fsa →
1.15.9+dfsg-4 →
armhf → 2018-07-21 05:18:28
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| fsa 1.15.9+dfsg-4 (armhf) Sat, 21 Jul 2018 05:00:48 +0000 |
+==============================================================================+
Package: fsa
Version: 1.15.9+dfsg-4
Source Version: 1.15.9+dfsg-4
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-6ee890f3-50d9-4b44-9e19-4b11cb3fbde9' 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 [10.9 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.7 MB]
Fetched 23.6 MB in 27s (859 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://salsa.debian.org/med-team/fsa.git
Please use:
git clone https://salsa.debian.org/med-team/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 buster-staging/main fsa 1.15.9+dfsg-4 (dsc) [1966 B]
Get:2 http://172.17.0.1/private buster-staging/main fsa 1.15.9+dfsg-4 (tar) [559 kB]
Get:3 http://172.17.0.1/private buster-staging/main fsa 1.15.9+dfsg-4 (diff) [13.1 kB]
Fetched 574 kB in 0s (2890 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/fsa-XmUzzC/fsa-1.15.9+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/fsa-XmUzzC' 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-zHTkkM/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-zHTkkM/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-zHTkkM/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-zHTkkM/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-zHTkkM/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-zHTkkM/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-zHTkkM/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-zHTkkM/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-zHTkkM/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (3224 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-zHTkkM/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-zHTkkM/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 47 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-zHTkkM/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15545 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 (>= 11~), mummer, exonerate, help2man
Filtered Build-Depends: debhelper (>= 11~), mummer, exonerate, help2man
dpkg-deb: building package 'sbuild-build-depends-fsa-dummy' in '/<<BUILDDIR>>/resolver-zHTkkM/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-zHTkkM/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-zHTkkM/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-zHTkkM/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-zHTkkM/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-zHTkkM/apt_archive ./ Sources [503 B]
Get:5 copy:/<<BUILDDIR>>/resolver-zHTkkM/apt_archive ./ Packages [585 B]
Fetched 2421 B in 1s (3733 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-zHTkkM/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-zHTkkM/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:
ca-certificates e2fsprogs-l10n libsasl2-modules libssl1.1 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 exonerate file gawk gettext
gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbsd0
libcroco3 libelf1 libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0
libgraphite2-3 libharfbuzz0b libicu-le-hb0 libicu60 liblocale-gettext-perl
libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool
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 m4-doc apparmor less
www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs 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 exonerate file gawk gettext
gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbsd0
libcroco3 libelf1 libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0
libgraphite2-3 libharfbuzz0b libicu-le-hb0 libicu60 liblocale-gettext-perl
libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool
libxml2 m4 man-db mummer po-debconf sbuild-build-depends-fsa-dummy
0 upgraded, 41 newly installed, 0 to remove and 47 not upgraded.
Need to get 23.7 MB of archives.
After this operation, 80.9 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-zHTkkM/apt_archive ./ sbuild-build-depends-fsa-dummy 0.invalid.0 [872 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 0.9.1-1 [104 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 man-db armhf 2.8.3-2 [1146 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf gawk armhf 1:4.1.4+dfsg-1+b1 [506 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.33-3 [234 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.33-3 [106 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.33-3 [64.7 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.042-1 [20.1 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.042-1 [12.1 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libfreetype6 armhf 2.8.1-2 [402 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.11-2 [73.5 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.8.2-2 [832 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-2 [132 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.5 [981 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf exonerate armhf 2.4.0-3 [1403 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf help2man armhf 1.47.6 [169 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf mummer armhf 3.23+dfsg-4 [767 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Processing triggers for libc-bin (2.27-3+rpi1) ...
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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
Setting up autopoint (0.19.8.1-6) ...
Setting up libfile-stripnondeterminism-perl (0.042-1) ...
Setting up mummer (3.23+dfsg-4) ...
