.17.0.1/private/ stretch-staging/main libtiff5 armhf 4.0.3-13 [193 kB]
Get:27 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:28 http://172.17.0.1/private/ stretch-staging/main libwebp5 armhf 0.4.3-1.3 [174 kB]
Get:29 http://172.17.0.1/private/ stretch-staging/main libwebpdemux1 armhf 0.4.3-1.3 [52.3 kB]
Get:30 http://172.17.0.1/private/ stretch-staging/main libwebpmux1 armhf 0.4.3-1.3 [57.7 kB]
Get:31 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.22+15-2 [59.9 kB]
Get:32 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.4-1 [117 kB]
Get:33 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.4-1 [1168 kB]
Get:34 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.2 [25.9 kB]
Get:35 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:36 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20150628 [817 kB]
Get:37 http://172.17.0.1/private/ stretch-staging/main help2man armhf 1.47.1 [150 kB]
Get:38 http://172.17.0.1/private/ stretch-staging/main python-pil armhf 2.8.1-1 [282 kB]
Get:39 http://172.17.0.1/private/ stretch-staging/main python-imaging all 2.8.1-1 [9546 B]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25-5 dpkg-dev_1.17.25 g++-4.9_4.9.2-10 gcc-4.9_4.9.2-10 libc6-dev_2.19-18 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 linux-libc-dev_3.16.7-ckt4-1+rpi1
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.8 base-files_8+rpi1 base-passwd_3.5.37 bash_4.3-11 binutils_2.25-5 bsdmainutils_9.0.6 bsdutils_1:2.25.2-6 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:4.9.2-2 cpp-4.9_4.9.2-10 dash_0.5.7-4 debconf_1.5.56 debconf-i18n_1.5.56 debfoster_2.7-2 debhelper_9.20150628 debianutils_4.4 diffutils_1:3.3-1 dmsetup_2:1.02.90-2.2 dpkg_1.17.25 dpkg-dev_1.17.25 e2fslibs_1.42.12-1.1 e2fsprogs_1.42.12-1.1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9 g++_4:4.9.2-2 g++-4.9_4.9.2-10 gcc_4:4.9.2-2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.4-1 gcc-4.9_4.9.2-10 gcc-4.9-base_4.9.2-10 gettext_0.19.4-1 gettext-base_0.19.4-1 gnupg_1.4.18-7 gpgv_1.4.18-7 grep_2.20-4.1 groff-base_1.22.3-1 gzip_1.6-4 help2man_1.47.1 hostname_3.15 init_1.22 init-system-helpers_1.22 initramfs-tools_0.120 initscripts_2.88dsf-59 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.2 klibc-utils_2.0.4-2+rpi1 kmod_18-3 libacl1_2.2.52-2 libapt-pkg4.12_1.0.9.8 libasan1_4.9.2-10 libasprintf0c2_0.19.4-1 libatomic1_4.9.2-10 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1 libblkid1_2.25.2-6 libbz2-1.0_1.0.6-7 libc-bin_2.19-18 libc-dev-bin_2.19-18 libc6_2.19-18 libc6-dev_2.19-18 libcap2_1:2.24-8 libcap2-bin_1:2.24-8 libcloog-isl4_0.18.2-1 libcomerr2_1.42.12-1.1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-9 libdbus-1-3_1.8.16-1 libdebconfclient0_0.192 libdevmapper1.02.1_2:1.02.90-2.2 libdpkg-perl_1.17.25 libdrm2_2.4.58-2 libexpat1_2.1.0-6 libfakeroot_1.20.2-1 libffi6_3.1-2 libfreetype6_2.5.2-4 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.2-10 libgcc1_1:4.9.2-10 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-6+rpi1 libgomp1_4.9.2-10 libgpg-error0_1.17-3 libisl10_0.12.2-2 libjbig0_2.1-3.1 libjpeg62-turbo_1:1.4.0-7 libklibc_2.0.4-2+rpi1 libkmod2_18-3 liblcms2-2_2.6-3 liblocale-gettext-perl_1.05-8+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.22+15-2 libmount1_2.25.2-6 libmpc3_1.0.2-1 libmpfr4_3.1.2-2 libncurses5_5.9+20140913-1 libncursesw5_5.9+20140913-1 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_2:8.35-3.3 libpipeline1_1.4.0-1 libpng12-0_1.2.50-2 libprocps3_2:3.3.9-9 libpython-stdlib_2.7.9-1 libpython2.7-minimal_2.7.10-3 libpython2.7-stdlib_2.7.10-3 libreadline6_6.3-8 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-2 libsmartcols1_2.25.2-6 libsqlite3-0_3.8.10.2-1 libss2_1.42.12-1.1 libssl1.0.0_1.0.2d-1 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 libsystemd0_215-17 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7 libtiff5_4.0.3-13 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140913-1 libubsan0_4.9.2-10 libudev1_215-17 