last-align →
938-1 →
armhf → 2018-05-25 05:46:15
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| last-align 938-1 (armhf) Fri, 25 May 2018 05:17:19 +0000 |
+==============================================================================+
Package: last-align
Version: 938-1
Source Version: 938-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/buster-staging-armhf-sbuild-1abfac56-1aa4-455d-a1fd-924147c8bf74' 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 [10.8 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.5 MB]
Fetched 23.3 MB in 27s (855 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| 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://salsa.debian.org/med-team/last-align.git
Please use:
git clone https://salsa.debian.org/med-team/last-align.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 405 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main last-align 938-1 (dsc) [2018 B]
Get:2 http://172.17.0.1/private buster-staging/main last-align 938-1 (tar) [394 kB]
Get:3 http://172.17.0.1/private buster-staging/main last-align 938-1 (diff) [9360 B]
Fetched 405 kB in 0s (2319 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/last-align-D4FAjL/last-align-938' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/last-align-D4FAjL' 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-hElmCZ/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-hElmCZ/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-hElmCZ/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-hElmCZ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hElmCZ/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hElmCZ/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-hElmCZ/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-hElmCZ/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hElmCZ/apt_archive ./ Packages [429 B]
Fetched 2105 B in 1s (2776 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-hElmCZ/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-hElmCZ/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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 e2fsprogs-l10n libsasl2-modules 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 63 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-hElmCZ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 15506 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) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), help2man, python-pil, zlib1g-dev
Filtered Build-Depends: debhelper (>= 11~), help2man, python-pil, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-last-align-dummy' in '/<<BUILDDIR>>/resolver-hElmCZ/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-hElmCZ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hElmCZ/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hElmCZ/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-hElmCZ/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-hElmCZ/apt_archive ./ Sources [517 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hElmCZ/apt_archive ./ Packages [593 B]
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Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-hElmCZ/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-hElmCZ/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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 e2fsprogs-l10n libsasl2-modules 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 dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3
libelf1 libexpat1 libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0
libicu57 libjbig0 libjpeg62-turbo liblcms2-2 liblocale-gettext-perl
libmagic-mgc libmagic1 libncursesw6 libpipeline1 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libtiff5
libtimedate-perl libtinfo6 libtool libwebp6 libwebpdemux2 libwebpmux3
libxml2 m4 man-db mime-support po-debconf python python-minimal
python-olefile python-pil python2.7 python2.7-minimal zlib1g zlib1g-dev
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
apparmor 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 libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libgpm2 libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3
libelf1 libexpat1 libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0
libicu57 libjbig0 libjpeg62-turbo liblcms2-2 liblocale-gettext-perl
libmagic-mgc libmagic1 libncursesw6 libpipeline1 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libtiff5
libtimedate-perl libtinfo6 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 zlib1g-dev
The following packages will be upgraded:
zlib1g
1 upgraded, 56 newly installed, 0 to remove and 62 not upgraded.
Need to get 25.5 MB/25.6 MB of archives.
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Get:1 copy:/<<BUILDDIR>>/resolver-hElmCZ/apt_archive ./ sbuild-build-depends-last-align-dummy 0.invalid.0 [884 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf liblocale-gettext-perl armhf 1.07-3+b2 [18.3 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.7-1 [96.8 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf zlib1g armhf 1:1.2.11.dfsg-1 [87.3 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.15-1 [393 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.15-1 [1077 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15~rc1-1 [41.1 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libtinfo6 armhf 6.1+20180210-3 [307 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libncursesw6 armhf 6.1+20180210-3 [103 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.15-1 [1841 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.15-1 [298 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15~rc1-1 [20.5 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.15~rc1-1 [155 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.33-2 [234 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.33-2 [106 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.33-2 [64.7 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.041-1 [19.9 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.041-1 [12.0 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.4 [160 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-9 [7414 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-6.1 [602 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-2 [132 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.2 [994 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf help2man armhf 1.47.6 [169 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libfreetype6 armhf 2.8.1-2 [402 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf liblcms2-2 armhf 2.9-1 [117 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libtiff5 armhf 4.0.9-5 [224 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libwebp6 armhf 0.6.1-2 [228 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libwebpdemux2 armhf 0.6.1-2 [86.7 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libwebpmux3 armhf 0.6.1-2 [94.2 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf python-olefile all 0.45.1-1 [35.4 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf python-pil armhf 4.3.0-2 [336 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
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Setting up dwz (0.12-2) ...
Setting up autotools-dev (20180224.1) ...
Setting up liblocale-gettext-perl (1.07-3+b2) ...
