fsa →
1.15.9+dfsg-3 →
armhf → 2016-12-27 05:30:02
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| fsa 1.15.9+dfsg-3 (armhf) Tue, 27 Dec 2016 05:04:12 +0000 |
+==============================================================================+
Package: fsa
Version: 1.15.9+dfsg-3
Source Version: 1.15.9+dfsg-3
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/stretch-staging-armhf-sbuild-f61684fd-d06d-4492-af82-76558e500f8e' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9655 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.6 MB]
Fetched 21.3 MB in 23s (908 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'fsa' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/fsa.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/fsa.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 574 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main fsa 1.15.9+dfsg-3 (dsc) [1975 B]
Get:2 http://172.17.0.1/private stretch-staging/main fsa 1.15.9+dfsg-3 (tar) [559 kB]
Get:3 http://172.17.0.1/private stretch-staging/main fsa 1.15.9+dfsg-3 (diff) [13.0 kB]
Fetched 574 kB in 0s (5170 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/fsa-TOm0v6/fsa-1.15.9+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/fsa-TOm0v6' 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-9XUsjo/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-9XUsjo/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-9XUsjo/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-9XUsjo/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-9XUsjo/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-9XUsjo/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-9XUsjo/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-9XUsjo/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-9XUsjo/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (3218 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-9XUsjo/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-9XUsjo/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:
fuse2fs gnupg-l10n libfuse2 manpages
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 42 not upgraded.
Need to get 772 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-9XUsjo/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 772 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12988 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
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 (>= 9), dh-autoreconf, mummer, exonerate, help2man
Filtered Build-Depends: debhelper (>= 9), dh-autoreconf, mummer, exonerate, help2man
dpkg-deb: building package 'sbuild-build-depends-fsa-dummy' in '/<<BUILDDIR>>/resolver-9XUsjo/apt_archive/sbuild-build-depends-fsa-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-fsa-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-9XUsjo/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-9XUsjo/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-9XUsjo/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-9XUsjo/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-9XUsjo/apt_archive ./ Sources [509 B]
Get:5 copy:/<<BUILDDIR>>/resolver-9XUsjo/apt_archive ./ Packages [595 B]
Fetched 2437 B in 0s (3700 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-9XUsjo/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-9XUsjo/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install fsa build dependencies (apt-based resolver)
---------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
fuse2fs gnupg-l10n libfuse2 manpages
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism exonerate file gawk gettext
gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbsd0
libcroco3 libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libicu57
liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libreadline6
libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db mummer
po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make wise gawk-doc gettext-doc libasprintf-dev libgettextpo-dev
groff libtool-doc gfortran | fortran95-compiler gcj-jdk less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
libltdl-dev xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism exonerate file gawk gettext
gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbsd0
libcroco3 libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libicu57
liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libreadline6
libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db mummer
po-debconf sbuild-build-depends-fsa-dummy
0 upgraded, 38 newly installed, 0 to remove and 42 not upgraded.
Need to get 21.8 MB/21.9 MB of archives.
After this operation, 78.0 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-9XUsjo/apt_archive ./ sbuild-build-depends-fsa-dummy 0.invalid.0 [796 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf liblocale-gettext-perl armhf 1.07-3+b1 [18.3 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.12 [178 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf gawk armhf 1:4.1.3+dfsg-0.1 [509 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-2 [221 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-2 [104 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-2 [63.1 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-5 [7427 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.1 [804 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-5 [733 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.2-2 [2527 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.2 [826 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf exonerate armhf 2.4.0-2 [1273 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf help2man armhf 1.47.4 [162 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf mummer armhf 3.23+dfsg-2 [765 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package liblocale-gettext-perl.
(Reading database ... 12988 files and directories currently installed.)
Preparing to unpack .../0-liblocale-gettext-perl_1.07-3+b1_armhf.deb ...
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Preparing to unpack .../1-groff-base_1.22.3-9_armhf.deb ...
Unpacking groff-base (1.22.3-9) ...
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Unpacking libsigsegv2:armhf (2.10-5) ...
Setting up libreadline6:armhf (6.3-9) ...
Setting up libsigsegv2:armhf (2.10-5) ...
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(Reading database ... 13591 files and directories currently installed.)
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Setting up libarchive-zip-perl (1.59-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up groff-base (1.22.3-9) ...
Setting up gettext-base (0.19.8.1-1) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up m4 (1.4.17-5) ...
Setting up gawk (1:4.1.3+dfsg-0.1) ...
Setting up libicu57:armhf (57.1-5) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2.1) ...
Setting up libmagic-mgc (1:5.29-2) ...
Setting up libmagic1:armhf (1:5.29-2) ...
Processing triggers for libc-bin (2.24-7+rpi1) ...
Setting up autotools-dev (20161112.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up liblocale-gettext-perl (1.07-3+b1) ...
Setting up libffi6:armhf (3.2.1-6) ...
Setting up bsdmainutils (9.0.12) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up autopoint (0.19.8.1-1) ...
Setting up libfile-stripnondeterminism-perl (0.028-1) ...
Setting up mummer (3.23+dfsg-2) ...
Setting up libglib2.0-0:armhf (2.50.2-2) ...
No schema files found: doing nothing.
Setting up exonerate (2.4.0-2) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.29-2) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Setting up automake (1:1.15-5) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up help2man (1.47.4) ...
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2) ...
Setting up gettext (0.19.8.1-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.20) ...
Setting up dh-autoreconf (12) ...
Setting up dh-strip-nondeterminism (0.028-1) ...
Setting up debhelper (10.2.2) ...
