last-align →
869-1 →
armhf → 2017-08-22 05:57:23
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| last-align 869-1 (armhf) Tue, 22 Aug 2017 05:31:33 +0000 |
+==============================================================================+
Package: last-align
Version: 869-1
Source Version: 869-1
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-a8cce2b8-78a4-4456-9eaf-18f714e78528' 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 [10.1 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.0 MB]
Fetched 22.1 MB in 28s (777 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 396 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main last-align 869-1 (dsc) [1656 B]
Get:2 http://172.17.0.1/private buster-staging/main last-align 869-1 (tar) [385 kB]
Get:3 http://172.17.0.1/private buster-staging/main last-align 869-1 (diff) [9168 B]
Fetched 396 kB in 0s (954 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/last-align-ucFwSq/last-align-869' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/last-align-ucFwSq' 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-OEVZD4/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-OEVZD4/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-OEVZD4/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-OEVZD4/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-OEVZD4/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-OEVZD4/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-OEVZD4/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-OEVZD4/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (2975 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 6 not upgraded.
Need to get 776 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-OEVZD4/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 14914 files and directories currently installed.)
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Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
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-pil
Filtered Build-Depends: debhelper (>= 10), help2man, python-pil
dpkg-deb: building package 'sbuild-build-depends-last-align-dummy' in '/<<BUILDDIR>>/resolver-OEVZD4/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-OEVZD4/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-OEVZD4/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-OEVZD4/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-OEVZD4/apt_archive ./ Sources [504 B]
Get:5 copy:/<<BUILDDIR>>/resolver-OEVZD4/apt_archive ./ Packages [584 B]
Fetched 2421 B in 0s (3509 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install last-align build dependencies (apt-based resolver)
----------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates openssl
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1
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
libtiff5 libtimedate-perl libtool libwebp6 libwebpdemux2 libwebpmux3 libxml2
m4 man-db mime-support po-debconf python python-minimal python-olefile
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 libarchive-cpio-perl 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
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
libtiff5 libtimedate-perl libtool libwebp6 libwebpdemux2 libwebpmux3 libxml2
m4 man-db mime-support po-debconf python python-minimal python-olefile
python-pil python2.7 python2.7-minimal sbuild-build-depends-last-align-dummy
0 upgraded, 50 newly installed, 0 to remove and 6 not upgraded.
Need to get 24.4 MB of archives.
After this operation, 83.9 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-OEVZD4/apt_archive ./ sbuild-build-depends-last-align-dummy 0.invalid.0 [788 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 0.8.6-1 [95.7 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 1.4.2-1 [24.2 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 2.2.3-1 [67.1 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.13-2 [1827 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.13-2 [285 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.13-2 [20.0 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.13-2 [154 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.31-1 [223 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.31-1 [105 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.31-1 [63.5 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-2+b1 [117 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-3 [601 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-2 [736 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-2 [433 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.038-1 [17.6 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.038-1 [11.1 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.53.4-3 [2628 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-2+b1 [1220 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.7.2 [975 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf help2man armhf 1.47.4 [162 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libfreetype6 armhf 2.8-0.2 [393 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo armhf 1:1.5.1-2 [109 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf liblcms2-2 armhf 2.8-4 [118 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libtiff5 armhf 4.0.8-4 [219 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libwebp6 armhf 0.6.0-3 [217 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libwebpdemux2 armhf 0.6.0-3 [80.7 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libwebpmux3 armhf 0.6.0-3 [88.2 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf python-olefile all 0.44-1 [37.3 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf python-pil armhf 4.2.1-1 [332 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libwebpdemux2:armhf.
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Unpacking libwebpdemux2:armhf (0.6.0-3) ...
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Unpacking libwebpmux3:armhf (0.6.0-3) ...
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Unpacking python-pil:armhf (4.2.1-1) ...
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Preparing to unpack .../35-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 (2.2.3-1) ...
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 (2.11-1) ...
Setting up groff-base (1.22.3-9) ...
Setting up libglib2.0-0:armhf (2.53.4-3) ...
No schema files found: doing nothing.
Setting up libtiff5:armhf (4.0.8-4) ...
