last-align →
830-2 →
armhf → 2017-06-22 18:08:43
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd.raspbian.org
+==============================================================================+
| last-align 830-2 (armhf) Thu, 22 Jun 2017 17:40:45 +0000 |
+==============================================================================+
Package: last-align
Version: 830-2
Source Version: 830-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-fe586113-77f5-460b-aca1-f309cca1c9c3' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [9974 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [11.9 MB]
Fetched 21.8 MB in 26s (810 kB/s)
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 392 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main last-align 830-2 (dsc) [2026 B]
Get:2 http://172.17.0.1/private buster-staging/main last-align 830-2 (tar) [381 kB]
Get:3 http://172.17.0.1/private buster-staging/main last-align 830-2 (diff) [8976 B]
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Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/last-align-ZFUV5G/last-align-830' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/last-align-ZFUV5G' 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-1yXmqg/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-1yXmqg/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-1yXmqg/gpg/trustdb.gpg: trustdb created
gpg: key 5FBC947B34E39F26: 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 5FBC947B34E39F26: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 5FBC947B34E39F26: 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-1yXmqg/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-1yXmqg/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-1yXmqg/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-1yXmqg/apt_archive ./ Sources [349 B]
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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...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
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Get:1 copy:/<<BUILDDIR>>/resolver-1yXmqg/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-1yXmqg/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-1yXmqg/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-1yXmqg/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-1yXmqg/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-1yXmqg/apt_archive ./ Sources [507 B]
Get:5 copy:/<<BUILDDIR>>/resolver-1yXmqg/apt_archive ./ Packages [587 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 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 libmagic-mgc libmagic1 libpipeline1
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2
libssl1.1 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 m4-doc 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 libmagic-mgc libmagic1 libpipeline1
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2
libssl1.1 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, 53 newly installed, 0 to remove and 1 not upgraded.
Need to get 26.0 MB of archives.
After this operation, 88.2 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-1yXmqg/apt_archive ./ sbuild-build-depends-last-align-dummy 0.invalid.0 [790 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.13-2 [389 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.13-2 [1178 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.13-2 [40.5 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libexpat1 armhf 2.2.1-1 [65.2 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libffi6 armhf 3.2.1-6 [18.7 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libssl1.1 armhf 1.1.0f-3 [1105 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.13-2 [1827 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.13-2 [285 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.13-2 [20.0 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.13-2 [154 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.30-1 [222 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.30-1 [105 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.30-1 [63.4 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-2 [116 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.2 [806 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15-6 [733 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-2 [433 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.034-1 [16.4 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.034-1 [10.5 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.50.3-2 [2527 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.11-3 [131 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-2 [1434 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.2.5 [961 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf help2man armhf 1.47.4 [162 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libfreetype6 armhf 2.6.3-3.2 [384 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo armhf 1:1.5.1-2 [109 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf liblcms2-2 armhf 2.8-4 [118 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libtiff5 armhf 4.0.8-2 [218 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libwebp6 armhf 0.5.2-1 [202 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libwebpdemux2 armhf 0.5.2-1 [72.5 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libwebpmux2 armhf 0.5.2-1 [80.1 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf python-pil armhf 4.0.0-4 [350 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf python-imaging all 4.0.0-4 [50.5 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libfreetype6:armhf (2.6.3-3.2) ...
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Unpacking libjpeg62-turbo:armhf (1:1.5.1-2) ...
Selecting previously unselected package liblcms2-2:armhf.
Preparing to unpack .../29-liblcms2-2_2.8-4_armhf.deb ...
Unpacking liblcms2-2:armhf (2.8-4) ...
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Preparing to unpack .../30-libtiff5_4.0.8-2_armhf.deb ...
Unpacking libtiff5:armhf (4.0.8-2) ...
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Preparing to unpack .../31-libwebp6_0.5.2-1_armhf.deb ...
Unpacking libwebp6:armhf (0.5.2-1) ...
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Preparing to unpack .../32-libwebpdemux2_0.5.2-1_armhf.deb ...
Unpacking libwebpdemux2:armhf (0.5.2-1) ...
Selecting previously unselected package libwebpmux2:armhf.
Preparing to unpack .../33-libwebpmux2_0.5.2-1_armhf.deb ...
Unpacking libwebpmux2:armhf (0.5.2-1) ...
Selecting previously unselected package python-pil:armhf.
Preparing to unpack .../34-python-pil_4.0.0-4_armhf.deb ...
Unpacking python-pil:armhf (4.0.0-4) ...