Setting up sbuild-build-depends-fsa-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-7+rpi1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.6.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.27.51.20161127-1 dpkg-dev_1.18.15 g++-6_6.2.1-5+rpi1 gcc-6_6.2.1-5+rpi1 libc6-dev_2.24-7+rpi1 libstdc++-6-dev_6.2.1-5+rpi1 libstdc++6_6.2.1-5+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.4~beta1 autoconf_2.69-10 automake_1:1.15-5 autopoint_0.19.8.1-1 autotools-dev_20161112.1 base-files_9.7+rpi1 base-passwd_3.5.41 bash_4.4-2 binutils_2.27.51.20161127-1 bsdmainutils_9.0.12 bsdutils_1:2.29-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-6 cpp_4:6.1.1-1 cpp-6_6.2.1-5+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.2 debianutils_4.8.1 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dmsetup_2:1.02.136-1 dpkg_1.18.15 dpkg-dev_1.18.15 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 exonerate_2.4.0-2 fakeroot_1.21-2 file_1:5.29-2 findutils_4.6.0+git+20161106-1 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.2.1-5+rpi1 gawk_1:4.1.3+dfsg-0.1 gcc_4:6.1.1-1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-6_6.2.1-5+rpi1 gcc-6-base_6.2.1-5+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_2.1.16-2 gnupg-agent_2.1.16-2 gnupg-l10n_2.1.16-2 gpgv_2.1.16-2 grep_2.26-1 groff-base_1.22.3-9 gzip_1.6-5 help2man_1.47.4 hostname_3.18 init_1.46 init-system-helpers_1.46 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_23-1 libacl1_2.2.52-3 libapparmor1_2.10.95-6 libapt-pkg5.0_1.4~beta1 libarchive-zip-perl_1.59-1 libasan3_6.2.1-5+rpi1 libassuan0_2.4.3-2 libatomic1_6.2.1-5+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblkid1_2.29-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-7+rpi1 libc-dev-bin_2.24-7+rpi1 libc6_2.24-7+rpi1 libc6-dev_2.24-7+rpi1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.2.1-5+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.3-2 libdb5.3_5.3.28-12 libdbus-1-3_1.10.14-1 libdebconfclient0_0.218 libdevmapper1.02.1_2:1.02.136-1 libdpkg-perl_1.18.15 libdrm2_2.4.74-1 libfakeroot_1.21-2 libfdisk1_2.29-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.2.1-5+rpi1 libgcc1_1:6.2.1-5+rpi1 libgcrypt20_1.7.3-2 libgdbm3_1.8.3-14 libglib2.0-0_2.50.2-2 libgmp10_2:6.1.1+dfsg-1 libgomp1_6.2.1-5+rpi1 libgpg-error0_1.25-1 libicu57_57.1-5 libidn11_1.33-1 libip4tc0_1.6.0-4 libisl15_0.17.1-1 libklibc_2.0.4-9+rpi1 libkmod2_23-1 libksba8_1.3.5-2 liblocale-gettext-perl_1.07-3+b1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-2 libmagic1_1:5.29-2 libmount1_2.29-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnpth0_1.3-1 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpcre3_2:8.39-2 libperl5.24_5.24.1~rc4-1 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libprocps6_2:3.3.12-3 libreadline6_6.3-9 libreadline7_7.0-1 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-1 libsemanage1_2.6-1 libsepol1_2.6-1 libsigsegv2_2.10-5 libsmartcols1_2.29-1 libsqlite3-0_3.15.2-1 libss2_1.43.3-1 libstdc++-6-dev_6.2.1-5+rpi1 libstdc++6_6.2.1-5+rpi1 libsystemd0_232-6 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtool_2.4.6-2 libubsan0_6.2.1-5+rpi1 libudev1_232-6 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1 libxml2_2.9.4+dfsg1-2.1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.3 lsb-base_9.20161125+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.6.1-2 manpages_4.08-1 mawk_1.3.3-17 mount_2.29-1 multiarch-support_2.24-7+rpi1 mummer_3.23+dfsg-2 nano_2.7.1-1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 passwd_1:4.2-3.3 patch_2.7.5-1 perl_5.24.1~rc4-1 perl-base_5.24.1~rc4-1 perl-modules-5.24_5.24.1~rc4-1 pinentry-curses_0.9.7-9 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-fsa-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_232-6 systemd-sysv_232-6 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1.1 tzdata_2016j-2 udev_232-6 util-linux_2.29-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri Dec 16 17:23:55 2016 UTC
gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./fsa_1.15.9+dfsg-3.dsc
dpkg-source: info: extracting fsa in /<<BUILDDIR>>/fsa-1.15.9+dfsg
dpkg-source: info: unpacking fsa_1.15.9+dfsg.orig.tar.xz
dpkg-source: info: unpacking fsa_1.15.9+dfsg-3.debian.tar.xz
dpkg-source: info: applying no-display.patch
dpkg-source: info: applying removed-pdf-only-docs.patch
dpkg-source: info: applying privacy_breach_logo.patch
dpkg-source: info: applying fixed-check-for-m64-flag.patch
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=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-f61684fd-d06d-4492-af82-76558e500f8e
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package fsa
dpkg-buildpackage: info: source version 1.15.9+dfsg-3
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build fsa-1.15.9+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with autoreconf
dh_testdir
dh_auto_clean
dh_autoreconf_clean
dh_clean
# found automatically: --with-mummer=/usr/bin/mummer --with-exonerate=/usr/bin/exonerate
debian/rules build-arch
dh build-arch --with autoreconf
dh_testdir -a
dh_update_autotools_config -a
dh_autoreconf -a
aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
dh_auto_configure -a
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '104' is supported by ustar format... yes
checking whether GID '109' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for ar... ar
checking the archiver (ar) interface... ar
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) none
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking for gawk... (cached) gawk
checking whether make sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for inline... inline
checking for pid_t... yes
checking for size_t... yes
checking for unsigned long long int... yes
checking for uintmax_t... yes
checking for ptrdiff_t... yes
checking tr1/unordered_map usability... yes
checking tr1/unordered_map presence... yes
checking for tr1/unordered_map... yes
checking tr1/unordered_set usability... yes
checking tr1/unordered_set presence... yes
checking for tr1/unordered_set... yes
checking vfork.h usability... no
checking vfork.h presence... no
checking for vfork.h... no
checking for fork... yes
checking for vfork... yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking for floor... yes
checking for memmove... yes
checking for pow... yes
checking for regcomp... yes
checking for sqrt... yes
checking for strchr... yes
checking for strcspn... yes
checking for strspn... yes
checking for strstr... yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking if gcc accepts -m64... no
checking for mummer... /usr/bin/mummer
checking for exonerate... /usr/bin/exonerate
checking for struct sysinfo.totalram... yes
checking for struct sysinfo.mem_unit... yes
checking whether sysctl is declared... yes
checking whether CTL_HW is declared... no
checking whether HW_PHYSMEM is declared... no
checking for javac... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/main/Makefile
config.status: creating src/manager/Makefile
config.status: creating src/fsa/Makefile
config.status: creating src/annealing/Makefile
config.status: creating src/math/Makefile
config.status: creating src/util/Makefile
config.status: creating src/seq/Makefile
config.status: creating perl/Makefile
config.status: creating examples/Makefile
config.status: creating html/Makefile
config.status: creating tests/Makefile
config.status: creating config.h
config.status: executing depfiles commands
-- FSA 1.15.9 Configuration Results --
C++ compiler: g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG
GCC version: gcc (Raspbian 6.2.1-5+rpi1) 6.2.1 20161124
Host System type: arm-unknown-linux-gnueabihf
Install prefix: /usr
See config.h for further configuration information.
