last-align →
746-1 →
armhf → 2016-07-20 11:12:10
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on testwandboard
+==============================================================================+
| last-align 746-1 (armhf) 20 Jul 2016 10:49 |
+==============================================================================+
Package: last-align
Version: 746-1
Source Version: 746-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/last-align-aKo1Gw/last-align-746' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/last-align-aKo1Gw' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-9dbb3c69-5e13-4630-8402-0d586e2a235c' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9179 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.1 MB]
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+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'last-align' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/last-align.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/last-align.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 382 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main last-align 746-1 (dsc) [1967 B]
Get:2 http://172.17.0.1/private stretch-staging/main last-align 746-1 (tar) [372 kB]
Get:3 http://172.17.0.1/private stretch-staging/main last-align 746-1 (diff) [8384 B]
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Download complete and in download only mode
Check architectures
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Check dependencies
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-CF7bGs/apt_archive/sbuild-build-depends-core-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
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+------------------------------------------------------------------------------+
| Install core build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
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The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 18 not upgraded.
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Filtered Build-Depends: debhelper (>= 9), help2man, python-imaging
dpkg-deb: building package 'sbuild-build-depends-last-align-dummy' in '/<<BUILDDIR>>/resolver-0h8xoH/apt_archive/sbuild-build-depends-last-align-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
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+------------------------------------------------------------------------------+
| Install last-align build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1
libffi6 libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0 libicu55
libjbig0 libjpeg62-turbo liblcms2-2 libmagic1 libpipeline1 libpng16-16
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2
libsqlite3-0 libssl1.0.2 libtiff5 libtimedate-perl libtool libunistring0
libwebp5 libwebpdemux1 libwebpmux1 libxml2 m4 man-db mime-support po-debconf
python python-imaging python-minimal python-pil python2.7 python2.7-minimal
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
liblcms2-utils libtool-doc gfortran | fortran95-compiler gcj-jdk 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
libltdl-dev xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1
libffi6 libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0 libicu55
libjbig0 libjpeg62-turbo liblcms2-2 libmagic1 libpipeline1 libpng16-16
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2
libsqlite3-0 libssl1.0.2 libtiff5 libtimedate-perl libtool libunistring0
libwebp5 libwebpdemux1 libwebpmux1 libxml2 m4 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, 54 newly installed, 0 to remove and 18 not upgraded.
Need to get 17.7 MB/25.9 MB of archives.
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Get:1 file:/<<BUILDDIR>>/resolver-0h8xoH/apt_archive ./ sbuild-build-depends-last-align-dummy 0.invalid.0 [788 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.12-1 [387 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.12-1 [1167 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-2 [40.3 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
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Get:20 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-2 [62.4 kB]
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Get:34 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.57-1 [95.1 kB]
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Get:39 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160403 [800 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf help2man armhf 1.47.4 [162 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libpng16-16 armhf 1.6.23-1 [260 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libfreetype6 armhf 2.6.3-3+b1 [385 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.0-1 [109 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf liblcms2-2 armhf 2.7-1 [116 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libtiff5 armhf 4.0.6-2 [203 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libwebp5 armhf 0.4.4-1.1 [175 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libwebpdemux1 armhf 0.4.4-1.1 [52.7 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libwebpmux1 armhf 0.4.4-1.1 [58.2 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf python-pil armhf 3.2.0-2 [333 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf python-imaging all 3.2.0-2 [45.3 kB]
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Unpacking sbuild-build-depends-last-align-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.23-1+rpi1) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libexpat1:armhf (2.2.0-1) ...
Setting up libjpeg62-turbo:armhf (1:1.5.0-1) ...
Setting up libarchive-zip-perl (1.57-1) ...
Setting up mime-support (3.60) ...
Setting up libpng16-16:armhf (1.6.23-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up liblcms2-2:armhf (2.7-1) ...
Setting up libjbig0:armhf (2.1-3.1) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up groff-base (1.22.3-8) ...
Setting up libtiff5:armhf (4.0.6-2) ...
Setting up gettext-base (0.19.8.1-1) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up m4 (1.4.17-5) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1.2) ...
Setting up libfreetype6:armhf (2.6.3-3+b1) ...