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Preparing to unpack .../35-python-imaging_4.0.0-4_all.deb ...
Unpacking python-imaging (4.0.0-4) ...
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Preparing to unpack .../36-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 (2.2.1-1) ...
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 libtimedate-perl (2.3000-2) ...
Setting up liblcms2-2:armhf (2.8-4) ...
Setting up libjbig0:armhf (2.1-3.1) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up groff-base (1.22.3-9) ...
Setting up libtiff5:armhf (4.0.8-2) ...
Setting up gettext-base (0.19.8.1-2) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-6) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2.2) ...
Setting up libfreetype6:armhf (2.6.3-3.2) ...
Setting up libmagic-mgc (1:5.30-1) ...
Setting up libmagic1:armhf (1:5.30-1) ...
Processing triggers for libc-bin (2.24-11+deb9u1) ...
Setting up autotools-dev (20161112.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up libssl1.1:armhf (1.1.0f-3) ...
Setting up help2man (1.47.4) ...
Setting up libffi6:armhf (3.2.1-6) ...
Setting up bsdmainutils (9.0.12+nmu1) ...
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 (2.7.13-2) ...
Setting up autopoint (0.19.8.1-2) ...
Setting up libwebp6:armhf (0.5.2-1) ...
Setting up libfile-stripnondeterminism-perl (0.034-1) ...
Setting up libglib2.0-0:armhf (2.50.3-2) ...
No schema files found: doing nothing.
Setting up python2.7 (2.7.13-2) ...
Setting up libwebpmux2:armhf (0.5.2-1) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.30-1) ...
Setting up libcroco3:armhf (0.6.11-3) ...
Setting up libpython-stdlib:armhf (2.7.13-2) ...
Setting up automake (1:1.15-6) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up libwebpdemux2:armhf (0.5.2-1) ...
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up python (2.7.13-2) ...
Setting up libtool (2.4.6-2) ...
Setting up gettext (0.19.8.1-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up python-pil:armhf (4.0.0-4) ...
Setting up po-debconf (1.0.20) ...
Setting up python-imaging (4.0.0-4) ...
Setting up dh-autoreconf (14) ...
Setting up dh-strip-nondeterminism (0.034-1) ...
Setting up debhelper (10.2.5) ...
Setting up sbuild-build-depends-last-align-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-11+deb9u1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.28-5 dpkg-dev_1.18.24 g++-6_6.3.0-18+rpi1 gcc-6_6.3.0-18+rpi1 libc6-dev_2.24-11+deb9u1 libstdc++-6-dev_6.3.0-18+rpi1 libstdc++6_6.3.0-18+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.4.6 autoconf_2.69-10 automake_1:1.15-6 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_9.9+rpi1 base-passwd_3.5.43 bash_4.4-5 binutils_2.28-5 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-1 build-essential_12.3 bzip2_1.0.6-8.1 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:6.3.0-4 cpp-6_6.3.0-18+rpi1 dash_0.5.8-2.4 debconf_1.5.61 debhelper_10.2.5 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.034-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-3.1 file_1:5.30-1 findutils_4.6.0+git+20161106-2 g++_4:6.3.0-4 g++-6_6.3.0-18+rpi1 gcc_4:6.3.0-4 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_5.4.1-4 gcc-6_6.3.0-18+rpi1 gcc-6-base_6.3.0-18+rpi1 gettext_0.19.8.1-2 gettext-base_0.19.8.1-2 gnupg_2.1.18-6 gnupg-agent_2.1.18-6 gpgv_2.1.18-6 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5 help2man_1.47.4 hostname_3.18 init-system-helpers_1.48 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_23-2 libacl1_2.2.52-3 libapparmor1_2.11.0-3 libapt-pkg5.0_1.4.6 libarchive-zip-perl_1.59-1 libasan3_6.3.0-18+rpi1 libassuan0_2.4.3-2 libatomic1_6.3.0-18+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-2 libaudit1_1:2.6.7-2 libblkid1_2.29.2-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-11+deb9u1 libc-dev-bin_2.24-11+deb9u1 libc6_2.24-11+deb9u1 libc6-dev_2.24-11+deb9u1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_6.3.0-18+rpi1 libcomerr2_1.43.4-2 libcroco3_0.6.11-3 libcryptsetup4_2:1.7.3-4 libdb5.3_5.3.28-12 libdbus-1-3_1.10.18-1 libdebconfclient0_0.227 libdevmapper1.02.1_2:1.02.137-2 libdpkg-perl_1.18.24 libdrm2_2.4.74-1 libexpat1_2.2.1-1 libfakeroot_1.21-3.1 libfdisk1_2.29.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.034-1 libfreetype6_2.6.3-3.2 libgcc-6-dev_6.3.0-18+rpi1 libgcc1_1:6.3.0-18+rpi1 libgcrypt20_1.7.6-2 libgdbm3_1.8.3-14 libglib2.0-0_2.50.3-2 libgmp10_2:6.1.2+dfsg-1 libgomp1_6.3.0-18+rpi1 libgpg-error0_1.26-2 libicu57_57.1-6 libidn11_1.33-1 libip4tc0_1.6.0+snapshot20161117-6 libisl15_0.18-1 libjbig0_2.1-3.1 libjpeg62-turbo_1:1.5.1-2 libklibc_2.0.4-9+rpi1 libkmod2_23-2 libksba8_1.3.5-2 liblcms2-2_2.8-4 liblocale-gettext-perl_1.07-3+b1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29.2-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20161126-1 libncursesw5_6.0+20161126-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.3-1 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-3 libperl5.24_5.24.1-3 libpipeline1_1.4.1-2 libplymouth4_0.9.2-4 libpng16-16_1.6.28-1 libprocps6_2:3.3.12-3 libpython-stdlib_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libreadline7_7.0-3 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.10-5 libsmartcols1_2.29.2-1 libsqlite3-0_3.16.2-5 libss2_1.43.4-2 libssl1.1_1.1.0f-3 libstdc++-6-dev_6.3.0-18+rpi1 libstdc++6_6.3.0-18+rpi1 libsystemd0_232-25 libtext-charwidth-perl_0.04-7+b7 libtext-iconv-perl_1.7-5+b8 libtext-wrapi18n-perl_0.06-7.1 libtiff5_4.0.8-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20161126-1 libtool_2.4.6-2 libubsan0_6.3.0-18+rpi1 libudev1_232-25 libunistring0_0.9.6+really0.9.3-0.1 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-1 libwebp6_0.5.2-1 libwebpdemux2_0.5.2-1 libwebpmux2_0.5.2-1 libxml2_2.9.4+dfsg1-2.2 linux-base_4.5 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-4.1 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mime-support_3.60 mount_2.29.2-1 mountall_2.54 multiarch-support_2.24-11+deb9u1 ncurses-base_6.0+20161126-1 ncurses-bin_6.0+20161126-1 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.24.1-3 perl-base_5.24.1-3 perl-modules-5.24_5.24.1-3 pinentry-curses_1.0.0-2 plymouth_0.9.2-4 po-debconf_1.0.20 procps_2:3.3.12-3 python_2.7.13-2 python-imaging_4.0.0-4 python-minimal_2.7.13-2 python-pil_4.0.0-4 python2.7_2.7.13-2 python2.7-minimal_2.7.13-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-last-align-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 systemd_232-25 sysvinit-utils_2.88dsf-59.9 tar_1.29b-1.1 tzdata_2017b-1 udev_232-25 util-linux_2.29.2-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Jun 6 08:14:41 2017 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./last-align_830-2.dsc