Setting up libharfbuzz0b:armhf (1.8.2-2) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.33-3) ...
Setting up automake (1:1.15.1-3.1) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up help2man (1.47.6) ...
Setting up man-db (2.8.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2.1) ...
Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ...
Setting up dh-strip-nondeterminism (0.042-1) ...
Setting up libicu60:armhf (60.2-6) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up gettext (0.19.8.1-6) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.20) ...
Setting up debhelper (11.3.5) ...
Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-fsa-dummy (0.invalid.0) ...
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_2.30-21+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-19 gcc-7_7.3.0-19 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-19 libstdc++6_8.1.0-8+rpi1 linux-libc-dev_4.16.12-1+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_4.4.18-3 binutils_2.30-21+rpi1 binutils-arm-linux-gnueabihf_2.30-21+rpi1 binutils-common_2.30-21+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32-0.1 build-essential_12.5 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.3.0-3+rpi1 cpp-7_7.3.0-19 dash_0.5.8-2.10 debconf_1.5.67 debhelper_11.3.5 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dirmngr_2.2.8-1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.2-1 e2fsprogs_1.44.2-1 e2fsprogs-l10n_1.44.2-1 exonerate_2.4.0-3 fakeroot_1.22-2 fdisk_2.32-0.1 file_1:5.33-3 findutils_4.6.0+git+20171230-2 g++_4:7.3.0-3+rpi1 g++-7_7.3.0-19 gawk_1:4.1.4+dfsg-1+b1 gcc_4:7.3.0-3+rpi1 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+b7 gcc-5-base_5.5.0-8 gcc-7_7.3.0-19 gcc-7-base_7.3.0-19 gcc-8-base_8.1.0-8+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gnupg_2.2.8-1 gnupg-agent_2.2.8-1 gnupg-l10n_2.2.8-1 gnupg-utils_2.2.8-1 gpg_2.2.8-1 gpg-agent_2.2.8-1 gpg-wks-client_2.2.8-1 gpg-wks-server_2.2.8-1 gpgconf_2.2.8-1 gpgsm_2.2.8-1 gpgv_2.2.8-1 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_7.3.0-19 libassuan0_2.5.1-2 libatomic1_8.1.0-8+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.30-21+rpi1 libblkid1_2.32-0.1 libbsd0_0.9.1-1 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_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-8+rpi1 libcilkrts5_7.3.0-19 libcom-err2_1.44.2-1 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_1.12.8-3 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.92-1+rpi1 libdrm2_2.4.92-1+rpi1 libelf1_0.170-0.5 libext2fs2_1.44.2-1 libfakeroot_1.22-2 libfdisk1_2.32-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libfreetype6_2.8.1-2 libgcc-7-dev_7.3.0-19 libgcc1_1:8.1.0-8+rpi1 libgcrypt20_1.8.3-1 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_8.1.0-8+rpi1 libgpg-error0_1.31-1 libgraphite2-3_1.3.11-2 libharfbuzz0b_1.8.2-2 libhogweed4_3.4-1 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl19_0.19-1 libjson-c3_0.12.1-1.3 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-3 libmagic1_1:5.33-3 libmount1_2.32-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1+20180210-4 libncurses6_6.1+20180210-4 libncursesw5_6.1+20180210-4 libncursesw6_6.1+20180210-4 libnettle6_3.4-1 libnpth0_1.5-4 libp11-kit0_0.23.12-2 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_5.26.2-6 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpng16-16_1.6.34-1 libprocps7_2:3.3.15-2 libreadline7_7.0-5 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_2.3.3-2 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32-0.1 libsqlite3-0_3.24.0-1 libss2_1.44.2-1 libssl1.1_1.1.0h-4 libstdc++-7-dev_7.3.0-19 libstdc++6_8.1.0-8+rpi1 libsystemd0_238-4 libtasn1-6_4.13-3 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-4 libtinfo6_6.1+20180210-4 libtool_2.4.6-2.1 libubsan0_7.3.0-19 libudev1_238-4 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32-0.1 libxml2_2.9.4+dfsg1-7 libzstd1_1.3.4+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.16.12-1+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 mount_2.32-0.1 multiarch-support_2.27-3+rpi1 mummer_3.23+dfsg-4 nano_2.9.8-1 ncurses-base_6.1+20180210-4 ncurses-bin_6.1+20180210-4 netbase_5.4 openssl_1.1.0h-4 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-6 perl-base_5.26.2-6 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-6 pinentry-curses_1.1.0-1 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-fsa-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-4 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 udev_238-4 util-linux_2.32-0.1 xz-utils_5.2.2-1.3 zlib1g_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 Jul 18 19:10:15 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 ./fsa_1.15.9+dfsg-4.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-4.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=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-6ee890f3-50d9-4b44-9e19-4b11cb3fbde9
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-4
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
dh_clean
# found automatically: --with-mummer=/usr/bin/mummer --with-exonerate=/usr/bin/exonerate
debian/rules build-arch
dh build-arch
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 --runstatedir=/run --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 7.3.0-19) 7.3.0
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 -j4
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
In file included from /usr/include/c++/7/vector:69:0,
from ../../src/seq/sequence.h:16,
from ../../src/seq/alignment.h:16,
from ../../src/seq/mercator.h:13,
from mercator.cc:11:
/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 'std::vector<fsa::Genomic_interval> fsa::Mercator_map::choose_random_intervals(const string&, size_t, size_t) const':
/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++ -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
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/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
^~~~~
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
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
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
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
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;
^~~~~~~~~~~~~~
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;
^~~~~~~~~~~~~~