Setting up libmagic1:armhf (1:5.28-2) ...
Setting up libssl1.0.2:armhf (1.0.2h-1) ...
Setting up autotools-dev (20160430.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up help2man (1.47.4) ...
Setting up libsqlite3-0:armhf (3.13.0-1) ...
Setting up libffi6:armhf (3.2.1-4) ...
Setting up bsdmainutils (9.0.10) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libwebp5:armhf (0.4.4-1.1) ...
Setting up libpython2.7-stdlib:armhf (2.7.12-1) ...
Setting up autopoint (0.19.8.1-1) ...
Setting up libfile-stripnondeterminism-perl (0.019-1) ...
Setting up libwebpmux1:armhf (0.4.4-1.1) ...
Setting up libglib2.0-0:armhf (2.48.1-2) ...
No schema files found: doing nothing.
Setting up python2.7 (2.7.12-1) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.28-2) ...
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up libpython-stdlib:armhf (2.7.11-2) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libwebpdemux1:armhf (0.4.4-1.1) ...
Setting up python (2.7.11-2) ...
Setting up libtool (2.4.6-0.1) ...
Setting up gettext (0.19.8.1-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up python-pil:armhf (3.2.0-2) ...
Setting up po-debconf (1.0.19) ...
Setting up python-imaging (3.2.0-2) ...
Setting up dh-autoreconf (12) ...
Setting up debhelper (9.20160403) ...
Setting up sbuild-build-depends-last-align-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.019-1) ...
Processing triggers for libc-bin (2.23-1+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.5.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26.1-1 dpkg-dev_1.18.7 g++-5_5.4.0-4 gcc-5_5.4.0-4 libc6-dev_2.23-1+rpi1 libstdc++-5-dev_5.4.0-4 libstdc++6_6.1.1-1+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3~pre2 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-15 binutils_2.26.1-1 bsdmainutils_9.0.10 bsdutils_1:2.28-5 build-essential_11.7 bzip2_1.0.6-8 console-setup_1.146 console-setup-linux_1.146 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-3 cpp-5_5.4.0-4 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160403 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.019-1 diffutils_1:3.3-3 dmsetup_2:1.02.127-1 dpkg_1.18.7 dpkg-dev_1.18.7 e2fslibs_1.43.1-1 e2fsprogs_1.43.1-1 fakeroot_1.21-1 file_1:5.28-2 findutils_4.6.0+git+20160517-5 fuse2fs_1.43.1-1 g++_4:5.3.1-3 g++-5_5.4.0-4 gcc_4:5.3.1-3 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5_5.4.0-4 gcc-5-base_5.4.0-4 gcc-6-base_6.1.1-1+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_1.4.20-6 gpgv_1.4.20-6 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 help2man_1.47.4 hostname_3.18 ifupdown_0.8.13 init_1.36 init-system-helpers_1.36 initscripts_2.88dsf-59.7 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 iproute2_4.3.0-1 kbd_2.0.3-2 keyboard-configuration_1.146 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10.95-4 libapt-pkg5.0_1.3~pre2 libarchive-zip-perl_1.57-1 libasan2_5.4.0-4 libatm1_1:2.5.1-1.6 libatomic1_6.1.1-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.5.2-1+rpi1 libaudit1_1:2.5.2-1+rpi1 libblkid1_2.28-5 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.23-1+rpi1 libc-dev-bin_2.23-1+rpi1 libc6_2.23-1+rpi1 libc6-dev_2.23-1+rpi1 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-1+rpi1 libcomerr2_1.43.1-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.8-1 libdebconfclient0_0.213 libdevmapper1.02.1_2:1.02.127-1 libdpkg-perl_1.18.7 libdrm2_2.4.68-1 libexpat1_2.2.0-1 libfakeroot_1.21-1 libfdisk1_2.28-5 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.019-1 libfreetype6_2.6.3-3+b1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-5-dev_5.4.0-4 libgcc1_1:6.1.1-1+rpi1 libgcrypt20_1.7.1-2 libgdbm3_1.8.3-14 libglib2.0-0_2.48.1-2 libgmp10_2:6.1.1+dfsg-1 libgomp1_6.1.1-1+rpi1 libgpg-error0_1.23-1 libicu55_55.1-7 libidn11_1.32-3.1 libisl15_0.17.1-1 libjbig0_2.1-3.1 libjpeg62-turbo_1:1.5.0-1 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 liblcms2-2_2.7-1 liblocale-gettext-perl_1.07-3 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.28-2 libmount1_2.28-5 libmpc3_1.0.3-1 libmpfr4_3.1.4-2 libncurses5_6.0+20160319-2 libncursesw5_6.0+20160319-2 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpcre3_2:8.38-3.1 libperl5.22_5.22.2-2 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng12-0_1.2.54-6 libpng16-16_1.6.23-1 libprocps5_2:3.3.11-3 libpython-stdlib_2.7.11-2 libpython2.7-minimal_2.7.12-1 libpython2.7-stdlib_2.7.12-1 libreadline6_6.3-8+b3 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28-5 libsqlite3-0_3.13.0-1 libss2_1.43.1-1 libssl1.0.2_1.0.2h-1 libstdc++-5-dev_5.4.0-4 libstdc++6_6.1.1-1+rpi1 libsystemd0_230-5 libtext-charwidth-perl_0.04-7+b6 libtext-iconv-perl_1.7-5+b7 libtext-wrapi18n-perl_0.06-7.1 