dpkg-source: info: extracting last-align in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking last-align_830.orig.tar.xz
dpkg-source: info: unpacking last-align_830-2.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=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=111
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-fe586113-77f5-460b-aca1-f309cca1c9c3
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 830-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build last-align-830
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 lastdb8 lastal8 last-split8 *.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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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
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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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
g++ -DLAST_INT_TYPE=unsigned -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
g++ -DLAST_INT_TYPE=unsigned -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 CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o fileMap.o io.o tantan.o LastdbArguments.o MultiSequence.o MultiSequenceQual.o SubsetSuffixArray.o SubsetSuffixArraySort.o lastdb.o
g++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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 -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
In file included from /usr/include/c++/6/algorithm:62:0,
from alp/sls_alp_regression.hpp:46,
from alp/sls_alp_regression.cpp:36:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1877:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__final_insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1877:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1877:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' will change in GCC 7.1
__move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1818:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' will change in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from alp/sls_alp_regression.hpp:46,
from alp/sls_alp_regression.cpp:36:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from alp/sls_alp_regression.hpp:46,
from alp/sls_alp_regression.cpp:36:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In static member function 'static void Sls::alp_reg::find_tetta_general(double (*)(double, void*), void*, double, double, long int, double, std::vector<double>&)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1968:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In static member function 'static double Sls::alp_reg::median(long int, double*)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1968:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
^~~
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from alp/sls_alp_regression.hpp:46,
from alp/sls_alp_regression.cpp:36:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >; _Distance = int; _Tp = std::pair<double, long int>; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from alp/sls_alp_regression.hpp:46,
from alp/sls_alp_regression.cpp:36:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' will change in GCC 7.1
std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
^~~
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In static member function 'static double Sls::alp_reg::robust_sum(double*, long int, long int, bool*&)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
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
In file included from /usr/include/c++/6/algorithm:62:0,
from alp/sls_alp_regression.hpp:46,
from alp/sls_alp_data.hpp:62,
from alp/sls_alp_data.cpp:36:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from alp/sls_alp_regression.hpp:46,
from alp/sls_alp_data.hpp:62,
from alp/sls_alp_data.cpp:36:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from alp/sls_alp_regression.hpp:46,
from alp/sls_alp_data.hpp:62,
from alp/sls_alp_data.cpp:36:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In constructor 'Sls::importance_sampling::importance_sampling(Sls::alp_data*, long int, long int, long int, long int**, double*, double*)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
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
In file included from /usr/include/c++/6/vector:69:0,
from alp/sls_fsa1_utils.hpp:40,
from alp/sls_fsa1_utils.cpp:36:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from alp/sls_fsa1_utils.hpp:40,
from alp/sls_fsa1_utils.cpp:36:
/usr/include/c++/6/bits/stl_vector.h: In static member function 'static void Sls::FSA_utils::multiply_matrix_and_vector(const std::vector<std::vector<double> >&, const std::vector<double>&, std::vector<double>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In static member function 'static void Sls::FSA_utils::multiply_matrices(const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, std::vector<std::vector<double> >&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
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;
^~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from alp/sls_alp_regression.hpp:46,
from alp/sls_fsa1.hpp:39,
