last-align →
809-1 →
armhf → 2016-12-06 18:13:39
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| last-align 809-1 (armhf) Tue, 06 Dec 2016 17:52:28 +0000 |
+==============================================================================+
Package: last-align
Version: 809-1
Source Version: 809-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-12a662aa-0c74-4a76-a8f2-be5bdda20832' 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 [9568 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.5 MB]
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Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: '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 388 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main last-align 809-1 (dsc) [2007 B]
Get:2 http://172.17.0.1/private stretch-staging/main last-align 809-1 (tar) [377 kB]
Get:3 http://172.17.0.1/private stretch-staging/main last-align 809-1 (diff) [8388 B]
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Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/last-align-N2m08g/last-align-809' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/last-align-N2m08g' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-UmTQBh/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-UmTQBh/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-UmTQBh/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-UmTQBh/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-UmTQBh/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-UmTQBh/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-UmTQBh/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-UmTQBh/apt_archive ./ Packages [433 B]
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Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
fuse2fs gnupg-l10n libfuse2 manpages
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 3 not upgraded.
Need to get 772 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-UmTQBh/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 10), help2man, python-imaging
Filtered Build-Depends: debhelper (>= 10), help2man, python-imaging
dpkg-deb: building package 'sbuild-build-depends-last-align-dummy' in '/<<BUILDDIR>>/resolver-UmTQBh/apt_archive/sbuild-build-depends-last-align-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-last-align-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-UmTQBh/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-UmTQBh/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-UmTQBh/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-UmTQBh/apt_archive ./ Sources [507 B]
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Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
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 packages were automatically installed and are no longer required:
fuse2fs gnupg-l10n libfuse2 manpages
Use 'apt autoremove' to remove them.
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 libssl1.0.2 libtiff5 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 libssl1.0.2 libtiff5 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, 54 newly installed, 0 to remove and 3 not upgraded.
Need to get 25.1 MB/26.0 MB of archives.
After this operation, 88.4 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-UmTQBh/apt_archive ./ sbuild-build-depends-last-align-dummy 0.invalid.0 [794 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf liblocale-gettext-perl armhf 1.07-3+b1 [18.3 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 9.0.12 [178 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 2.7.5-2 [971 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.12-7 [389 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.12-7 [1177 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 libpython2.7-stdlib armhf 2.7.12-7 [1853 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.12-7 [284 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-2 [19.8 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.11-2 [153 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-1 [219 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-1 [104 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-1 [63.3 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-5 [7427 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.1 [804 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-5 [733 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.2-2 [2527 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.2 [826 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf help2man armhf 1.47.4 [162 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libpng16-16 armhf 1.6.26-2 [263 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libfreetype6 armhf 2.6.3-3+b1 [385 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.1-2 [109 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf liblcms2-2 armhf 2.7-1 [116 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libtiff5 armhf 4.0.7-1 [209 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libwebp6 armhf 0.5.1-2 [200 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libwebpdemux2 armhf 0.5.1-2 [71.1 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libwebpmux2 armhf 0.5.1-2 [78.6 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf python-pil armhf 3.4.2-1 [346 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf python-imaging all 3.4.2-1 [48.2 kB]
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Unpacking liblcms2-2:armhf (2.7-1) ...
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Unpacking libtiff5:armhf (4.0.7-1) ...
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Preparing to unpack .../34-libwebpmux2_0.5.1-2_armhf.deb ...
Unpacking libwebpmux2:armhf (0.5.1-2) ...
Selecting previously unselected package python-pil:armhf.
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Unpacking python-pil:armhf (3.4.2-1) ...
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Preparing to unpack .../37-sbuild-build-depends-last-align-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-last-align-dummy (0.invalid.0) ...
Setting up libexpat1:armhf (2.2.0-1) ...
Setting up libjpeg62-turbo:armhf (1:1.5.1-2) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up mime-support (3.60) ...
Setting up libpng16-16:armhf (1.6.26-2) ...
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 (4.0.7-1) ...
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 (57.1-5) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2.1) ...
Setting up libfreetype6:armhf (2.6.3-3+b1) ...
Setting up libmagic-mgc (1:5.29-1) ...
Setting up libmagic1:armhf (1:5.29-1) ...
Setting up libssl1.0.2:armhf (1.0.2j-4) ...
Processing triggers for libc-bin (2.24-7+rpi1) ...