libtiff5_4.0.6-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160319-2 libtool_2.4.6-0.1 libubsan0_6.1.1-1+rpi1 libudev1_230-5 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28-5 libwebp5_0.4.4-1.1 libwebpdemux1_0.4.4-1.1 libwebpmux1_0.4.4-1.1 libxml2_2.9.3+dfsg1-1.2 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.06-1 mawk_1.3.3-17 mime-support_3.60 mount_2.28-5 multiarch-support_2.23-1+rpi1 ncurses-base_6.0+20160319-2 ncurses-bin_6.0+20160319-2 netbase_5.3 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-2 perl-base_5.22.2-2 perl-modules-5.22_5.22.2-2 po-debconf_1.0.19 procps_2:3.3.11-3 psmisc_22.21-2.1 python_2.7.11-2 python-imaging_3.2.0-2 python-minimal_2.7.11-2 python-pil_3.2.0-2 python2.7_2.7.12-1 python2.7-minimal_2.7.12-1 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_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_230-5 systemd-sysv_230-5 sysv-rc_2.88dsf-59.7 sysvinit-utils_2.88dsf-59.7 tar_1.29-1+rpi1 tzdata_2016f-1 udev_230-5 util-linux_2.28-5 xkb-data_2.17-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Fri Jul 15 05:34:24 2016 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./last-align_746-1.dsc
dpkg-source: info: extracting last-align in last-align-746
dpkg-source: info: unpacking last-align_746.orig.tar.xz
dpkg-source: info: unpacking last-align_746-1.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-9dbb3c69-5e13-4630-8402-0d586e2a235c
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package last-align
dpkg-buildpackage: info: source version 746-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build last-align-746
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j1 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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_update_autotools_config -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make all CXXFLAGS="-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11" CFLAGS="-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security" CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS="-fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o Alphabet.o Alphabet.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o MultiSequence.o MultiSequence.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o LastdbArguments.o LastdbArguments.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o io.o io.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o fileMap.o fileMap.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o TantanMasker.o TantanMasker.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o ScoreMatrix.o ScoreMatrix.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o LambdaCalculator.o LambdaCalculator.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o tantan.o tantan.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc
SubsetSuffixArraySort.cc: In member function 'void cbrc::SubsetSuffixArray::sortIndex(const uchar*, cbrc::SubsetSuffixArray::indexT, int)':
SubsetSuffixArraySort.cc:327:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if( end - beg <= maxUnsortedInterval && depth >= minLength ) continue;
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o lastdb.o lastdb.cc
In file included from lastdb.cc:14:0:
threadUtil.hh:16:23: warning: unused parameter 'programName' [-Wunused-parameter]
const char *programName,
^
threadUtil.hh:17:16: warning: unused parameter 'isVerbose' [-Wunused-parameter]
bool isVerbose) {
^
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -o lastdb Alphabet.o MultiSequence.o CyclicSubsetSeed.o SubsetSuffixArray.o LastdbArguments.o io.o fileMap.o TantanMasker.o ScoreMatrix.o SubsetMinimizerFinder.o LambdaCalculator.o tantan.o SubsetSuffixArraySort.o MultiSequenceQual.o lastdb.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o LastalArguments.o LastalArguments.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o DiagonalTable.o DiagonalTable.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o SegmentPair.o SegmentPair.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o Alignment.o Alignment.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o SegmentPairPot.o SegmentPairPot.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o AlignmentPot.o AlignmentPot.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o GeneralizedAffineGapCosts.o GeneralizedAffineGapCosts.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o Centroid.o Centroid.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o GeneticCode.o GeneticCode.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o LastEvaluer.o LastEvaluer.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o gaplessXdrop.o gaplessXdrop.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o gaplessPssmXdrop.o gaplessPssmXdrop.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o gaplessTwoQualityXdrop.o gaplessTwoQualityXdrop.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o AlignmentWrite.o AlignmentWrite.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o lastal.o lastal.cc