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-3 libuuid1_2.25.2-6 libwebp5_0.4.3-1.3 libwebpdemux1_0.4.3-1.3 libwebpmux1_0.4.3-1.3 libxml2_2.9.1+dfsg1-5 linux-libc-dev_3.16.7-ckt4-1+rpi1 login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.1 makedev_2.3.1-93 man-db_2.7.0.2-5 mawk_1.3.3-17 mime-support_3.58 mount_2.25.2-6 mountall_2.54 multiarch-support_2.19-18 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-3 perl-base_5.20.2-3 perl-modules_5.20.2-3 plymouth_0.9.0-9 po-debconf_1.0.18 procps_2:3.3.9-9 python_2.7.9-1 python-imaging_2.8.1-1 python-minimal_2.7.9-1 python-pil_2.8.1-1 python2.7_2.7.10-3 python2.7-minimal_2.7.10-3 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_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 systemd_215-17 systemd-sysv_215-17 sysv-rc_2.88dsf-59 sysvinit-utils_2.88dsf-59 tar_1.27.1-2 tzdata_2015c-1 udev_215-17 util-linux_2.25.2-6 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Mon Jul 6 17:01:51 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_588-1.dsc
dpkg-source: info: extracting last-align in last-align-588
dpkg-source: info: unpacking last-align_588.orig.tar.xz
dpkg-source: info: unpacking last-align_588-1.debian.tar.xz
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-f6bdc5f8-b971-4510-aed6-c2bc18f504f4
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package last-align
dpkg-buildpackage: source version 588-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build last-align-588
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:311:19: 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 'bool readBatch(std::istream&, char, double, const std::set<std::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="588" \
--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="588" \
--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="588" \
--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="588" \
--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="588" \
--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="588" \
--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="588" \
# --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="588" \
# --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="588" \
# --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="588" \
--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="588" \
--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="588" \
--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="588" \
--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/lastal 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/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-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/last-pair-probs 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_588-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../last-align_588-1_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build last-align-588
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20150712-1200
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
last-align_588-1_armhf.changes:
───────────────────────────────
Format: 1.8
Date: Mon, 06 Jul 2015 18:00:21 +0200
Source: last-align
Binary: last-align
Architecture: armhf
Version: 588-1
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 (588-1) unstable; urgency=medium
.
* New upstream version
* Binaries lastex and last-pair-probs do not belong to the package any more
* Removed paragraphs from copyright where files are not part of the
source any more
Checksums-Sha1:
13240b8e9c9a8996ebc489e701981dc6081a4f44 523266 last-align_588-1_armhf.deb
Checksums-Sha256:
67912955e93fc16210ba19087b3250ed0fe04e3330ca0d265a7f5009dee9ea85 523266 last-align_588-1_armhf.deb
Files:
41ca6cc7b03cd1c5390a9661f9215bd6 523266 science optional last-align_588-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
last-align_588-1_armhf.deb
──────────────────────────
new debian package, version 2.0.
size 523266 bytes: control archive=3257 bytes.