Email <fsa@math.berkeley.edu> with questions and bug reports.
dh_auto_build -a
make -j1
make[1]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg'
make all-recursive
make[2]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg'
Making all in src/util
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/util'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o dexception.o dexception.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o logfile.o logfile.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o memcheck.o memcheck.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o misc.o misc.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o opts_list.o opts_list.cc
opts_list.cc:99:25: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
SET_VERSION_INFO(*this);
^
opts_list.cc:99:25: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o regexp.o regexp.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o sstring.o sstring.cc
rm -f libutil.a
ar cru libutil.a dexception.o logfile.o memcheck.o misc.o opts_list.o regexp.o sstring.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libutil.a
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/util'
Making all in src/math
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/math'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o mathematics.o mathematics.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o mst.o mst.cc
rm -f libmath.a
ar cru libmath.a mathematics.o mst.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libmath.a
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/math'
Making all in src/seq
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/seq'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o alphabet.o alphabet.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o alignment.o alignment.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o gff.o gff.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o mercator.o mercator.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o sequence.o sequence.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o similarity_matrix.o similarity_matrix.cc
rm -f libseq.a
ar cru libseq.a alphabet.o alignment.o gff.o mercator.o sequence.o similarity_matrix.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libseq.a
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/seq'
Making all in src/manager
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/manager'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o manager.o manager.cc
In file included from ../../src/manager/manager.h:12:0,
from manager.cc:6:
../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)':
../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable]
int yprev = -1; // the previous y-coordinate
^~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o mw_adapter.o mw_adapter.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o db_adapter.o db_adapter.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o db_misc.o db_misc.cc
In file included from ../../src/fsa/anchors.h:17:0,
from ../../src/fsa/fsa.h:71,
from db_misc.cc:7:
../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)':
../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable]
int yprev = -1; // the previous y-coordinate
^~~~~
rm -f libmanager.a
ar cru libmanager.a manager.o mw_adapter.o db_adapter.o db_misc.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libmanager.a
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/manager'
Making all in src/fsa
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/fsa'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o algebras.o algebras.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o aminoacid_indel2dp.o aminoacid_indel2dp.cc
aminoacid_indel2dp.cc: In function 'Algebra<BFloatMethods> Forward(AminoAcidIndel2AlignDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&)':
aminoacid_indel2dp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
int iPrevSlowCoord;
^~~~~~~~~~~~~~
aminoacid_indel2dp.cc: In function 'Algebra<BFloatMethods> Backward(AminoAcidIndel2AlignDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&)':
aminoacid_indel2dp.cc:1320:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
int iPrevSlowCoord;
^~~~~~~~~~~~~~
aminoacid_indel2dp.cc: In function 'Algebra<BFloatMethods> ForwardBanding(AminoAcidIndel2AlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
aminoacid_indel2dp.cc:1568:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
int iPrevSlowCoord;
^~~~~~~~~~~~~~
aminoacid_indel2dp.cc: In function 'Algebra<BFloatMethods> BackwardBanding(AminoAcidIndel2AlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
aminoacid_indel2dp.cc:2189:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
int iPrevSlowCoord;
^~~~~~~~~~~~~~
aminoacid_indel2dp.cc: In function 'Algebra<BFloatMethods> ForwardBanding(AminoAcidIndel2AlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
aminoacid_indel2dp.cc:1691:17: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
if (iLastSlowCoord > position[1]) {
^~
aminoacid_indel2dp.cc: In function 'Algebra<BFloatMethods> BackwardBanding(AminoAcidIndel2AlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
aminoacid_indel2dp.cc:2310:48: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
if (iCheckSlowCoordTraversal != -1 && iCheckSlowCoordTraversal < position[1]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aminoacid_indel2dp.cc: In function 'Algebra<BFloatMethods> BackwardBaumWelchBanding(AminoAcidIndel2AlignWithBandingBaumWelch&, AminoAcidIndel2AlignWithBandingDPTable*, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
aminoacid_indel2dp.cc:1973:48: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
if (iCheckSlowCoordTraversal != -1 && iCheckSlowCoordTraversal < position[1]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o aminoaciddp.o aminoaciddp.cc
aminoaciddp.cc: In function 'Algebra<BFloatMethods> Forward(AminoAcidAlignDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&)':
aminoaciddp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
int iPrevSlowCoord;
^~~~~~~~~~~~~~
aminoaciddp.cc: In function 'Algebra<BFloatMethods> Backward(AminoAcidAlignDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&)':
aminoaciddp.cc:1230:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
int iPrevSlowCoord;
^~~~~~~~~~~~~~
aminoaciddp.cc: In function 'Algebra<BFloatMethods> ForwardBanding(AminoAcidAlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