In file included from lastal.cc:32:0:
threadUtil.hh:16:23: warning: unused parameter 'programName' [-Wunused-parameter]
const char *programName,
^
threadUtil.hh:17:16: warning: unused parameter 'isVerbose' [-Wunused-parameter]
bool isVerbose) {
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_alp.o alp/sls_alp.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_basic.o alp/sls_basic.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/njn_random.o alp/njn_random.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -o lastal Alphabet.o MultiSequence.o CyclicSubsetSeed.o SubsetSuffixArray.o LastalArguments.o io.o fileMap.o TantanMasker.o ScoreMatrix.o SubsetMinimizerFinder.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 GreedyXdropAligner.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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o split/cbrc_linalg.o split/cbrc_linalg.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o split/last-split-main.o split/last-split-main.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o last-merge-batches.o last-merge-batches.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -o last-merge-batches last-merge-batches.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -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>>'
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
debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installman
help2man --no-info --version-string="746" \
--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="746" \
--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="746" \
# --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="746" \
--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="746" \
--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="746" \
# --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="746" \
# --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="746" \
# --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="746" \
# --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="746" \
--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="746" \
--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="746" \
--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="746" \
--name="Read 2 fastq files, and write them interleaved" \
/<<PKGBUILDDIR>>/scripts/fastq-interleave > /<<PKGBUILDDIR>>/debian/last-align/usr/share/man/man1//fastq-interleave.1
help2man --no-info --version-string="746" \
--name="Read files of lastal output, merge corresponding batches, and write them" \
/<<PKGBUILDDIR>>/src/last-merge-batches > /<<PKGBUILDDIR>>/debian/last-align/usr/share/man/man1//last-merge-batches.1
#help2man --no-info --version-string="746" \
# --name="Read alignments of paired DNA reads to a genome, and do estimations" \
# /<<PKGBUILDDIR>>/src/last-pair-probs > /<<PKGBUILDDIR>>/debian/last-align/usr/share/man/man1//last-pair-probs.1
help2man --no-info --version-string="746" \
--name="Get alignments that have a segment with score >= threshold, with gentle masking of lowercase letters" \
/<<PKGBUILDDIR>>/scripts/last-postmask > /<<PKGBUILDDIR>>/debian/last-align/usr/share/man/man1//last-postmask.1
help2man --no-info --version-string="746" \
--name="Try to find suitable score parameters for aligning the given sequences" \
/<<PKGBUILDDIR>>/scripts/last-train > /<<PKGBUILDDIR>>/debian/last-align/usr/share/man/man1//last-train.1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'last-align-dbgsym' in '../last-align-dbgsym_746-1_armhf.deb'.
dpkg-deb: building package 'last-align' in '../last-align_746-1_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../last-align_746-1_armhf.changes
dpkg-genchanges: warning: package last-align-dbgsym listed in files list but not in control info
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build last-align-746
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160720-1112
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
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+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
last-align_746-1_armhf.changes:
-------------------------------
Format: 1.8
Date: Fri, 15 Jul 2016 14:24:00 +0900
Source: last-align
Binary: last-align
Architecture: armhf
Version: 746-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Charles Plessy <plessy@debian.org>
Description:
last-align - genome-scale comparison of biological sequences
Changes:
last-align (746-1) unstable; urgency=medium
.
