fsa →
1.15.9+dfsg-6 →
armhf → 2020-11-18 05:29:36
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| fsa 1.15.9+dfsg-6 (armhf) Wed, 18 Nov 2020 05:11:00 +0000 |
+==============================================================================+
Package: fsa
Version: 1.15.9+dfsg-6
Source Version: 1.15.9+dfsg-6
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-e37a657d-347b-458f-8198-9ee460961b1c' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.9 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.7 MB in 27s (909 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: '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 bullseye-staging/main fsa 1.15.9+dfsg-6 (dsc) [1971 B]
Get:2 http://172.17.0.1/private bullseye-staging/main fsa 1.15.9+dfsg-6 (tar) [559 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main fsa 1.15.9+dfsg-6 (diff) [13.4 kB]
Fetched 574 kB in 0s (1393 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/fsa-98yGY2/fsa-1.15.9+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/fsa-98yGY2' 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-uuXLbl/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-uuXLbl/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-uuXLbl/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-uuXLbl/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-uuXLbl/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-uuXLbl/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-uuXLbl/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-uuXLbl/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2831 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
bsdextrautils krb5-locales libpam-cap netbase sensible-utils
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 30 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-uuXLbl/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 (23.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12732 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) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), mummer, exonerate, help2man
Filtered Build-Depends: debhelper-compat (= 13), mummer, exonerate, help2man
dpkg-deb: building package 'sbuild-build-depends-fsa-dummy' in '/<<BUILDDIR>>/resolver-uuXLbl/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-uuXLbl/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-uuXLbl/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-uuXLbl/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-uuXLbl/apt_archive ./ Sources [505 B]
Get:5 copy:/<<BUILDDIR>>/resolver-uuXLbl/apt_archive ./ Packages [587 B]
Fetched 2425 B in 1s (3223 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
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:
krb5-locales libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz exonerate file gawk gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libcroco3
libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0
libicu67 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1
libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
mummer po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc 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 debhelper dh-autoreconf
dh-strip-nondeterminism dwz exonerate file gawk gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libcroco3
libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0
libicu67 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1
libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
mummer po-debconf sbuild-build-depends-fsa-dummy
0 upgraded, 37 newly installed, 0 to remove and 30 not upgraded.
Need to get 21.1 MB of archives.
After this operation, 81.9 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-uuXLbl/apt_archive ./ sbuild-build-depends-fsa-dummy 0.invalid.0 [880 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf liblocale-gettext-perl armhf 1.07-4 [18.1 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf gawk armhf 1:5.0.1+dfsg-1 [540 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2.1 [188 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182-1 [162 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.2-1 [1176 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.2 [578 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf exonerate armhf 2.4.0-4 [1326 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf help2man armhf 1.47.16 [181 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf mummer armhf 3.23+dfsg-6 [621 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package liblocale-gettext-perl.
(Reading database ... 12732 files and directories currently installed.)
Preparing to unpack .../0-liblocale-gettext-perl_1.07-4_armhf.deb ...
Unpacking liblocale-gettext-perl (1.07-4) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../1-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
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Unpacking libpipeline1:armhf (1.5.3-1) ...
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Unpacking man-db (2.9.3-2) ...
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Unpacking libsigsegv2:armhf (2.12-2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Selecting previously unselected package gawk.
(Reading database ... 13281 files and directories currently installed.)
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Preparing to unpack .../05-m4_1.4.18-4_armhf.deb ...
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Unpacking gettext (0.19.8.1-10) ...
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Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libicu67:armhf (67.1-4) ...
Setting up libmagic-mgc (1:5.38-5) ...
Setting up gawk (1:5.0.1+dfsg-1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.66.2-1) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.2.1) ...
Setting up libmagic1:armhf (1:5.38-5) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up m4 (1.4.18-4) ...
Setting up file (1:5.38-5) ...
Setting up autotools-dev (20180224.1) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up autoconf (2.69-11.1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up mummer (3.23+dfsg-6) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libelf1:armhf (0.182-1) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.2) ...
Setting up exonerate (2.4.0-4) ...
Setting up liblocale-gettext-perl (1.07-4) ...
Setting up automake (1:1.16.2-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
Setting up libtool (2.4.6-14) ...
Setting up help2man (1.47.16) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-5) ...
Setting up gettext (0.19.8.1-10) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up po-debconf (1.0.21) ...
Setting up debhelper (13.2.1) ...
Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-fsa-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.1-2+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-13+rpi1 gcc-10_10.2.0-13+rpi1 libc6-dev_2.31-4+rpi1 libstdc++-10-dev_10.2.0-13+rpi1 libstdc++6_10.2.0-13+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.10 aptitude_0.8.13-2 aptitude-common_0.8.13-2 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1~rc1-2 binutils_2.35.1-2+rpi1 binutils-arm-linux-gnueabihf_2.35.1-2+rpi1 binutils-common_2.35.1-2+rpi1 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.0-1+rpi1 cpp-10_10.2.0-13+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 exonerate_2.4.0-4 fakeroot_1.25.3-1 fdisk_2.36-3 file_1:5.38-5 findutils_4.7.0-1 g++_4:10.2.0-1+rpi1 g++-10_10.2.0-13+rpi1 gawk_1:5.0.1+dfsg-1 gcc_4:10.2.0-1+rpi1 gcc-10_10.2.0-13+rpi1 gcc-10-base_10.2.0-13+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 help2man_1.47.16 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 krb5-locales_1.17-10 libacl1_2.2.53-8 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libasan6_10.2.0-13+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-13+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3.1 libaudit1_1:2.8.5-3.1 libbinutils_2.35.1-2+rpi1 libblkid1_2.36-3 libboost-iostreams1.71.0_1.71.0-7 libbz2-1.0_1.0.8-4 libc-bin_2.31-4+rpi1 libc-dev-bin_2.31-4+rpi1 libc6_2.31-4+rpi1 libc6-dev_2.31-4+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_10.2.0-13+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-2+rpi1 libctf0_2.35.1-2+rpi1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.254 libdebhelper-perl_13.2.1 libdpkg-perl_1.20.5+rpi1 libelf1_0.182-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1 libfdisk1_2.36-3 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-13+rpi1 libgcc-s1_10.2.0-13+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.2-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.15-4 libgomp1_10.2.0-13+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10+b3 libhogweed6_3.6-2 libicu67_67.1-4 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libk5crypto3_1.17-10+b3 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10+b3 libkrb5support0_1.17-10+b3 libksba8_1.4.0-2 libldap-2.4-2_2.4.53+dfsg-1+rpi1 libldap-common_2.4.53+dfsg-1+rpi1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-3 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20200918-1 libnettle8_3.6-2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.21-2 libpam-cap_1:2.44-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.3-1 libreadline8_8.0-4 librust-rand-core-dev_0.5.1-1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.4-1+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.4-2 libsigsegv2_2.12-2 libsmartcols1_2.36-3 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libstdc++-10-dev_10.2.0-13+rpi1 libstdc++6_10.2.0-13+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.4-1+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20200918-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-14 libubsan1_10.2.0-13+rpi1 libuchardet0_0.0.7-1 libudev1_246.4-1+rpi1 libunistring2_0.9.10-4 libuuid1_2.36-3 libxapian30_1.4.17-1 libxml2_2.9.10+dfsg-6.2 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36-3 mummer_3.23+dfsg-6 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 netbase_6.2 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-fsa-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-5 tar_1.30+dfsg-7 tzdata_2020d-1 util-linux_2.36-3 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.lbrlTpGL/trustedkeys.kbx': General error
gpgv: Signature made Sun Nov 15 17:07:02 2020 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-6.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-6.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-e37a657d-347b-458f-8198-9ee460961b1c
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-6
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_clean
# found automatically: --with-mummer=/usr/bin/mummer --with-exonerate=/usr/bin/exonerate
debian/rules binary-arch
dh binary-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-option-checking --disable-silent-rules --libdir=\${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 whether make supports the include directive... yes (GNU style)
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 10.2.0-13+rpi1) 10.2.0
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]
99 | SET_VERSION_INFO(*this);
| ^
In file included from opts_list.cc:2:
../../src/util/opts_list.h:146:153: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
146 | #define SET_VERSION_INFO(OPTS) (OPTS).version_info.clear(); (OPTS).version_info << PACKAGE_STRING << " (" << DART_DEBUG_MODE_STRING << ") compiled " << __DATE__ << " " << __TIME__ << "\n";
| ^~~~~~~~
opts_list.cc:99:3: note: in expansion of macro 'SET_VERSION_INFO'
99 | SET_VERSION_INFO(*this);
| ^~~~~~~~~~~~~~~~
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++/10/vector:72,
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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _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,
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]
241 | int yprev = -1; // the previous y-coordinate
| ^~~~~
In file included from ../../src/fsa/anchors.h:17,
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]
241 | 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
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]
768 | 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]
1320 | 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]
1568 | 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]
2189 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
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]
768 | 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]
1230 | 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]
1448 | 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]
1979 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
In file included from ../../src/fsa/anchors.h:17,
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]
241 | int yprev = -1; // the previous y-coordinate
| ^~~~~
anchors.cc: In member function 'fsa::Anchors fsa::Exonerate_adapter::call_exonerate(const string&, const string&, int) const':
anchors.cc:863:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
863 | 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]
864 | 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]
1100 | 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]
1101 | 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
fsa.cc:25:125: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
25 | INIT_CONSTRUCTED_OPTS_LIST (opts, -1, "[options] <sequence file(s)>", "Distance-based alignment of DNA, RNA and proteins.");