Setting up autotools-dev (20161112.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up liblocale-gettext-perl (1.07-3+b1) ...
Setting up libffi6:armhf (3.2.1-6) ...
Setting up bsdmainutils (9.0.12) ...
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 (2.7.12-7) ...
Setting up autopoint (0.19.8.1-1) ...
Setting up libwebp6:armhf (0.5.1-2) ...
Setting up libfile-stripnondeterminism-perl (0.028-1) ...
Setting up libglib2.0-0:armhf (2.50.2-2) ...
No schema files found: doing nothing.
Setting up python2.7 (2.7.12-7) ...
Setting up libwebpmux2:armhf (0.5.1-2) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.29-1) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Setting up libpython-stdlib:armhf (2.7.11-2) ...
Setting up automake (1:1.15-5) ...
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 (2.7.5-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up python (2.7.11-2) ...
Setting up libtool (2.4.6-2) ...
Setting up gettext (0.19.8.1-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up python-pil:armhf (3.4.2-1) ...
Setting up po-debconf (1.0.20) ...
Setting up python-imaging (3.4.2-1) ...
Setting up dh-autoreconf (12) ...
Setting up dh-strip-nondeterminism (0.028-1) ...
Setting up debhelper (10.2.2) ...
Setting up sbuild-build-depends-last-align-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-7+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.27.51.20161127-1 dpkg-dev_1.18.15 g++-6_6.2.1-5+rpi1 gcc-6_6.2.1-5+rpi1 libc6-dev_2.24-7+rpi1 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.2.1-5+rpi1 libstdc++6_6.2.1-5+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-3 adduser_3.115 apt_1.4~beta1 autoconf_2.69-10 automake_1:1.15-5 autopoint_0.19.8.1-1 autotools-dev_20161112.1 base-files_9.7+rpi1 base-passwd_3.5.41 bash_4.4-2 binutils_2.27.51.20161127-1 bsdmainutils_9.0.12 bsdutils_1:2.29-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-6 cpp_4:6.1.1-1 cpp-6_6.2.1-5+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.2 debianutils_4.8.1 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dmsetup_2:1.02.136-1 dpkg_1.18.15 dpkg-dev_1.18.15 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.29-1 findutils_4.6.0+git+20161106-1 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.2.1-5+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-6_6.2.1-5+rpi1 gcc-6-base_6.2.1-5+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_2.1.16-2 gnupg-agent_2.1.16-2 gnupg-l10n_2.1.16-2 gpgv_2.1.16-2 grep_2.26-1 groff-base_1.22.3-8 gzip_1.6-5 help2man_1.47.4 hostname_3.18 init_1.46 init-system-helpers_1.46 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_23-1 libacl1_2.2.52-3 libapparmor1_2.10.95-6 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.4~beta1 libarchive-zip-perl_1.59-1 libasan1_4.9.3-14 libasan3_6.2.1-5+rpi1 libassuan0_2.4.3-2 libatomic1_6.2.1-5+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblkid1_2.29-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-7+rpi1 libc-dev-bin_2.24-7+rpi1 libc6_2.24-7+rpi1 libc6-dev_2.24-7+rpi1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.2.1-5+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.3-2 libdb5.3_5.3.28-12 libdbus-1-3_1.10.14-1 libdebconfclient0_0.218 libdevmapper1.02.1_2:1.02.136-1 libdpkg-perl_1.18.15 libdrm2_2.4.74-1 libexpat1_2.2.0-1 libfakeroot_1.21-2 libfdisk1_2.29-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libfreetype6_2.6.3-3+b1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-4.9-dev_4.9.3-14 libgcc-6-dev_6.2.1-5+rpi1 libgcc1_1:6.2.1-5+rpi1 libgcrypt20_1.7.3-2 libgdbm3_1.8.3-14 libglib2.0-0_2.50.2-2 libgmp10_2:6.1.1+dfsg-1 libgomp1_6.2.1-5+rpi1 libgpg-error0_1.25-1 libicu57_57.1-5 libidn11_1.33-1 libip4tc0_1.6.0-4 libisl15_0.17.1-1 libjbig0_2.1-3.1 libjpeg62-turbo_1:1.5.1-2 libklibc_2.0.4-9+rpi1 libkmod2_23-1 libksba8_1.3.5-2 liblcms2-2_2.7-1 liblocale-gettext-perl_1.07-3+b1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-1 libmagic1_1:5.29-1 libmount1_2.29-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnpth0_1.3-1 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_2:8.39-2 libperl5.24_5.24.1~rc4-1 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libpng16-16_1.6.26-2 libprocps3_2:3.3.9-9 libprocps6_2:3.3.12-3 libpython-stdlib_2.7.11-2 libpython2.7-minimal_2.7.12-7 libpython2.7-stdlib_2.7.12-7 libreadline7_7.0-1 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-1 libsemanage1_2.6-1 libsepol1_2.6-1 libsigsegv2_2.10-5 libslang2_2.3.1-5 libsmartcols1_2.29-1 libsqlite3-0_3.15.2-1 libss2_1.43.3-1 libssl1.0.2_1.0.2j-4 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.2.1-5+rpi1 libstdc++6_6.2.1-5+rpi1 libsystemd0_232-6 libtiff5_4.0.7-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtool_2.4.6-2 libubsan0_6.2.1-5+rpi1 libudev1_232-6 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1 libwebp6_0.5.1-2 libwebpdemux2_0.5.1-2 libwebpmux2_0.5.1-2 libxml2_2.9.4+dfsg1-2.1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.3 lsb-base_9.20161125+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-2 manpages_4.08-1 mawk_1.3.3-17 mime-support_3.60 mount_2.29-1 multiarch-support_2.24-7+rpi1 nano_2.7.1-1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 passwd_1:4.2-3.3 patch_2.7.5-1 perl_5.24.1~rc4-1 perl-base_5.24.1~rc4-1 perl-modules-5.24_5.24.1~rc4-1 pinentry-curses_0.9.7-9 po-debconf_1.0.20 procps_2:3.3.12-3 python_2.7.11-2 python-imaging_3.4.2-1 python-minimal_2.7.11-2 python-pil_3.4.2-1 python2.7_2.7.12-7 python2.7-minimal_2.7.12-7 raspbian-archive-keyring_20120528.2 readline-common_7.0-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-last-align-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_232-6 systemd-sysv_232-6 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1.1 tzdata_2016j-2 udev_232-6 util-linux_2.29-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Nov 30 15:11:06 2016 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./last-align_809-1.dsc
