augustus →
3.4.0+dfsg2-3+b2 →
armhf → 2022-09-05 17:51:59
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| augustus 3.4.0+dfsg2-3+b2 (armhf) Mon, 05 Sep 2022 16:34:48 +0000 |
+==============================================================================+
Package: augustus
Version: 3.4.0+dfsg2-3+b2
Source Version: 3.4.0+dfsg2-3
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-6b43066d-b0dd-4201-84a1-5d80be9612cb' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.2 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.1 MB]
Fetched 27.4 MB in 10s (2798 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'augustus' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/augustus.git
Please use:
git clone https://salsa.debian.org/med-team/augustus.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 148 MB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main augustus 3.4.0+dfsg2-3 (dsc) [2355 B]
Get:2 http://172.17.4.1/private bookworm-staging/main augustus 3.4.0+dfsg2-3 (tar) [148 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main augustus 3.4.0+dfsg2-3 (diff) [19.2 kB]
Fetched 148 MB in 15s (9605 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/augustus-VTpi4J/augustus-3.4.0+dfsg2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/augustus-VTpi4J' 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-FISwLO/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-FISwLO/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-FISwLO/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-FISwLO/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-FISwLO/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-FISwLO/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-FISwLO/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-FISwLO/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (7202 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:
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 20 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-FISwLO/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (73.1 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12802 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 all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, libboost-serialization-dev, libssl-dev, libmysql++-dev, asciidoctor, python3, samtools
Filtered Build-Depends: debhelper-compat (= 13), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, libboost-serialization-dev, libssl-dev, libmysql++-dev, asciidoctor, python3, samtools
dpkg-deb: building package 'sbuild-build-depends-augustus-dummy' in '/<<BUILDDIR>>/resolver-FISwLO/apt_archive/sbuild-build-depends-augustus-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-augustus-dummy sbuild-build-depends-core-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-FISwLO/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-FISwLO/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-FISwLO/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-FISwLO/apt_archive ./ Sources [600 B]
Get:5 copy:/<<BUILDDIR>>/resolver-FISwLO/apt_archive ./ Packages [681 B]
Fetched 2614 B in 0s (12.9 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install augustus 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:
asciidoctor autoconf automake autopoint autotools-dev bsdextrautils
ca-certificates cpp-12 debhelper default-libmysqlclient-dev dh-autoreconf
dh-strip-nondeterminism dmsetup dwz file g++-12 gcc-12 gcc-12-base gettext
gettext-base groff-base icu-devtools intltool-debian libamd2 libapparmor1
libarchive-zip-perl libargon2-1 libasan8 libatomic1 libbamtools-dev
libbamtools2.5.2 libblas-dev libblas3 libboost-iostreams-dev
libboost-iostreams1.74-dev libboost-iostreams1.74.0 libboost-regex1.74-dev
libboost-regex1.74.0 libboost-serialization-dev
libboost-serialization1.74-dev libboost-serialization1.74.0 libboost1.74-dev
libbrotli1 libbsd0 libbtf1 libbz2-dev libcamd2 libcc1-0 libccolamd2
libcholmod3 libcolamd2 libcryptsetup12 libcurl3-gnutls libcurl4-gnutls-dev
libcxsparse3 libdebhelper-perl libdeflate-dev libdeflate0 libdevmapper1.02.1
libedit2 libelf1 libexpat1 libfdisk1 libfile-stripnondeterminism-perl
libgcc-12-dev libgcc-s1 libgfortran5 libgomp1 libgsl-dev libgsl27
libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu-dev libicu71 libip4tc2
libjson-c5 libklu1 libkmod2 liblapack-dev liblapack3 libldl2
liblpsolve55-dev liblzma-dev libmagic-mgc libmagic1 libmariadb-dev
libmariadb-dev-compat libmariadb3 libmd0 libmetis5 libmongoose2 libmpdec3
libmysql++-dev libmysql++3v5 libncurses-dev libncurses5-dev libncurses6
libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.10-minimal
libpython3.10-stdlib librbio2 librtmp1 libruby3.0 libsliplu1 libspqr2
libsqlite3-dev libssh2-1 libssl-dev libstdc++-12-dev libstdc++6
libsub-override-perl libsuitesparse-dev libsuitesparseconfig5
libsystemd-shared libtool libubsan1 libuchardet0 libumfpack5 libxml2
libyaml-0-2 lzma-dev m4 man-db mariadb-common media-types mysql-common
openssl po-debconf python3 python3-minimal python3.10 python3.10-minimal
rake ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-webrick
ruby-xmlrpc ruby3.0 rubygems-integration samtools systemd zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc gcc-12-locales dh-make
gcc-12-doc gettext-doc libasprintf-dev libgettextpo-dev groff
libbamtools-doc liblapack-doc libboost1.74-doc libboost-atomic1.74-dev
libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev
libboost-contract1.74-dev libboost-coroutine1.74-dev
libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-locale1.74-dev libboost-log1.74-dev
libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev
libboost-numpy1.74-dev libboost-program-options1.74-dev
libboost-python1.74-dev libboost-random1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev
librtmp-dev libssh2-1-dev pkg-config gsl-ref-psdoc | gsl-doc-pdf
| gsl-doc-info | gsl-ref-html icu-doc liblzma-doc libmysql++-doc ncurses-doc
sqlite3-doc libssl-doc libstdc++-12-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv python3.10-venv
python3.10-doc binfmt-support ri ruby-dev bundler cwltool systemd-container
systemd-homed systemd-userdbd systemd-boot libfido2-1 libtss2-esys-3.0.2-0
libtss2-mu0 libtss2-rc0 policykit-1
Recommended packages:
curl | wget | lynx bzip2-doc libarchive-cpio-perl libgpm2 publicsuffix
libgraphblas-dev libltdl-dev libmail-sendmail-perl zip fonts-lato
libjs-jquery default-dbus-system-bus | dbus-system-bus systemd-timesyncd
| time-daemon
The following NEW packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdextrautils
ca-certificates debhelper default-libmysqlclient-dev dh-autoreconf
dh-strip-nondeterminism dmsetup dwz file gettext gettext-base groff-base
icu-devtools intltool-debian libamd2 libapparmor1 libarchive-zip-perl
libargon2-1 libbamtools-dev libbamtools2.5.2 libblas-dev libblas3
libboost-iostreams-dev libboost-iostreams1.74-dev libboost-iostreams1.74.0
libboost-regex1.74-dev libboost-regex1.74.0 libboost-serialization-dev
libboost-serialization1.74-dev libboost-serialization1.74.0 libboost1.74-dev
libbrotli1 libbsd0 libbtf1 libbz2-dev libcamd2 libccolamd2 libcholmod3
libcolamd2 libcryptsetup12 libcurl3-gnutls libcurl4-gnutls-dev libcxsparse3
libdebhelper-perl libdeflate-dev libdeflate0 libdevmapper1.02.1 libedit2
libelf1 libexpat1 libfdisk1 libfile-stripnondeterminism-perl libgfortran5
libgsl-dev libgsl27 libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu-dev
libicu71 libip4tc2 libjson-c5 libklu1 libkmod2 liblapack-dev liblapack3
libldl2 liblpsolve55-dev liblzma-dev libmagic-mgc libmagic1 libmariadb-dev
libmariadb-dev-compat libmariadb3 libmd0 libmetis5 libmongoose2 libmpdec3
libmysql++-dev libmysql++3v5 libncurses-dev libncurses5-dev libncurses6
libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.10-minimal
libpython3.10-stdlib librbio2 librtmp1 libruby3.0 libsliplu1 libspqr2
libsqlite3-dev libssh2-1 libssl-dev libsub-override-perl libsuitesparse-dev
libsuitesparseconfig5 libsystemd-shared libtool libuchardet0 libumfpack5
libxml2 libyaml-0-2 lzma-dev m4 man-db mariadb-common media-types
mysql-common openssl po-debconf python3 python3-minimal python3.10
python3.10-minimal rake ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems
ruby-webrick ruby-xmlrpc ruby3.0 rubygems-integration samtools
sbuild-build-depends-augustus-dummy systemd zlib1g-dev
The following packages will be upgraded:
cpp-12 g++-12 gcc-12 gcc-12-base libasan8 libatomic1 libcc1-0 libgcc-12-dev
libgcc-s1 libgomp1 libstdc++-12-dev libstdc++6 libubsan1
13 upgraded, 137 newly installed, 0 to remove and 7 not upgraded.
Need to get 245 MB of archives.
After this operation, 421 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-FISwLO/apt_archive ./ sbuild-build-depends-augustus-dummy 0.invalid.0 [964 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libargon2-1 armhf 0~20171227-0.3 [19.6 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf dmsetup armhf 2:1.02.185-1 [91.8 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf libdevmapper1.02.1 armhf 2:1.02.185-1 [134 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libjson-c5 armhf 0.16-1 [40.0 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf libcryptsetup12 armhf 2:2.5.0-2 [225 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libfdisk1 armhf 2.38.1-1 [237 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libkmod2 armhf 30+20220630-3 [51.8 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libapparmor1 armhf 3.0.7-1 [98.9 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libip4tc2 armhf 1.8.8-1 [32.9 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libsystemd-shared armhf 251.3-1+rpi1 [1526 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf systemd armhf 251.3-1+rpi1 [2985 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-minimal armhf 3.10.6-1 [813 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libubsan1 armhf 12.1.0-8+rpi1 [861 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf gcc-12-base armhf 12.1.0-8+rpi1 [208 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libgcc-s1 armhf 12.1.0-8+rpi1 [36.2 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libgomp1 armhf 12.1.0-8+rpi1 [95.9 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libatomic1 armhf 12.1.0-8+rpi1 [8236 B]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libasan8 armhf 12.1.0-8+rpi1 [2090 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf cpp-12 armhf 12.1.0-8+rpi1 [50.1 MB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libcc1-0 armhf 12.1.0-8+rpi1 [32.2 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf g++-12 armhf 12.1.0-8+rpi1 [54.0 MB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf gcc-12 armhf 12.1.0-8+rpi1 [55.9 MB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libgcc-12-dev armhf 12.1.0-8+rpi1 [725 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libstdc++-12-dev armhf 12.1.0-8+rpi1 [2026 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libstdc++6 armhf 12.1.0-8+rpi1 [505 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.8-1 [84.1 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf python3.10-minimal armhf 3.10.6-1 [1520 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.10.6-1 [38.7 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf media-types all 8.0.0 [33.4 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-stdlib armhf 3.10.6-1 [1596 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf python3.10 armhf 3.10.6-1 [545 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.10.6-1 [21.7 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.10.6-1 [38.2 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-1 [137 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-2 [34.2 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.2-2 [1364 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf openssl armhf 3.0.5-2 [1372 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf ca-certificates all 20211016 [156 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-8 [171 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf rubygems-integration all 1.18 [6704 B]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf rake all 13.0.6-3 [83.9 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf ruby-net-telnet all 0.1.1-2.1 [12.7 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf ruby-webrick all 1.7.0-3 [50.8 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf ruby-xmlrpc all 0.3.2-2 [24.4 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-2 [28.6 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.6-1 [109 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20210910-1 [81.2 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libyaml-0-2 armhf 0.2.5-1 [44.6 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libruby3.0 armhf 3.0.4-7 [5083 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf ruby3.0 armhf 3.0.4-7 [682 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf ruby-rubygems all 3.3.15-1 [293 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf ruby armhf 1:3.0+1 [12.1 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf ruby-asciidoctor all 2.0.16-2 [210 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf asciidoctor all 2.0.16-2 [87.6 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-8 [510 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.9.1 [196 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-3 [10.4 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-1 [175 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-8 [1219 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.9.1 [1071 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf mysql-common all 5.8+1.0.8 [7528 B]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf mariadb-common all 1:10.6.9-1 [37.0 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libmariadb3 armhf 1:10.6.9-1 [163 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf libssl-dev armhf 3.0.5-2 [2116 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4.1 [183 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libmariadb-dev armhf 1:10.6.9-1 [253 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libmariadb-dev-compat armhf 1:10.6.9-1 [35.9 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf default-libmysqlclient-dev armhf 1.0.8 [3980 B]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf icu-devtools armhf 71.1-3 [177 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libsuitesparseconfig5 armhf 1:5.12.0+dfsg-2 [23.6 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libamd2 armhf 1:5.12.0+dfsg-2 [30.2 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf libbamtools2.5.2 armhf 2.5.2+dfsg-2 [127 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libbamtools-dev armhf 2.5.2+dfsg-2 [183 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.10.1-2 [109 kB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf libblas-dev armhf 3.10.1-2 [114 kB]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-17 [9534 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf libboost-regex1.74.0 armhf 1.74.0-17 [444 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf libicu-dev armhf 71.1-3 [9799 kB]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf libboost-regex1.74-dev armhf 1.74.0-17 [550 kB]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf libboost-iostreams1.74.0 armhf 1.74.0-17 [260 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf libboost-iostreams1.74-dev armhf 1.74.0-17 [270 kB]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf libboost-iostreams-dev armhf 1.74.0.3+b4 [4592 B]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf libboost-serialization1.74.0 armhf 1.74.0-17 [322 kB]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf libboost-serialization1.74-dev armhf 1.74.0-17 [387 kB]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf libboost-serialization-dev armhf 1.74.0.3+b4 [4832 B]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf libbtf1 armhf 1:5.12.0+dfsg-2 [24.1 kB]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf libbz2-dev armhf 1.0.8-5+b2 [26.8 kB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf libcamd2 armhf 1:5.12.0+dfsg-2 [30.7 kB]
Get:112 http://172.17.4.1/private bookworm-staging/main armhf libccolamd2 armhf 1:5.12.0+dfsg-2 [31.7 kB]
Get:113 http://172.17.4.1/private bookworm-staging/main armhf libcolamd2 armhf 1:5.12.0+dfsg-2 [28.3 kB]
Get:114 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.1.0-8+rpi1 [238 kB]
Get:115 http://172.17.4.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.1-2 [1587 kB]
Get:116 http://172.17.4.1/private bookworm-staging/main armhf libmetis5 armhf 5.1.0.dfsg-7 [133 kB]
Get:117 http://172.17.4.1/private bookworm-staging/main armhf libcholmod3 armhf 1:5.12.0+dfsg-2 [212 kB]
Get:118 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.49.0-1 [69.8 kB]
Get:119 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:120 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:121 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:122 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.84.0-2 [315 kB]
Get:123 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.84.0-2 [392 kB]
Get:124 http://172.17.4.1/private bookworm-staging/main armhf libcxsparse3 armhf 1:5.12.0+dfsg-2 [52.1 kB]
Get:125 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.12-1 [60.5 kB]
Get:126 http://172.17.4.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.12-1 [51.8 kB]
Get:127 http://172.17.4.1/private bookworm-staging/main armhf libgslcblas0 armhf 2.7.1+dfsg-3 [81.4 kB]
Get:128 http://172.17.4.1/private bookworm-staging/main armhf libgsl27 armhf 2.7.1+dfsg-3 [758 kB]
Get:129 http://172.17.4.1/private bookworm-staging/main armhf libgsl-dev armhf 2.7.1+dfsg-3 [958 kB]
Get:130 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.2.2-1 [53.1 kB]
Get:131 http://172.17.4.1/private bookworm-staging/main armhf libhts3 armhf 1.13+ds-2+b1 [339 kB]
Get:132 http://172.17.4.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2.1 [218 kB]
Get:133 http://172.17.4.1/private bookworm-staging/main armhf libhts-dev armhf 1.13+ds-2+b1 [4045 kB]
Get:134 http://172.17.4.1/private bookworm-staging/main armhf libklu1 armhf 1:5.12.0+dfsg-2 [51.8 kB]
Get:135 http://172.17.4.1/private bookworm-staging/main armhf liblapack-dev armhf 3.10.1-2 [2847 kB]
Get:136 http://172.17.4.1/private bookworm-staging/main armhf libldl2 armhf 1:5.12.0+dfsg-2 [23.8 kB]
Get:137 http://172.17.4.1/private bookworm-staging/main armhf libmongoose2 armhf 1:5.12.0+dfsg-2 [43.8 kB]
Get:138 http://172.17.4.1/private bookworm-staging/main armhf libumfpack5 armhf 1:5.12.0+dfsg-2 [128 kB]
Get:139 http://172.17.4.1/private bookworm-staging/main armhf librbio2 armhf 1:5.12.0+dfsg-2 [32.9 kB]
Get:140 http://172.17.4.1/private bookworm-staging/main armhf libspqr2 armhf 1:5.12.0+dfsg-2 [68.2 kB]
Get:141 http://172.17.4.1/private bookworm-staging/main armhf libsliplu1 armhf 1:5.12.0+dfsg-2 [49.5 kB]
Get:142 http://172.17.4.1/private bookworm-staging/main armhf libsuitesparse-dev armhf 1:5.12.0+dfsg-2 [614 kB]
Get:143 http://172.17.4.1/private bookworm-staging/main armhf liblpsolve55-dev armhf 5.5.2.5-2 [349 kB]
Get:144 http://172.17.4.1/private bookworm-staging/main armhf libmysql++3v5 armhf 3.2.5-2.1 [144 kB]
Get:145 http://172.17.4.1/private bookworm-staging/main armhf libmysql++-dev armhf 3.2.5-2.1 [150 kB]
Get:146 http://172.17.4.1/private bookworm-staging/main armhf libncurses-dev armhf 6.3+20220423-2 [289 kB]
Get:147 http://172.17.4.1/private bookworm-staging/main armhf libncurses5-dev armhf 6.3+20220423-2 [940 B]
Get:148 http://172.17.4.1/private bookworm-staging/main armhf libsqlite3-dev armhf 3.39.2-1 [896 kB]
Get:149 http://172.17.4.1/private bookworm-staging/main armhf lzma-dev all 9.22-2.2 [44.8 kB]
Get:150 http://172.17.4.1/private bookworm-staging/main armhf samtools armhf 1.13-4 [525 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up gcc-12-base:armhf (12.1.0-8+rpi1) ...
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Setting up libsuitesparseconfig5:armhf (1:5.12.0+dfsg-2) ...
Setting up libcc1-0:armhf (12.1.0-8+rpi1) ...
Setting up libblas-dev:armhf (3.10.1-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up librbio2:armhf (1:5.12.0+dfsg-2) ...
Setting up libkmod2:armhf (30+20220630-3) ...
Setting up libbz2-dev:armhf (1.0.8-5+b2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.0-1) ...
Setting up libamd2:armhf (1:5.12.0+dfsg-2) ...
Setting up liblapack3:armhf (3.10.1-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libncurses-dev:armhf (6.3+20220423-2) ...
Setting up gettext (0.21-8) ...
Setting up libgsl-dev (2.7.1+dfsg-3) ...
Setting up libcolamd2:armhf (1:5.12.0+dfsg-2) ...
Setting up libtool (2.4.7-4) ...
Setting up libedit2:armhf (3.1-20210910-1) ...
Setting up libcurl3-gnutls:armhf (7.84.0-2) ...
Setting up libcurl4-gnutls-dev:armhf (7.84.0-2) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libsliplu1:armhf (1:5.12.0+dfsg-2) ...
Setting up libpython3.10-stdlib:armhf (3.10.6-1) ...
Setting up dh-autoreconf (20) ...
Setting up ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
127 added, 0 removed; done.
Setting up libcamd2:armhf (1:5.12.0+dfsg-2) ...
Setting up libmongoose2:armhf (1:5.12.0+dfsg-2) ...
Setting up libbamtools-dev:armhf (2.5.2+dfsg-2) ...
Setting up libgcc-12-dev:armhf (12.1.0-8+rpi1) ...
Setting up liblapack-dev:armhf (3.10.1-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libsystemd-shared:armhf (251.3-1+rpi1) ...
Setting up lzma-dev (9.22-2.2) ...
Setting up libmariadb-dev (1:10.6.9-1) ...
Setting up dh-strip-nondeterminism (1.13.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-8) ...
Setting up libklu1:armhf (1:5.12.0+dfsg-2) ...
Setting up libccolamd2:armhf (1:5.12.0+dfsg-2) ...
Setting up libncurses5-dev:armhf (6.3+20220423-2) ...
Setting up libcholmod3:armhf (1:5.12.0+dfsg-2) ...
Setting up libpython3-stdlib:armhf (3.10.6-1) ...
Setting up libmariadb-dev-compat:armhf (1:10.6.9-1) ...
Setting up libspqr2:armhf (1:5.12.0+dfsg-2) ...
Setting up libhts3:armhf (1.13+ds-2+b1) ...
Setting up python3.10 (3.10.6-1) ...
Setting up libstdc++-12-dev:armhf (12.1.0-8+rpi1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhts-dev:armhf (1.13+ds-2+b1) ...
Setting up python3 (3.10.6-1) ...
Setting up rubygems-integration (1.18) ...
Setting up samtools (1.13-4) ...
Setting up libumfpack5:armhf (1:5.12.0+dfsg-2) ...
Setting up gcc-12 (12.1.0-8+rpi1) ...
Setting up g++-12 (12.1.0-8+rpi1) ...
Setting up default-libmysqlclient-dev:armhf (1.0.8) ...
Setting up libboost1.74-dev:armhf (1.74.0-17) ...
Setting up libsuitesparse-dev:armhf (1:5.12.0+dfsg-2) ...
Setting up libmysql++-dev:armhf (3.2.5-2.1) ...
Setting up liblpsolve55-dev (5.5.2.5-2) ...
Setting up libboost-serialization1.74-dev:armhf (1.74.0-17) ...
Setting up libboost-regex1.74-dev:armhf (1.74.0-17) ...
Setting up libboost-iostreams1.74-dev:armhf (1.74.0-17) ...
Setting up libboost-serialization-dev:armhf (1.74.0.3+b4) ...
Setting up libboost-iostreams-dev:armhf (1.74.0.3+b4) ...
Setting up rake (13.0.6-3) ...
Setting up libdevmapper1.02.1:armhf (2:1.02.185-1) ...
Setting up dmsetup (2:1.02.185-1) ...
Setting up libcryptsetup12:armhf (2:2.5.0-2) ...
Setting up libruby3.0:armhf (3.0.4-7) ...
Setting up systemd (251.3-1+rpi1) ...
Created symlink /etc/systemd/system/getty.target.wants/getty@tty1.service -> /lib/systemd/system/getty@.service.
Created symlink /etc/systemd/system/multi-user.target.wants/remote-fs.target -> /lib/systemd/system/remote-fs.target.
Created symlink /etc/systemd/system/sysinit.target.wants/systemd-pstore.service -> /lib/systemd/system/systemd-pstore.service.
Initializing machine ID from random generator.
Setting up ruby-rubygems (3.3.15-1) ...
Setting up man-db (2.10.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer -> /lib/systemd/system/man-db.timer.
Setting up ruby3.0 (3.0.4-7) ...
Setting up debhelper (13.9.1) ...
Setting up ruby (1:3.0+1) ...
Setting up ruby-asciidoctor (2.0.16-2) ...
Setting up asciidoctor (2.0.16-2) ...
Setting up sbuild-build-depends-augustus-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.33-8+rpi1) ...