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
^~~~~
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]) {
^~
anchors.cc: In member function 'fsa::Anchors fsa::Exonerate_adapter::call_exonerate(const string&, const string&, int) const':
anchors.cc:863:13: 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:864:13: 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:1100:13: 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:1101:13: 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 fsa.o fsa.cc
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]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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]
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]) {
^~
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
^~~~~
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]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from ../../src/seq/sequence.h:16,
from ../../src/seq/alignment.h:16,
from anchors.cc:15:
/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 fsa::Anchor&}; _Tp = fsa::Anchor; _Alloc = std::allocator<fsa::Anchor>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<fsa::Anchor>::iterator {aka __gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../../src/seq/sequence.h:16,
from ../../src/seq/alignment.h:16,
from anchors.cc:15:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator<fsa::Anchor>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static fsa::Anchors fsa::Anchors::convert_constraints_to_anchors(const fsa::Constraints&, const fsa::Sequence&, const fsa::Sequence&, bool)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' 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<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'fsa::Anchors fsa::Cabbage_adapter::get_candidate_anchors() const':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' 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<fsa::Anchor*, std::vector<fsa::Anchor> >' 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<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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
/usr/include/c++/7/bits/stl_vector.h: In member function 'fsa::Anchors fsa::Mummer_adapter::get_candidate_anchors(size_t) const':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from ../../src/seq/sequence.h:16,
from ../../src/seq/alignment.h:16,
from anchors.cc:15:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const fsa::Anchor*, std::vector<fsa::Anchor> >; _Tp = fsa::Anchor; _Alloc = std::allocator<fsa::Anchor>]':
/usr/include/c++/7/bits/vector.tcc:630:7: note: parameter passing for argument of type 'std::vector<fsa::Anchor>::iterator {aka __gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:630:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
/usr/include/c++/7/bits/vector.tcc:630:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
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
^~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >; _Tp = fsa::Anchor; _Alloc = std::allocator<fsa::Anchor>]':
/usr/include/c++/7/bits/vector.tcc:278:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:278:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from ../../src/seq/sequence.h:16,
from ../../src/seq/alignment.h:16,
from anchors.cc:15:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void fsa::Anchors::remove_overlaps(size_t, unsigned int)':
/usr/include/c++/7/bits/stl_vector.h:1369:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
{ _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'void fsa::Anchors::enforce_immutable_unique()':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:1369:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
{ _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from anchors.cc:13:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const fsa::Anchor&, const fsa::Anchor&)>]':
/usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' 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<fsa::Anchor*, std::vector<fsa::Anchor> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const fsa::Anchor&, const fsa::Anchor&)>]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' 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<fsa::Anchor*, std::vector<fsa::Anchor> >' 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<fsa::Anchor*, std::vector<fsa::Anchor> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const fsa::Anchor&, const fsa::Anchor&)>]':
/usr/include/c++/7/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' 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<fsa::Anchor*, std::vector<fsa::Anchor> >' 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<fsa::Anchor*, std::vector<fsa::Anchor> >' 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<fsa::Anchor*, std::vector<fsa::Anchor> >' 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 anchors.cc:13:
/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<fsa::Anchor*, std::vector<fsa::Anchor> >; _Distance = int; _Tp = fsa::Anchor; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const fsa::Anchor&, const fsa::Anchor&)>]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from anchors.cc:13:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const fsa::Anchor&, const fsa::Anchor&)>]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' 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<fsa::Anchor*, std::vector<fsa::Anchor> >' 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<fsa::Anchor*, std::vector<fsa::Anchor> >' 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<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'bool fsa::Anchors::resolve_parallel(size_t, bool)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' 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<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../../src/seq/sequence.h:16,
from ../../src/seq/alignment.h:16,
from anchors.cc:15:
/usr/include/c++/7/bits/stl_vector.h:1369:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
{ _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from anchors.cc:13:
/usr/include/c++/7/bits/stl_algo.h: In member function 'void fsa::Anchors::remove_overlaps(size_t)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' 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<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' 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<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' 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<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' 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<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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
In file included from /usr/include/c++/7/vector:64:0,
from ../../src/seq/sequence.h:16,
from ../../src/seq/alignment.h:16,
from anchors.cc:15:
/usr/include/c++/7/bits/stl_vector.h: In member function 'const std::vector<fsa::Anchors> fsa::Anchor_resolver::get_resolved_anchors(const fsa::Tree_weights&, size_t, size_t, bool, bool, int, bool, bool, size_t, bool, std::__cxx11::string) const':
/usr/include/c++/7/bits/stl_vector.h:1406:19: note: parameter passing for argument of type 'std::vector<fsa::Anchor>::iterator {aka __gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >}' changed in GCC 7.1
_M_range_insert(__pos, __first, __last,
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
std::__iterator_category(__first));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:1406:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_vector.h:1406:19: note: parameter passing for argument of type 'std::vector<fsa::Anchor>::iterator {aka __gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >}' changed in GCC 7.1
_M_range_insert(__pos, __first, __last,
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
std::__iterator_category(__first));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:1406:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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;
^~~~~~~~~~~~~~
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;
^~~~~~~~~~~~~~
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
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]) {
^~
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]) {
^~
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]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/queue:62:0,
from sequence_pair_selector.cc:8:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >; _Distance = int; _Tp = std::pair<double, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<fsa::Util::Duple_less<double, unsigned int> >]':
/usr/include/c++/7/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >' changed in GCC 7.1
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/c++/7/queue:61,
from sequence_pair_selector.cc:8:
/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 = {std::pair<double, unsigned int>}; _Tp = std::pair<double, unsigned int>; _Alloc = std::allocator<std::pair<double, unsigned int> >]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<std::pair<double, unsigned int> >::iterator {aka __gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void fsa::Sequence_pair_selector::choose_kmer_similarity(size_t)':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from ../../src/util/misc.h:17,
from ../../src/math/mst.h:11,
from fsa.cc:9:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:278:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:278:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from ../../src/util/misc.h:17,
from ../../src/math/mst.h:11,
from fsa.cc:9:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void fsa::FSA::init_subst_params(fsa::Params&, const std::vector<double>&, unsigned int, double)':
/usr/include/c++/7/bits/stl_vector.h:1369:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
{ _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:1369:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
{ _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
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
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
^~~~~
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
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
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++ -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
In file included from /usr/include/c++/7/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++/7/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/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
^~~~~
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++ -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++ -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++ -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++ -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++ -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++ -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++ -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 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++ -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++ -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++ -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++ -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++ -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++ -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++ -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++ -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++ -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++ -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'
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Making all in html
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Making all in tests
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/tests'
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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'
create-stamp debian/debhelper-build-stamp
# found automatically: --with-mummer=/usr/bin/mummer --with-exonerate=/usr/bin/exonerate
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
make -j4 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'
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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'
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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'
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Making install in src/manager
make[2]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/manager'
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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'.