aminoaciddp.cc:1448:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
int iPrevSlowCoord;
^~~~~~~~~~~~~~
aminoaciddp.cc: In function 'Algebra<BFloatMethods> BackwardBanding(AminoAcidAlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
aminoaciddp.cc:1979:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
int iPrevSlowCoord;
^~~~~~~~~~~~~~
aminoaciddp.cc: In function 'Algebra<BFloatMethods> ForwardBanding(AminoAcidAlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
aminoaciddp.cc:1551:17: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
if (iLastSlowCoord > position[1]) {
^~
aminoaciddp.cc: In function 'Algebra<BFloatMethods> BackwardBanding(AminoAcidAlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
aminoaciddp.cc:2080:48: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
if (iCheckSlowCoordTraversal != -1 && iCheckSlowCoordTraversal < position[1]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aminoaciddp.cc: In function 'Algebra<BFloatMethods> BackwardBaumWelchBanding(AminoAcidAlignWithBandingBaumWelch&, AminoAcidAlignWithBandingDPTable*, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
aminoaciddp.cc:1803:48: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
if (iCheckSlowCoordTraversal != -1 && iCheckSlowCoordTraversal < position[1]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o anchors.o anchors.cc
In file included from ../../src/fsa/anchors.h:17:0,
from anchors.cc:16:
../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)':
../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable]
int yprev = -1; // the previous y-coordinate
^~~~~
anchors.cc: In member function 'fsa::Anchors fsa::Exonerate_adapter::call_exonerate(const string&, const string&, int) const':
anchors.cc:863:47: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
freopen (output_file.c_str(), "w", stdout); // capture stdout (send to file output_file) to store exonerate results
^
anchors.cc:864:39: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
freopen ("/dev/null", "a", stderr); // capture stderr (send to trash) so that it doesn't mess up our logging
^
anchors.cc: In member function 'fsa::Anchors fsa::Mummer_adapter::call_mummer(const string&, const string&, size_t) const':
anchors.cc:1100:47: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
freopen (output_file.c_str(), "w", stdout); // capture stdout (send to file output_file) to store mummer results
^
anchors.cc:1101:39: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
freopen ("/dev/null", "a", stderr); // capture stderr (send to trash) so that it doesn't mess up our logging
^
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o constraints.o constraints.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o fsa.o fsa.cc
fsa.cc:25:125: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
INIT_CONSTRUCTED_OPTS_LIST (opts, -1, "[options] <sequence file(s)>", "Distance-based alignment of DNA, RNA and proteins.");
^
fsa.cc:25:125: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
In file included from ../../src/fsa/anchors.h:17:0,
from ../../src/fsa/fsa.h:71,
from fsa.cc:11:
../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)':
../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable]
int yprev = -1; // the previous y-coordinate
^~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o model.o model.cc
In file included from ../../src/fsa/model.h:32:0,
from model.cc:8:
../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)':
../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable]
int yprev = -1; // the previous y-coordinate
^~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o nucleotide_indel2dp.o nucleotide_indel2dp.cc
nucleotide_indel2dp.cc: In function 'Algebra<BFloatMethods> Forward(NucleotideIndel2AlignDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&)':
nucleotide_indel2dp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
int iPrevSlowCoord;
^~~~~~~~~~~~~~
nucleotide_indel2dp.cc: In function 'Algebra<BFloatMethods> Backward(NucleotideIndel2AlignDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&)':
nucleotide_indel2dp.cc:1256:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
int iPrevSlowCoord;
^~~~~~~~~~~~~~
nucleotide_indel2dp.cc: In function 'Algebra<BFloatMethods> ForwardBanding(NucleotideIndel2AlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
nucleotide_indel2dp.cc:1472:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
int iPrevSlowCoord;
^~~~~~~~~~~~~~
nucleotide_indel2dp.cc: In function 'Algebra<BFloatMethods> BackwardBanding(NucleotideIndel2AlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
nucleotide_indel2dp.cc:2029:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
int iPrevSlowCoord;
^~~~~~~~~~~~~~
nucleotide_indel2dp.cc: In function 'Algebra<BFloatMethods> ForwardBanding(NucleotideIndel2AlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
nucleotide_indel2dp.cc:1563:17: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
if (iLastSlowCoord > position[1]) {
^~
nucleotide_indel2dp.cc: In function 'Algebra<BFloatMethods> BackwardBanding(NucleotideIndel2AlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
nucleotide_indel2dp.cc:2118:48: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
if (iCheckSlowCoordTraversal != -1 && iCheckSlowCoordTraversal < position[1]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nucleotide_indel2dp.cc: In function 'Algebra<BFloatMethods> BackwardBaumWelchBanding(NucleotideIndel2AlignWithBandingBaumWelch&, NucleotideIndel2AlignWithBandingDPTable*, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
nucleotide_indel2dp.cc:1813:48: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
if (iCheckSlowCoordTraversal != -1 && iCheckSlowCoordTraversal < position[1]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o nucleotidedp.o nucleotidedp.cc
nucleotidedp.cc: In function 'Algebra<BFloatMethods> Forward(NucleotideAlignDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&)':
nucleotidedp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
int iPrevSlowCoord;
^~~~~~~~~~~~~~
nucleotidedp.cc: In function 'Algebra<BFloatMethods> Backward(NucleotideAlignDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&)':
nucleotidedp.cc:1166:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
int iPrevSlowCoord;
^~~~~~~~~~~~~~
nucleotidedp.cc: In function 'Algebra<BFloatMethods> ForwardBanding(NucleotideAlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