Processing triggers for ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.38.90.20220713-2+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.1.0-8+rpi1 gcc-12_12.1.0-8+rpi1 libc6-dev_2.33-8+rpi1 libstdc++-12-dev_12.1.0-8+rpi1 libstdc++6_12.1.0-8+rpi1 linux-libc-dev_5.18.14-1+rpi1
Package versions: adduser_3.123 apt_2.5.2 asciidoctor_2.0.16-2 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-8 autotools-dev_20220109.1 base-files_12.2+rpi1 base-passwd_3.6.0 bash_5.1-6.1 binutils_2.38.90.20220713-2+rpi1 binutils-arm-linux-gnueabihf_2.38.90.20220713-2+rpi1 binutils-common_2.38.90.20220713-2+rpi1 bsdextrautils_2.38.1-1 bsdutils_1:2.38.1-1 build-essential_12.9 bzip2_1.0.8-5+b2 ca-certificates_20211016 coreutils_8.32-4.1 cpp_4:12.1.0-3+rpi1 cpp-12_12.1.0-8+rpi1 dash_0.5.11+git20210903+057cd650a4ed-8 debconf_1.5.79 debhelper_13.9.1 debianutils_5.7-0.3 default-libmysqlclient-dev_1.0.8 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dirmngr_2.2.35-3 dmsetup_2:1.02.185-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.5-2 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.1.0-3+rpi1 g++-12_12.1.0-8+rpi1 gcc_4:12.1.0-3+rpi1 gcc-12_12.1.0-8+rpi1 gcc-12-base_12.1.0-8+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-8 gettext-base_0.21-8 gnupg_2.2.35-3 gnupg-l10n_2.2.35-3 gnupg-utils_2.2.35-3 gpg_2.2.35-3 gpg-agent_2.2.35-3 gpg-wks-client_2.2.35-3 gpg-wks-server_2.2.35-3 gpgconf_2.2.35-3 gpgsm_2.2.35-3 gpgv_2.2.35-3 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 hostname_3.23 icu-devtools_71.1-3 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20211215-1 krb5-locales_1.20-1 libacl1_2.3.1-1 libamd2_1:5.12.0+dfsg-2 libapparmor1_3.0.7-1 libapt-pkg6.0_2.5.2 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan8_12.1.0-8+rpi1 libassuan0_2.5.5-4 libatomic1_12.1.0-8+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1 libaudit1_1:3.0.7-1+b1 libbamtools-dev_2.5.2+dfsg-2 libbamtools2.5.2_2.5.2+dfsg-2 libbinutils_2.38.90.20220713-2+rpi1 libblas-dev_3.10.1-2 libblas3_3.10.1-2 libblkid1_2.38.1-1 libboost-iostreams-dev_1.74.0.3+b4 libboost-iostreams1.74-dev_1.74.0-17 libboost-iostreams1.74.0_1.74.0-17 libboost-regex1.74-dev_1.74.0-17 libboost-regex1.74.0_1.74.0-17 libboost-serialization-dev_1.74.0.3+b4 libboost-serialization1.74-dev_1.74.0-17 libboost-serialization1.74.0_1.74.0-17 libboost1.74-dev_1.74.0-17 libbrotli1_1.0.9-2+b2 libbsd0_0.11.6-1 libbtf1_1:5.12.0+dfsg-2 libbz2-1.0_1.0.8-5+b2 libbz2-dev_1.0.8-5+b2 libc-bin_2.33-8+rpi1 libc-dev-bin_2.33-8+rpi1 libc6_2.33-8+rpi1 libc6-dev_2.33-8+rpi1 libcamd2_1:5.12.0+dfsg-2 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_12.1.0-8+rpi1 libccolamd2_1:5.12.0+dfsg-2 libcholmod3_1:5.12.0+dfsg-2 libcolamd2_1:5.12.0+dfsg-2 libcom-err2_1.46.5-2 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libcryptsetup12_2:2.5.0-2 libctf-nobfd0_2.38.90.20220713-2+rpi1 libctf0_2.38.90.20220713-2+rpi1 libcurl3-gnutls_7.84.0-2 libcurl4-gnutls-dev_7.84.0-2 libcxsparse3_1:5.12.0+dfsg-2 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.263 libdebhelper-perl_13.9.1 libdeflate-dev_1.12-1 libdeflate0_1.12-1 libdevmapper1.02.1_2:1.02.185-1 libdpkg-perl_1.21.9+rpi1 libedit2_3.1-20210910-1 libelf1_0.187-1 libexpat1_2.4.8-1 libext2fs2_1.46.5-2 libfakeroot_1.29-1 libfdisk1_2.38.1-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-12-dev_12.1.0-8+rpi1 libgcc-s1_12.1.0-8+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgfortran5_12.1.0-8+rpi1 libgmp10_2:6.2.1+dfsg1-1 libgnutls30_3.7.7-2 libgomp1_12.1.0-8+rpi1 libgpg-error0_1.45-2 libgsl-dev_2.7.1+dfsg-3 libgsl27_2.7.1+dfsg-3 libgslcblas0_2.7.1+dfsg-3 libgssapi-krb5-2_1.20-1 libhogweed6_3.8.1-2 libhts-dev_1.13+ds-2+b1 libhts3_1.13+ds-2+b1 libhtscodecs2_1.2.2-1 libicu-dev_71.1-3 libicu71_71.1-3 libidn2-0_2.3.3-1 libip4tc2_1.8.8-1 libisl23_0.25-1 libjson-c5_0.16-1 libk5crypto3_1.20-1 libkeyutils1_1.6.3-1 libklu1_1:5.12.0+dfsg-2 libkmod2_30+20220630-3 libkrb5-3_1.20-1 libkrb5support0_1.20-1 libksba8_1.6.0-3 liblapack-dev_3.10.1-2 liblapack3_3.10.1-2 libldap-2.5-0_2.5.12+dfsg-2 libldl2_1:5.12.0+dfsg-2 liblpsolve55-dev_5.5.2.5-2 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2.1 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmariadb-dev_1:10.6.9-1 libmariadb-dev-compat_1:10.6.9-1 libmariadb3_1:10.6.9-1 libmd0_1.0.4-2 libmetis5_5.1.0.dfsg-7 libmongoose2_1:5.12.0+dfsg-2 libmount1_2.38.1-1 libmpc3_1.2.1-2 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libmysql++-dev_3.2.5-2.1 libmysql++3v5_3.2.5-2.1 libncurses-dev_6.3+20220423-2 libncurses5-dev_6.3+20220423-2 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnghttp2-14_1.49.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-2 libpam-modules-bin_1.5.2-2 libpam-runtime_1.5.2-2 libpam0g_1.5.2-2 libpcre2-8-0_10.40-1+b2 libpcre3_2:8.39-14 libperl5.34_5.34.0-5 libpipeline1_1.5.6-2 libpsl5_0.21.0-1.2 libpython3-stdlib_3.10.6-1 libpython3.10-minimal_3.10.6-1 libpython3.10-stdlib_3.10.6-1 librbio2_1:5.12.0+dfsg-2 libreadline8_8.1.2-1.2 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libruby3.0_3.0.4-7 libsasl2-2_2.1.28+dfsg-7 libsasl2-modules-db_2.1.28+dfsg-7 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol1_3.1-1 libsepol2_3.4-2 libsliplu1_1:5.12.0+dfsg-2 libsmartcols1_2.38.1-1 libspqr2_1:5.12.0+dfsg-2 libsqlite3-0_3.39.2-1 libsqlite3-dev_3.39.2-1 libss2_1.46.5-2 libssh2-1_1.10.0-3+b1 libssl-dev_3.0.5-2 libssl1.1_1.1.1o-1 libssl3_3.0.5-2 libstdc++-12-dev_12.1.0-8+rpi1 libstdc++6_12.1.0-8+rpi1 libsub-override-perl_0.09-3 libsuitesparse-dev_1:5.12.0+dfsg-2 libsuitesparseconfig5_1:5.12.0+dfsg-2 libsystemd-shared_251.3-1+rpi1 libsystemd0_251.3-1+rpi1 libtasn1-6_4.18.0-4 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-4 libubsan1_12.1.0-8+rpi1 libuchardet0_0.0.7-1 libudev1_251.3-1+rpi1 libumfpack5_1:5.12.0+dfsg-2 libunistring2_1.0-1 libuuid1_2.38.1-1 libxml2_2.9.14+dfsg-1 libxxhash0_0.8.1-1 libyaml-0-2_0.2.5-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.18.14-1+rpi1 login_1:4.11.1+dfsg1-2 logsave_1.46.5-2 lsb-base_11.2+rpi1 lzma-dev_9.22-2.2 m4_1.4.19-1 make_4.3-4.1 man-db_2.10.2-2 mariadb-common_1:10.6.9-1 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mount_2.38.1-1 mysql-common_5.8+1.0.8 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 netbase_6.3 openssl_3.0.5-2 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-5 perl-base_5.34.0-5 perl-modules-5.34_5.34.0-5 pinentry-curses_1.2.0-2 po-debconf_1.0.21+nmu1 python3_3.10.6-1 python3-minimal_3.10.6-1 python3.10_3.10.6-1 python3.10-minimal_3.10.6-1 rake_13.0.6-3 raspbian-archive-keyring_20120528.2 readline-common_8.1.2-1.2 rpcsvc-proto_1.4.2-4 ruby_1:3.0+1 ruby-asciidoctor_2.0.16-2 ruby-net-telnet_0.1.1-2.1 ruby-rubygems_3.3.15-1 ruby-webrick_1.7.0-3 ruby-xmlrpc_0.3.2-2 ruby3.0_3.0.4-7 rubygems-integration_1.18 samtools_1.13-4 sbuild-build-depends-augustus-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.30 systemd_251.3-1+rpi1 sysvinit-utils_3.04-1 tar_1.34+dfsg-1 tzdata_2022c-1 util-linux_2.38.1-1 util-linux-extra_2.38.1-1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.wIbqAgKX/trustedkeys.kbx': General error
gpgv: Signature made Tue Sep 28 20:37:41 2021 UTC
gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./augustus_3.4.0+dfsg2-3.dsc
dpkg-source: info: extracting augustus in /<<BUILDDIR>>/augustus-3.4.0+dfsg2
dpkg-source: info: unpacking augustus_3.4.0+dfsg2.orig.tar.xz
dpkg-source: info: unpacking augustus_3.4.0+dfsg2-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying search_config_path
dpkg-source: info: applying set_installdir
dpkg-source: info: applying interpreter_paths.patch
dpkg-source: info: applying switch_cgp_testing_off.patch
dpkg-source: info: applying disable-compare.patch
Check disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 3.4.0+dfsg2-3+b2
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=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-6b43066d-b0dd-4201-84a1-5d80be9612cb
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package augustus
dpkg-buildpackage: info: source version 3.4.0+dfsg2-3+b2
dpkg-buildpackage: info: source distribution bookworm-staging
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
/usr/bin/make -C auxprogs/bam2hints clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2hints'
rm -f bam2hints.o bam2hints ../../bin/bam2hints
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/homGeneMapping clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping'
cd src; make clean
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src'
rm -f homGeneMapping gene.o genome.o sqliteDB.o
rm -f ../../../bin/homGeneMapping
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src'
cd ../..; tests/auxprogs/homGeneMapping/test_homGeneMapping.py --clean
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping'
/usr/bin/make -C auxprogs/joingenes clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/joingenes'
rm -rf *.o joingenes; rm -rf ../../bin/joingenes
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/joingenes'
/usr/bin/make -C auxprogs/aln2wig clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/aln2wig'
rm -f aln2wig aln2wig.o; rm -f ../../bin/aln2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2wig clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2wig'
rm -f bam2wig bam2wig.o bam2wig
rm -f ../../bin/bam2wig
cd ../..; tests/auxprogs/bam2wig/test_bam2wig.py --clean
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/compileSpliceCands clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands'
rm -f compileSpliceCands compileSpliceCands.o ../../bin/compileSpliceCands list.o
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam'
(cd src; make clean;)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src'
rm -f *~ filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o
rm -f filterBam
rm -f ../../../bin/filterBam
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam'
rm -rf bin
rm -f debian/*substvars
rm -f debian/mansrc/*.1
find . -name "__pycache__" | xargs -r rm -r
find src -name "*.o" | xargs -r rm
find auxprogs -name "*.o" | xargs -r rm
rm -f auxprogs/utrrnaseq/Debug/utrrnaseq src/augustus src/etraining src/fastBlockSearch src/getSeq src/load2db src/load2sqlitedb src/pp_simScore src/prepareAlign
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
mkdir -p bin
/usr/bin/make -C auxprogs/aln2wig
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/aln2wig'
cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -ansi -pedantic -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -c aln2wig.c
aln2wig.c: In function 'main':
aln2wig.c:454:41: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation]
454 | strncpy(completedChromosomes[completedChromosomeCount-1],oldname,TOKEN_SIZE-1);
| ^
aln2wig.c:460:41: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation]
460 | strncpy(oldname,name,TOKEN_SIZE-1);
| ^
aln2wig.c:327:41: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation]
327 | strncpy(completedChromosomes[completedChromosomeCount-1],oldname,TOKEN_SIZE-1);
| ^
aln2wig.c:334:41: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation]
334 | strncpy(oldname,name,TOKEN_SIZE-1);
| ^
cc -Wall -Wno-sign-compare -ansi -pedantic -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o aln2wig aln2wig.o
mkdir -p ../../bin
cp aln2wig ../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2hints
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2hints'
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c bam2hints.cc -o bam2hints.o -I/usr/include/bamtools
In file included from /usr/include/c++/12/list:63,
from bam2hints.cc:9:
In member function 'std::_List_iterator< <template-parameter-1-1> >::_Self std::_List_iterator< <template-parameter-1-1> >::operator++(int) [with _Tp = hint_t]',
inlined from 'void printHints(FILE*, const char*)' at bam2hints.cc:326:121:
/usr/include/c++/12/bits/stl_list.h:297:28: warning: pointer used after 'void operator delete(void*, std::size_t)' [-Wuse-after-free]
297 | _M_node = _M_node->_M_next;
| ~~~~~~~~~^~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/c++/12/bits/c++allocator.h:33,
from /usr/include/c++/12/bits/allocator.h:46,
from /usr/include/c++/12/list:61:
In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = std::_List_node<hint_t>]',
inlined from 'static void std::allocator_traits<std::allocator<_Tp1> >::deallocate(allocator_type&, pointer, size_type) [with _Tp = std::_List_node<hint_t>]' at /usr/include/c++/12/bits/alloc_traits.h:496:23,
inlined from 'void std::__cxx11::_List_base<_Tp, _Alloc>::_M_put_node(typename _Node_alloc_traits::pointer) [with _Tp = hint_t; _Alloc = std::allocator<hint_t>]' at /usr/include/c++/12/bits/stl_list.h:522:39,
inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = hint_t; _Alloc = std::allocator<hint_t>]' at /usr/include/c++/12/bits/stl_list.h:2024:13,
inlined from 'std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::erase(const_iterator) [with _Tp = hint_t; _Alloc = std::allocator<hint_t>]' at /usr/include/c++/12/bits/list.tcc:158:15,
inlined from 'void printHints(FILE*, const char*)' at bam2hints.cc:334:26:
/usr/include/c++/12/bits/new_allocator.h:158:33: note: call to 'void operator delete(void*, std::size_t)' here
158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n));
| ^
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o bam2hints bam2hints.o -lbamtools -lz
mkdir -p ../../bin
cp bam2hints ../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/bam2wig
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2wig'
cc -Wall -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bam2wig.c -o bam2wig.o -I/usr/include/htslib
bam2wig.c: In function 'main':
bam2wig.c:172:35: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
172 | printf("%ld %d\n", pos+1, coverage);
| ~~^ ~~~~~
| | |
| long int hts_pos_t {aka long long int}
| %lld
cc -Wall -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now bam2wig.o -o bam2wig -lhts -lz -lpthread
mkdir -p ../../bin
cp bam2wig ../../bin/bam2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/compileSpliceCands
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands'
cc -Wall -pedantic -ansi -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compileSpliceCands.c
compileSpliceCands.c: In function 'getChromosome':
compileSpliceCands.c:226:9: warning: this decimal constant is unsigned only in ISO C90
226 | s = malloc(3500000000);
| ^
compileSpliceCands.c:216:9: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=]
216 | strncat(checkstring,chromosomename,strlen(chromosomename));
| ^
compileSpliceCands.c:216:9: note: length computed here
216 | strncat(checkstring,chromosomename,strlen(chromosomename));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compileSpliceCands.c:226:13: warning: argument 1 value '3500000000' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
226 | s = malloc(3500000000);
| ^~~~~~~~~~~~~~~~~~
In file included from compileSpliceCands.c:14:
/usr/include/stdlib.h:539:14: note: in a call to allocation function 'malloc' declared here