from alp/sls_fsa1.cpp:36:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1877:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__final_insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1877:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1877:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from alp/sls_alp_regression.hpp:46,
from alp/sls_fsa1.hpp:39,
from alp/sls_fsa1.cpp:36:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from alp/sls_alp_regression.hpp:46,
from alp/sls_fsa1.hpp:39,
from alp/sls_fsa1.cpp:36:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In static member function 'static void Sls::test::calculate_ungapped_lambda(long int, double*, double*, long int**, double&)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1968:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In static member function 'static void Sls::test::calculate_ungapped_lambda_general(double (*)(double, void*), void*, double&)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1968:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
^~~
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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -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 CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o fileMap.o io.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GeneralizedAffineGapCosts.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.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 Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o SegmentPairPot.o SubsetSuffixArray.o SubsetSuffixArraySearch.o lastal.o
g++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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++ -DLAST_INT_TYPE=unsigned -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:729:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (a.rend > chromEnd - chromBeg)
~~~~~~~^~~~~~~~~~~~~~~~~~~~~
g++ -DLAST_INT_TYPE=unsigned -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
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 fileMap.o split/cbrc_linalg.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/last-split.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++ -DLAST_INT_TYPE=unsigned -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
In file included from /usr/include/c++/6/bits/char_traits.h:39:0,
from /usr/include/c++/6/string:40,
from last-pair-probs.hh:27,
from last-pair-probs.cc:4:
/usr/include/c++/6/bits/stl_algobase.h: In function '_ForwardIterator std::__lower_bound(_ForwardIterator, _ForwardIterator, const _Tp&, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >; _Tp = Alignment; _Compare = __gnu_cxx::__ops::_Iter_less_val]':
/usr/include/c++/6/bits/stl_algobase.h:946:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
__lower_bound(_ForwardIterator __first, _ForwardIterator __last,
^~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algobase.h:946:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
In file included from /usr/include/c++/6/algorithm:62:0,
from last-pair-probs.cc:9:
/usr/include/c++/6/bits/stl_algo.h: In function '_ForwardIterator std::__upper_bound(_ForwardIterator, _ForwardIterator, const _Tp&, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >; _Tp = Alignment; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:2036:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
__upper_bound(_ForwardIterator __first, _ForwardIterator __last,
^~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:2036:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
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]
In file included from /usr/include/c++/6/algorithm:62:0,
from last-pair-probs.cc:9:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1818:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h: In function '_RandomAccessIterator std::_V2::__rotate(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >]':
/usr/include/c++/6/bits/stl_algo.h:1325:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
__rotate(_RandomAccessIterator __first,
^~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1325:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1325:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1325:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1325:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:2473:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
__merge_without_buffer(_BidirectionalIterator __first,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:2473:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2473:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2497:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
__second_cut
^~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:2506:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
__first_cut
^~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1441:40: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__iterator_category(__first));
^
/usr/include/c++/6/bits/stl_algo.h:1441:40: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1441:40: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2515:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__merge_without_buffer(__first, __first_cut, __new_middle,
^~~
/usr/include/c++/6/bits/stl_algo.h:2515:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2515:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2517:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__merge_without_buffer(__new_middle, __second_cut, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:2517:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2517:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:2758:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