nucleotidedp.cc:1352:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
int iPrevSlowCoord;
^~~~~~~~~~~~~~
nucleotidedp.cc: In function 'Algebra<BFloatMethods> BackwardBanding(NucleotideAlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
nucleotidedp.cc:1819:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
int iPrevSlowCoord;
^~~~~~~~~~~~~~
nucleotidedp.cc: In function 'Algebra<BFloatMethods> ForwardBanding(NucleotideAlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
nucleotidedp.cc:1423:17: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
if (iLastSlowCoord > position[1]) {
^~
nucleotidedp.cc: In function 'Algebra<BFloatMethods> BackwardBanding(NucleotideAlignWithBandingDPTable**, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
nucleotidedp.cc:1888:48: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
if (iCheckSlowCoordTraversal != -1 && iCheckSlowCoordTraversal < position[1]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nucleotidedp.cc: In function 'Algebra<BFloatMethods> BackwardBaumWelchBanding(NucleotideAlignWithBandingBaumWelch&, NucleotideAlignWithBandingDPTable*, const string&, const string&, const std::vector<double>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, int)':
nucleotidedp.cc:1643:48: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
if (iCheckSlowCoordTraversal != -1 && iCheckSlowCoordTraversal < position[1]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o sequence_pair_selector.o sequence_pair_selector.cc
rm -f libfsa.a
ar cru libfsa.a algebras.o aminoacid_indel2dp.o aminoaciddp.o anchors.o constraints.o fsa.o model.o nucleotide_indel2dp.o nucleotidedp.o sequence_pair_selector.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libfsa.a
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/fsa'
Making all in src/annealing
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/annealing'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o alignment_DAG.o alignment_DAG.cc
In file included from ../../src/annealing/alignment_DAG.h:58:0,
from alignment_DAG.cc:12:
../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)':
../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable]
int yprev = -1; // the previous y-coordinate
^~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o dotplot.o dotplot.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o tree_weights.o tree_weights.cc
rm -f libannealing.a
ar cru libannealing.a alignment_DAG.o dotplot.o tree_weights.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libannealing.a
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/annealing'
Making all in src/main
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/main'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o main.o main.cc
In file included from /usr/include/c++/6/ext/hash_map:60:0,
from ../../src/fsa/dptables.h:43,
from ../../src/fsa/mybanding.h:25,
from ../../src/fsa/model.h:24,
from ../../src/fsa/anchors.h:20,
from ../../src/fsa/fsa.h:71,
from main.cc:8:
/usr/include/c++/6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
#warning \
^~~~~~~
In file included from ../../src/fsa/anchors.h:17:0,
from ../../src/fsa/fsa.h:71,
from main.cc:8:
../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)':
../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable]
int yprev = -1; // the previous y-coordinate
^~~~~
g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o fsa main.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o gapcleaner.o gapcleaner.cc
In file included from ../../src/annealing/alignment_DAG.h:58:0,
from gapcleaner.cc:11:
../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)':
../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable]
int yprev = -1; // the previous y-coordinate
^~~~~
g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o gapcleaner gapcleaner.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o isect_mercator_alignment_gff.o isect_mercator_alignment_gff.cc
g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o isect_mercator_alignment_gff isect_mercator_alignment_gff.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o map_coords.o map_coords.cc
g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o map_coords map_coords.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o map_gff_coords.o map_gff_coords.cc
g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o map_gff_coords map_gff_coords.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o percentid.o percentid.cc
g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o percentid percentid.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o prot2codon.o prot2codon.cc
g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o prot2codon prot2codon.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o slice_fasta.o slice_fasta.cc
g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o slice_fasta slice_fasta.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o slice_fasta_gff.o slice_fasta_gff.cc
g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o slice_fasta_gff slice_fasta_gff.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o slice_mercator_alignment.o slice_mercator_alignment.cc
g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o slice_mercator_alignment slice_mercator_alignment.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o translate.o translate.cc
g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o translate translate.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/main'
Making all in perl
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/perl'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/perl'
Making all in examples
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/examples'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/examples'
Making all in html
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/html'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/html'
Making all in tests
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/tests'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/tests'
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg'
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg'
echo "Tests seem to miss some files:"
Tests seem to miss some files:
echo "make[4]: *** No rule to make target 'apps/isect_d.unmappable.bash', needed by 'apps/isect_d.unmappable.bash.log'. Stop."
make[4]: *** No rule to make target 'apps/isect_d.unmappable.bash', needed by 'apps/isect_d.unmappable.bash.log'. Stop.