1176 bytes, 25 lines control
5593 bytes, 79 lines md5sums
Package: last-align
Version: 588-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1468
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.9)
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 2015-07-12 12:00 ./
drwxr-xr-x root/root 0 2015-07-12 11:59 ./usr/
drwxr-xr-x root/root 0 2015-07-12 12:00 ./usr/bin/
-rwxr-xr-x root/root 408 2015-07-12 11:59 ./usr/bin/fastq-interleave
-rwxr-xr-x root/root 11475 2015-07-12 11:59 ./usr/bin/last-dotplot
-rwxr-xr-x root/root 4703 2015-07-12 11:59 ./usr/bin/last-map-probs
-rwxr-xr-x root/root 5600 2015-07-12 12:00 ./usr/bin/last-merge-batches
-rwxr-xr-x root/root 55200 2015-07-12 12:00 ./usr/bin/last-pair-probs
-rwxr-xr-x root/root 3931 2015-07-12 11:59 ./usr/bin/last-postmask
-rwxr-xr-x root/root 120888 2015-07-12 12:00 ./usr/bin/last-split
-rwxr-xr-x root/root 12466 2015-07-12 11:59 ./usr/bin/last-train
-rwxr-xr-x root/root 751440 2015-07-12 12:00 ./usr/bin/lastal
-rwxr-xr-x root/root 149328 2015-07-12 12:00 ./usr/bin/lastdb
-rwxr-xr-x root/root 25453 2015-07-12 11:59 ./usr/bin/maf-convert
-rwxr-xr-x root/root 4266 2015-07-12 11:59 ./usr/bin/maf-cull
-rwxr-xr-x root/root 8992 2015-07-12 11:59 ./usr/bin/maf-join
-rwxr-xr-x root/root 2027 2015-07-12 11:59 ./usr/bin/maf-sort
-rwxr-xr-x root/root 4762 2015-07-12 11:59 ./usr/bin/maf-swap
-rwxr-xr-x root/root 234 2015-07-12 11:59 ./usr/bin/parallel-fasta
-rwxr-xr-x root/root 295 2015-07-12 11:59 ./usr/bin/parallel-fastq
drwxr-xr-x root/root 0 2015-07-12 11:59 ./usr/share/
drwxr-xr-x root/root 0 2015-07-12 11:59 ./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 2015-07-12 11:59 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-07-12 11:59 ./usr/share/doc/last-align/
-rw-r--r-- root/root 11779 2015-06-17 15:16 ./usr/share/doc/last-align/FAQ.html
-rw-r--r-- root/root 2734 2015-06-17 15:16 ./usr/share/doc/last-align/FAQ.txt
-rw-r--r-- root/root 696 2015-06-17 15:16 ./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 9913 2015-06-17 15:16 ./usr/share/doc/last-align/bisulfite.html
-rw-r--r-- root/root 2585 2015-06-17 15:16 ./usr/share/doc/last-align/bisulfite.txt
-rw-r--r-- root/root 3854 2015-07-06 16:49 ./usr/share/doc/last-align/changelog.Debian.gz
-rw-r--r-- root/root 24644 2015-06-17 15:16 ./usr/share/doc/last-align/changelog.gz
-rw-r--r-- root/root 1075 2015-07-06 16:59 ./usr/share/doc/last-align/copyright
drwxr-xr-x root/root 0 2015-07-12 11:59 ./usr/share/doc/last-align/examples/
-rw-r--r-- root/root 5504 2015-06-17 15:16 ./usr/share/doc/last-align/examples/chickenMito.fa.gz
-rw-r--r-- root/root 5675 2015-06-17 15:16 ./usr/share/doc/last-align/examples/fuguMito.fa.gz
-rw-r--r-- root/root 749 2015-06-17 15:16 ./usr/share/doc/last-align/examples/hoxd70.mat
-rw-r--r-- root/root 5562 2015-06-17 15:16 ./usr/share/doc/last-align/examples/humanMito.fa.gz
-rwxr-xr-x root/root 1484 2015-06-17 15:16 ./usr/share/doc/last-align/examples/last-bisulfite-paired.sh
-rwxr-xr-x root/root 905 2015-06-17 15:16 ./usr/share/doc/last-align/examples/last-bisulfite.sh
-rw-r--r-- root/root 5424 2015-06-17 15:16 ./usr/share/doc/last-align/examples/mouseMito.fa.gz
-rw-r--r-- root/root 50644 2015-06-17 15:16 ./usr/share/doc/last-align/examples/multiMito.maf.gz
-rwxr-xr-x root/root 964 2015-06-17 15:16 ./usr/share/doc/last-align/examples/multiMito.sh
-rw-r--r-- root/root 9249 2015-06-17 15:16 ./usr/share/doc/last-align/examples/myalns.maf.gz
-rw-r--r-- root/root 712 2015-06-17 15:16 ./usr/share/doc/last-align/examples/titv212.mat
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 35112
Build-Time: 722
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 250
Job: last-align_588-1
Machine Architecture: armhf
Package: last-align
Package-Time: 1029
Source-Version: 588-1
Space: 35112
Status: successful
Version: 588-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20150712-1200
Build needed 00:17:09, 35112k disc space