Setting up gettext-base (0.19.8.1-2+b1) ...
Setting up libpipeline1:armhf (1.4.2-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-6) ...
Setting up libbsd0:armhf (0.8.6-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-3) ...
Setting up libfreetype6:armhf (2.8-0.2) ...
Setting up libmagic-mgc (1:5.31-1) ...
Setting up libmagic1:armhf (1:5.31-1) ...
Setting up libcroco3:armhf (0.6.12-1) ...
Processing triggers for libc-bin (2.24-12) ...
Setting up autotools-dev (20161112.1) ...
Setting up help2man (1.47.4) ...
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 (0.6.0-3) ...
Setting up libfile-stripnondeterminism-perl (0.038-1) ...
Setting up gettext (0.19.8.1-2+b1) ...
Setting up python2.7 (2.7.13-2) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.31-1) ...
Setting up libpython-stdlib:armhf (2.7.13-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libwebpmux3:armhf (0.6.0-3) ...
Setting up automake (1:1.15.1-2) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up libwebpdemux2:armhf (0.6.0-3) ...
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 po-debconf (1.0.20) ...
Setting up python-olefile (0.44-1) ...
Setting up python-pil:armhf (4.2.1-1) ...
Setting up dh-strip-nondeterminism (0.038-1) ...
Setting up debhelper (10.7.2) ...
Setting up dh-autoreconf (14) ...
Setting up sbuild-build-depends-last-align-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-12) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.8.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.29-4+rpi1 dpkg-dev_1.18.24 g++-7_7.1.0-13+rpi1 gcc-7_7.1.0-13+rpi1 libc6-dev_2.24-12 libstdc++-7-dev_7.1.0-13+rpi1 libstdc++6_7.1.0-13+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.116 apt_1.5~beta1+b3 autoconf_2.69-10 automake_1:1.15.1-2 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_10+rpi1 base-passwd_3.5.43 bash_4.4-5 binutils_2.29-4+rpi1 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-2+rpi1 build-essential_12.3 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:7.1.0-2 cpp-7_7.1.0-13+rpi1 dash_0.5.8-2.5 debconf_1.5.63 debhelper_10.7.2 debianutils_4.8.2 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.6-1 dmsetup_2:1.02.137-2 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.5-1 e2fsprogs_1.43.5-1 fakeroot_1.21-3.1 file_1:5.31-1 findutils_4.6.0+git+20170729-2 g++_4:7.1.0-2 g++-7_7.1.0-13+rpi1 gcc_4:7.1.0-2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-7_7.1.0-13+rpi1 gcc-7-base_7.1.0-13+rpi1 gettext_0.19.8.1-2+b1 gettext-base_0.19.8.1-2+b1 gnupg_2.1.18-8 gnupg-agent_2.1.18-8 gpgv_2.1.18-8 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 help2man_1.47.4 hostname_3.18 init-system-helpers_1.49 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.0-10 libapt-pkg5.0_1.5~beta1+b3 libarchive-zip-perl_1.59-1 libasan4_7.1.0-13+rpi1 libassuan0_2.4.3-3 libatomic1_7.1.0-13+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1+b1 libblkid1_2.29.2-2+rpi1 libbsd0_0.8.6-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12 libc-dev-bin_2.24-12 libc6_2.24-12 libc6-dev_2.24-12 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.1.0-13+rpi1 libcilkrts5_7.1.0-13+rpi1 libcomerr2_1.43.5-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.3-4 libdb5.3_5.3.28-13+rpi1 libdbus-1-3_1.11.16+really1.10.22-1 libdebconfclient0_0.229 libdevmapper1.02.1_2:1.02.137-2 libdpkg-perl_1.18.24 libdrm-common_2.4.82-1+rpi1 libdrm2_2.4.82-1+rpi1 libexpat1_2.2.3-1 libfakeroot_1.21-3.1 libfdisk1_2.29.2-2+rpi1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libfreetype6_2.8-0.2 libgcc-7-dev_7.1.0-13+rpi1 libgcc1_1:7.1.0-13+rpi1 libgcrypt20_1.7.8-2 libgdbm3_1.8.3-14 libglib2.0-0_2.53.4-3 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.14-2 libgomp1_7.1.0-13+rpi1 libgpg-error0_1.27-3 libhogweed4_3.3-1 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_2.0.2-1 libip4tc0_1.6.1-2 libisl15_0.18-1 libjbig0_2.1-3.1 libjpeg62-turbo_1:1.5.1-2 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libksba8_1.3.5-2 liblcms2-2_2.8-4 liblocale-gettext-perl_1.07-3+b2 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.31-1 libmagic1_1:5.31-1 libmount1_2.29.2-2+rpi1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20170715-2 libncursesw5_6.0+20170715-2 libnettle6_3.3-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.7-3 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_2:8.39-4 libperl5.24_5.24.1-4 libperl5.26_5.26.0-5 libpipeline1_1.4.2-1 libplymouth4_0.9.2-4 libpng16-16_1.6.31-1 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 libreadline5_5.2+dfsg-3 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_2.11-1 libsmartcols1_2.29.2-2+rpi1 libsqlite3-0_3.19.3-3 libss2_1.43.5-1 libssl1.1_1.1.0f-4 libstdc++-7-dev_7.1.0-13+rpi1 libstdc++6_7.1.0-13+rpi1 libsystemd0_234-2 libtasn1-6_4.12-2.1 libtext-charwidth-perl_0.04-7+b8 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libtiff5_4.0.8-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170715-2 libtool_2.4.6-2 libubsan0_7.1.0-13+rpi1 libudev1_234-2 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-2+rpi1 libwebp6_0.6.0-3 libwebpdemux2_0.6.0-3 libwebpmux3_0.6.0-3 libxml2_2.9.4+dfsg1-3 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_2.29.2-2+rpi1 mountall_2.54 multiarch-support_2.24-12 ncurses-base_6.0+20170715-2 ncurses-bin_6.0+20170715-2 openssl_1.1.0f-4 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.26.0-5 perl-base_5.26.0-5 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.0-5 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-minimal_2.7.13-2 python-olefile_0.44-1 python-pil_4.2.1-1 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_0.0.10 systemd_234-2 sysvinit-utils_2.88dsf-59.9 tar_1.29b-2 tzdata_2017b-2 udev_234-2 util-linux_2.29.2-2+rpi1 xz-utils_5.2.2-1.3 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 Fri Aug 11 19:32:07 2017 UTC
gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./last-align_869-1.dsc
dpkg-source: info: extracting last-align in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking last-align_869.orig.tar.xz
dpkg-source: info: unpacking last-align_869-1.debian.tar.xz
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=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=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-a8cce2b8-78a4-4456-9eaf-18f714e78528
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package last-align
dpkg-buildpackage: info: source version 869-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build last-align-869