* New upstream version
Checksums-Sha1:
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ab1da06a7a05e1279bc4f8bdf0f3d8429eb84a19 573460 last-align_746-1_armhf.deb
Checksums-Sha256:
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Files:
aea3c08055e4bdc565751994f60ff56b 4023392 debug extra last-align-dbgsym_746-1_armhf.deb
04951aeb60782f3b9d0b66aa031d5a00 573460 science optional last-align_746-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
last-align-dbgsym_746-1_armhf.deb
---------------------------------
new debian package, version 2.0.
size 4023392 bytes: control archive=715 bytes.
571 bytes, 13 lines control
530 bytes, 5 lines md5sums
Package: last-align-dbgsym
Source: last-align
Version: 746-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4149
Depends: last-align (= 746-1)
Section: debug
Priority: extra
Homepage: http://last.cbrc.jp/
Description: Debug symbols for last-align
Auto-Built-Package: debug-symbols
Build-Ids: 2b2181fa30350010a6f2af93a316adc727951482 334b242d1d82801602de7ef962f20317fa2fb70f 713e3ea229e79bb65c7f143d76ccfb863b985081 ce4f798c905ff8781373705444554edddef94332 ee08bbdfca1ab4b2294621767a6408307acf9fd4
drwxr-xr-x root/root 0 2016-07-20 11:11 ./
drwxr-xr-x root/root 0 2016-07-20 11:11 ./usr/
drwxr-xr-x root/root 0 2016-07-20 11:11 ./usr/lib/
drwxr-xr-x root/root 0 2016-07-20 11:11 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-07-20 11:11 ./usr/lib/debug/.build-id/
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-rw-r--r-- root/root 9752 2016-07-20 11:11 ./usr/lib/debug/.build-id/2b/2181fa30350010a6f2af93a316adc727951482.debug
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-rw-r--r-- root/root 553468 2016-07-20 11:11 ./usr/lib/debug/.build-id/33/4b242d1d82801602de7ef962f20317fa2fb70f.debug
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-rw-r--r-- root/root 223320 2016-07-20 11:11 ./usr/lib/debug/.build-id/71/3e3ea229e79bb65c7f143d76ccfb863b985081.debug
drwxr-xr-x root/root 0 2016-07-20 11:11 ./usr/lib/debug/.build-id/ce/
-rw-r--r-- root/root 2685288 2016-07-20 11:11 ./usr/lib/debug/.build-id/ce/4f798c905ff8781373705444554edddef94332.debug
drwxr-xr-x root/root 0 2016-07-20 11:11 ./usr/lib/debug/.build-id/ee/
-rw-r--r-- root/root 759680 2016-07-20 11:11 ./usr/lib/debug/.build-id/ee/08bbdfca1ab4b2294621767a6408307acf9fd4.debug
drwxr-xr-x root/root 0 2016-07-20 11:11 ./usr/share/
drwxr-xr-x root/root 0 2016-07-20 11:11 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-07-20 11:11 ./usr/share/doc/last-align-dbgsym -> last-align
last-align_746-1_armhf.deb
--------------------------
new debian package, version 2.0.
size 573460 bytes: control archive=3495 bytes.
