last-align →
752-1 →
armhf → 2016-08-22 11:11:21
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on testbuildd.raspbian.org
+==============================================================================+
| last-align 752-1 (armhf) 22 Aug 2016 10:50 |
+==============================================================================+
Package: last-align
Version: 752-1
Source Version: 752-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/last-align-FPgQ8Q/last-align-752' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/last-align-FPgQ8Q' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-4faa8024-a4d3-43c0-928b-6ac4d7b7c3c5' 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 [9238 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.2 MB]
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W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: '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 384 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main last-align 752-1 (dsc) [1967 B]
Get:2 http://172.17.0.1/private stretch-staging/main last-align 752-1 (tar) [374 kB]
Get:3 http://172.17.0.1/private stretch-staging/main last-align 752-1 (diff) [8392 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-kWnPoS/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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Get:5 file:/<<BUILDDIR>>/resolver-kWnPoS/apt_archive ./ Packages [527 B]
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Reading package lists...
+------------------------------------------------------------------------------+
| Install core build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
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Building dependency tree...
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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 15 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-PBCZAC/apt_archive/sbuild-build-depends-last-align-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Get:1 file:/<<BUILDDIR>>/resolver-PBCZAC/apt_archive ./ InRelease
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Get:4 file:/<<BUILDDIR>>/resolver-PBCZAC/apt_archive ./ Sources [229 B]
Get:5 file:/<<BUILDDIR>>/resolver-PBCZAC/apt_archive ./ Packages [546 B]
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W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-PBCZAC/apt_archive/./Release.gpg: Signature by key 085A60275B95EE7E758335885FBC947B34E39F26 uses weak digest algorithm (SHA1)
Reading package lists...
+------------------------------------------------------------------------------+
| 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 libicu57
libjbig0 libjpeg62-turbo liblcms2-2 liblocale-gettext-perl libmagic-mgc
libmagic1 libpipeline1 libpng16-16 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libsigsegv2 libsqlite3-0 libssl1.0.2 libtiff5
libtimedate-perl libtool libunistring0 libwebp6 libwebpdemux2 libwebpmux2
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 libicu57
libjbig0 libjpeg62-turbo liblcms2-2 liblocale-gettext-perl libmagic-mgc
libmagic1 libpipeline1 libpng16-16 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libsigsegv2 libsqlite3-0 libssl1.0.2 libtiff5
libtimedate-perl libtool libunistring0 libwebp6 libwebpdemux2 libwebpmux2
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, 56 newly installed, 0 to remove and 15 not upgraded.
Need to get 26.1 MB/26.1 MB of archives.
After this operation, 88.7 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-PBCZAC/apt_archive ./ sbuild-build-depends-last-align-dummy 0.invalid.0 [786 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf liblocale-gettext-perl armhf 1.07-3 [18.0 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.12-2 [388 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.12-2 [1173 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-2 [40.3 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-1 [61.7 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-0 armhf 3.13.0-1 [479 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libssl1.0.2 armhf 1.0.2h-1 [889 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.12-2 [1843 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.12-2 [277 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-2 [19.8 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.11-2 [153 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.28-4 [210 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-4 [104 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-4 [62.7 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-2 [7404 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-1+b1 [803 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.1-2 [2546 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.022-1 [13.1 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.022-1 [7902 B]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-0.1 [200 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160814 [800 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf help2man armhf 1.47.4 [162 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libpng16-16 armhf 1.6.24-2 [262 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libfreetype6 armhf 2.6.3-3+b1 [385 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.0-1 [109 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf liblcms2-2 armhf 2.7-1 [116 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libtiff5 armhf 4.0.6-2 [203 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libwebp6 armhf 0.5.1-2 [200 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libwebpdemux2 armhf 0.5.1-2 [71.1 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libwebpmux2 armhf 0.5.1-2 [78.6 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf python-pil armhf 3.3.0-1 [337 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf python-imaging all 3.3.0-1 [47.1 kB]
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Processing triggers for libc-bin (2.23-4) ...
Setting up libexpat1:armhf (2.2.0-1) ...