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
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_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
In file included from /usr/include/c++/7/vector:69:0,
from LambdaCalculator.hh:16,
from LambdaCalculator.cc:3:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 were 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 were guarded by the 'if'
if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0;
^~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from alp/sls_pvalues.hpp:41,
from alp/sls_alignment_evaluer.hpp:39,
from alp/sls_alignment_evaluer.cpp:37:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++/7/vector:69:0,
from alp/sls_alp_regression.hpp:43,
from alp/sls_alp_regression.cpp:36:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from alp/sls_alp_regression.hpp:46,
from alp/sls_alp_regression.cpp:36:
/usr/include/c++/7/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++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/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++/7/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__final_insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/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++/7/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> > >' changed in GCC 7.1
__move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/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> > >' changed in GCC 7.1
/usr/include/c++/7/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> > >' changed in GCC 7.1
/usr/include/c++/7/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> > >' changed in GCC 7.1
/usr/include/c++/7/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++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/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++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from alp/sls_alp_regression.hpp:46,
from alp/sls_alp_regression.cpp:36:
/usr/include/c++/7/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++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from alp/sls_alp_regression.hpp:46,
from alp/sls_alp_regression.cpp:36:
/usr/include/c++/7/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++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from alp/sls_alp_regression.hpp:43,
from alp/sls_alp_regression.cpp:36:
/usr/include/c++/7/bits/stl_vector.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++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from alp/sls_alp_regression.hpp:46,
from alp/sls_alp_regression.cpp:36:
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In static member function 'static double Sls::alp_reg::median(long int, double*)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from alp/sls_alp_regression.hpp:46,
from alp/sls_alp_regression.cpp:36:
/usr/include/c++/7/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++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from alp/sls_alp_regression.hpp:46,
from alp/sls_alp_regression.cpp:36:
/usr/include/c++/7/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++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In static member function 'static double Sls::alp_reg::robust_sum(double*, long int, long int, bool*&)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed 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++/7/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++/7/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++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/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++/7/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++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/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++/7/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++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In constructor 'Sls::importance_sampling::importance_sampling(Sls::alp_data*, long int, long int, double, long int, long int**, double*, double*)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were guarded by the 'if'
if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0;
^~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from alp/sls_fsa1_pvalues.hpp:41,
from alp/sls_falp_alignment_evaluer.hpp:40,
from alp/sls_falp_alignment_evaluer.cpp:37:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++/7/vector:69:0,
from alp/sls_fsa1_utils.hpp:40,
from alp/sls_fsa1_utils.cpp:36:
/usr/include/c++/7/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++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from alp/sls_fsa1_utils.hpp:40,
from alp/sls_fsa1_utils.cpp:36:
/usr/include/c++/7/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++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/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++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __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 were 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 were guarded by the 'if'
if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0;
^~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from alp/sls_alp_regression.hpp:43,
from alp/sls_fsa1.hpp:39,
from alp/sls_fsa1.cpp:36:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from alp/sls_alp_regression.hpp:43,
from alp/sls_fsa1.hpp:39,
from alp/sls_fsa1.cpp:36:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from alp/sls_alp_regression.hpp:43,
from alp/sls_fsa1.hpp:39,
from alp/sls_fsa1.cpp:36:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from alp/sls_alp_regression.hpp:43,
from alp/sls_fsa1.hpp:39,
from alp/sls_fsa1.cpp:36:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void Sls::IS1_general_simulation::calculate_weight_W1_for_fixed_lengths_using_recursions(long int, long int, double&, bool, std::vector<std::vector<double> >*, std::vector<std::vector<double> >*)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/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++/7/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++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/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++/7/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__final_insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from alp/sls_alp_regression.hpp:46,
from alp/sls_fsa1.hpp:39,
from alp/sls_fsa1.cpp:36:
/usr/include/c++/7/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++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/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++/7/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++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/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++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In static member function 'static void Sls::test::calculate_ungapped_lambda_general(double (*)(double, void*), void*, double&)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed 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)
~~~~~~~^~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from split/cbrc_unsplit_alignment.hh:12,
from split/cbrc_split_aligner.hh:7,
from split/cbrc_split_aligner.cc:4:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from split/cbrc_unsplit_alignment.hh:12,
from split/cbrc_split_aligner.hh:7,
from split/cbrc_split_aligner.cc:4:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> cbrc::SplitAligner::marginalProbs(unsigned int, unsigned int, unsigned int, unsigned int) const':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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++/7/bits/char_traits.h:39:0,
from /usr/include/c++/7/string:40,
from last-pair-probs.hh:27,
from last-pair-probs.cc:4:
/usr/include/c++/7/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++/7/bits/stl_algobase.h:946:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
__lower_bound(_ForwardIterator __first, _ForwardIterator __last,
^~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algobase.h:946:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
In file included from /usr/include/c++/7/algorithm:62:0,
from last-pair-probs.cc:9:
/usr/include/c++/7/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++/7/bits/stl_algo.h:2039:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
__upper_bound(_ForwardIterator __first, _ForwardIterator __last,
^~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2039:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed 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);
^
In file included from /usr/include/c++/7/vector:69:0,
from last-pair-probs.hh:28,
from last-pair-probs.cc:4:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Alignment}; _Tp = Alignment; _Alloc = std::allocator<Alignment>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<Alignment>::iterator {aka __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<Alignment>::iterator {aka __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >}' changed in GCC 7.1
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Alignment}; _Tp = Alignment; _Alloc = std::allocator<Alignment>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from last-pair-probs.cc:9:
/usr/include/c++/7/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++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/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++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__move_merge_adaptive_backward(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator2, _BidirectionalIterator2, _BidirectionalIterator3, _Compare) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >; _BidirectionalIterator2 = Alignment*; _BidirectionalIterator3 = __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:2330:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
__move_merge_adaptive_backward(_BidirectionalIterator1 __first1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2330:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:2330:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/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++/7/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
__rotate(_RandomAccessIterator __first,
^~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/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++/7/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
__merge_without_buffer(_BidirectionalIterator __first,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:2500:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
__second_cut
^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2509:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
__first_cut
^~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1444:40: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__iterator_category(__first));
^
/usr/include/c++/7/bits/stl_algo.h:2518:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__merge_without_buffer(__first, __first_cut, __new_middle,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__len11, __len22, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2520:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__merge_without_buffer(__new_middle, __second_cut, __last,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__len1 - __len11, __len2 - __len22, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/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++/7/bits/stl_algo.h:2761:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
__inplace_stable_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2761:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__inplace_stable_sort(__first, __middle, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__inplace_stable_sort(__middle, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__merge_without_buffer(__first, __middle, __last,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
__middle - __first,
~~~~~~~~~~~~~~~~~~~
__last - __middle,
~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/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++/7/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
__merge_adaptive(_BidirectionalIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:2431:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__move_merge_adaptive_backward(__first, __middle, __buffer,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__buffer_end, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2431:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:2444:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
__second_cut
^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2453:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
__first_cut
^~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1444:40: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__iterator_category(__first));
^