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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'.
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make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/annealing'
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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'
make[3]: Nothing to be done for 'install-data-am'.
/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]: 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'
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Making install in examples
make[2]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/examples'
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Making install in html
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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'
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make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/tests'
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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_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
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: 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/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/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/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/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/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/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/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/gapcleaner 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_mercator_alignment debian/fsa/usr/bin/isect_mercator_alignment_gff debian/fsa/usr/bin/percentid debian/fsa/usr/bin/fsa debian/fsa/usr/bin/prot2codon debian/fsa/usr/bin/fsa-translate debian/fsa/usr/bin/slice_fasta_gff debian/fsa/usr/bin/slice_fasta debian/fsa/usr/bin/map_gff_coords debian/fsa/usr/bin/map_coords debian/fsa/usr/bin/gapcleaner 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 'fsa-dbgsym' in '../fsa-dbgsym_1.15.9+dfsg-4_armhf.deb'.
dpkg-deb: building package 'fsa' in '../fsa_1.15.9+dfsg-4_armhf.deb'.
# found automatically: --with-mummer=/usr/bin/mummer --with-exonerate=/usr/bin/exonerate
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../fsa_1.15.9+dfsg-4_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 2018-07-21T05:18:14Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
fsa_1.15.9+dfsg-4_armhf.changes:
--------------------------------
Format: 1.8
Date: Wed, 18 Jul 2018 21:07:06 +0200
Source: fsa
Binary: fsa
Architecture: armhf
Version: 1.15.9+dfsg-4
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
fsa - Fast Statistical Alignment of protein, RNA or DNA sequences
Changes:
fsa (1.15.9+dfsg-4) unstable; urgency=medium
.
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.5
* d/rules:
- Drop unneeded get-orig-source target
- Do not parse d/changelog
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a245159f65b6eb039e1a348f5e39d5b2715b782f 4778 fsa_1.15.9+dfsg-4_armhf.buildinfo
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Checksums-Sha256:
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607bf8861ad27ce423c9e9817a550f9db184e07957ac23ecf6743ff3d7dc79af 4778 fsa_1.15.9+dfsg-4_armhf.buildinfo
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Files:
9c4eccfa629b550d08b1a12cdca7980a 13449488 debug optional fsa-dbgsym_1.15.9+dfsg-4_armhf.deb
4fc7b7315b2f1ae5101510c357812af9 4778 science optional fsa_1.15.9+dfsg-4_armhf.buildinfo
c3f09f62efbfbac8188cd0ce89cfd9bc 577992 science optional fsa_1.15.9+dfsg-4_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
fsa-dbgsym_1.15.9+dfsg-4_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 13449488 bytes: control archive=1048 bytes.