Setting up libjpeg62-turbo:armhf (1:1.5.0-1) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up mime-support (3.60) ...
Setting up libpng16-16:armhf (1.6.24-2) ...
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 libicu57:armhf (57.1-2) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-1+b1) ...
Setting up libfreetype6:armhf (2.6.3-3+b1) ...
Setting up libmagic-mgc (1:5.28-4) ...
Setting up libmagic1:armhf (1:5.28-4) ...
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 libsqlite3-0:armhf (3.13.0-1) ...
Setting up liblocale-gettext-perl (1.07-3) ...
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 libpython2.7-stdlib:armhf (2.7.12-2) ...
Setting up autopoint (0.19.8.1-1) ...
Setting up libwebp6:armhf (0.5.1-2) ...
Setting up libfile-stripnondeterminism-perl (0.022-1) ...
Setting up libglib2.0-0:armhf (2.48.1-2) ...
No schema files found: doing nothing.
Setting up python2.7 (2.7.12-2) ...
Setting up libwebpmux2:armhf (0.5.1-2) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.28-4) ...
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 help2man (1.47.4) ...
Setting up libwebpdemux2:armhf (0.5.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
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 (3.3.0-1) ...
Setting up po-debconf (1.0.19) ...
Setting up python-imaging (3.3.0-1) ...
Setting up dh-autoreconf (12) ...
Setting up debhelper (9.20160814) ...
Setting up sbuild-build-depends-last-align-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.022-1) ...
Processing triggers for libc-bin (2.23-4) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26.1-1 dpkg-dev_1.18.10 g++-6_6.1.1-11+rpi1 gcc-6_6.1.1-11+rpi1 libc6-dev_2.23-4 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3~pre3 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_1:2.28-6 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.1.1-11+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_9.20160814 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.022-1 diffutils_1:3.3-3 dmsetup_2:1.02.130-1 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.1-1 e2fsprogs_1.43.1-1 fakeroot_1.21-1 file_1:5.28-4 findutils_4.6.0+git+20160703-2 fuse2fs_1.43.1-1 g++_4:6.1.1-1 g++-6_6.1.1-11+rpi1 gcc_4:6.1.1-1 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-base_5.4.0-4 gcc-6_6.1.1-11+rpi1 gcc-6-base_6.1.1-11+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 init_1.42 init-system-helpers_1.42 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 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~pre3 libarchive-zip-perl_1.59-1 libasan3_6.1.1-11+rpi1 libatomic1_6.1.1-11+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.5-1 libaudit1_1:2.6.5-1 libblkid1_2.28-6 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.23-4 libc-dev-bin_2.23-4 libc6_2.23-4 libc6-dev_2.23-4 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-11+rpi1 libcomerr2_1.43.1-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-12 libdbus-1-3_1.10.8-1 libdebconfclient0_0.215 libdevmapper1.02.1_2:1.02.130-1 libdpkg-perl_1.18.10 libdrm2_2.4.70-1 libexpat1_2.2.0-1 libfakeroot_1.21-1 libfdisk1_2.28-6 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.022-1 libfreetype6_2.6.3-3+b1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.1.1-11+rpi1 libgcc1_1:6.1.1-11+rpi1 libgcrypt20_1.7.2-2 libgdbm3_1.8.3-14 libglib2.0-0_2.48.1-2 libgmp10_2:6.1.1+dfsg-1 libgomp1_6.1.1-11+rpi1 libgpg-error0_1.24-1 libicu57_57.1-2 libidn11_1.33-1 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 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmount1_2.28-6 libmpc3_1.0.3-1 libmpfr4_3.1.4-2 libncurses5_6.0+20160625-1 libncursesw5_6.0+20160625-1 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_2:8.39-1 libperl5.22_5.22.2-3 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libpng16-16_1.6.24-2 libprocps6_2:3.3.12-2 libpython-stdlib_2.7.11-2 libpython2.7-minimal_2.7.12-2 libpython2.7-stdlib_2.7.12-2 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_2.28-6 libsqlite3-0_3.13.0-1 libss2_1.43.1-1 libssl1.0.2_1.0.2h-1 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 libsystemd0_230-7+b1 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+20160625-1 libtool_2.4.6-0.1 libubsan0_6.1.1-11+rpi1 libudev1_230-7+b1 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_2.28-6 libwebp6_0.5.1-2 libwebpdemux2_0.5.1-2 libwebpmux2_0.5.1-2 libxml2_2.9.4+dfsg1-1+b1 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_4.07-1 mawk_1.3.3-17 mime-support_3.60 mount_2.28-6 multiarch-support_2.23-4 nano_2.6.2-1 ncurses-base_6.0+20160625-1 ncurses-bin_6.0+20160625-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-3 perl-base_5.22.2-3 perl-modules-5.22_5.22.2-3 po-debconf_1.0.19 procps_2:3.3.12-2 python_2.7.11-2 python-imaging_3.3.0-1 python-minimal_2.7.11-2 python-pil_3.3.0-1 python2.7_2.7.12-2 python2.7-minimal_2.7.12-2 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_0.59-3.1 systemd_230-7+b1 systemd-sysv_230-7+b1 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016f-1 udev_230-7+b1 util-linux_2.28-6 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Tue Aug 16 12:37:41 2016 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_752-1.dsc