539 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
| ^~~~~~
compileSpliceCands.c: In function 'parseLine':
compileSpliceCands.c:292:9: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation]
292 | strncpy(d->name,tokens[0],LINEBUFFER);
| ^
compileSpliceCands.c: In function 'parseList':
compileSpliceCands.c:337:36: warning: 'left' may be used uninitialized [-Wmaybe-uninitialized]
337 | if(isCompatibleStrand(left->strand,right->strand))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compileSpliceCands.c:314:14: note: 'left' was declared here
314 | Data left;
| ^~~~
compileSpliceCands.c: In function 'main':
compileSpliceCands.c:563:17: warning: 'chromosomeLength' may be used uninitialized [-Wmaybe-uninitialized]
563 | parseList(&L,actualChromosome,chromosomeLength,oldname,maxSpliceSiteDiff,threshold,maxIntronLength);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compileSpliceCands.c:416:18: note: 'chromosomeLength' was declared here
416 | long int chromosomeLength;
| ^~~~~~~~~~~~~~~~
cc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o list.o list.c
cc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o compileSpliceCands compileSpliceCands.o list.o
cp compileSpliceCands ../../bin/compileSpliceCands
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src'
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c filterBam.cc -o filterBam.o -I/usr/include/bamtools -Iheaders -I./bamtools
In file included from filterBam.cc:17:
/usr/include/bamtools/api/algorithms/Sort.h:64:18: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
64 | typedef std::binary_function<BamAlignment, BamAlignment, bool> AlignmentSortBase;
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/bamtools/api/BamReader.h:13,
from filterBam.cc:14:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/MatePairs.cc -o MatePairs.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/getReferenceName.cc -o getReferenceName.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/initOptions.cc -o initOptions.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/SingleAlignment.cc -o SingleAlignment.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/printElapsedTime.cc -o printElapsedTime.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumMandIOperations.cc -o sumMandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumDandIOperations.cc -o sumDandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/PairednessCoverage.cc -o PairednessCoverage.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz
filterBam compiled with BAMTOOLS=/usr/include/bamtools
mkdir -p ../../../bin
mv filterBam ../../../bin/filterBam
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam'
/usr/bin/make -C auxprogs/homGeneMapping/src
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src'
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -o gene.o gene.cc -I../include
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -o genome.o genome.cc -I../include
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -o sqliteDB.o sqliteDB.cc -I../include
g++ -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wl,-z,relro -Wl,-z,now -o homGeneMapping main.cc gene.o genome.o sqliteDB.o -I../include -lsqlite3
mkdir -p ../../../bin/
cp homGeneMapping ../../../bin/homGeneMapping
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src'
/usr/bin/make -C auxprogs/joingenes
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/joingenes'
g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 joingenes.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 jg_transcript.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 jg_ios.cpp
jg_ios.cpp: In function 'void load(std::unordered_map<std::__cxx11::basic_string<char>, Gene*>&, std::string&, int&, std::unordered_map<std::__cxx11::basic_string<char>, bool>&, Properties&)':
jg_ios.cpp:251:14: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation]
251 | strncpy(copybuff, buff, 1014);
| ^
jg_ios.cpp:79:14: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation]
79 | strncpy(copybuff, buff, 1014);
| ^
jg_ios.cpp:148:16: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound 300 equals destination size [-Wstringop-truncation]
148 | strncpy(attribute, temp, 300);
| ^
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now joingenes.o jg_transcript.o jg_ios.o -o joingenes
mkdir -p ../../bin/
cp joingenes ../../bin/
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/joingenes'
dh_auto_build
make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
mkdir -p bin
cd src && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o genbank.o genbank.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o properties.o properties.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_profile.o pp_profile.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_hitseq.o pp_hitseq.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_scoring.o pp_scoring.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/12/vector:70,
from ../include/types.hh:36,
from ../include/geneticcode.hh:12,
from ../include/pp_profile.hh:16,
from pp_profile.cc:11:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const PP::Column&}; _Tp = PP::Column; _Alloc = std::allocator<PP::Column>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<PP::Column>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = PP::Column; _Alloc = std::allocator<PP::Column>]',
inlined from 'PP::Block::Block(PP::DistanceType, const std::vector<std::__cxx11::basic_string<char> >&, std::string)' at pp_profile.cc:206:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PP::Column*, std::vector<PP::Column> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'bool PP::Block::initThresholds()' at pp_profile.cc:257:30:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]',
inlined from 'bool PP::Block::initThresholds()' at pp_profile.cc:260:27:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]',
inlined from 'bool PP::Block::initThresholds()' at pp_profile.cc:263:34:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]',
inlined from 'bool PP::Block::initThresholds()' at pp_profile.cc:264:27:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:60,
from ../include/types.hh:39:
/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, LLDouble>; _KeyOfValue = std::_Select1st<std::pair<const int, LLDouble> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, LLDouble> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, LLDouble>, std::_Select1st<std::pair<const int, LLDouble> >, std::less<int>, std::allocator<std::pair<const int, LLDouble> > >::const_iterator' changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]',
inlined from 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map<int, LLDouble>*)' at pp_profile.cc:365:39:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]',
inlined from 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map<int, LLDouble>*)' at pp_profile.cc:376:39:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]',
inlined from 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map<int, LLDouble>*)' at pp_profile.cc:380:24:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = LLDouble; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, LLDouble> >]',
inlined from 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map<int, LLDouble>*)' at pp_profile.cc:388:30:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, LLDouble>, std::_Select1st<std::pair<const int, LLDouble> >, std::less<int>, std::allocator<std::pair<const int, LLDouble> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = LLDouble; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, LLDouble> >]',
inlined from 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map<int, LLDouble>*)' at pp_profile.cc:390:22:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, LLDouble>, std::_Select1st<std::pair<const int, LLDouble> >, std::less<int>, std::allocator<std::pair<const int, LLDouble> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {PP::Block}; _Tp = PP::Block; _Alloc = std::allocator<PP::Block>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<PP::Block>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {PP::Block}; _Tp = PP::Block; _Alloc = std::allocator<PP::Block>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = PP::Block; _Alloc = std::allocator<PP::Block>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void PP::Profile::parse_stream(std::istream&)' at pp_profile.cc:682:29:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PP::Block*, std::vector<PP::Block> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o statemodel.o statemodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/12/vector:70,
from ../include/types.hh:36,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const PP::BonusProbEntry&}; _Tp = PP::BonusProbEntry; _Alloc = std::allocator<PP::BonusProbEntry>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<PP::BonusProbEntry>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:60,
from ../include/types.hh:39:
/usr/include/c++/12/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(const_iterator, const_iterator) [with _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/12/bits/stl_tree.h:2502:5: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
2502 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_tree.h:2502:5: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::size_type std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const _Key&) [with _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/12/bits/stl_tree.h:2520:19: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
2520 | _M_erase_aux(__p.first, __p.second);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = PP::BonusProbEntry; _Alloc = std::allocator<PP::BonusProbEntry>]',
inlined from 'void PP::BonusProbType::push_back(int, const Double&)' at ../include/pp_scoring.hh:68:17,
inlined from 'void PP::MultiTargetExonScorer::initBonusProbs(PP::BonusProbType&, int, int)' at pp_scoring.cc:266:19:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PP::BonusProbEntry*, std::vector<PP::BonusProbEntry> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o namgene.o namgene.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
/usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair<SubstateId, ViterbiSubmapEntry>&}; _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]' at /usr/include/c++/12/bits/stl_map.h:1137:26,
inlined from 'void ViterbiSubmapType::erase(iterator, iterator) const' at ../include/vitmatrix.hh:329:15,
inlined from 'void PP::SubstateModel::scoreAssOrRDss(ViterbiSubmapType&, bool, int, const Double&)' at pp_scoring.cc:88:18:
/usr/include/c++/12/bits/stl_tree.h:1238:21: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
1238 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
In member function 'std::__enable_if_t<std::is_constructible<std::pair<const _Key, _Tp>, _Pair>::value, typename std::_Rb_tree<_Key, std::pair<const _Key, _Tp>, std::_Select1st<std::pair<const _Key, _Tp> >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind<std::pair<const _Key, _Tp> >::other>::iterator> std::map<_Key, _Tp, _Compare, _Alloc>::insert(const_iterator, _Pair&&) [with _Pair = std::pair<SubstateId, ViterbiSubmapEntry>&; _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'ViterbiSubmapType::iterator ViterbiSubmapType::insert(iterator, std::pair<SubstateId, ViterbiSubmapEntry>) const' at ../include/vitmatrix.hh:317:27,
inlined from 'ViterbiSubmapType::iterator ViterbiSubmapType::insert(iterator, SubstateId, const Double&, ViterbiSubmapType*) const' at ../include/vitmatrix.hh:322:19,
inlined from 'void ViterbiSubmapType::push_back(SubstateId, const Double&, ViterbiSubmapType*) const' at ../include/vitmatrix.hh:326:12,
inlined from 'void PP::SubstateModel::scoreAssOrRDss(ViterbiSubmapType&, bool, int, const Double&)' at pp_scoring.cc:114:23:
/usr/include/c++/12/bits/stl_map.h:925:45: note: parameter passing for argument of type 'std::map<SubstateId, ViterbiSubmapEntry>::const_iterator' {aka 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator'} changed in GCC 7.1
925 | return _M_t._M_emplace_hint_unique(__position,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
926 | std::forward<_Pair>(__x));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::__enable_if_t<std::is_constructible<std::pair<const _Key, _Tp>, _Pair>::value, typename std::_Rb_tree<_Key, std::pair<const _Key, _Tp>, std::_Select1st<std::pair<const _Key, _Tp> >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind<std::pair<const _Key, _Tp> >::other>::iterator> std::map<_Key, _Tp, _Compare, _Alloc>::insert(const_iterator, _Pair&&) [with _Pair = std::pair<SubstateId, ViterbiSubmapEntry>&; _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'ViterbiSubmapType::iterator ViterbiSubmapType::insert(iterator, std::pair<SubstateId, ViterbiSubmapEntry>) const' at ../include/vitmatrix.hh:317:27,
inlined from 'ViterbiSubmapType::iterator ViterbiSubmapType::insert(iterator, SubstateId, const Double&, ViterbiSubmapType*) const' at ../include/vitmatrix.hh:322:19,
inlined from 'void ViterbiSubmapType::push_back(SubstateId, const Double&, ViterbiSubmapType*) const' at ../include/vitmatrix.hh:326:12,
inlined from 'void PP::SubstateModel::scoreAssOrRDss(ViterbiSubmapType&, bool, int, const Double&)' at pp_scoring.cc:122:22:
/usr/include/c++/12/bits/stl_map.h:925:45: note: parameter passing for argument of type 'std::map<SubstateId, ViterbiSubmapEntry>::const_iterator' {aka 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator'} changed in GCC 7.1
925 | return _M_t._M_emplace_hint_unique(__position,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
926 | std::forward<_Pair>(__x));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const SubstateId&>, std::tuple<>}; _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'short int& ViterbiSubmapType::succCount(SubstateId)' at ../include/vitmatrix.hh:335:27,
inlined from 'void ViterbiSubmapType::eraseAndDecCounts(iterator) const' at ../include/vitmatrix.hh:418:17,
inlined from 'void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)' at pp_scoring.cc:183:28:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'short int& ViterbiSubmapType::succCount(SubstateId)' at ../include/vitmatrix.hh:335:27,
inlined from 'void ViterbiSubmapType::eraseAndDecCounts(iterator) const' at ../include/vitmatrix.hh:418:17,
inlined from 'void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)' at pp_scoring.cc:196:28:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'short int& ViterbiSubmapType::succCount(SubstateId)' at ../include/vitmatrix.hh:335:27,
inlined from 'void ViterbiSubmapType::eraseAndDecCounts(iterator) const' at ../include/vitmatrix.hh:418:17,
inlined from 'void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)' at pp_scoring.cc:220:31:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'short int& ViterbiSubmapType::succCount(SubstateId)' at ../include/vitmatrix.hh:335:27,