dpkg-source: info: extracting last-align in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking last-align_809.orig.tar.xz
dpkg-source: info: unpacking last-align_809-1.debian.tar.xz
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-12a662aa-0c74-4a76-a8f2-be5bdda20832
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package last-align
dpkg-buildpackage: info: source version 809-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build last-align-809
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j4 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_autoreconf_clean
dh_clean
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_update_autotools_config -a
dh_autoreconf -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>>=. -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>>=. -fstack-protector-strong -Wformat -Werror=format-security" CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS="-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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -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>>=. -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>>=. -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:160:28: 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>>=. -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
split/cbrc_split_aligner.cc: In member function 'void cbrc::SplitAligner::initSpliceSignals(unsigned int)':
split/cbrc_split_aligner.cc:721:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (a.rend > chromEnd - chromBeg)
~~~~~~~^~~~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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>>=. -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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -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>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o last-merge-batches.o last-merge-batches.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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>>=. -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>>=. -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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -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="809" \
--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="809" \
--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="809" \
# --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="809" \
--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="809" \
--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="809" \
# --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="809" \
# --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="809" \
# --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="809" \
# --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="809" \
--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="809" \
--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="809" \
--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="809" \
--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="809" \
--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="809" \
# --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="809" \
--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="809" \
--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
dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastdb contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastal contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/last-align/usr/bin/last-pair-probs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/last-align/usr/bin/last-split contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/last-align/usr/bin/lastdb debian/last-align/usr/bin/last-merge-batches debian/last-align/usr/bin/lastal debian/last-align/usr/bin/last-pair-probs debian/last-align/usr/bin/last-split were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'last-align-dbgsym' in '../last-align-dbgsym_809-1_armhf.deb'.
dpkg-deb: building package 'last-align' in '../last-align_809-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../last-align_809-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build last-align-809
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2016-12-06T18:12:14Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
last-align_809-1_armhf.changes:
-------------------------------
Format: 1.8
Date: Wed, 30 Nov 2016 16:04:04 +0100
Source: last-align
Binary: last-align
Architecture: armhf
Version: 809-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
last-align - genome-scale comparison of biological sequences
Changes:
last-align (809-1) unstable; urgency=medium
.