1165 bytes, 24 lines control
6684 bytes, 93 lines md5sums
Package: last-align
Version: 746-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1684
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), parallel
Recommends: python, python-imaging
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 2016-07-20 11:11 ./
drwxr-xr-x root/root 0 2016-07-20 11:10 ./usr/
drwxr-xr-x root/root 0 2016-07-20 11:11 ./usr/bin/
-rwxr-xr-x root/root 475 2016-07-20 11:10 ./usr/bin/fastq-interleave
-rwxr-xr-x root/root 17142 2016-07-20 11:10 ./usr/bin/last-dotplot
-rwxr-xr-x root/root 4703 2016-07-20 11:10 ./usr/bin/last-map-probs
-rwxr-xr-x root/root 9724 2016-07-20 11:11 ./usr/bin/last-merge-batches
-rwxr-xr-x root/root 54944 2016-07-20 11:11 ./usr/bin/last-pair-probs
-rwxr-xr-x root/root 3931 2016-07-20 11:10 ./usr/bin/last-postmask
-rwxr-xr-x root/root 112344 2016-07-20 11:11 ./usr/bin/last-split
-rwxr-xr-x root/root 13627 2016-07-20 11:10 ./usr/bin/last-train
-rwxr-xr-x root/root 779628 2016-07-20 11:11 ./usr/bin/lastal
-rwxr-xr-x root/root 153152 2016-07-20 11:11 ./usr/bin/lastdb
-rwxr-xr-x root/root 25732 2016-07-20 11:10 ./usr/bin/maf-convert
-rwxr-xr-x root/root 8992 2016-07-20 11:10 ./usr/bin/maf-join
-rwxr-xr-x root/root 2027 2016-07-20 11:10 ./usr/bin/maf-sort
-rwxr-xr-x root/root 4762 2016-07-20 11:10 ./usr/bin/maf-swap
-rwxr-xr-x root/root 234 2016-07-20 11:10 ./usr/bin/parallel-fasta
-rwxr-xr-x root/root 295 2016-07-20 11:10 ./usr/bin/parallel-fastq
drwxr-xr-x root/root 0 2016-07-20 11:11 ./usr/share/
drwxr-xr-x root/root 0 2016-07-20 11:10 ./usr/share/doc-base/
-rw-r--r-- root/root 281 2016-07-15 05:23 ./usr/share/doc-base/last-align-manual
-rw-r--r-- root/root 291 2016-07-15 05:23 ./usr/share/doc-base/last-align-scripts
-rw-r--r-- root/root 294 2016-07-15 05:23 ./usr/share/doc-base/last-align-seeds
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drwxr-xr-x root/root 0 2016-07-20 11:11 ./usr/share/doc/last-align/
-rw-r--r-- root/root 12338 2016-07-15 04:31 ./usr/share/doc/last-align/FAQ.html
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-rw-r--r-- root/root 888 2016-07-15 04:31 ./usr/share/doc/last-align/Makefile
-rw-r--r-- root/root 201 2016-07-15 05:23 ./usr/share/doc/last-align/NEWS.Debian.gz
-rw-r--r-- root/root 10092 2016-07-15 04:31 ./usr/share/doc/last-align/bisulfite.html
-rw-r--r-- root/root 2719 2016-07-15 04:31 ./usr/share/doc/last-align/bisulfite.txt
-rw-r--r-- root/root 4080 2016-07-15 05:24 ./usr/share/doc/last-align/changelog.Debian.gz
-rw-r--r-- root/root 28930 2016-07-15 04:31 ./usr/share/doc/last-align/changelog.gz
-rw-r--r-- root/root 1016 2016-07-15 05:23 ./usr/share/doc/last-align/copyright
drwxr-xr-x root/root 0 2016-07-20 11:11 ./usr/share/doc/last-align/examples/
-rw-r--r-- root/root 5504 2016-07-15 04:31 ./usr/share/doc/last-align/examples/chickenMito.fa.gz
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-rw-r--r-- root/root 5562 2016-07-15 04:31 ./usr/share/doc/last-align/examples/humanMito.fa.gz
-rwxr-xr-x root/root 1484 2016-07-15 04:31 ./usr/share/doc/last-align/examples/last-bisulfite-paired.sh
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-rw-r--r-- root/root 408 2016-07-15 04:31 ./usr/share/doc/last-align/examples/ublast.seed
-rw-r--r-- root/root 539 2016-07-15 04:31 ./usr/share/doc/last-align/examples/vertebrateMito.gc
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-rw-r--r-- root/root 11019 2016-07-15 04:31 ./usr/share/doc/last-align/last.html
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 45236
Build-Time: 882
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 360
Job: last-align_746-1
Machine Architecture: armhf
Package: last-align
Package-Time: 1343
Source-Version: 746-1
Space: 45236
Status: successful
Version: 746-1
--------------------------------------------------------------------------------
Finished at 20160720-1112
Build needed 00:22:23, 45236k disc space