Setting up bsdmainutils (11.1.2) ...
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
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Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
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Setting up gettext (0.19.8.1-6) ...
Setting up libncursesw6:armhf (6.1+20180210-3) ...
Setting up autoconf (2.69-11) ...
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Not building database; man-db/auto-update is not 'true'.
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Processing triggers for libc-bin (2.27-3+rpi1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.30-15+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-12 gcc-7_7.3.0-12 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180414-1+rpi1 linux-libc-dev_4.15.17-1+rpi1
Package versions: adduser_3.117 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-2+b1 binutils_2.30-15+rpi1 binutils-arm-linux-gnueabihf_2.30-15+rpi1 binutils-common_2.30-15+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.5 build-essential_12.4+b1 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.3.0-12 dash_0.5.8-2.10 debconf_1.5.66 debhelper_11.3.2 debianutils_4.8.4 dh-autoreconf_19 dh-strip-nondeterminism_0.041-1 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.1-2 e2fsprogs_1.44.1-2 e2fsprogs-l10n_1.44.1-2 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.33-2 findutils_4.6.0+git+20171230-2 g++_4:7.2.0-1d1 g++-7_7.3.0-12 gcc_4:7.2.0-1d1 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_4.9.4-2+rpi1 gcc-5-base_5.5.0-8 gcc-7_7.3.0-12 gcc-7-base_7.3.0-12 gcc-8-base_8-20180414-1+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gnupg_2.2.5-1 gnupg-agent_2.2.5-1 gnupg-l10n_2.2.5-1 gnupg-utils_2.2.5-1 gpg_2.2.5-1 gpg-agent_2.2.5-1 gpg-wks-client_2.2.5-1 gpg-wks-server_2.2.5-1 gpgconf_2.2.5-1 gpgsm_2.2.5-1 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 help2man_1.47.6 hostname_3.20 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-4 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-2 libasan4_7.3.0-12 libassuan0_2.5.1-2 libatomic1_8-20180414-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libbinutils_2.30-15+rpi1 libblkid1_2.31.1-0.5 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3+rpi1 libc-dev-bin_2.27-3+rpi1 libc6_2.27-3+rpi1 libc6-dev_2.27-3+rpi1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_8-20180414-1+rpi1 libcilkrts5_7.3.0-12 libcom-err2_1.44.1-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.6-2 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.91-2+rpi1 libdrm2_2.4.91-2+rpi1 libelf1_0.170-0.4 libexpat1_2.2.5-3 libext2fs2_1.44.1-2 libfakeroot_1.22-2 libfdisk1_2.31.1-0.5 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.041-1 libfreetype6_2.8.1-2 libgcc-7-dev_7.3.0-12 libgcc1_1:8-20180414-1+rpi1 libgcrypt20_1.8.2-2 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libglib2.0-0_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180414-1+rpi1 libgpg-error0_1.29-4 libhogweed4_3.4-1 libicu57_57.1-9 libidn11_1.33-2.2 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl15_0.18-4 libjbig0_2.1-3.1+b2 libjpeg62-turbo_1:1.5.2-2+b1 libjson-c3_0.12.1-1.3 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libksba8_1.3.5-2 liblcms2-2_2.9-1 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_1.8.1.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-2 libmagic1_1:5.33-2 libmount1_2.31.1-0.5 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1-1 libncursesw5_6.1-1 libncursesw6_6.1+20180210-3 libnettle6_3.4-1 libnpth0_1.5-3 libp11-kit0_0.23.10-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam0g_1.1.8-3.7 libpcre3_2:8.39-9 libperl5.24_5.24.1-7 libperl5.26_5.26.2-2 libpipeline1_1.5.0-1 libplymouth4_0.9.3-2 libpng16-16_1.6.34-1 libprocps6_2:3.3.14-1 libpython-stdlib_2.7.15~rc1-1 libpython2.7-minimal_2.7.15-1 libpython2.7-stdlib_2.7.15-1 libreadline7_7.0-3 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-2 libsmartcols1_2.31.1-0.5 libsqlite3-0_3.23.1-1 libss2_1.44.1-2 libssl1.1_1.1.0h-2 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180414-1+rpi1 libsystemd0_238-4 libtasn1-6_4.13-2 libtiff5_4.0.9-5 libtimedate-perl_2.3000-2 libtinfo5_6.1-1 libtinfo6_6.1+20180210-3 libtool_2.4.6-2.1 libubsan0_7.3.0-12 libudev1_238-4 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.5 libwebp6_0.6.1-2 libwebpdemux2_0.6.1-2 libwebpmux3_0.6.1-2 libxml2_2.9.4+dfsg1-6.1 libzstd1_1.3.3+dfsg-2+rpi1 linux-base_4.5 linux-libc-dev_4.15.17-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.3-2 mawk_1.3.3-17 mime-support_3.60 mount_2.31.1-0.5 multiarch-support_2.27-3+rpi1 nano_2.9.5-1 ncurses-base_6.1-1 ncurses-bin_6.1-1 netbase_5.4 openssl_1.1.0h-2 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-2 perl-base_5.26.2-2 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-3 pinentry-curses_1.1.0-1 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.14-1 python_2.7.15~rc1-1 python-minimal_2.7.15~rc1-1 python-olefile_0.45.1-1 python-pil_4.3.0-2 python2.7_2.7.15-1 python2.7-minimal_2.7.15-1 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_4.4-2 sensible-utils_0.0.12 systemd_238-4 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018d-1 udev_238-4 util-linux_2.31.1-0.5 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed May 23 05:13:52 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./last-align_938-1.dsc
dpkg-source: info: extracting last-align in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking last-align_938.orig.tar.xz
dpkg-source: info: unpacking last-align_938-1.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-1abfac56-1aa4-455d-a1fd-924147c8bf74
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 938-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build last-align-938
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_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 -DHAS_CXX_THREADS" LDFLAGS="-Wl,-z,relro -Wl,-z,now -pthread"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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