/usr/include/c++/7/bits/stl_algo.h:2463:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__merge_adaptive(__first, __first_cut, __new_middle, __len11,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__len22, __buffer, __buffer_size, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2465:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__merge_adaptive(__new_middle, __second_cut, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__len1 - __len11,
~~~~~~~~~~~~~~~~~
__len2 - __len22, __buffer,
~~~~~~~~~~~~~~~~~~~~~~~~~~~
__buffer_size, __comp);
~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/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++/7/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
__move_merge(_InputIterator __first1, _InputIterator __last1,
^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/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++/7/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/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++/7/bits/stl_algo.h:2705:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
__merge_sort_with_buffer(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2705:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:2695:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + __chunk_size, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2698:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2674:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
__result = std::__move_merge(__first, __first + __step_size,
^~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2674:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__move_merge(__first, __first + __step_size,
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__first + __step_size, __last, __result, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:2674:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
__result = std::__move_merge(__first, __first + __step_size,
^~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__move_merge(__first, __first + __step_size,
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__first + __step_size, __last, __result, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:2698:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/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++/7/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
__stable_sort_adaptive(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:2741:31: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__stable_sort_adaptive(__first, __middle, __buffer,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__buffer_size, __comp);
~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2743:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__stable_sort_adaptive(__middle, __last, __buffer,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
__buffer_size, __comp);
~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2748:33: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:2751:28: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__merge_adaptive(__first, __middle, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
_Distance(__middle - __first),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_Distance(__last - __middle),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__buffer, __buffer_size,
~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: 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>&)':
/usr/include/c++/7/bits/stl_algo.h:5008:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__stable_sort_adaptive(__first, __last, __buf.begin(),
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_DistanceType(__buf.size()), __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:5006:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >' changed in GCC 7.1
std::__inplace_stable_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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)
~~~~~~~^~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from split/cbrc_unsplit_alignment.hh:12,
from split/cbrc_split_aligner.hh:7,
from split/cbrc_split_aligner.cc:4:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from split/cbrc_unsplit_alignment.hh:12,
from split/cbrc_split_aligner.hh:7,
from split/cbrc_split_aligner.cc:4:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> cbrc::SplitAligner::marginalProbs(unsigned int, unsigned int, unsigned int, unsigned int) const':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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="869" \
--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="869" \
--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="869" \
--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="869" \
# --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="869" \
--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="869" \
--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="869" \
# --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="869" \
# --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="869" \
# --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="869" \
# --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="869" \
--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="869" \
--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="869" \
--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="869" \
--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="869" \
--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="869" \
--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="869" \
# --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="869" \
--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="869" \
--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_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
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/lastdb contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/last-align/usr/bin/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/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/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/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/lastal 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-pair-probs debian/last-align/usr/bin/last-merge-batches debian/last-align/usr/bin/lastdb debian/last-align/usr/bin/lastal8 debian/last-align/usr/bin/last-split8 debian/last-align/usr/bin/last-split debian/last-align/usr/bin/lastdb8 debian/last-align/usr/bin/lastal 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' in '../last-align_869-1_armhf.deb'.