dpkg-source: info: extracting last-align in last-align-752
dpkg-source: info: unpacking last-align_752.orig.tar.xz
dpkg-source: info: unpacking last-align_752-1.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=111
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-4faa8024-a4d3-43c0-928b-6ac4d7b7c3c5
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package last-align
dpkg-buildpackage: info: source version 752-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build last-align-752
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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: In function 'unsigned int cbrc::decideNumberOfThreads(unsigned int, const char*, bool)':
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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: In function 'unsigned int cbrc::decideNumberOfThreads(unsigned int, const char*, bool)':
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
In file included from alp/njn_matrix.hpp:43:0,
from alp/njn_localmaxstatutil.hpp:39,
from alp/sls_alignment_evaluer.cpp:44:
alp/njn_vector.hpp: In member function 'virtual void Njn::Vector<T>::free2()':
alp/njn_vector.hpp:333:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (getM () > 0) delete [] d_vector_p; d_vector_p = 0;
^~
alp/njn_vector.hpp:333:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (getM () > 0) delete [] d_vector_p; d_vector_p = 0;
^~~~~~~~~~
In file included from alp/njn_localmaxstatutil.hpp:39:0,
from alp/sls_alignment_evaluer.cpp:44:
alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix<T>::free2()':
alp/njn_matrix.hpp:600:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0;
^~
alp/njn_matrix.hpp:600:54: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0;
^~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
In file included from alp/njn_matrix.hpp:43:0,
from alp/njn_localmaxstatutil.hpp:39,
from alp/njn_localmaxstatmatrix.cpp:37:
alp/njn_vector.hpp: In member function 'virtual void Njn::Vector<T>::free2()':
alp/njn_vector.hpp:333:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (getM () > 0) delete [] d_vector_p; d_vector_p = 0;
^~
alp/njn_vector.hpp:333:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (getM () > 0) delete [] d_vector_p; d_vector_p = 0;
^~~~~~~~~~
In file included from alp/njn_localmaxstatutil.hpp:39:0,
from alp/njn_localmaxstatmatrix.cpp:37:
alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix<T>::free2()':
alp/njn_matrix.hpp:600:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0;
^~
alp/njn_matrix.hpp:600:54: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0;
^~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
In file included from alp/njn_matrix.hpp:43:0,
from alp/njn_localmaxstatutil.hpp:39,
from alp/njn_localmaxstat.cpp:42:
alp/njn_vector.hpp: In member function 'virtual void Njn::Vector<T>::free2()':
alp/njn_vector.hpp:333:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (getM () > 0) delete [] d_vector_p; d_vector_p = 0;
^~
alp/njn_vector.hpp:333:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (getM () > 0) delete [] d_vector_p; d_vector_p = 0;
^~~~~~~~~~
In file included from alp/njn_localmaxstatutil.hpp:39:0,
from alp/njn_localmaxstat.cpp:42:
alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix<T>::free2()':
alp/njn_matrix.hpp:600:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0;
^~
alp/njn_matrix.hpp:600:54: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0;
^~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
In file included from alp/njn_matrix.hpp:43:0,
from alp/njn_localmaxstatutil.hpp:39,
from alp/njn_localmaxstatutil.cpp:37:
alp/njn_vector.hpp: In member function 'virtual void Njn::Vector<T>::free2()':
alp/njn_vector.hpp:333:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (getM () > 0) delete [] d_vector_p; d_vector_p = 0;
^~