778 bytes, 12 lines control
1166 bytes, 11 lines md5sums
Package: fsa-dbgsym
Source: fsa
Version: 1.15.9+dfsg-4
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 13821
Depends: fsa (= 1.15.9+dfsg-4)
Section: debug
Priority: optional
Description: debug symbols for fsa
Build-Ids: 147b6622adc3313b018d39d554622ffa31bff22d 2725cf359bcda160e07e0621397c3cf1b621f0e3 400c5b72ba2959ba3e0ff48da1be3227b390662c 5d6f6046f3e4c7b099bdd4a170fbcce39460a4eb 74c5c24a1806ca6d51166f14ba1b184dd689313b 7aa6689a381a7808c4e4257f92a9f16911139a1c 83586e3de86781260658f289fe73ab957d03e4ce 83e37c0df35aee0a09865a72ac8eea2ac0e07949 ae3ba16aebb8256e36168befe27c673c7d795700 ca1e0aa90a731f932e0542320fe6d74fa03b771a f7bd88de481c7cb6e4d2faa8933f3029bdd5aeed
drwxr-xr-x root/root 0 2018-07-18 19:07 ./
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/debug/.build-id/14/
-rw-r--r-- root/root 1248228 2018-07-18 19:07 ./usr/lib/debug/.build-id/14/7b6622adc3313b018d39d554622ffa31bff22d.debug
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/debug/.build-id/27/
-rw-r--r-- root/root 676232 2018-07-18 19:07 ./usr/lib/debug/.build-id/27/25cf359bcda160e07e0621397c3cf1b621f0e3.debug
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/debug/.build-id/40/
-rw-r--r-- root/root 1225800 2018-07-18 19:07 ./usr/lib/debug/.build-id/40/0c5b72ba2959ba3e0ff48da1be3227b390662c.debug
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/debug/.build-id/5d/
-rw-r--r-- root/root 1257520 2018-07-18 19:07 ./usr/lib/debug/.build-id/5d/6f6046f3e4c7b099bdd4a170fbcce39460a4eb.debug
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/debug/.build-id/74/
-rw-r--r-- root/root 653112 2018-07-18 19:07 ./usr/lib/debug/.build-id/74/c5c24a1806ca6d51166f14ba1b184dd689313b.debug
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/debug/.build-id/7a/
-rw-r--r-- root/root 3958220 2018-07-18 19:07 ./usr/lib/debug/.build-id/7a/a6689a381a7808c4e4257f92a9f16911139a1c.debug
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/debug/.build-id/83/
-rw-r--r-- root/root 1244904 2018-07-18 19:07 ./usr/lib/debug/.build-id/83/586e3de86781260658f289fe73ab957d03e4ce.debug
-rw-r--r-- root/root 668548 2018-07-18 19:07 ./usr/lib/debug/.build-id/83/e37c0df35aee0a09865a72ac8eea2ac0e07949.debug
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/debug/.build-id/ae/
-rw-r--r-- root/root 901084 2018-07-18 19:07 ./usr/lib/debug/.build-id/ae/3ba16aebb8256e36168befe27c673c7d795700.debug
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/debug/.build-id/ca/
-rw-r--r-- root/root 1621900 2018-07-18 19:07 ./usr/lib/debug/.build-id/ca/1e0aa90a731f932e0542320fe6d74fa03b771a.debug
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/debug/.build-id/f7/
-rw-r--r-- root/root 673188 2018-07-18 19:07 ./usr/lib/debug/.build-id/f7/bd88de481c7cb6e4d2faa8933f3029bdd5aeed.debug
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/share/
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-07-18 19:07 ./usr/share/doc/fsa-dbgsym -> fsa
fsa_1.15.9+dfsg-4_armhf.deb
---------------------------
new Debian package, version 2.0.
size 577992 bytes: control archive=2716 bytes.