| ^
In file included from ../../src/fsa/fsa.h:66,
from fsa.cc:11:
../../src/util/opts_list.h:146:153: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
146 | #define SET_VERSION_INFO(OPTS) (OPTS).version_info.clear(); (OPTS).version_info << PACKAGE_STRING << " (" << DART_DEBUG_MODE_STRING << ") compiled " << __DATE__ << " " << __TIME__ << "\n";
| ^~~~~~~~
../../src/util/opts_list.h:152:153: note: in expansion of macro 'SET_VERSION_INFO'
152 | #define INIT_CONSTRUCTED_OPTS_LIST(OPTS,ARGS,SYNTAX,SHORTDESC) OPTS.short_description = (SHORTDESC); OPTS.syntax = (SYNTAX); OPTS.expect_args = (ARGS); SET_VERSION_INFO(OPTS); Log_stream::add_opts(OPTS);
| ^~~~~~~~~~~~~~~~
fsa.cc:25:3: note: in expansion of macro 'INIT_CONSTRUCTED_OPTS_LIST'
25 | INIT_CONSTRUCTED_OPTS_LIST (opts, -1, "[options] <sequence file(s)>", "Distance-based alignment of DNA, RNA and proteins.");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../../src/seq/sequence.h:16,
from ../../src/seq/alignment.h:16,
from anchors.cc:15:
/usr/include/c++/10/bits/vector.tcc: In 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++/10/bits/vector.tcc:300:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
300 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:300:7: 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++/10/bits/vector.tcc: In 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++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<fsa::Anchor>::iterator' changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:721:7: 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++/10/bits/vector.tcc:721:7: 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/anchors.h:17,
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]
241 | int yprev = -1; // the previous y-coordinate
| ^~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<fsa::Anchor>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../../src/seq/sequence.h:16,
from ../../src/seq/alignment.h:16,
from anchors.cc:15:
/usr/include/c++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'fsa::Anchors fsa::Cabbage_adapter::get_candidate_anchors() const':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void fsa::Anchors::enforce_immutable_unique()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1628:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1628 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void fsa::Anchors::remove_overlaps(size_t, unsigned int)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1628:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1628 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
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
/usr/include/c++/10/bits/stl_vector.h: In member function 'fsa::Anchors fsa::Mummer_adapter::get_candidate_anchors(size_t) const':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from ../../src/fsa/model.h:32,
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]
241 | int yprev = -1; // the previous y-coordinate
| ^~~~~
In file included from /usr/include/c++/10/vector:72,
from ../../src/util/misc.h:17,
from ../../src/math/mst.h:11,
from fsa.cc:9:
/usr/include/c++/10/bits/vector.tcc: In 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++/10/bits/vector.tcc:300:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
300 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:300:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
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]
768 | 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]
1256 | 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]
1472 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from anchors.cc:13:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __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++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:79:5: 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++/10/bits/stl_algo.h:79:5: 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++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
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:2029:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable]
2029 | int iPrevSlowCoord;
| ^~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: 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++/10/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++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1881 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1881:5: 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++/10/bits/stl_algo.h:1881:5: 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++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from anchors.cc:13:
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from anchors.cc:13:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _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++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1662 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1662:5: 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++/10/bits/stl_algo.h:1662:5: 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++/10/bits/stl_algo.h:1662:5: 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++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: 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++/10/bits/stl_algo.h:1945:5: 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++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1924 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1925 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1924:34: 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++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1937 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In member function 'bool fsa::Anchors::resolve_parallel(size_t, bool)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../../src/seq/sequence.h:16,
from ../../src/seq/alignment.h:16,
from anchors.cc:15:
/usr/include/c++/10/bits/stl_vector.h:1628:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1628 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from anchors.cc:13:
/usr/include/c++/10/bits/stl_algo.h: In member function 'void fsa::Anchors::remove_overlaps(size_t)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../../src/seq/sequence.h:16,
from ../../src/seq/alignment.h:16,
from anchors.cc:15:
/usr/include/c++/10/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::string) const':
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type 'std::vector<fsa::Anchor>::iterator' changed in GCC 7.1
1665 | _M_range_insert(__pos, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
1666 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1665:19: 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++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type 'std::vector<fsa::Anchor>::iterator' changed in GCC 7.1