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 -pthread -o lastdb Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o fileMap.o tantan.o LastdbArguments.o MultiSequence.o MultiSequenceQual.o SubsetSuffixArray.o SubsetSuffixArraySort.o lastdb.o -lz
g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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/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);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In static member function 'static void Sls::alp_reg::find_tetta_general(double (*)(double, void*), void*, double, double, long int, double, std::vector<double>&)':
/usr/include/c++/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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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
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 -pthread -o lastal Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o fileMap.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 -lz
g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -pthread -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
cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o last-merge-batches.o last-merge-batches.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -pthread -o last-merge-batches last-merge-batches.o
g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -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:429:74: 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 -DHAS_CXX_THREADS -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 -pthread -o last-pair-probs last-pair-probs.o last-pair-probs-main.o -lz
g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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
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 -pthread -o lastdb8 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o fileMap.o tantan.o LastdbArguments.o MultiSequence.o8 MultiSequenceQual.o8 SubsetSuffixArray.o8 SubsetSuffixArraySort.o8 lastdb.o8 -lz
g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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
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 -pthread -o lastal8 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o fileMap.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 -lz
g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -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 -DHAS_CXX_THREADS -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 -pthread -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>>'
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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="938" \
--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="938" \
--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="938" \
--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="938" \
# --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="938" \
--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="938" \
--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="938" \
# --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="938" \
# --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="938" \
# --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="938" \
# --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="938" \
--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="938" \
--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="938" \
--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="938" \
--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="938" \
--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="938" \
--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="938" \
# --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="938" \
--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="938" \
--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/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/last-split contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastal contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/last-align/usr/bin/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/lastdb8 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/last-align/usr/bin/last-pair-probs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/last-align/usr/bin/last-split8 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/last-align/usr/bin/lastdb debian/last-align/usr/bin/last-split debian/last-align/usr/bin/lastal debian/last-align/usr/bin/lastal8 debian/last-align/usr/bin/lastdb8 debian/last-align/usr/bin/last-merge-batches debian/last-align/usr/bin/last-pair-probs debian/last-align/usr/bin/last-split8 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_938-1_armhf.deb'.
dpkg-deb: building package 'last-align-dbgsym' in '../last-align-dbgsym_938-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../last-align_938-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build last-align-938
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-05-25T05:45:12Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
last-align_938-1_armhf.changes:
-------------------------------
Format: 1.8
Date: Wed, 23 May 2018 07:10:11 +0200
Source: last-align
Binary: last-align
Architecture: armhf
Version: 938-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
last-align - genome-scale comparison of biological sequences
Changes:
last-align (938-1) unstable; urgency=medium
.
* New upstream version
Checksums-Sha1:
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e145ed27e82b330b80e6eacb8a06931ded588b79 5342 last-align_938-1_armhf.buildinfo
9f2328123b762b3fbe94343173074a13020beb6b 589900 last-align_938-1_armhf.deb
Checksums-Sha256:
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Files:
d52e5d3253abded93820201c025fddea 5646260 debug optional last-align-dbgsym_938-1_armhf.deb
52a7d6d172c8f459b345977c372ff54c 5342 science optional last-align_938-1_armhf.buildinfo
aee2c53f1f76028304f752330a35973c 589900 science optional last-align_938-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
last-align-dbgsym_938-1_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 5646260 bytes: control archive=912 bytes.