2335 bytes, 40 lines control
3531 bytes, 49 lines md5sums
Package: fsa
Version: 1.15.9+dfsg-4
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 2018-07-18 19:07 ./
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/bin/
-rwxr-xr-x root/root 906968 2018-07-18 19:07 ./usr/bin/fsa
-rwxr-xr-x root/root 108288 2018-07-18 19:07 ./usr/bin/fsa-translate
-rwxr-xr-x root/root 276232 2018-07-18 19:07 ./usr/bin/gapcleaner
-rwxr-xr-x root/root 210816 2018-07-18 19:07 ./usr/bin/isect_mercator_alignment_gff
-rwxr-xr-x root/root 210768 2018-07-18 19:07 ./usr/bin/map_coords
-rwxr-xr-x root/root 210816 2018-07-18 19:07 ./usr/bin/map_gff_coords
-rwxr-xr-x root/root 108288 2018-07-18 19:07 ./usr/bin/percentid
-rwxr-xr-x root/root 108288 2018-07-18 19:07 ./usr/bin/prot2codon
-rwxr-xr-x root/root 112384 2018-07-18 19:07 ./usr/bin/slice_fasta
-rwxr-xr-x root/root 161552 2018-07-18 19:07 ./usr/bin/slice_fasta_gff
-rwxr-xr-x root/root 210816 2018-07-18 19:07 ./usr/bin/slice_mercator_alignment
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/debian-med/
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/debian-med/bin/
lrwxrwxrwx root/root 0 2018-07-18 19:07 ./usr/lib/debian-med/bin/tranlate -> ../../../bin/fsa-translate
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/debian-med/share/
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/debian-med/share/man/
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/lib/debian-med/share/man/man1/
lrwxrwxrwx root/root 0 2018-07-18 19:07 ./usr/lib/debian-med/share/man/man1/translate.1.gz -> ../../../../../share/man/man1/fsa-translate.1.gz
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/share/
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/share/doc/fsa/
-rw-r--r-- root/root 24437 2018-07-18 19:07 ./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 462 2018-07-18 19:07 ./usr/share/doc/fsa/changelog.Debian.gz
-rw-r--r-- root/root 3602 2018-07-18 19:07 ./usr/share/doc/fsa/copyright
drwxr-xr-x root/root 0 2018-07-18 19:07 ./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 2018-07-18 19:07 ./usr/share/man/
drwxr-xr-x root/root 0 2018-07-18 19:07 ./usr/share/man/man1/
-rw-r--r-- root/root 402 2018-07-18 19:07 ./usr/share/man/man1/fsa-translate.1.gz
-rw-r--r-- root/root 393 2018-07-18 19:07 ./usr/share/man/man1/fsa.1.gz
-rw-r--r-- root/root 467 2018-07-18 19:07 ./usr/share/man/man1/gapcleaner.1.gz
-rw-r--r-- root/root 1077 2018-07-18 19:07 ./usr/share/man/man1/isect_mercator_alignment_gff.1.gz
-rw-r--r-- root/root 695 2018-07-18 19:07 ./usr/share/man/man1/map_coords.1.gz
-rw-r--r-- root/root 1074 2018-07-18 19:07 ./usr/share/man/man1/map_gff_coords.1.gz
-rw-r--r-- root/root 378 2018-07-18 19:07 ./usr/share/man/man1/percentid.1.gz
-rw-r--r-- root/root 411 2018-07-18 19:07 ./usr/share/man/man1/prot2codon.1.gz
-rw-r--r-- root/root 443 2018-07-18 19:07 ./usr/share/man/man1/slice_fasta.1.gz
-rw-r--r-- root/root 533 2018-07-18 19:07 ./usr/share/man/man1/slice_fasta_gff.1.gz
-rw-r--r-- root/root 870 2018-07-18 19:07 ./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: 137936
Build-Time: 647
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 346
Job: fsa_1.15.9+dfsg-4
Machine Architecture: armhf
Package: fsa
Package-Time: 1046
Source-Version: 1.15.9+dfsg-4
Space: 137936
Status: successful
Version: 1.15.9+dfsg-4
--------------------------------------------------------------------------------
Finished at 2018-07-21T05:18:14Z
Build needed 00:17:26, 137936k disc space