1665 | _M_range_insert(__pos, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
1666 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1665:19: 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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fsa::Anchor*, std::vector<fsa::Anchor> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../../src/util/misc.h:17,
from ../../src/math/mst.h:11,
from fsa.cc:9:
/usr/include/c++/10/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++/10/bits/stl_vector.h:1628:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
1628 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1628:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
1628 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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]
768 | 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]
1166 | 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]
1352 | 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]
1819 | 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
In file included from /usr/include/c++/10/queue:62,
from sequence_pair_selector.cc:8:
/usr/include/c++/10/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++/10/bits/stl_heap.h:134:5: 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
134 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/queue:61,
from sequence_pair_selector.cc:8:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<double, unsigned int> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void fsa::Sequence_pair_selector::choose_kmer_similarity(size_t)':
/usr/include/c++/10/bits/vector.tcc:121:21: 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
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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,
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]
241 | 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++/10/ext/hash_map:60,
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++/10/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]
32 | #warning \
| ^~~~~~~
In file included from ../../src/fsa/anchors.h:17,
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]
241 | int yprev = -1; // the previous y-coordinate
| ^~~~~
In file included from ../../src/annealing/alignment_DAG.h:58,
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]
241 | 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 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
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
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'
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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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make[3]: Nothing to be done for 'all'.
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Making all in 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
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]: Nothing to be done for 'install-exec-am'.
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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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make[2]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/math'
Making install in src/seq
make[2]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/seq'
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/seq'
make[3]: Nothing to be done for 'install-exec-am'.
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make[3]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/seq'
make[2]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/seq'
Making install in src/manager
make[2]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/manager'
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/manager'
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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'
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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[2]: Leaving directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/annealing'
Making install in src/main
make[2]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/main'
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/src/main'
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'
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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'
make[3]: Entering directory '/<<BUILDDIR>>/fsa-1.15.9+dfsg/examples'
make[3]: Nothing to be done for 'install-exec-am'.
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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'
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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_dwz -a -a
dh_strip -a -a
dh_makeshlibs -a -a
dh_shlibdeps -a -a
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/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/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/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/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_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/gapcleaner contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/fsa/usr/bin/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/slice_fasta_gff 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/map_coords debian/fsa/usr/bin/prot2codon debian/fsa/usr/bin/slice_fasta debian/fsa/usr/bin/map_gff_coords debian/fsa/usr/bin/percentid debian/fsa/usr/bin/fsa debian/fsa/usr/bin/fsa-translate debian/fsa/usr/bin/slice_mercator_alignment debian/fsa/usr/bin/gapcleaner debian/fsa/usr/bin/isect_mercator_alignment_gff debian/fsa/usr/bin/slice_fasta_gff 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' in '../fsa_1.15.9+dfsg-6_armhf.deb'.
dpkg-deb: building package 'fsa-dbgsym' in '../fsa-dbgsym_1.15.9+dfsg-6_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-6_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-11-18T05:29:24Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
fsa_1.15.9+dfsg-6_armhf.changes:
--------------------------------
Format: 1.8
Date: Sun, 15 Nov 2020 17:45:20 +0100
Source: fsa
Binary: fsa fsa-dbgsym
Architecture: armhf
Version: 1.15.9+dfsg-6
Distribution: bullseye-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-6) unstable; urgency=medium
.
* Fix typo
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Files:
57eee9b2b1c282327532b0f34f9e2b1b 14263068 debug optional fsa-dbgsym_1.15.9+dfsg-6_armhf.deb
113fec31a1cbca59f2f9f3402331b95d 5128 science optional fsa_1.15.9+dfsg-6_armhf.buildinfo
5de8993b6df2ca9dddf4fd0c70c5ce59 526776 science optional fsa_1.15.9+dfsg-6_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
fsa-dbgsym_1.15.9+dfsg-6_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 14263068 bytes: control archive=1100 bytes.