__inplace_stable_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:2758:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2763:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:2767:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__inplace_stable_sort(__first, __middle, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:2768:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__inplace_stable_sort(__middle, __last, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:2769:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__merge_without_buffer(__first, __middle, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:2769:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2769:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >; _Distance = int; _Pointer = Alignment*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:2412:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
__merge_adaptive(_BidirectionalIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:2412:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2412:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2441:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
__second_cut
^~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:2450:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
__first_cut
^~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1441:40: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__iterator_category(__first));
^
/usr/include/c++/6/bits/stl_algo.h:1441:40: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1441:40: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2460:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__merge_adaptive(__first, __first_cut, __new_middle, __len11,
^~~
/usr/include/c++/6/bits/stl_algo.h:2460:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2460:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2462:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__merge_adaptive(__new_middle, __second_cut, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:2462:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2462:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >; _OutputIterator = Alignment*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:2636:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
__move_merge(_InputIterator __first1, _InputIterator __last1,
^~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:2636:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2636:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2636:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = Alignment*; _OutputIterator = __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:2636:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >; _Pointer = Alignment*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:2702:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
__merge_sort_with_buffer(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:2702:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2692:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + __chunk_size, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:2695:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:2671:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
__result = std::__move_merge(__first, __first + __step_size,
^~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:2671:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2671:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2671:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2679:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__move_merge(__first, __first + __step_size,
^~~
/usr/include/c++/6/bits/stl_algo.h:2679:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2679:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2679:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2671:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
__result = std::__move_merge(__first, __first + __step_size,
^~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:2679:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__move_merge(__first, __first + __step_size,
^~~
/usr/include/c++/6/bits/stl_algo.h:2679:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >; _Pointer = Alignment*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:2729:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
__stable_sort_adaptive(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:2729:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2738:4: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__stable_sort_adaptive(__first, __middle, __buffer,
^~~
/usr/include/c++/6/bits/stl_algo.h:2740:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__stable_sort_adaptive(__middle, __last, __buffer,
^~~
/usr/include/c++/6/bits/stl_algo.h:2745:4: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:2746:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:2748:7: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__merge_adaptive(__first, __middle, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:2748:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:2748:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
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;
^~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from last-pair-probs.cc:9:
/usr/include/c++/6/bits/stl_algo.h:4877:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__inplace_stable_sort(__first, __last, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:4879:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' will change in GCC 7.1
std::__stable_sort_adaptive(__first, __last, __buf.begin(),
^~~
g++ -DLAST_INT_TYPE=unsigned -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
g++ -DLAST_INT_TYPE=size_t -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.o8 MultiSequence.cc
g++ -DLAST_INT_TYPE=size_t -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.o8 MultiSequenceQual.cc
g++ -DLAST_INT_TYPE=size_t -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.o8 SubsetSuffixArray.cc
g++ -DLAST_INT_TYPE=size_t -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.o8 SubsetSuffixArraySort.cc
g++ -DLAST_INT_TYPE=size_t -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.o8 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 lastdb8 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o fileMap.o io.o tantan.o LastdbArguments.o MultiSequence.o8 MultiSequenceQual.o8 SubsetSuffixArray.o8 SubsetSuffixArraySort.o8 lastdb.o8