dpkg-deb: building package 'last-align-dbgsym' in '../last-align-dbgsym_869-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../last-align_869-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build last-align-869
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-08-22T05:57:12Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
last-align_869-1_armhf.changes:
-------------------------------
Format: 1.8
Date: Fri, 11 Aug 2017 15:17:15 -0400
Source: last-align
Binary: last-align
Architecture: armhf
Version: 869-1
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
last-align - genome-scale comparison of biological sequences
Closes: 866438
Changes:
last-align (869-1) unstable; urgency=low
.
* Team upload.
.
[ Steffen Moeller ]
* [debian/upstream/metadata] Added references to
OMICtools, bio.tools, RRID
.
[ Sascha Steinbiss ]
* New upstream release.
* Use python-pil instead of python-imaging as dependency.
Closes: #866438
* Add needs-recommends to d/t/control to fix autopkgtests.
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Files:
145ce3cf02b1a8bdb88e673e2ae97a74 5216482 debug extra last-align-dbgsym_869-1_armhf.deb
d9e452b8c2f4881e9ad39e9095c7c0ec 5072 science optional last-align_869-1_armhf.buildinfo
4dd34cd6d7319505c603629ea8b7be66 570714 science optional last-align_869-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
last-align-dbgsym_869-1_armhf.deb
---------------------------------
new debian package, version 2.0.
size 5216482 bytes: control archive=845 bytes.
663 bytes, 12 lines control
848 bytes, 8 lines md5sums
Package: last-align-dbgsym
Source: last-align
Version: 869-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8321
Depends: last-align (= 869-1)
Section: debug
Priority: extra
Description: Debug symbols for last-align
Build-Ids: 2728dbf85f134bba08c90fc2c2356dd1340b263a 37153d2ed2109937a56faabd9df8d8c356aa44cd 492afa4ad212247c3cf916809e23bd4025f92a6a 7b251fc7b4d21ecbc6e32d25e819757a9359bfa3 896280fb2aefccd6e61c9a61207f1f77e553ee74 bf20d274889aa070b50457301ff9973b3ba85659 defdd82fb7620aa6e00dea6099bc452f57adb25f ee46f453348a450cb13246e2ba86ae0861f92f47
drwxr-xr-x root/root 0 2017-08-11 19:17 ./
drwxr-xr-x root/root 0 2017-08-11 19:17 ./usr/
drwxr-xr-x root/root 0 2017-08-11 19:17 ./usr/lib/
drwxr-xr-x root/root 0 2017-08-11 19:17 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-08-11 19:17 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-08-11 19:17 ./usr/lib/debug/.build-id/27/
-rw-r--r-- root/root 792964 2017-08-11 19:17 ./usr/lib/debug/.build-id/27/28dbf85f134bba08c90fc2c2356dd1340b263a.debug
drwxr-xr-x root/root 0 2017-08-11 19:17 ./usr/lib/debug/.build-id/37/
-rw-r--r-- root/root 587948 2017-08-11 19:17 ./usr/lib/debug/.build-id/37/153d2ed2109937a56faabd9df8d8c356aa44cd.debug
drwxr-xr-x root/root 0 2017-08-11 19:17 ./usr/lib/debug/.build-id/49/
-rw-r--r-- root/root 792964 2017-08-11 19:17 ./usr/lib/debug/.build-id/49/2afa4ad212247c3cf916809e23bd4025f92a6a.debug
drwxr-xr-x root/root 0 2017-08-11 19:17 ./usr/lib/debug/.build-id/7b/
-rw-r--r-- root/root 2748508 2017-08-11 19:17 ./usr/lib/debug/.build-id/7b/251fc7b4d21ecbc6e32d25e819757a9359bfa3.debug