make[1]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg'
# found automatically: --with-mummer=/usr/bin/mummer --with-exonerate=/usr/bin/exonerate
fakeroot debian/rules binary-arch
dh binary-arch --with autoreconf
dh_testroot -a
dh_prep -a
dh_auto_install -a
make -j1 install DESTDIR=/<<BUILDDIR>>/fsa-1.15.9\+dfsg/debian/fsa AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg'
Making install in src/util
make[2]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/util'
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/util'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/util'
make[2]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/util'
Making install in src/math
make[2]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/math'
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/math'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/math'
make[2]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/math'
Making install in src/seq
make[2]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/seq'
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/seq'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/seq'
make[2]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/seq'
Making install in src/manager
make[2]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/manager'
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/manager'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/manager'
make[2]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/manager'
Making install in src/fsa
make[2]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/fsa'
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/fsa'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/fsa'
make[2]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/fsa'
Making install in src/annealing
make[2]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/annealing'
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/annealing'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/annealing'
make[2]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/annealing'
Making install in src/main
make[2]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/main'
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/main'
/bin/mkdir -p '/<<BUILDDIR>>/fsa-1.15.9+dfsg/debian/fsa/usr/bin'
/usr/bin/install -c fsa gapcleaner isect_mercator_alignment_gff map_coords map_gff_coords percentid prot2codon slice_fasta slice_fasta_gff slice_mercator_alignment translate '/<<BUILDDIR>>/fsa-1.15.9+dfsg/debian/fsa/usr/bin'
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/main'
make[2]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/main'
Making install in perl
make[2]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/perl'
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/perl'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/perl'
make[2]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/perl'
Making install in examples
make[2]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/examples'
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/examples'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/examples'
make[2]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/examples'
Making install in html
make[2]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/html'
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/html'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/html'
make[2]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/html'
Making install in tests
make[2]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/tests'
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/tests'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/tests'
make[2]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/tests'
make[2]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg'
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg'
dh_install
mv /<<BUILDDIR>>/fsa-1.15.9+dfsg/debian/fsa/usr/bin/translate /<<BUILDDIR>>/fsa-1.15.9+dfsg/debian/fsa/usr/bin/fsa-translate
make[1]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg'
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/fsa/usr/bin/slice_fasta contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/fsa/usr/bin/prot2codon contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/fsa/usr/bin/percentid contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/fsa/usr/bin/map_gff_coords contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/fsa/usr/bin/isect_mercator_alignment_gff contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/fsa/usr/bin/fsa-translate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/fsa/usr/bin/slice_fasta_gff contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/fsa/usr/bin/gapcleaner contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/fsa/usr/bin/fsa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/fsa/usr/bin/map_coords contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/fsa/usr/bin/slice_mercator_alignment 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/fsa/usr/bin/slice_fasta debian/fsa/usr/bin/prot2codon debian/fsa/usr/bin/percentid debian/fsa/usr/bin/map_gff_coords debian/fsa/usr/bin/isect_mercator_alignment_gff debian/fsa/usr/bin/fsa-translate debian/fsa/usr/bin/slice_fasta_gff debian/fsa/usr/bin/gapcleaner debian/fsa/usr/bin/fsa debian/fsa/usr/bin/map_coords debian/fsa/usr/bin/slice_mercator_alignment were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'fsa-dbgsym' in '../fsa-dbgsym_1.15.9+dfsg-3_armhf.deb'.
dpkg-deb: building package 'fsa' in '../fsa_1.15.9+dfsg-3_armhf.deb'.
# found automatically: --with-mummer=/usr/bin/mummer --with-exonerate=/usr/bin/exonerate
dpkg-genbuildinfo --build=any
dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../fsa_1.15.9+dfsg-3_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build fsa-1.15.9+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2016-12-27T05:29:38Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
fsa_1.15.9+dfsg-3_armhf.changes:
--------------------------------
Format: 1.8
Date: Fri, 16 Dec 2016 16:41:29 +0000
Source: fsa
Binary: fsa
Architecture: armhf
Version: 1.15.9+dfsg-3
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
fsa - Fast Statistical Alignment of protein, RNA or DNA sequences
Closes: 848328
Changes:
fsa (1.15.9+dfsg-3) unstable; urgency=medium
.
* Team upload.
* Add autopkgtests.
Closes: #848328
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Checksums-Sha256:
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Files:
4d9815e1d2a730547fab7cf2b87eff18 13373084 debug extra fsa-dbgsym_1.15.9+dfsg-3_armhf.deb
c3adb7f8354196af22ed85334f52e7c3 4579 science optional fsa_1.15.9+dfsg-3_armhf.buildinfo
08ba3a5dd5360e3344b48849f63508ea 587954 science optional fsa_1.15.9+dfsg-3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
fsa-dbgsym_1.15.9+dfsg-3_armhf.deb
----------------------------------
new debian package, version 2.0.
size 13373084 bytes: control archive=1031 bytes.
813 bytes, 13 lines control
1166 bytes, 11 lines md5sums
Package: fsa-dbgsym
Source: fsa
Version: 1.15.9+dfsg-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 13664
Depends: fsa (= 1.15.9+dfsg-3)
Section: debug
Priority: extra
Homepage: http://fsa.sourceforge.net/
Description: Debug symbols for fsa
Auto-Built-Package: debug-symbols
Build-Ids: 0bed4caaa02f93592babbf1a183df33e4d434edc 165cb8b4b04c787afe46023e1043c09780f796f1 2af8042fa96be42aead83fc9966472a1e3140936 2cd38c7b740b2740edd1d9de594dcb4cda572957 7fcc5f79bb1e35183179d80d4d05e4f7e41f2882 a70485d0c1c2e9e8d0ebfe1bc211a0487c187d9c b0fd4fc0c382bbabd75cc1fcd03213f6a0541d74 be667406cce35136d3d56a2d5152b297a9631823 cb69c71731d3ac3d70f1492785b05943d89d4707 ddc548f7ba5dd6db134f95b00a57126405abf376 e840b2e8591787f351683e5db63a21180300ed66
drwxr-xr-x root/root 0 2016-12-16 16:41 ./
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/debug/.build-id/0b/
-rw-r--r-- root/root 642880 2016-12-16 16:41 ./usr/lib/debug/.build-id/0b/ed4caaa02f93592babbf1a183df33e4d434edc.debug
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/debug/.build-id/16/
-rw-r--r-- root/root 1235820 2016-12-16 16:41 ./usr/lib/debug/.build-id/16/5cb8b4b04c787afe46023e1043c09780f796f1.debug
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/debug/.build-id/2a/
-rw-r--r-- root/root 657760 2016-12-16 16:41 ./usr/lib/debug/.build-id/2a/f8042fa96be42aead83fc9966472a1e3140936.debug
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/debug/.build-id/2c/
-rw-r--r-- root/root 1619956 2016-12-16 16:41 ./usr/lib/debug/.build-id/2c/d38c7b740b2740edd1d9de594dcb4cda572957.debug
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/debug/.build-id/7f/
-rw-r--r-- root/root 1226224 2016-12-16 16:41 ./usr/lib/debug/.build-id/7f/cc5f79bb1e35183179d80d4d05e4f7e41f2882.debug
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/debug/.build-id/a7/
-rw-r--r-- root/root 1203272 2016-12-16 16:41 ./usr/lib/debug/.build-id/a7/0485d0c1c2e9e8d0ebfe1bc211a0487c187d9c.debug
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/debug/.build-id/b0/
-rw-r--r-- root/root 884100 2016-12-16 16:41 ./usr/lib/debug/.build-id/b0/fd4fc0c382bbabd75cc1fcd03213f6a0541d74.debug
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/debug/.build-id/be/
-rw-r--r-- root/root 663216 2016-12-16 16:41 ./usr/lib/debug/.build-id/be/667406cce35136d3d56a2d5152b297a9631823.debug
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/debug/.build-id/cb/
-rw-r--r-- root/root 666404 2016-12-16 16:41 ./usr/lib/debug/.build-id/cb/69c71731d3ac3d70f1492785b05943d89d4707.debug
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/debug/.build-id/dd/
-rw-r--r-- root/root 3944516 2016-12-16 16:41 ./usr/lib/debug/.build-id/dd/c548f7ba5dd6db134f95b00a57126405abf376.debug
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/debug/.build-id/e8/
-rw-r--r-- root/root 1222036 2016-12-16 16:41 ./usr/lib/debug/.build-id/e8/40b2e8591787f351683e5db63a21180300ed66.debug
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/share/
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-12-16 16:41 ./usr/share/doc/fsa-dbgsym -> fsa
fsa_1.15.9+dfsg-3_armhf.deb
---------------------------
new debian package, version 2.0.
size 587954 bytes: control archive=2749 bytes.
2335 bytes, 40 lines control
3531 bytes, 49 lines md5sums
Package: fsa
Version: 1.15.9+dfsg-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2818
Depends: libc6 (>= 2.15), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), mummer, exonerate
Recommends: med-config (>= 2.1)
Section: science
Priority: optional
Homepage: http://fsa.sourceforge.net/
Description: Fast Statistical Alignment of protein, RNA or DNA sequences
FSA is a probabilistic multiple sequence alignment algorithm which uses
a "distance-based" approach to aligning homologous protein, RNA or DNA
sequences. Much as distance-based phylogenetic reconstruction methods
like Neighbor-Joining build a phylogeny using only pairwise divergence
estimates, FSA builds a multiple alignment using only pairwise
estimations of homology. This is made possible by the sequence annealing
technique for constructing a multiple alignment from pairwise
comparisons, developed by Ariel Schwartz.
.
FSA brings the high accuracies previously available only for
small-scale analyses of proteins or RNAs to large-scale problems such as
aligning thousands of sequences or megabase-long sequences. FSA
introduces several novel methods for constructing better alignments:
* FSA uses machine-learning techniques to estimate gap and
substitution parameters on the fly for each set of input sequences.
This "query-specific learning" alignment method makes FSA very robust:
it can produce superior alignments of sets of homologous sequences
which are subject to very different evolutionary constraints.
* FSA is capable of aligning hundreds or even thousands of sequences
using a randomized inference algorithm to reduce the computational
cost of multiple alignment. This randomized inference can be over ten
times faster than a direct approach with little loss of accuracy.