g++ -DLAST_INT_TYPE=size_t -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.o8 Alignment.cc
g++ -DLAST_INT_TYPE=size_t -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.o8 AlignmentPot.cc
g++ -DLAST_INT_TYPE=size_t -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.o8 AlignmentWrite.cc
g++ -DLAST_INT_TYPE=size_t -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.o8 Centroid.cc
g++ -DLAST_INT_TYPE=size_t -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.o8 DiagonalTable.cc
g++ -DLAST_INT_TYPE=size_t -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.o8 SegmentPair.cc
g++ -DLAST_INT_TYPE=size_t -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.o8 SegmentPairPot.cc
g++ -DLAST_INT_TYPE=size_t -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.o8 SubsetSuffixArraySearch.cc
g++ -DLAST_INT_TYPE=size_t -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.o8 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++ -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 lastal8 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o fileMap.o io.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GeneralizedAffineGapCosts.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.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 Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8
g++ -DLAST_INT_TYPE=size_t -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.o8 split/cbrc_split_aligner.cc
split/cbrc_split_aligner.cc: In member function 'void cbrc::SplitAligner::initSpliceSignals(unsigned int)':
split/cbrc_split_aligner.cc:729:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (a.rend > chromEnd - chromBeg)
~~~~~~~^~~~~~~~~~~~~~~~~~~~~
g++ -DLAST_INT_TYPE=size_t -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.o8 split/last-split.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-split8 Alphabet.o fileMap.o split/cbrc_linalg.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o8 split/cbrc_split_aligner.o8 split/last-split.o8
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
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/lastdb src/lastal src/last-split src/last-merge-batches src/last-pair-probs src/lastdb8 src/lastal8 src/last-split8 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="830" \
--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="830" \
--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="830" \
--name="genome-scale comparison of biological sequences" \
--help-option="-h" \
/<<PKGBUILDDIR>>/src/lastal8 > /<<PKGBUILDDIR>>/debian/last-align/usr/share/man/man1//lastal8.1
#help2man --no-info --version-string="830" \
# --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="830" \
--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="830" \
--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="830" \
# --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="830" \
# --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="830" \
# --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="830" \
# --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="830" \
--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="830" \
--name='Estimates "split" or "spliced" alignments.' \
/<<PKGBUILDDIR>>/src/last-split8 > /<<PKGBUILDDIR>>/debian/last-align/usr/share/man/man1//last-split8.1
help2man --no-info --version-string="830" \
--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="830" \
--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="830" \
--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="830" \
--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="830" \
# --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="830" \
--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="830" \
--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/last-split contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastal contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
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/lastdb8 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-split8 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/lastal8 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastdb contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/last-align/usr/bin/last-split debian/last-align/usr/bin/lastal debian/last-align/usr/bin/last-pair-probs debian/last-align/usr/bin/lastdb8 debian/last-align/usr/bin/last-split8 debian/last-align/usr/bin/last-merge-batches debian/last-align/usr/bin/lastal8 debian/last-align/usr/bin/lastdb were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'last-align-dbgsym' in '../last-align-dbgsym_830-2_armhf.deb'.
dpkg-deb: building package 'last-align' in '../last-align_830-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian nitrogen6x test autobuilder <root@raspbian.org> >../last-align_830-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build last-align-830
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-06-22T18:08:30Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
last-align_830-2_armhf.changes:
-------------------------------
Format: 1.8
Date: Tue, 06 Jun 2017 01:56:56 -0400
Source: last-align
Binary: last-align
Architecture: armhf
Version: 830-2
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian nitrogen6x test autobuilder <root@raspbian.org>
Changed-By: Nadiya Sitdykova <rovenskasa@gmail.com>
Description:
last-align - genome-scale comparison of biological sequences
Changes:
last-align (830-2) unstable; urgency=low
.
* Team upload.
.
[ Nadiya Sitdykova ]
* Add autopkgtest test-suite
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217394a975dd3bd2169ea8d03dd79340 570292 science optional last-align_830-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
last-align-dbgsym_830-2_armhf.deb
---------------------------------
new debian package, version 2.0.
size 7819902 bytes: control archive=869 bytes.