778 bytes, 12 lines control
1249 bytes, 12 lines md5sums
Package: fsa-dbgsym
Source: fsa
Version: 1.15.9+dfsg-6
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 14866
Depends: fsa (= 1.15.9+dfsg-6)
Section: debug
Priority: optional
Description: debug symbols for fsa
Build-Ids: 03e217e24e758c66b2079d2a8ddb64348862b4cc 086c5291c8f2b91ae74d9d6c89a620bb5ce5b17d 11c19fcbdbde6eed1d59f6d14b4ae775fa420f8e 43ccdc09d36777a057caa07475893f5525b6739c 54570ae542c06fc3d97476ebbbcabf85d52805f3 75d4be2fc1a5bec6416081bf9fff0b5325d0407b 936ce624b68068565bf2f80a6f682e3d667eaf56 b1397b86af49e8440d8b89a34270e56b597ba42a c2aa5c9ea52d35fefd4b37ae349662d916600780 cbf398bc783a06185908f3d41ea9fdfb614506e8 ef371f44f0448f84e73a250714e08119aade3c35
drwxr-xr-x root/root 0 2020-11-15 16:45 ./
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debug/.build-id/03/
-rw-r--r-- root/root 667564 2020-11-15 16:45 ./usr/lib/debug/.build-id/03/e217e24e758c66b2079d2a8ddb64348862b4cc.debug
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debug/.build-id/08/
-rw-r--r-- root/root 1273624 2020-11-15 16:45 ./usr/lib/debug/.build-id/08/6c5291c8f2b91ae74d9d6c89a620bb5ce5b17d.debug
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debug/.build-id/11/
-rw-r--r-- root/root 637020 2020-11-15 16:45 ./usr/lib/debug/.build-id/11/c19fcbdbde6eed1d59f6d14b4ae775fa420f8e.debug
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debug/.build-id/43/
-rw-r--r-- root/root 1281628 2020-11-15 16:45 ./usr/lib/debug/.build-id/43/ccdc09d36777a057caa07475893f5525b6739c.debug
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debug/.build-id/54/
-rw-r--r-- root/root 1370412 2020-11-15 16:45 ./usr/lib/debug/.build-id/54/570ae542c06fc3d97476ebbbcabf85d52805f3.debug
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debug/.build-id/75/
-rw-r--r-- root/root 646880 2020-11-15 16:45 ./usr/lib/debug/.build-id/75/d4be2fc1a5bec6416081bf9fff0b5325d0407b.debug
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debug/.build-id/93/
-rw-r--r-- root/root 650872 2020-11-15 16:45 ./usr/lib/debug/.build-id/93/6ce624b68068565bf2f80a6f682e3d667eaf56.debug
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debug/.build-id/b1/
-rw-r--r-- root/root 1274056 2020-11-15 16:45 ./usr/lib/debug/.build-id/b1/397b86af49e8440d8b89a34270e56b597ba42a.debug
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debug/.build-id/c2/
-rw-r--r-- root/root 898336 2020-11-15 16:45 ./usr/lib/debug/.build-id/c2/aa5c9ea52d35fefd4b37ae349662d916600780.debug
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debug/.build-id/cb/
-rw-r--r-- root/root 1310740 2020-11-15 16:45 ./usr/lib/debug/.build-id/cb/f398bc783a06185908f3d41ea9fdfb614506e8.debug
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debug/.build-id/ef/
-rw-r--r-- root/root 4279948 2020-11-15 16:45 ./usr/lib/debug/.build-id/ef/371f44f0448f84e73a250714e08119aade3c35.debug
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 902484 2020-11-15 16:45 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/fsa.debug
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/share/
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-11-15 16:45 ./usr/share/doc/fsa-dbgsym -> fsa
fsa_1.15.9+dfsg-6_armhf.deb
---------------------------
new Debian package, version 2.0.
size 526776 bytes: control archive=2720 bytes.