inlined from 'void ViterbiSubmapType::eraseAndDecCounts(iterator) const' at ../include/vitmatrix.hh:418:17,
inlined from 'void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)' at pp_scoring.cc:234:27:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'short int& ViterbiSubmapType::succCount(SubstateId)' at ../include/vitmatrix.hh:335:27,
inlined from 'void ViterbiSubmapType::eraseAndDecCounts(iterator) const' at ../include/vitmatrix.hh:418:17,
inlined from 'void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)' at pp_scoring.cc:247:31:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::__enable_if_t<std::is_constructible<std::pair<const _Key, _Tp>, _Pair>::value, typename std::_Rb_tree<_Key, std::pair<const _Key, _Tp>, std::_Select1st<std::pair<const _Key, _Tp> >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind<std::pair<const _Key, _Tp> >::other>::iterator> std::map<_Key, _Tp, _Compare, _Alloc>::insert(const_iterator, _Pair&&) [with _Pair = std::pair<SubstateId, ViterbiSubmapEntry>&; _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'ViterbiSubmapType::iterator ViterbiSubmapType::insert(iterator, std::pair<SubstateId, ViterbiSubmapEntry>) const' at ../include/vitmatrix.hh:317:27,
inlined from 'ViterbiSubmapType::iterator ViterbiSubmapType::insert(iterator, SubstateId, const Double&, ViterbiSubmapType*) const' at ../include/vitmatrix.hh:322:19,
inlined from 'void PP::BonusProbType::mergeIntoSubmap(int, ViterbiSubmapType&, SubstateIdMap*)' at pp_scoring.cc:310:16:
/usr/include/c++/12/bits/stl_map.h:925:45: note: parameter passing for argument of type 'std::map<SubstateId, ViterbiSubmapEntry>::const_iterator' {aka 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator'} changed in GCC 7.1
925 | return _M_t._M_emplace_hint_unique(__position,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
926 | std::forward<_Pair>(__x));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]' at /usr/include/c++/12/bits/stl_map.h:1137:26,
inlined from 'void ViterbiSubmapType::erase(iterator, iterator) const' at ../include/vitmatrix.hh:329:15,
inlined from 'virtual void PP::MultiTargetExonScorer::postProcessing(const Double&)' at pp_scoring.cc:549:21:
/usr/include/c++/12/bits/stl_tree.h:1238:21: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
1238 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'bool ViterbiSubmapType::setMax(SubstateId, Double, ViterbiSubmapType*) const' at ../include/vitmatrix.hh:428:52,
inlined from 'virtual void PP::SingleTargetExonScorer::exportSubstates(ViterbiSubmapType&)' at pp_scoring.cc:806:18,
inlined from 'virtual void PP::SingleTargetExonScorer::exportSubstates(ViterbiSubmapType&)' at pp_scoring.cc:791:6:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'bool ViterbiSubmapType::setMax(SubstateId, Double, ViterbiSubmapType*) const' at ../include/vitmatrix.hh:428:52,
inlined from 'void PP::MultiTargetExonScorer::updateBonusProbs(PP::Position, const Double&)' at pp_scoring.cc:386:22:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]' at /usr/include/c++/12/bits/stl_map.h:1137:26,
inlined from 'void ViterbiSubmapType::erase(iterator, iterator) const' at ../include/vitmatrix.hh:329:15,
inlined from 'virtual void PP::MultiTargetExonScorer::scoreInternal(ViterbiColumnType&, int, const Double&)' at pp_scoring.cc:499:19:
/usr/include/c++/12/bits/stl_tree.h:1238:21: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
1238 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'bool ViterbiSubmapType::setMax(SubstateId, Double, ViterbiSubmapType*) const' at ../include/vitmatrix.hh:428:52,
inlined from 'virtual void PP::MultiTargetExonScorer::scoreInternal(ViterbiColumnType&, int, const Double&)' at pp_scoring.cc:524:26:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o types.o types.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/12/vector:70,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from statemodel.cc:8:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {Ancestor}; _Tp = Ancestor; _Alloc = std::allocator<Ancestor>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<Ancestor>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Ancestor}; _Tp = Ancestor; _Alloc = std::allocator<Ancestor>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Ancestor; _Alloc = std::allocator<Ancestor>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void StateModel::initPredecessors(Matrix<LLDouble>&, int)' at statemodel.cc:45:24:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Ancestor*, std::vector<Ancestor> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o gene.o gene.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o evaluation.o evaluation.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/algorithm:61,
from ../include/types.hh:38,
from types.cc:8:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >; _Distance = int; _Tp = LLDouble; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'Double quantile(const std::vector<LLDouble>&, float)' at types.cc:513:12:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'Double quantile(const std::vector<LLDouble>&, float)' at types.cc:513:12:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from ../include/types.hh:36:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'static void Constant::init()' at types.cc:356:21:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'static void Constant::init()' at types.cc:363:21:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'static void Constant::init()' at types.cc:370:17:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o motif.o motif.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/algorithm:61,
from ../include/types.hh:38,
from ../include/geneticcode.hh:12,
from ../include/motif.hh:13,
from ../include/gene.hh:12,
from gene.cc:8:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o geneticcode.o geneticcode.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/12/vector:70,
from ../include/matrix.hh:12,
from ../include/motif.hh:12,
from motif.cc:10:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]',
inlined from 'Double Motif::getProbThreshold(double, int)' at motif.cc:452:28:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o hints.o hints.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o extrinsicinfo.o extrinsicinfo.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/12/list:64,
from ../include/vitmatrix.hh:17,
from ../include/pp_scoring.hh:16,
from ../include/gene.hh:13:
/usr/include/c++/12/bits/list.tcc: In function 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator<PP::Match>; _Tp = PP::Match; _Alloc = std::allocator<PP::Match>]':
/usr/include/c++/12/bits/list.tcc:308:7: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
308 | list<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/list.tcc:308:7: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
hints.cc: In function 'std::istream& operator>>(std::istream&, Feature&)':
hints.cc:82:16: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation]
82 | strncpy(copybuff, buff, 1014);
| ^
In member function 'std::__cxx11::list<_Tp, _Alloc>& std::__cxx11::list<_Tp, _Alloc>::operator=(const std::__cxx11::list<_Tp, _Alloc>&) [with _Tp = PP::Match; _Alloc = std::allocator<PP::Match>]',
inlined from 'std::__cxx11::list<_Tp, _Alloc>& std::__cxx11::list<_Tp, _Alloc>::operator=(const std::__cxx11::list<_Tp, _Alloc>&) [with _Tp = PP::Match; _Alloc = std::allocator<PP::Match>]' at /usr/include/c++/12/bits/list.tcc:267:5,
inlined from 'static StatePath* StatePath::condenseStatePath(StatePath*)' at gene.cc:995:37:
/usr/include/c++/12/bits/list.tcc:286:29: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
286 | _M_assign_dispatch(__x.begin(), __x.end(), __false_type());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o projectio.o projectio.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In member function 'std::__cxx11::list<_Tp, _Alloc>& std::__cxx11::list<_Tp, _Alloc>::operator=(const std::__cxx11::list<_Tp, _Alloc>&) [with _Tp = PP::Match; _Alloc = std::allocator<PP::Match>]',
inlined from 'std::__cxx11::list<_Tp, _Alloc>& std::__cxx11::list<_Tp, _Alloc>::operator=(const std::__cxx11::list<_Tp, _Alloc>&) [with _Tp = PP::Match; _Alloc = std::allocator<PP::Match>]' at /usr/include/c++/12/bits/list.tcc:267:5,
inlined from 'Gene::Gene(const Gene&)' at gene.cc:1391:28:
/usr/include/c++/12/bits/list.tcc:286:29: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
286 | _M_assign_dispatch(__x.begin(), __x.end(), __false_type());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o intronmodel.o intronmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o exonmodel.o exonmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/12/vector:70,
from ../include/matrix.hh:12,
from ../include/motif.hh:12:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void examineBaseCountOfGeneSeq(AnnoSequence*)' at gene.cc:3431:22:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'void examineBaseCountOfGeneSeq(AnnoSequence*)' at gene.cc:3440:14:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'void examineBaseCountOfGeneSeq(AnnoSequence*)' at gene.cc:3440:14:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o igenicmodel.o igenicmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/12/map:60,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from ../include/statemodel.hh:13,
from ../include/intronmodel.hh:11,
from intronmodel.cc:8:
/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, LLDouble>; _KeyOfValue = std::_Select1st<std::pair<const int, LLDouble> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, LLDouble> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, LLDouble>, std::_Select1st<std::pair<const int, LLDouble> >, std::less<int>, std::allocator<std::pair<const int, LLDouble> > >::const_iterator' changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = LLDouble; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, LLDouble> >]',
inlined from 'static Double IntronModel::dSSProb(int, bool)' at intronmodel.cc:1232:16:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, LLDouble>, std::_Select1st<std::pair<const int, LLDouble> >, std::less<int>, std::allocator<std::pair<const int, LLDouble> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = LLDouble; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, LLDouble> >]',
inlined from 'static Double IntronModel::dSSProb(int, bool)' at intronmodel.cc:1234:16:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, LLDouble>, std::_Select1st<std::pair<const int, LLDouble> >, std::less<int>, std::allocator<std::pair<const int, LLDouble> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = LLDouble; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, LLDouble> >]',
inlined from 'static Double IntronModel::aSSProb(int, bool)' at intronmodel.cc:1175:12:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, LLDouble>, std::_Select1st<std::pair<const int, LLDouble> >, std::less<int>, std::allocator<std::pair<const int, LLDouble> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = LLDouble; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, LLDouble> >]',
inlined from 'static Double IntronModel::aSSProb(int, bool)' at intronmodel.cc:1177:12:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, LLDouble>, std::_Select1st<std::pair<const int, LLDouble> >, std::less<int>, std::allocator<std::pair<const int, LLDouble> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o utrmodel.o utrmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/12/map:60,
from ../include/types.hh:39,
from ../include/hints.hh:12,
from ../include/extrinsicinfo.hh:15,
from extrinsicinfo.cc:10:
/usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = Feature; _Val = Feature; _KeyOfValue = std::_Identity<Feature>; _Compare = std::less<Feature>; _Alloc = std::allocator<Feature>]':
/usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::const_iterator' changed in GCC 7.1
2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o merkmal.o merkmal.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/12/algorithm:61,
from ../include/types.hh:38:
/usr/include/c++/12/bits/stl_algo.h: In function '_OutputIterator std::__set_difference(_InputIterator1, _InputIterator1, _InputIterator2, _InputIterator2, _OutputIterator, _Compare) [with _InputIterator1 = _Rb_tree_const_iterator<Feature>; _InputIterator2 = _Rb_tree_const_iterator<Feature>; _OutputIterator = insert_iterator<set<Feature> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:5334:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5334 | __set_difference(_InputIterator1 __first1, _InputIterator1 __last1,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:5334:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:5334:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:5334:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o vitmatrix.o vitmatrix.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator<Feature>; _IIter2 = _Rb_tree_const_iterator<Feature>; _OIter = insert_iterator<set<Feature> >]',
inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2519:20:
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5399 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator<Feature>; _IIter2 = _Rb_tree_const_iterator<Feature>; _OIter = insert_iterator<set<Feature> >]',
inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2525:17:
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5399 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator<Feature>; _IIter2 = _Rb_tree_const_iterator<Feature>; _OIter = insert_iterator<set<Feature> >]',
inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2538:20:
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5399 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator<Feature>; _IIter2 = _Rb_tree_const_iterator<Feature>; _OIter = insert_iterator<set<Feature> >]',
inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2559:20:
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5399 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator<Feature>; _IIter2 = _Rb_tree_const_iterator<Feature>; _OIter = insert_iterator<set<Feature> >]',
inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2565:17:
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5399 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator<Feature>; _IIter2 = _Rb_tree_const_iterator<Feature>; _OIter = insert_iterator<set<Feature> >]',
inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2577:20:
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5399 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator<Feature>; _IIter2 = _Rb_tree_const_iterator<Feature>; _OIter = insert_iterator<set<Feature> >]',
inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2597:20:
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5399 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator<Feature>; _IIter2 = _Rb_tree_const_iterator<Feature>; _OIter = insert_iterator<set<Feature> >]',
inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2603:17:
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5399 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator<Feature>; _IIter2 = _Rb_tree_const_iterator<Feature>; _OIter = insert_iterator<set<Feature> >]',
inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2615:20:
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5399 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator<Feature>; _IIter2 = _Rb_tree_const_iterator<Feature>; _OIter = insert_iterator<set<Feature> >]',
inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2643:20:
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5399 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator<Feature>; _IIter2 = _Rb_tree_const_iterator<Feature>; _OIter = insert_iterator<set<Feature> >]',
inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2649:17:
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5399 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator<Feature>; _IIter2 = _Rb_tree_const_iterator<Feature>; _OIter = insert_iterator<set<Feature> >]',
inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2661:20:
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5399 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:70,
from ../include/types.hh:36,
from ../include/vitmatrix.hh:12,
from vitmatrix.cc:10:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ViterbiSubmapType&}; _Tp = ViterbiSubmapType; _Alloc = std::allocator<ViterbiSubmapType>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<ViterbiSubmapType>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:60,
from ../include/types.hh:39:
/usr/include/c++/12/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(const_iterator, const_iterator) [with _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/12/bits/stl_tree.h:2502:5: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
2502 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_tree.h:2502:5: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]' at /usr/include/c++/12/bits/stl_map.h:1137:26,
inlined from 'void ViterbiSubmapType::erase(iterator, iterator) const' at ../include/vitmatrix.hh:329:15,
inlined from 'void ViterbiSubmapType::useMaximum(Double&)' at vitmatrix.cc:164:10:
/usr/include/c++/12/bits/stl_tree.h:1238:21: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
1238 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]' at /usr/include/c++/12/bits/stl_map.h:1137:26,
inlined from 'void ViterbiSubmapType::erase(iterator, iterator) const' at ../include/vitmatrix.hh:329:15,
inlined from 'void ViterbiSubmapType::useMaximum(Double&)' at vitmatrix.cc:166:7:
/usr/include/c++/12/bits/stl_tree.h:1238:21: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
1238 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::size_type std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const _Key&) [with _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::size_type std::map<_Key, _Tp, _Compare, _Alloc>::erase(const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]' at /usr/include/c++/12/bits/stl_map.h:1117:26,
inlined from 'int ViterbiSubmapType::eraseUnneededSubstate(SubstateId)' at vitmatrix.cc:103:18:
/usr/include/c++/12/bits/stl_tree.h:2520:19: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
2520 | _M_erase_aux(__p.first, __p.second);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {ViterbiEntryType}; _Tp = ViterbiEntryType; _Alloc = std::allocator<ViterbiEntryType>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<ViterbiEntryType>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {ViterbiEntryType}; _Tp = ViterbiEntryType; _Alloc = std::allocator<ViterbiEntryType>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = ViterbiEntryType; _Alloc = std::allocator<ViterbiEntryType>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void ViterbiColumnType::addState(int, signed char)' at vitmatrix.cc:289:14:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ViterbiEntryType*, std::vector<ViterbiEntryType> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ViterbiSubmapType; _Alloc = std::allocator<ViterbiSubmapType>]',
inlined from 'ViterbiSubmapType& ViterbiColumnType::addSubstates(const ViterbiSubmapType&)' at vitmatrix.cc:234:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ViterbiSubmapType*, std::vector<ViterbiSubmapType> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair<SubstateId, ViterbiSubmapEntry>&}; _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
In member function 'std::__enable_if_t<std::is_constructible<std::pair<const _Key, _Tp>, _Pair>::value, typename std::_Rb_tree<_Key, std::pair<const _Key, _Tp>, std::_Select1st<std::pair<const _Key, _Tp> >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind<std::pair<const _Key, _Tp> >::other>::iterator> std::map<_Key, _Tp, _Compare, _Alloc>::insert(const_iterator, _Pair&&) [with _Pair = std::pair<SubstateId, ViterbiSubmapEntry>&; _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'ViterbiSubmapType::iterator ViterbiSubmapType::insert(iterator, std::pair<SubstateId, ViterbiSubmapEntry>) const' at ../include/vitmatrix.hh:317:27,
inlined from 'ViterbiSubmapType::iterator ViterbiSubmapType::insert(iterator, SubstateId, const Double&, ViterbiSubmapType*) const' at ../include/vitmatrix.hh:322:19,
inlined from 'void ViterbiSubmapType::merge(ViterbiSubmapType&, Double)' at vitmatrix.cc:73:9:
/usr/include/c++/12/bits/stl_map.h:925:45: note: parameter passing for argument of type 'std::map<SubstateId, ViterbiSubmapEntry>::const_iterator' {aka 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator'} changed in GCC 7.1
925 | return _M_t._M_emplace_hint_unique(__position,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
926 | std::forward<_Pair>(__x));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const SubstateId&>, std::tuple<>}; _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'short int& ViterbiSubmapType::succCount(SubstateId)' at ../include/vitmatrix.hh:335:27,
inlined from 'void ViterbiSubmapType::registerPredecessors()' at vitmatrix.cc:131:35:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]',
inlined from 'short int& ViterbiSubmapType::succCount(SubstateId)' at ../include/vitmatrix.hh:335:27,
inlined from 'void ViterbiSubmapType::registerPredecessors()' at vitmatrix.cc:148:21:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o lldouble.o lldouble.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/algorithm:61,
from ../include/types.hh:38,
from ../include/merkmal.hh:14,
from merkmal.cc:10:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >; _Distance = int; _Tp = LLDouble; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o mea.o mea.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o graph.o graph.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'static std::vector<double> CRF::capOutliers(std::vector<double>)' at merkmal.cc:841:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'static std::vector<double> CRF::capOutliers(std::vector<double>)' at merkmal.cc:841:11:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from ../include/types.hh:36:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'void BinnedMMGroup::trainBins(int)' at merkmal.cc:111:14:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'void BinnedMMGroup::trainBins(int)' at merkmal.cc:111:14:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'static void CRF::onlineLargeMarginTraining(Parameters*, std::vector<AnnoSequence*>, FeatureCollection&)' at merkmal.cc:396:14:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from ../include/matrix.hh:12,
from ../include/motif.hh:12,
from ../include/gene.hh:12,
from ../include/mea.hh:11,
from mea.cc:8:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'AugustusGraph::AugustusGraph(std::__cxx11::list<Status>*, const char*)' at ../include/graph.hh:344:25:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o meaPath.o meaPath.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o exoncand.o exoncand.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o randseqaccess.o randseqaccess.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o fasta.o fasta.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o ncmodel.o ncmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o parser/parse.o parser/parse.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o scanner/lex.o scanner/lex.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o genomicMSA.o genomicMSA.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o geneMSA.o geneMSA.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/12/vector:70,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from ../include/ncmodel.hh:11,
from ncmodel.cc:8:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]',
inlined from 'void NcModel::computeLengthDistributions()' at ncmodel.cc:142:25:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o contTimeMC.o contTimeMC.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/algorithm:61,
from ../include/types.hh:38,
from ../include/geneticcode.hh:12,
from contTimeMC.cc:10:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'void Evo::setBranchLengths(std::vector<double>, int)' at contTimeMC.cc:52:9:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'void Evo::setBranchLengths(std::vector<double>, int)' at contTimeMC.cc:52:9:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from ../include/matrix.hh:12,
from ../include/motif.hh:12,
from ../include/gene.hh:12,
from ../include/randseqaccess.hh:12,
from randseqaccess.cc:10:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {hints}; _Tp = hints; _Alloc = std::allocator<hints>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<hints>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from ../include/matrix.hh:12,
from ../include/contTimeMC.hh:13,
from contTimeMC.cc:9:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'virtual void ExonEvo::addBranchLength(double)' at contTimeMC.cc:384:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {hints}; _Tp = hints; _Alloc = std::allocator<hints>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = hints; _Alloc = std::allocator<hints>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mysqlpp::Query::storein_sequence(Sequence&, const mysqlpp::SQLTypeAdapter&) [with Sequence = std::vector<hints>]' at /usr/include/mysql++/query.h:763:18:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<hints*, std::vector<hints> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o codonevo.o codonevo.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o compgenepred.o compgenepred.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/12/vector:70,
from ../include/matrix.hh:12,
from ../include/contTimeMC.hh:13,
from ../include/codonevo.hh:11,
from codonevo.cc:9:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void CodonEvo::setPrior(double)' at codonevo.cc:64:22:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void CodonEvo::setOmegas(int)' at codonevo.cc:42:18:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void CodonEvo::setOmegas(int)' at codonevo.cc:43:21:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void CodonEvo::setOmegas(int)' at codonevo.cc:45:18:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void CodonEvo::setOmegas(int)' at codonevo.cc:48:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'Parsimony::Parsimony()' at ../include/contTimeMC.hh:177:23,
inlined from 'double CodonEvo::estOmegaOnSeqTuple(std::vector<std::__cxx11::basic_string<char> >&, PhyloTree*, int&)' at codonevo.cc:553:15:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void CodonEvo::setAAPostProbs()' at codonevo.cc:92:17:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o phylotree.o phylotree.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/12/vector:70,
from ../include/types.hh:36,
from ../include/geneticcode.hh:12,
from geneMSA.cc:10:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void GeneMSA::calcConsScore(std::__cxx11::list<OrthoExon>&, const std::vector<AnnoSequence*>&, std::string)' at geneMSA.cc:1696:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from ../include/phylotree.hh:13,
from phylotree.cc:12:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void Treenode::resizeTable(int, double)' at phylotree.cc:55:17:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void Treenode::resizeTable(int, double)' at phylotree.cc:55:17,
inlined from 'double PhyloTree::pruningAlgor(std::vector<int>&, Evo*, int)' at phylotree.cc:246:23:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void Treenode::resizeTable(int, double)' at phylotree.cc:55:17,
inlined from 'double PhyloTree::pruningAlgor(std::vector<int>&, Evo*, int)' at phylotree.cc:249:23:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void Treenode::resizeTable(int, double)' at phylotree.cc:55:17,
inlined from 'double PhyloTree::pruningAlgor(std::vector<int>&, Evo*, int)' at phylotree.cc:255:26:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void Treenode::resizeTable(int, double)' at phylotree.cc:55:17,
inlined from 'int PhyloTree::fitch(std::vector<int>&, int)' at phylotree.cc:540:26:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void Treenode::resizeTable(int, double)' at phylotree.cc:55:17,
inlined from 'int PhyloTree::fitch(std::vector<int>&, int)' at phylotree.cc:547:26:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void Treenode::resizeTable(int, double)' at phylotree.cc:55:17,
inlined from 'double PhyloTree::MAP(std::vector<int>&, std::vector<double>&, Evo*, bool)' at phylotree.cc:399:26:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void Treenode::resizeTable(int, double)' at phylotree.cc:55:17,
inlined from 'double PhyloTree::MAP(std::vector<int>&, std::vector<double>&, Evo*, bool)' at phylotree.cc:412:26:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void PhyloTree::getBranchLengths(std::vector<double>&) const' at phylotree.cc:317:25:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o orthograph.o orthograph.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o orthoexon.o orthoexon.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void cumValues::addLogliks(std::vector<double>*)' at ../include/geneMSA.hh:41:21,
inlined from 'void GeneMSA::computeOmegasEff(std::__cxx11::list<OrthoExon>&, const std::vector<AnnoSequence*>&, PhyloTree*, std::ofstream*)' at geneMSA.cc:1551:17:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from ../include/types.hh:36,
from ../include/hints.hh:12,
from ../include/extrinsicinfo.hh:15,
from ../include/compgenepred.hh:12,
from compgenepred.cc:8:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'AugustusGraph::AugustusGraph(std::__cxx11::list<Status>*, const char*)' at ../include/graph.hh:344:25:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from ../include/types.hh:36,