694 bytes, 13 lines control
848 bytes, 8 lines md5sums
Package: last-align-dbgsym
Source: last-align
Version: 830-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8327
Depends: last-align (= 830-2)
Section: debug
Priority: extra
Homepage: http://last.cbrc.jp/
Description: Debug symbols for last-align
Build-Ids: 04cb35795f271f01d6ec3dfd6d806f6a598c41b3 15b88b09d218931ba875c0e599f7d3fcef738b77 333f650256d6dcf21375b83156c0340c3ff7a464 3a79f583daca680619e846d9a152b3c2f74dc192 710bf73a87d05e66d9d13e6125362f19c1080468 b98a700548e90c54a466c1aebfffd82732defa67 c7335197cea3e6542ca5058954f540c65cda5b31 faaa31300a98ddeb315b16633a89b4b43f537921
drwxr-xr-x root/root 0 2017-06-06 05:56 ./
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/lib/
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/lib/debug/.build-id/04/
-rw-r--r-- root/root 2758344 2017-06-06 05:56 ./usr/lib/debug/.build-id/04/cb35795f271f01d6ec3dfd6d806f6a598c41b3.debug
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/lib/debug/.build-id/15/
-rw-r--r-- root/root 788924 2017-06-06 05:56 ./usr/lib/debug/.build-id/15/b88b09d218931ba875c0e599f7d3fcef738b77.debug
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-rw-r--r-- root/root 2758348 2017-06-06 05:56 ./usr/lib/debug/.build-id/33/3f650256d6dcf21375b83156c0340c3ff7a464.debug
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/lib/debug/.build-id/3a/
-rw-r--r-- root/root 788924 2017-06-06 05:56 ./usr/lib/debug/.build-id/3a/79f583daca680619e846d9a152b3c2f74dc192.debug
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/lib/debug/.build-id/71/
-rw-r--r-- root/root 585560 2017-06-06 05:56 ./usr/lib/debug/.build-id/71/0bf73a87d05e66d9d13e6125362f19c1080468.debug
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/lib/debug/.build-id/b9/
-rw-r--r-- root/root 230980 2017-06-06 05:56 ./usr/lib/debug/.build-id/b9/8a700548e90c54a466c1aebfffd82732defa67.debug
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/lib/debug/.build-id/c7/
-rw-r--r-- root/root 9924 2017-06-06 05:56 ./usr/lib/debug/.build-id/c7/335197cea3e6542ca5058954f540c65cda5b31.debug
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/lib/debug/.build-id/fa/
-rw-r--r-- root/root 585560 2017-06-06 05:56 ./usr/lib/debug/.build-id/fa/aa31300a98ddeb315b16633a89b4b43f537921.debug
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/share/
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-06-06 05:56 ./usr/share/doc/last-align-dbgsym -> last-align
last-align_830-2_armhf.deb
--------------------------
new debian package, version 2.0.
size 570292 bytes: control archive=3675 bytes.
1165 bytes, 24 lines control
7118 bytes, 100 lines md5sums
Package: last-align
Version: 830-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2644
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 2017-06-06 05:56 ./
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/bin/
-rwxr-xr-x root/root 475 2017-06-06 05:56 ./usr/bin/fastq-interleave
-rwxr-xr-x root/root 17152 2017-06-06 05:56 ./usr/bin/last-dotplot
-rwxr-xr-x root/root 4703 2017-06-06 05:56 ./usr/bin/last-map-probs
-rwxr-xr-x root/root 9776 2017-06-06 05:56 ./usr/bin/last-merge-batches
-rwxr-xr-x root/root 50900 2017-06-06 05:56 ./usr/bin/last-pair-probs
-rwxr-xr-x root/root 4154 2017-06-06 05:56 ./usr/bin/last-postmask
-rwxr-xr-x root/root 116508 2017-06-06 05:56 ./usr/bin/last-split
-rwxr-xr-x root/root 116508 2017-06-06 05:56 ./usr/bin/last-split8
-rwxr-xr-x root/root 17806 2017-06-06 05:56 ./usr/bin/last-train
-rwxr-xr-x root/root 738668 2017-06-06 05:56 ./usr/bin/lastal
-rwxr-xr-x root/root 738668 2017-06-06 05:56 ./usr/bin/lastal8
-rwxr-xr-x root/root 149056 2017-06-06 05:56 ./usr/bin/lastdb
-rwxr-xr-x root/root 149056 2017-06-06 05:56 ./usr/bin/lastdb8
-rwxr-xr-x root/root 27469 2017-06-06 05:56 ./usr/bin/maf-convert
-rwxr-xr-x root/root 8992 2017-06-06 05:56 ./usr/bin/maf-join
-rwxr-xr-x root/root 2027 2017-06-06 05:56 ./usr/bin/maf-sort
-rwxr-xr-x root/root 4762 2017-06-06 05:56 ./usr/bin/maf-swap