* New upstream version
* debhelper 10
* d/watch: version=4
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Files:
082387d5a57c3f3e768e7f5639756a4d 4166536 debug extra last-align-dbgsym_809-1_armhf.deb
3aadf62a8ce20841e6eec6b7c76a9cbf 5078 science optional last-align_809-1_armhf.buildinfo
47705cf59927dfcb8ff1f6b1b8baf9b7 561610 science optional last-align_809-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
last-align-dbgsym_809-1_armhf.deb
---------------------------------
new debian package, version 2.0.
size 4166536 bytes: control archive=707 bytes.
571 bytes, 13 lines control
530 bytes, 5 lines md5sums
Package: last-align-dbgsym
Source: last-align
Version: 809-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4281
Depends: last-align (= 809-1)
Section: debug
Priority: extra
Homepage: http://last.cbrc.jp/
Description: Debug symbols for last-align
Auto-Built-Package: debug-symbols
Build-Ids: 06297f95994066b2c5343bcaed7c742eb5ab0b23 1a05a2dcf301f8f248f4705e6ac7f125a49dfe97 4fc5fdcb8d47f00e41d6d44fcb8afb22ed9fbfd4 e567a35ec8889341e1f64bda2c7fc10ea61001f2 ea2aacf9e4932f5f3e987936d5127797fc309dd7
drwxr-xr-x root/root 0 2016-11-30 15:04 ./
drwxr-xr-x root/root 0 2016-11-30 15:04 ./usr/
drwxr-xr-x root/root 0 2016-11-30 15:04 ./usr/lib/
drwxr-xr-x root/root 0 2016-11-30 15:04 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-11-30 15:04 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-11-30 15:04 ./usr/lib/debug/.build-id/06/
-rw-r--r-- root/root 9856 2016-11-30 15:04 ./usr/lib/debug/.build-id/06/297f95994066b2c5343bcaed7c742eb5ab0b23.debug
drwxr-xr-x root/root 0 2016-11-30 15:04 ./usr/lib/debug/.build-id/1a/
-rw-r--r-- root/root 2756116 2016-11-30 15:04 ./usr/lib/debug/.build-id/1a/05a2dcf301f8f248f4705e6ac7f125a49dfe97.debug
drwxr-xr-x root/root 0 2016-11-30 15:04 ./usr/lib/debug/.build-id/4f/
-rw-r--r-- root/root 790164 2016-11-30 15:04 ./usr/lib/debug/.build-id/4f/c5fdcb8d47f00e41d6d44fcb8afb22ed9fbfd4.debug
drwxr-xr-x root/root 0 2016-11-30 15:04 ./usr/lib/debug/.build-id/e5/
-rw-r--r-- root/root 230744 2016-11-30 15:04 ./usr/lib/debug/.build-id/e5/67a35ec8889341e1f64bda2c7fc10ea61001f2.debug
drwxr-xr-x root/root 0 2016-11-30 15:04 ./usr/lib/debug/.build-id/ea/
-rw-r--r-- root/root 580268 2016-11-30 15:04 ./usr/lib/debug/.build-id/ea/2aacf9e4932f5f3e987936d5127797fc309dd7.debug
drwxr-xr-x root/root 0 2016-11-30 15:04 ./usr/share/
drwxr-xr-x root/root 0 2016-11-30 15:04 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-11-30 15:04 ./usr/share/doc/last-align-dbgsym -> last-align
last-align_809-1_armhf.deb
--------------------------
new debian package, version 2.0.
size 561610 bytes: control archive=3486 bytes.
1165 bytes, 24 lines control
6684 bytes, 93 lines md5sums
Package: last-align
Version: 809-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1643
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 2016-11-30 15:04 ./
drwxr-xr-x root/root 0 2016-11-30 15:04 ./usr/
drwxr-xr-x root/root 0 2016-11-30 15:04 ./usr/bin/
-rwxr-xr-x root/root 475 2016-11-30 15:04 ./usr/bin/fastq-interleave
-rwxr-xr-x root/root 17152 2016-11-30 15:04 ./usr/bin/last-dotplot
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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: 46288
Build-Time: 822
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 318
Job: last-align_809-1
Machine Architecture: armhf
Package: last-align
Package-Time: 1186
Source-Version: 809-1
Space: 46288
Status: successful
Version: 809-1
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Finished at 2016-12-06T18:12:14Z
Build needed 00:19:46, 46288k disc space