from ../include/exoncand.hh:13,
from ../include/orthoexon.hh:11,
from orthoexon.cc:10:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void OrthoExon::setOmega(std::vector<double>*, CodonEvo*, bool)' at orthoexon.cc:168:25:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void CompGenePred::runPredictionOrTest()' at compgenepred.cc:280:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void CompGenePred::runPredictionOrTest()' at compgenepred.cc:282:41:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void CompGenePred::runPredictionOrTest()' at compgenepred.cc:286:27:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void CompGenePred::runPredictionOrTest()' at compgenepred.cc:293:26:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'OrthoExon::OrthoExon(int_fast64_t, size_t)' at orthoexon.cc:21:19:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o alignment.o alignment.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o speciesgraph.o speciesgraph.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o codonMSA.o codonMSA.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o train_logReg_param.o train_logReg_param.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o tokenizer.o tokenizer.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o sqliteDB.o sqliteDB.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o commontrain.o commontrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o igenictrain.o igenictrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o introntrain.o introntrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o exontrain.o exontrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o utrtrain.o utrtrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o dummy.o dummy.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/12/vector:70,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from ../include/intronmodel.hh:11,
from introntrain.cc:8:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from ../include/exonmodel.hh:11,
from exontrain.cc:8:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]',
inlined from 'void BinnedMMGroup::addProb(Double)' at ../include/merkmal.hh:126:47,
inlined from 'void IntronModel::makeDSSProbs()' at introntrain.cc:583:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]',
inlined from 'void BinnedMMGroup::addProb(Double)' at ../include/merkmal.hh:126:47,
inlined from 'void IntronModel::buildProbabilities(const AnnoSequence*)' at introntrain.cc:415:28:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]',
inlined from 'void BinnedMMGroup::addProb(Double)' at ../include/merkmal.hh:126:47,
inlined from 'void ExonModel::buildProbabilities()' at exontrain.cc:130:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]',
inlined from 'void BinnedMMGroup::addProb(Double)' at ../include/merkmal.hh:126:47,
inlined from 'void ExonModel::buildProbabilities()' at exontrain.cc:135:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o pp_simScore pp_simscore.cc fasta.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o load2db load2db.cc fasta.o hints.o types.o properties.o lldouble.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o getSeq getSeq.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
cp prepareAlign ../bin/
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o load2sqlitedb load2sqlitedb.cc fasta.o hints.o types.o properties.o lldouble.o sqliteDB.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
cp load2sqlitedb ../bin/
echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
In file included from /usr/include/c++/12/vector:70,
from ../include/types.hh:36,
from ../include/properties.hh:14,
from ../include/pp_simscore.hh:21,
from pp_simscore.cc:10:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void SS::SimilarityScore::printAlignment()' at pp_simscore.cc:723:56:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cp load2db ../bin/
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
cp getSeq ../bin/
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
cp pp_simScore ../bin/
In file included from /usr/include/c++/12/vector:70,
from ../include/types.hh:36,
from etraining.cc:9:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'static void CRF::compareWeights(Parameters*, std::vector<T>&, std::vector<V>&, int) [with U = double; V = double]' at ../include/merkmal.hh:277:27:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cp etraining ../bin/
cp fastBlockSearch ../bin/
cp augustus ../bin/
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/src'
cd auxprogs && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs'
cd aln2wig; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/aln2wig'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: 'aln2wig' is up to date.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/aln2wig'
cd bam2hints; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2hints'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: 'bam2hints' is up to date.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2hints'
cd compileSpliceCands; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: 'compileSpliceCands' is up to date.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands'
cd filterBam; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src;make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src'
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz
filterBam compiled with BAMTOOLS=/usr/include/bamtools
mkdir -p ../../../bin
mv filterBam ../../../bin/filterBam
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam'
cd homGeneMapping; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src; make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src'
make[5]: Nothing to be done for 'all'.
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping'
cd joingenes; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/joingenes'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/joingenes'
cd utrrnaseq/Debug; make all;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/utrrnaseq/Debug'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
Building file: ../src/Compute_UTRs.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Compute_UTRs.d" -MT"src/Compute_UTRs.o" -o "src/Compute_UTRs.o" "../src/Compute_UTRs.cpp"
In file included from /usr/include/c++/12/map:61,
from ../src/Compute_UTRs.hpp:14,
from ../src/Compute_UTRs.cpp:8:
/usr/include/c++/12/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = double; _Compare = std::less<unsigned int>; _Alloc = std::allocator<std::pair<const unsigned int, double> >]':
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<unsigned int, std::pair<const unsigned int, double>, std::_Select1st<std::pair<const unsigned int, double> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = unsigned int; _Tp = double; _Compare = std::less<unsigned int>; _Alloc = std::allocator<std::pair<const unsigned int, double> >]':
/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree<unsigned int, std::pair<const unsigned int, double>, std::_Select1st<std::pair<const unsigned int, double> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, double> > >::const_iterator' changed in GCC 7.1
530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
531 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
532 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:60:
/usr/include/c++/12/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const unsigned int&>, std::tuple<>}; _Key = unsigned int; _Val = std::pair<const unsigned int, double>; _KeyOfValue = std::_Select1st<std::pair<const unsigned int, double> >; _Compare = std::less<unsigned int>; _Alloc = std::allocator<std::pair<const unsigned int, double> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<unsigned int, std::pair<const unsigned int, double>, std::_Select1st<std::pair<const unsigned int, double> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, double> > >::const_iterator' changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<unsigned int&&>, std::tuple<>}; _Key = unsigned int; _Val = std::pair<const unsigned int, double>; _KeyOfValue = std::_Select1st<std::pair<const unsigned int, double> >; _Compare = std::less<unsigned int>; _Alloc = std::allocator<std::pair<const unsigned int, double> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<unsigned int, std::pair<const unsigned int, double>, std::_Select1st<std::pair<const unsigned int, double> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, double> > >::const_iterator' changed in GCC 7.1
/usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = unsigned int; _Val = std::pair<const unsigned int, double>; _KeyOfValue = std::_Select1st<std::pair<const unsigned int, double> >; _Compare = std::less<unsigned int>; _Alloc = std::allocator<std::pair<const unsigned int, double> >]':
/usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree<unsigned int, std::pair<const unsigned int, double>, std::_Select1st<std::pair<const unsigned int, double> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, double> > >::const_iterator' changed in GCC 7.1
2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Finished building: ../src/Compute_UTRs.cpp
Building file: ../src/Coord_Transform.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Coord_Transform.d" -MT"src/Coord_Transform.o" -o "src/Coord_Transform.o" "../src/Coord_Transform.cpp"
../src/Coord_Transform.cpp:25:59: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
25 | template <class Intron> struct finding_intron_greater_s : binary_function<Genomic_Data::Intron,unsigned,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from ../src/flex_vec.hpp:8,
from ../src/Coord_Transform.cpp:5:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Coord_Transform.cpp:33:58: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
33 | template <class Intron> struct finding_intron_lesser_s : binary_function<Genomic_Data::Intron,unsigned,bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Coord_Transform.cpp:41:59: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
41 | template <class Intron> struct finding_intron_greater_e : binary_function<Genomic_Data::Intron,unsigned,bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Coord_Transform.cpp:49:58: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
49 | template <class Intron> struct finding_intron_lesser_e : binary_function<Genomic_Data::Intron,unsigned,bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Coord_Transform.cpp: In constructor 'Coord_Transform::Coord_Transform(unsigned int, int, unsigned int, unsigned int, unsigned int, unsigned int, std::vector<Genomic_Data::Intron>*)':
../src/Coord_Transform.cpp:77:56: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_greater_s<Genomic_Data::Intron>; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
77 | bind2nd(finding_intron_greater_s<Genomic_Data::Intron>(), i));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_function.h:1438:
/usr/include/c++/12/backward/binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
../src/Coord_Transform.cpp:81:56: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_greater_e<Genomic_Data::Intron>; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
81 | bind2nd(finding_intron_greater_e<Genomic_Data::Intron>(), i));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/backward/binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
../src/Coord_Transform.cpp:89:56: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_lesser_e<Genomic_Data::Intron>; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
89 | bind2nd(finding_intron_lesser_e<Genomic_Data::Intron>(), i));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/backward/binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
../src/Coord_Transform.cpp:93:56: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_lesser_s<Genomic_Data::Intron>; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
93 | bind2nd(finding_intron_lesser_s<Genomic_Data::Intron>(), i));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/backward/binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
Finished building: ../src/Coord_Transform.cpp
Building file: ../src/Genomic_Data.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Genomic_Data.d" -MT"src/Genomic_Data.o" -o "src/Genomic_Data.o" "../src/Genomic_Data.cpp"
Finished building: ../src/Genomic_Data.cpp
Building file: ../src/Splice_Sites.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Splice_Sites.d" -MT"src/Splice_Sites.o" -o "src/Splice_Sites.o" "../src/Splice_Sites.cpp"
Finished building: ../src/Splice_Sites.cpp
Building file: ../src/Supporting_Methods.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Supporting_Methods.d" -MT"src/Supporting_Methods.o" -o "src/Supporting_Methods.o" "../src/Supporting_Methods.cpp"
Finished building: ../src/Supporting_Methods.cpp
Building file: ../src/Test.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Test.d" -MT"src/Test.o" -o "src/Test.o" "../src/Test.cpp"
Finished building: ../src/Test.cpp
Building file: ../src/UTRs.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/UTRs.d" -MT"src/UTRs.o" -o "src/UTRs.o" "../src/UTRs.cpp"
../src/UTRs.cpp:83:9: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
83 | binary_function<Genomic_Data::CRB,unsigned,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from ../src/Genomic_Data.hpp:8,
from ../src/UTRs.cpp:5:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/UTRs.cpp:92:9: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
92 | binary_function<Genomic_Data::CRB,unsigned,bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/UTRs.cpp:100:59: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
100 | template <class Intron> struct finding_intron_greater_s : binary_function<Genomic_Data::Intron,unsigned,bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/UTRs.cpp:108:58: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
108 | template <class Intron> struct finding_intron_lesser_s : binary_function<Genomic_Data::Intron,unsigned,bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/UTRs.cpp:116:59: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
116 | template <class Intron> struct finding_intron_greater_e : binary_function<Genomic_Data::Intron,unsigned,bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/UTRs.cpp:124:58: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
124 | template <class Intron> struct finding_intron_lesser_e : binary_function<Genomic_Data::Intron,unsigned,bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/UTRs.cpp:133:49: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
133 | template <class Repeat> struct finding_repeat : binary_function<Genomic_Data::Repeat,unsigned,bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/UTRs.cpp: In static member function 'static unsigned int UTRs::get_max_pos(unsigned int, int, unsigned int, unsigned int, std::vector<Genomic_Data::CRB>*)':