-rwxr-xr-x root/root 234 2017-06-06 05:56 ./usr/bin/parallel-fasta
-rwxr-xr-x root/root 295 2017-06-06 05:56 ./usr/bin/parallel-fastq
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/share/
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/share/doc-base/
-rw-r--r-- root/root 281 2017-06-06 05:56 ./usr/share/doc-base/last-align-manual
-rw-r--r-- root/root 291 2017-06-06 05:56 ./usr/share/doc-base/last-align-scripts
-rw-r--r-- root/root 295 2017-06-06 05:56 ./usr/share/doc-base/last-align-seeds
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/share/doc/last-align/
-rw-r--r-- root/root 12338 2015-12-16 18:25 ./usr/share/doc/last-align/FAQ.html
-rw-r--r-- root/root 2947 2015-12-16 18:25 ./usr/share/doc/last-align/FAQ.txt
-rw-r--r-- root/root 888 2015-12-07 16:10 ./usr/share/doc/last-align/Makefile
-rw-r--r-- root/root 201 2017-06-06 05:56 ./usr/share/doc/last-align/NEWS.Debian.gz
-rw-r--r-- root/root 179 2017-06-06 05:56 ./usr/share/doc/last-align/README.test
-rw-r--r-- root/root 10092 2016-03-11 15:47 ./usr/share/doc/last-align/bisulfite.html
-rw-r--r-- root/root 2719 2016-03-11 15:47 ./usr/share/doc/last-align/bisulfite.txt
-rw-r--r-- root/root 4281 2017-06-06 05:56 ./usr/share/doc/last-align/changelog.Debian.gz
-rw-r--r-- root/root 30970 2017-01-19 16:54 ./usr/share/doc/last-align/changelog.gz
-rw-r--r-- root/root 1016 2017-06-06 05:56 ./usr/share/doc/last-align/copyright
drwxr-xr-x root/root 0 2017-06-06 05:56 ./usr/share/doc/last-align/examples/
-rw-r--r-- root/root 5504 2013-05-23 07:23 ./usr/share/doc/last-align/examples/chickenMito.fa.gz
-rw-r--r-- root/root 5675 2013-05-23 07:23 ./usr/share/doc/last-align/examples/fuguMito.fa.gz
-rw-r--r-- root/root 5562 2013-05-23 07:23 ./usr/share/doc/last-align/examples/humanMito.fa.gz
-rwxr-xr-x root/root 1488 2016-09-01 16:26 ./usr/share/doc/last-align/examples/last-bisulfite-paired.sh
-rwxr-xr-x root/root 907 2016-09-01 16:26 ./usr/share/doc/last-align/examples/last-bisulfite.sh
-rw-r--r-- root/root 5424 2013-05-23 07:23 ./usr/share/doc/last-align/examples/mouseMito.fa.gz
-rw-r--r-- root/root 50644 2014-07-30 18:08 ./usr/share/doc/last-align/examples/multiMito.maf.gz
-rwxr-xr-x root/root 964 2014-10-07 18:04 ./usr/share/doc/last-align/examples/multiMito.sh
-rw-r--r-- root/root 9249 2015-01-30 18:22 ./usr/share/doc/last-align/examples/myalns.maf.gz
-rw-r--r-- root/root 712 2013-05-23 07:23 ./usr/share/doc/last-align/examples/titv212.mat
-rw-r--r-- root/root 408 2015-09-18 16:28 ./usr/share/doc/last-align/examples/ublast.seed
-rw-r--r-- root/root 539 2013-05-23 07:23 ./usr/share/doc/last-align/examples/vertebrateMito.gc
-rw-r--r-- root/root 260 2015-09-18 16:28 ./usr/share/doc/last-align/last-doc.css
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-rw-r--r-- root/root 12084 2015-12-07 16:11 ./usr/share/doc/last-align/last-evalues.html
-rw-r--r-- root/root 1870 2015-08-31 16:57 ./usr/share/doc/last-align/last-evalues.txt.gz
-rw-r--r-- root/root 10452 2016-09-01 16:26 ./usr/share/doc/last-align/last-map-probs.html
-rw-r--r-- root/root 2687 2016-09-01 16:26 ./usr/share/doc/last-align/last-map-probs.txt
-rw-r--r-- root/root 18722 2015-12-07 16:11 ./usr/share/doc/last-align/last-matrices.html
-rw-r--r-- root/root 3058 2015-09-18 16:29 ./usr/share/doc/last-align/last-matrices.txt.gz
-rw-r--r-- root/root 14658 2016-09-01 16:26 ./usr/share/doc/last-align/last-pair-probs.html
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-rw-r--r-- root/root 12217 2015-12-07 16:11 ./usr/share/doc/last-align/last-papers.html
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+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 74208
Build-Time: 1032
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 581
Job: last-align_830-2
Machine Architecture: armhf
Package: last-align
Package-Time: 1665
Source-Version: 830-2
Space: 74208
Status: successful
Version: 830-2
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Finished at 2017-06-22T18:08:30Z
Build needed 00:27:45, 74208k disc space