666 bytes, 12 lines control
848 bytes, 8 lines md5sums
Package: last-align-dbgsym
Source: last-align
Version: 938-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8804
Depends: last-align (= 938-1)
Section: debug
Priority: optional
Description: debug symbols for last-align
Build-Ids: 01581d01e28b66f2edb56e0368a6caaf3001e257 0a350b65b0a4bc380d559800e1299b93eca98ed6 2ae731069b9c7e489626e0e0e364cd7d94871528 794523e27f9cdb3b71c038d8d8c30657430f5f16 932bc0b64684244a8fb430b2aa0f0216c0c5ba7f acfd45b309bb5a9b675744f73eb989205fc9815e cb41e666d017a0099aa78b723f7eb53707168718 dd6efbaaa9cde90a99b0ba6242048a8d3752d301
drwxr-xr-x root/root 0 2018-05-23 05:10 ./
drwxr-xr-x root/root 0 2018-05-23 05:10 ./usr/
drwxr-xr-x root/root 0 2018-05-23 05:10 ./usr/lib/
drwxr-xr-x root/root 0 2018-05-23 05:10 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-05-23 05:10 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-05-23 05:10 ./usr/lib/debug/.build-id/01/
-rw-r--r-- root/root 603084 2018-05-23 05:10 ./usr/lib/debug/.build-id/01/581d01e28b66f2edb56e0368a6caaf3001e257.debug
drwxr-xr-x root/root 0 2018-05-23 05:10 ./usr/lib/debug/.build-id/0a/
-rw-r--r-- root/root 914972 2018-05-23 05:10 ./usr/lib/debug/.build-id/0a/350b65b0a4bc380d559800e1299b93eca98ed6.debug
drwxr-xr-x root/root 0 2018-05-23 05:10 ./usr/lib/debug/.build-id/2a/
-rw-r--r-- root/root 603084 2018-05-23 05:10 ./usr/lib/debug/.build-id/2a/e731069b9c7e489626e0e0e364cd7d94871528.debug
drwxr-xr-x root/root 0 2018-05-23 05:10 ./usr/lib/debug/.build-id/79/
-rw-r--r-- root/root 221464 2018-05-23 05:10 ./usr/lib/debug/.build-id/79/4523e27f9cdb3b71c038d8d8c30657430f5f16.debug
drwxr-xr-x root/root 0 2018-05-23 05:10 ./usr/lib/debug/.build-id/93/
-rw-r--r-- root/root 914972 2018-05-23 05:10 ./usr/lib/debug/.build-id/93/2bc0b64684244a8fb430b2aa0f0216c0c5ba7f.debug
drwxr-xr-x root/root 0 2018-05-23 05:10 ./usr/lib/debug/.build-id/ac/
-rw-r--r-- root/root 2863228 2018-05-23 05:10 ./usr/lib/debug/.build-id/ac/fd45b309bb5a9b675744f73eb989205fc9815e.debug
drwxr-xr-x root/root 0 2018-05-23 05:10 ./usr/lib/debug/.build-id/cb/
-rw-r--r-- root/root 9536 2018-05-23 05:10 ./usr/lib/debug/.build-id/cb/41e666d017a0099aa78b723f7eb53707168718.debug
drwxr-xr-x root/root 0 2018-05-23 05:10 ./usr/lib/debug/.build-id/dd/
-rw-r--r-- root/root 2863200 2018-05-23 05:10 ./usr/lib/debug/.build-id/dd/6efbaaa9cde90a99b0ba6242048a8d3752d301.debug
drwxr-xr-x root/root 0 2018-05-23 05:10 ./usr/share/
drwxr-xr-x root/root 0 2018-05-23 05:10 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-05-23 05:10 ./usr/share/doc/last-align-dbgsym -> last-align
last-align_938-1_armhf.deb
--------------------------
new Debian package, version 2.0.
size 589900 bytes: control archive=3548 bytes.
1180 bytes, 24 lines control
7317 bytes, 103 lines md5sums
Package: last-align
Version: 938-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2730
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libstdc++6 (>= 6), zlib1g (>= 1:1.1.4), 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.
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Build Architecture: armhf
Build-Space: 76180
Build-Time: 1164
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 455
Job: last-align_938-1
Machine Architecture: armhf
Package: last-align
Package-Time: 1673
Source-Version: 938-1
Space: 76180
Status: successful
Version: 938-1
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Finished at 2018-05-25T05:45:12Z
Build needed 00:27:53, 76180k disc space