../src/UTRs.cpp:181:64: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_coding_region_greater<Genomic_Data::CRB>; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
181 | bind2nd(finding_coding_region_greater<Genomic_Data::CRB>(), pos)) :
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_function.h:1438:
/usr/include/c++/12/backward/binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
../src/UTRs.cpp:183:65: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_coding_region_lesser<Genomic_Data::CRB>; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
183 | bind2nd(finding_coding_region_lesser<Genomic_Data::CRB>(), pos));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/backward/binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
../src/UTRs.cpp: In static member function 'static bool UTRs::repeat_in_UTR(unsigned int, unsigned int, std::vector<Genomic_Data::Repeat>*)':
../src/UTRs.cpp:196:63: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_repeat<Genomic_Data::Repeat>; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
196 | it = find_if(repeats->begin(), repeats->end(), bind2nd(finding_repeat<Genomic_Data::Repeat>(), start));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/backward/binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
../src/UTRs.cpp: In static member function 'static std::vector<int> UTRs::find_introns_in_range(unsigned int, unsigned int, int, std::vector<Genomic_Data::Intron>*)':
../src/UTRs.cpp:233:79: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_greater_s<Genomic_Data::Intron>; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
233 | it = find_if(introns->begin(), introns->end(), bind2nd(finding_intron_greater_s<Genomic_Data::Intron>(), start));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/backward/binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
../src/UTRs.cpp:240:79: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_greater_e<Genomic_Data::Intron>; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
240 | it = find_if(introns->begin(), introns->end(), bind2nd(finding_intron_greater_e<Genomic_Data::Intron>(), start));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/backward/binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
../src/UTRs.cpp:252:93: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_lesser_e<Genomic_Data::Intron>; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
252 | it = find_if(reverse_introns.begin(), reverse_introns.end(), bind2nd(finding_intron_lesser_e<Genomic_Data::Intron>(), start));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/backward/binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
../src/UTRs.cpp:259:93: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_lesser_s<Genomic_Data::Intron>; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
259 | it = find_if(reverse_introns.begin(), reverse_introns.end(), bind2nd(finding_intron_lesser_s<Genomic_Data::Intron>(), start));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/backward/binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
../src/UTRs.cpp: In static member function 'static void UTRs::compute_UTRs(const Genomic_Data::Scaff_plus_Gen_Data&, const std::map<unsigned int, double>&)':
../src/UTRs.cpp:387:66: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
387 | vector<double>::iterator jt = min_element(d.begin(), d.end());
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/algorithm:61,
from ../src/UTRs.cpp:20:
/usr/include/c++/12/bits/stl_algo.h: In function 'constexpr _FIter std::min_element(_FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >]':
/usr/include/c++/12/bits/stl_algo.h:5617:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
5617 | inline min_element(_ForwardIterator __first, _ForwardIterator __last)
| ^~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:5617:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:5626:43: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
5626 | return _GLIBCXX_STD_A::__min_element(__first, __last,
| ^
/usr/include/c++/12/bits/stl_algo.h: In function 'constexpr _ForwardIterator std::__min_element(_ForwardIterator, _ForwardIterator, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:5595:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
5595 | __min_element(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:5595:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:5602:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
5602 | if (__comp(__first, __result))
| ~~~~~~^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_algobase.h:71,
from /usr/include/c++/12/string:50:
/usr/include/c++/12/bits/predefined_ops.h: In member function 'constexpr bool __gnu_cxx::__ops::_Iter_less_iter::operator()(_Iterator1, _Iterator2) const [with _Iterator1 = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >; _Iterator2 = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >]':
/usr/include/c++/12/bits/predefined_ops.h:44:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
44 | operator()(_Iterator1 __it1, _Iterator2 __it2) const
| ^~~~~~~~
/usr/include/c++/12/bits/predefined_ops.h:44:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:70,
from ../src/Genomic_Data.hpp:9:
/usr/include/c++/12/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
Finished building: ../src/UTRs.cpp
Building file: ../src/main.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/main.d" -MT"src/main.o" -o "src/main.o" "../src/main.cpp"
Finished building: ../src/main.cpp
Building target: utrrnaseq
Invoking: GCC C++ Linker
g++ -o "utrrnaseq" ./src/Compute_UTRs.o ./src/Coord_Transform.o ./src/Genomic_Data.o ./src/Splice_Sites.o ./src/Supporting_Methods.o ./src/Test.o ./src/UTRs.o ./src/main.o
Finished building target: utrrnaseq
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/utrrnaseq/Debug'
cd bam2wig; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2wig'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: 'bam2wig' is up to date.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2wig'
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
asciidoctor -a docdate='' -b manpage --destination-dir=debian/mansrc/ mansrc/*adoc
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_auto_test -a
make -j4 test
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
cd tests/examples && ./testcases.py --html
test_utr_on (__main__.TestAugustus) ... ok
test_hints_MPE (__main__.TestAugustus) ... ok
test_training_new_species (__main__.TestAugustus) ... ok
test_ab_initio_prediction (__main__.TestAugustus) ... ok
test_format_and_error_out (__main__.TestAugustus) ... ok
test_cgp (__main__.TestAugustus) ... ok
test_cgp_sqlite (__main__.TestAugustus) ... ok
test_cgp_sqlite_hints (__main__.TestAugustus) ... ok
----------------------------------------------------------------------
Ran 8 tests in 3329.867s
OK
Removing generated test files...
----------------------------------------------------------------------
Executing small test suite
----------------------------------------------------------------------
Creating SQLite database for cgp test cases...
tests/auxprogs/bam2wig/test_bam2wig.py --html
test_bam2wig (__main__.TestBam2Wig) ... ok
test_bam2wig_region (__main__.TestBam2Wig) ... ok
----------------------------------------------------------------------
Ran 2 tests in 0.084s
OK
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
create-stamp debian/debhelper-build-stamp
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
mkdir -p debian/augustus/usr/bin
install bin/* debian/augustus/usr/bin
install auxprogs/bam2wig/bam2wig \
debian/augustus/usr/bin
install auxprogs/compileSpliceCands/compileSpliceCands \
debian/augustus/usr/bin
install auxprogs/homGeneMapping/src/homGeneMapping \
debian/augustus/usr/bin
install auxprogs/joingenes/joingenes \
debian/augustus/usr/bin
mkdir -p debian/augustus/usr/share/augustus
cp -r scripts debian/augustus/usr/share/augustus
chmod -R -x debian/augustus/usr/share/augustus/scripts/*
rm -rf debian/augustus/usr/share/augustus/scripts/*.patch \
debian/augustus/usr/share/augustus/scripts/executeTestCGP.py \
debian/augustus/usr/share/augustus/scripts/*.txt
chmod +x debian/augustus/usr/share/augustus/scripts/checkUTR \
debian/augustus/usr/share/augustus/scripts/*.pl*
mkdir -p debian/augustus-doc/usr/share/doc/augustus
cp README* debian/augustus-doc/usr/share/doc/augustus
cp docs/*.txt debian/augustus-doc/usr/share/doc/augustus
cp docs/RUNNING* debian/augustus-doc/usr/share/doc/augustus
cp docs/README* debian/augustus-doc/usr/share/doc/augustus
cp docs/EXONCAND-MSAS-CGP.md \
debian/augustus-doc/usr/share/doc/augustus
cp -r docs/tutorial \
debian/augustus-doc/usr/share/doc/augustus
cp -r docs/tutorial-cgp \
debian/augustus-doc/usr/share/doc/augustus
mkdir -p debian/augustus-data/usr/share/augustus
cp -r config debian/augustus-data/usr/share/augustus
find debian/augustus-data/usr/share/augustus \
-type f -exec chmod -x {} \;
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_installchangelogs -k docs/HISTORY.TXT
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
debian/rules override_dh_compress
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_compress -Xtutorial
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/augustus/usr/bin/bam2hints contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/prepareAlign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/fastBlockSearch contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/joingenes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/homGeneMapping contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/filterBam contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/getSeq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/etraining contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/augustus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/pp_simScore contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/load2sqlitedb contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/load2db 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/augustus/usr/bin/bam2hints debian/augustus/usr/bin/prepareAlign debian/augustus/usr/bin/fastBlockSearch debian/augustus/usr/bin/joingenes debian/augustus/usr/bin/homGeneMapping debian/augustus/usr/bin/aln2wig debian/augustus/usr/bin/filterBam debian/augustus/usr/bin/getSeq debian/augustus/usr/bin/compileSpliceCands debian/augustus/usr/bin/etraining debian/augustus/usr/bin/augustus debian/augustus/usr/bin/pp_simScore debian/augustus/usr/bin/load2sqlitedb debian/augustus/usr/bin/load2db debian/augustus/usr/bin/bam2wig were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.4.0+dfsg2-3+b2_armhf.deb'.
dpkg-deb: building package 'augustus' in '../augustus_3.4.0+dfsg2-3+b2_armhf.deb'.
dpkg-genbuildinfo --build=any -O../augustus_3.4.0+dfsg2-3+b2_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../augustus_3.4.0+dfsg2-3+b2_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 2022-09-05T17:51:51Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
augustus_3.4.0+dfsg2-3+b2_armhf.changes:
----------------------------------------
Format: 1.8
Date: Tue, 28 Sep 2021 22:14:24 +0200
Source: augustus (3.4.0+dfsg2-3)
Binary: augustus augustus-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 3.4.0+dfsg2-3+b2
Distribution: bookworm-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
augustus - gene prediction in eukaryotic genomes
Changes:
augustus (3.4.0+dfsg2-3+b2) bookworm-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
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| Package contents |
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augustus-dbgsym_3.4.0+dfsg2-3+b2_armhf.deb
------------------------------------------
new Debian package, version 2.0.
size 34758576 bytes: control archive=1284 bytes.
984 bytes, 12 lines control
1678 bytes, 16 lines md5sums
Package: augustus-dbgsym
Source: augustus (3.4.0+dfsg2-3)
Version: 3.4.0+dfsg2-3+b2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 35424
Depends: augustus (= 3.4.0+dfsg2-3+b2)
Section: debug
Priority: optional
Description: debug symbols for augustus
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lrwxrwxrwx root/root 0 2021-09-28 20:14 ./usr/share/doc/augustus-dbgsym -> augustus
augustus_3.4.0+dfsg2-3+b2_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 1461012 bytes: control archive=5004 bytes.
1561 bytes, 24 lines control
10389 bytes, 139 lines md5sums
Package: augustus
Source: augustus (3.4.0+dfsg2-3)
Version: 3.4.0+dfsg2-3+b2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8854
Depends: libbamtools2.5.2 (>= 2.5.2+dfsg), libboost-iostreams1.74.0 (>= 1.74.0), libc6 (>= 2.33), libcolamd2 (>= 1:4.5.2), libgcc-s1 (>= 3.5), libgsl27 (>= 2.7.1), libhts3 (>= 1.10), libmariadb3 (>= 3.0.0), libmysql++3v5 (>= 3.2.5-1~), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 11), augustus-data
Recommends: samtools
Suggests: cdbfasta, diamond-aligner, libfile-which-perl, libparallel-forkmanager-perl, libyaml-perl, libdbd-mysql-perl, python3-biopython
Section: science
Priority: optional
Homepage: https://bioinf.uni-greifswald.de/augustus/
Description: gene prediction in eukaryotic genomes
AUGUSTUS is a software for gene prediction in eukaryotic genomic sequences
that is based on a generalized hidden Markov model (HMM), a probabilistic
model of a sequence and its gene structure. After learning gene structures
from a reference annotation, AUGUSTUS uses the HMM to recognize genes in a new
sequence and annotates it with the regions of identified genes. External hints,
e.g. from RNA sequencing, EST or protein alignments etc. can be used to guide
and improve the gene finding process. The result is the set of most likely gene
structures that comply with all given user constraints, if such gene
structures exist.
AUGUSTUS already includes prebuilt HMMs for many species, as well as scripts
to train custom models using annotated genomes.
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drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/share/doc/augustus/
lrwxrwxrwx root/root 0 2021-09-28 20:14 ./usr/share/doc/augustus/HISTORY.TXT.gz -> changelog.gz
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-rw-r--r-- root/root 3366 2021-09-28 20:13 ./usr/share/doc/augustus/copyright
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/share/man/
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/share/man/man1/
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 1483480
Build-Time: 3852
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 713
Job: augustus_3.4.0+dfsg2-3
Machine Architecture: armhf
Package: augustus
Package-Time: 4623
Source-Version: 3.4.0+dfsg2-3
Space: 1483480
Status: successful
Version: 3.4.0+dfsg2-3+b2
--------------------------------------------------------------------------------
Finished at 2022-09-05T17:51:51Z
Build needed 01:17:03, 1483480k disk space