alp/njn_vector.hpp:333:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (getM () > 0) delete [] d_vector_p; d_vector_p = 0;
^~~~~~~~~~
In file included from alp/njn_localmaxstatutil.hpp:39:0,
from alp/njn_localmaxstatutil.cpp:37:
alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix<T>::free2()':
alp/njn_matrix.hpp:600:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0;
^~
alp/njn_matrix.hpp:600:54: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0;
^~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
In file included from alp/njn_matrix.hpp:43:0,
from alp/njn_localmaxstatutil.hpp:39,
from alp/sls_falp_alignment_evaluer.cpp:43:
alp/njn_vector.hpp: In member function 'virtual void Njn::Vector<T>::free2()':
alp/njn_vector.hpp:333:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (getM () > 0) delete [] d_vector_p; d_vector_p = 0;
^~
alp/njn_vector.hpp:333:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (getM () > 0) delete [] d_vector_p; d_vector_p = 0;
^~~~~~~~~~
In file included from alp/njn_localmaxstatutil.hpp:39:0,
from alp/sls_falp_alignment_evaluer.cpp:43:
alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix<T>::free2()':
alp/njn_matrix.hpp:600:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0;
^~
alp/njn_matrix.hpp:600:54: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0;
^~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
In file included from alp/njn_matrix.hpp:43:0,
from alp/njn_localmaxstatutil.hpp:39,
from alp/sls_fsa1.hpp:45,
from alp/sls_fsa1.cpp:36:
alp/njn_vector.hpp: In member function 'virtual void Njn::Vector<T>::free2()':
alp/njn_vector.hpp:333:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (getM () > 0) delete [] d_vector_p; d_vector_p = 0;
^~
alp/njn_vector.hpp:333:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (getM () > 0) delete [] d_vector_p; d_vector_p = 0;
^~~~~~~~~~
In file included from alp/njn_localmaxstatutil.hpp:39:0,
from alp/sls_fsa1.hpp:45,
from alp/sls_fsa1.cpp:36:
alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix<T>::free2()':
alp/njn_matrix.hpp:600:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0;
^~
alp/njn_matrix.hpp:600:54: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0;
^~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o last-merge-batches.o last-merge-batches.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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: 'qName' may be used uninitialized in this function [-Wmaybe-uninitialized]
last-pair-probs.cc:430:74: warning: 'rName' 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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="752" \
--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="752" \
--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="752" \
# --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="752" \
--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="752" \
--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="752" \
# --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="752" \
# --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="752" \
# --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="752" \
# --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="752" \
--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="752" \
--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="752" \
--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="752" \
--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="752" \
--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="752" \
# --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="752" \
--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="752" \
--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_752-1_armhf.deb'.
dpkg-deb: building package 'last-align' in '../last-align_752-1_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian nitrogen6x test autobuilder <root@raspbian.org> >../last-align_752-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build last-align-752
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160822-1110
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
last-align_752-1_armhf.changes:
-------------------------------
Format: 1.8
Date: Tue, 16 Aug 2016 14:35:15 +0200
Source: last-align
Binary: last-align
Architecture: armhf
Version: 752-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian nitrogen6x test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
last-align - genome-scale comparison of biological sequences
Changes:
last-align (752-1) unstable; urgency=medium
.