drwxr-xr-x root/root 0 2017-08-11 19:17 ./usr/lib/debug/.build-id/89/
-rw-r--r-- root/root 9660 2017-08-11 19:17 ./usr/lib/debug/.build-id/89/6280fb2aefccd6e61c9a61207f1f77e553ee74.debug
drwxr-xr-x root/root 0 2017-08-11 19:17 ./usr/lib/debug/.build-id/bf/
-rw-r--r-- root/root 587952 2017-08-11 19:17 ./usr/lib/debug/.build-id/bf/20d274889aa070b50457301ff9973b3ba85659.debug
drwxr-xr-x root/root 0 2017-08-11 19:17 ./usr/lib/debug/.build-id/de/
-rw-r--r-- root/root 229376 2017-08-11 19:17 ./usr/lib/debug/.build-id/de/fdd82fb7620aa6e00dea6099bc452f57adb25f.debug
drwxr-xr-x root/root 0 2017-08-11 19:17 ./usr/lib/debug/.build-id/ee/
-rw-r--r-- root/root 2748556 2017-08-11 19:17 ./usr/lib/debug/.build-id/ee/46f453348a450cb13246e2ba86ae0861f92f47.debug
drwxr-xr-x root/root 0 2017-08-11 19:17 ./usr/share/
drwxr-xr-x root/root 0 2017-08-11 19:17 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-08-11 19:17 ./usr/share/doc/last-align-dbgsym -> last-align
last-align_869-1_armhf.deb
--------------------------
new debian package, version 2.0.
size 570714 bytes: control archive=3674 bytes.
1161 bytes, 24 lines control
7121 bytes, 100 lines md5sums
Package: last-align
Version: 869-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2634
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), parallel
Recommends: python, python-pil
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 2017-08-11 19:17 ./
drwxr-xr-x root/root 0 2017-08-11 19:17 ./usr/
drwxr-xr-x root/root 0 2017-08-11 19:17 ./usr/bin/
-rwxr-xr-x root/root 475 2017-08-11 19:17 ./usr/bin/fastq-interleave
-rwxr-xr-x root/root 25766 2017-08-11 19:17 ./usr/bin/last-dotplot
-rwxr-xr-x root/root 4703 2017-08-11 19:17 ./usr/bin/last-map-probs
-rwxr-xr-x root/root 5636 2017-08-11 19:17 ./usr/bin/last-merge-batches
-rwxr-xr-x root/root 50856 2017-08-11 19:17 ./usr/bin/last-pair-probs
-rwxr-xr-x root/root 4150 2017-08-11 19:17 ./usr/bin/last-postmask
-rwxr-xr-x root/root 112368 2017-08-11 19:17 ./usr/bin/last-split
-rwxr-xr-x root/root 112368 2017-08-11 19:17 ./usr/bin/last-split8
-rwxr-xr-x root/root 19371 2017-08-11 19:17 ./usr/bin/last-train
-rwxr-xr-x root/root 730432 2017-08-11 19:17 ./usr/bin/lastal
-rwxr-xr-x root/root 730432 2017-08-11 19:17 ./usr/bin/lastal8
-rwxr-xr-x root/root 149012 2017-08-11 19:17 ./usr/bin/lastdb
-rwxr-xr-x root/root 149012 2017-08-11 19:17 ./usr/bin/lastdb8
-rwxr-xr-x root/root 27843 2017-08-11 19:17 ./usr/bin/maf-convert
-rwxr-xr-x root/root 8992 2017-08-11 19:17 ./usr/bin/maf-join
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| Post Build |
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+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 71572
Build-Time: 1096
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 392
Job: last-align_869-1
Machine Architecture: armhf
Package: last-align
Package-Time: 1539
Source-Version: 869-1
Space: 71572
Status: successful
Version: 869-1
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Finished at 2017-08-22T05:57:12Z
Build needed 00:25:39, 71572k disc space