* FSA can quickly align very long sequences using the "anchor
annealing" technique for resolving anchors and projecting them with
transitive anchoring. It then stitches together the alignment between
the anchors using the methods described above.
* The included GUI, MAD (Multiple Alignment Display), can display the
intermediate alignments produced by FSA, where each character is
colored according to the probability that it is correctly aligned
drwxr-xr-x root/root 0 2016-12-16 16:41 ./
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/bin/
-rwxr-xr-x root/root 911056 2016-12-16 16:41 ./usr/bin/fsa
-rwxr-xr-x root/root 108280 2016-12-16 16:41 ./usr/bin/fsa-translate
-rwxr-xr-x root/root 276224 2016-12-16 16:41 ./usr/bin/gapcleaner
-rwxr-xr-x root/root 210808 2016-12-16 16:41 ./usr/bin/isect_mercator_alignment_gff
-rwxr-xr-x root/root 210760 2016-12-16 16:41 ./usr/bin/map_coords
-rwxr-xr-x root/root 210808 2016-12-16 16:41 ./usr/bin/map_gff_coords
-rwxr-xr-x root/root 108280 2016-12-16 16:41 ./usr/bin/percentid
-rwxr-xr-x root/root 108280 2016-12-16 16:41 ./usr/bin/prot2codon
-rwxr-xr-x root/root 112376 2016-12-16 16:41 ./usr/bin/slice_fasta
-rwxr-xr-x root/root 157448 2016-12-16 16:41 ./usr/bin/slice_fasta_gff
-rwxr-xr-x root/root 210808 2016-12-16 16:41 ./usr/bin/slice_mercator_alignment
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/debian-med/
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/debian-med/bin/
lrwxrwxrwx root/root 0 2016-12-16 16:41 ./usr/lib/debian-med/bin/tranlate -> ../../../bin/fsa-translate
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/debian-med/share/
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/debian-med/share/man/
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/lib/debian-med/share/man/man1/
lrwxrwxrwx root/root 0 2016-12-16 16:41 ./usr/lib/debian-med/share/man/man1/translate.1.gz -> ../../../../../share/man/man1/fsa-translate.1.gz
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/share/
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/share/doc/fsa/
-rw-r--r-- root/root 24437 2016-12-16 16:41 ./usr/share/doc/fsa/FAQ.html
-rw-r--r-- root/root 5889 2014-05-16 17:25 ./usr/share/doc/fsa/README.gz
-rw-r--r-- root/root 334 2016-12-16 16:41 ./usr/share/doc/fsa/changelog.Debian.gz
-rw-r--r-- root/root 3602 2016-12-16 16:41 ./usr/share/doc/fsa/copyright
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/share/doc/fsa/examples/
-rw-r--r-- root/root 1244 2012-03-22 17:09 ./usr/share/doc/fsa/examples/README
-rw-r--r-- root/root 1505 2012-03-22 17:09 ./usr/share/doc/fsa/examples/RV12.BBS12030.fasta
-rw-r--r-- root/root 9906 2012-03-22 17:09 ./usr/share/doc/fsa/examples/RV12.BBS12030.fasta.gui.gz
-rw-r--r-- root/root 79537 2012-03-22 17:09 ./usr/share/doc/fsa/examples/RV12.BBS12030.fasta.probs.gz
-rw-r--r-- root/root 1547 2012-03-22 17:09 ./usr/share/doc/fsa/examples/RV12.BBS12030.mfa
-rw-r--r-- root/root 1546 2012-03-22 17:09 ./usr/share/doc/fsa/examples/RV12.BBS12030.reference.mfa
-rw-r--r-- root/root 1543 2012-03-22 17:09 ./usr/share/doc/fsa/examples/RV12.BBS12030.reference.stock
-rw-r--r-- root/root 1876 2012-03-22 17:09 ./usr/share/doc/fsa/examples/RV12.BBS12030.stock
-rw-r--r-- root/root 715 2012-03-22 17:09 ./usr/share/doc/fsa/examples/U5.aln1.fasta
-rw-r--r-- root/root 3894 2012-03-22 17:09 ./usr/share/doc/fsa/examples/U5.aln1.fasta.gui.gz
-rw-r--r-- root/root 40577 2012-03-22 17:09 ./usr/share/doc/fsa/examples/U5.aln1.fasta.probs.gz
-rw-r--r-- root/root 800 2012-03-22 17:09 ./usr/share/doc/fsa/examples/U5.aln1.mfa
-rw-r--r-- root/root 774 2012-03-22 17:09 ./usr/share/doc/fsa/examples/U5.aln1.reference.mfa
-rw-r--r-- root/root 1812 2012-03-22 17:09 ./usr/share/doc/fsa/examples/U5.aln1.reference.stock
-rw-r--r-- root/root 1025 2012-03-22 17:09 ./usr/share/doc/fsa/examples/U5.aln1.stock
-rw-r--r-- root/root 471 2012-03-22 17:09 ./usr/share/doc/fsa/examples/tRNA.aln1.fasta
-rw-r--r-- root/root 2400 2012-03-22 17:09 ./usr/share/doc/fsa/examples/tRNA.aln1.fasta.gui.gz
-rw-r--r-- root/root 24959 2012-03-22 17:09 ./usr/share/doc/fsa/examples/tRNA.aln1.fasta.probs.gz
-rw-r--r-- root/root 488 2012-03-22 17:09 ./usr/share/doc/fsa/examples/tRNA.aln1.mfa
-rw-r--r-- root/root 492 2012-03-22 17:09 ./usr/share/doc/fsa/examples/tRNA.aln1.reference.mfa
-rw-r--r-- root/root 1185 2012-03-22 17:09 ./usr/share/doc/fsa/examples/tRNA.aln1.reference.stock
-rw-r--r-- root/root 639 2012-03-22 17:09 ./usr/share/doc/fsa/examples/tRNA.aln1.stock
-rw-r--r-- root/root 266 2012-03-22 17:09 ./usr/share/doc/fsa/pretty.css
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/share/man/
drwxr-xr-x root/root 0 2016-12-16 16:41 ./usr/share/man/man1/
-rw-r--r-- root/root 402 2016-12-16 16:41 ./usr/share/man/man1/fsa-translate.1.gz
-rw-r--r-- root/root 393 2016-12-16 16:41 ./usr/share/man/man1/fsa.1.gz
-rw-r--r-- root/root 467 2016-12-16 16:41 ./usr/share/man/man1/gapcleaner.1.gz
-rw-r--r-- root/root 1077 2016-12-16 16:41 ./usr/share/man/man1/isect_mercator_alignment_gff.1.gz
-rw-r--r-- root/root 695 2016-12-16 16:41 ./usr/share/man/man1/map_coords.1.gz
-rw-r--r-- root/root 1074 2016-12-16 16:41 ./usr/share/man/man1/map_gff_coords.1.gz
-rw-r--r-- root/root 378 2016-12-16 16:41 ./usr/share/man/man1/percentid.1.gz
-rw-r--r-- root/root 411 2016-12-16 16:41 ./usr/share/man/man1/prot2codon.1.gz
-rw-r--r-- root/root 443 2016-12-16 16:41 ./usr/share/man/man1/slice_fasta.1.gz
-rw-r--r-- root/root 533 2016-12-16 16:41 ./usr/share/man/man1/slice_fasta_gff.1.gz
-rw-r--r-- root/root 870 2016-12-16 16:41 ./usr/share/man/man1/slice_mercator_alignment.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 137136
Build-Time: 1164
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 316
Job: fsa_1.15.9+dfsg-3
Machine Architecture: armhf
Package: fsa
Package-Time: 1526
Source-Version: 1.15.9+dfsg-3
Space: 137136
Status: successful
Version: 1.15.9+dfsg-3
--------------------------------------------------------------------------------
Finished at 2016-12-27T05:29:38Z
Build needed 00:25:26, 137136k disc space