* New upstream version
Checksums-Sha1:
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7cff811f548181b8124250512bc66288025fb56e 575582 last-align_752-1_armhf.deb
Checksums-Sha256:
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fccde84a7dac75c090e1e6c612bf5def23ef8e4c4e47a5f5586ed4a9bee13886 575582 last-align_752-1_armhf.deb
Files:
49b2405e5f069bc6ea4b7c4bf6e7c79e 4145548 debug extra last-align-dbgsym_752-1_armhf.deb
0b657bc518a6d490308c919a465a9308 575582 science optional last-align_752-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
last-align-dbgsym_752-1_armhf.deb
---------------------------------
new debian package, version 2.0.
size 4145548 bytes: control archive=707 bytes.
571 bytes, 13 lines control
530 bytes, 5 lines md5sums
Package: last-align-dbgsym
Source: last-align
Version: 752-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4263
Depends: last-align (= 752-1)
Section: debug
Priority: extra
Homepage: http://last.cbrc.jp/
Description: Debug symbols for last-align
Auto-Built-Package: debug-symbols
Build-Ids: 222b9bae33bd96b4432229a46a0cef5ff0fa5a4d 297e804b3eed52eb9b81597cb51d01ee1804eac0 b8fb61ac1eabb9568c5c2e20f0c2be7816369b6b f2186e766db0edaaab209b558d20840176e8a7fe fdcfb55ace4802475cb2fab9fe104d045825d288
drwxr-xr-x root/root 0 2016-08-16 12:35 ./
drwxr-xr-x root/root 0 2016-08-16 12:35 ./usr/
drwxr-xr-x root/root 0 2016-08-16 12:35 ./usr/lib/
drwxr-xr-x root/root 0 2016-08-16 12:35 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-08-16 12:35 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-08-16 12:35 ./usr/lib/debug/.build-id/22/
-rw-r--r-- root/root 786136 2016-08-16 12:35 ./usr/lib/debug/.build-id/22/2b9bae33bd96b4432229a46a0cef5ff0fa5a4d.debug
drwxr-xr-x root/root 0 2016-08-16 12:35 ./usr/lib/debug/.build-id/29/
-rw-r--r-- root/root 570996 2016-08-16 12:35 ./usr/lib/debug/.build-id/29/7e804b3eed52eb9b81597cb51d01ee1804eac0.debug
drwxr-xr-x root/root 0 2016-08-16 12:35 ./usr/lib/debug/.build-id/b8/
-rw-r--r-- root/root 9872 2016-08-16 12:35 ./usr/lib/debug/.build-id/b8/fb61ac1eabb9568c5c2e20f0c2be7816369b6b.debug
drwxr-xr-x root/root 0 2016-08-16 12:35 ./usr/lib/debug/.build-id/f2/
-rw-r--r-- root/root 2752212 2016-08-16 12:35 ./usr/lib/debug/.build-id/f2/186e766db0edaaab209b558d20840176e8a7fe.debug
drwxr-xr-x root/root 0 2016-08-16 12:35 ./usr/lib/debug/.build-id/fd/
-rw-r--r-- root/root 229620 2016-08-16 12:35 ./usr/lib/debug/.build-id/fd/cfb55ace4802475cb2fab9fe104d045825d288.debug
drwxr-xr-x root/root 0 2016-08-16 12:35 ./usr/share/
drwxr-xr-x root/root 0 2016-08-16 12:35 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-08-16 12:35 ./usr/share/doc/last-align-dbgsym -> last-align
last-align_752-1_armhf.deb
--------------------------
new debian package, version 2.0.
size 575582 bytes: control archive=3497 bytes.
1165 bytes, 24 lines control
6684 bytes, 93 lines md5sums
Package: last-align
Version: 752-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1692
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 2016-08-16 12:35 ./
drwxr-xr-x root/root 0 2016-08-16 12:35 ./usr/
drwxr-xr-x root/root 0 2016-08-16 12:35 ./usr/bin/
-rwxr-xr-x root/root 475 2016-08-16 12:35 ./usr/bin/fastq-interleave
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 46208
Build-Time: 812
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 328
Job: last-align_752-1
Machine Architecture: armhf
Package: last-align
Package-Time: 1186
Source-Version: 752-1
Space: 46208
Status: successful
Version: 752-1
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Finished at 20160822-1110
Build needed 00:19:46, 46208k disc space