2335 bytes, 40 lines control
3513 bytes, 49 lines md5sums
Package: fsa
Version: 1.15.9+dfsg-6
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3487
Depends: libc6 (>= 2.29), libgcc-s1 (>= 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 2020-11-15 16:45 ./
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/bin/
-rwxr-xr-x root/root 898908 2020-11-15 16:45 ./usr/bin/fsa
-rwxr-xr-x root/root 120708 2020-11-15 16:45 ./usr/bin/fsa-translate
-rwxr-xr-x root/root 300940 2020-11-15 16:45 ./usr/bin/gapcleaner
-rwxr-xr-x root/root 219140 2020-11-15 16:45 ./usr/bin/isect_mercator_alignment_gff
-rwxr-xr-x root/root 219092 2020-11-15 16:45 ./usr/bin/map_coords
-rwxr-xr-x root/root 219140 2020-11-15 16:45 ./usr/bin/map_gff_coords
-rwxr-xr-x root/root 120708 2020-11-15 16:45 ./usr/bin/percentid
-rwxr-xr-x root/root 124804 2020-11-15 16:45 ./usr/bin/prot2codon
-rwxr-xr-x root/root 124804 2020-11-15 16:45 ./usr/bin/slice_fasta
-rwxr-xr-x root/root 157588 2020-11-15 16:45 ./usr/bin/slice_fasta_gff
-rwxr-xr-x root/root 219140 2020-11-15 16:45 ./usr/bin/slice_mercator_alignment
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debian-med/
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debian-med/bin/
lrwxrwxrwx root/root 0 2020-11-15 16:45 ./usr/lib/debian-med/bin/translate -> ../../../bin/fsa-translate
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debian-med/share/
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debian-med/share/man/
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/lib/debian-med/share/man/man1/
lrwxrwxrwx root/root 0 2020-11-15 16:45 ./usr/lib/debian-med/share/man/man1/translate.1.gz -> ../../../../../share/man/man1/fsa-translate.1.gz
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/share/
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/share/doc/fsa/
-rw-r--r-- root/root 24437 2020-11-15 16:45 ./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 696 2020-11-15 16:45 ./usr/share/doc/fsa/changelog.Debian.gz
-rw-r--r-- root/root 3603 2020-11-15 16:45 ./usr/share/doc/fsa/copyright
drwxr-xr-x root/root 0 2020-11-15 16:45 ./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 33181 2012-03-22 17:09 ./usr/share/doc/fsa/examples/RV12.BBS12030.fasta.gui
-rw-r--r-- root/root 393175 2012-03-22 17:09 ./usr/share/doc/fsa/examples/RV12.BBS12030.fasta.probs
-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 12629 2012-03-22 17:09 ./usr/share/doc/fsa/examples/U5.aln1.fasta.gui
-rw-r--r-- root/root 185198 2012-03-22 17:09 ./usr/share/doc/fsa/examples/U5.aln1.fasta.probs
-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 7534 2012-03-22 17:09 ./usr/share/doc/fsa/examples/tRNA.aln1.fasta.gui
-rw-r--r-- root/root 113663 2012-03-22 17:09 ./usr/share/doc/fsa/examples/tRNA.aln1.fasta.probs
-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 2020-11-15 16:45 ./usr/share/man/
drwxr-xr-x root/root 0 2020-11-15 16:45 ./usr/share/man/man1/
-rw-r--r-- root/root 402 2020-11-15 16:45 ./usr/share/man/man1/fsa-translate.1.gz
-rw-r--r-- root/root 393 2020-11-15 16:45 ./usr/share/man/man1/fsa.1.gz
-rw-r--r-- root/root 467 2020-11-15 16:45 ./usr/share/man/man1/gapcleaner.1.gz
-rw-r--r-- root/root 1077 2020-11-15 16:45 ./usr/share/man/man1/isect_mercator_alignment_gff.1.gz
-rw-r--r-- root/root 695 2020-11-15 16:45 ./usr/share/man/man1/map_coords.1.gz
-rw-r--r-- root/root 1074 2020-11-15 16:45 ./usr/share/man/man1/map_gff_coords.1.gz
-rw-r--r-- root/root 378 2020-11-15 16:45 ./usr/share/man/man1/percentid.1.gz
-rw-r--r-- root/root 411 2020-11-15 16:45 ./usr/share/man/man1/prot2codon.1.gz
-rw-r--r-- root/root 443 2020-11-15 16:45 ./usr/share/man/man1/slice_fasta.1.gz
-rw-r--r-- root/root 533 2020-11-15 16:45 ./usr/share/man/man1/slice_fasta_gff.1.gz
-rw-r--r-- root/root 870 2020-11-15 16:45 ./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: 183720
Build-Time: 764
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 290
Job: fsa_1.15.9+dfsg-6
Machine Architecture: armhf
Package: fsa
Package-Time: 1104
Source-Version: 1.15.9+dfsg-6
Space: 183720
Status: successful
Version: 1.15.9+dfsg-6
--------------------------------------------------------------------------------
Finished at 2020-11-18T05:29:24Z
Build needed 00:18:24, 183720k disc space