augustus →
3.5.0+dfsg-3 →
armhf → 2023-09-22 16:16:27
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| augustus 3.5.0+dfsg-3 (armhf) Fri, 22 Sep 2023 14:59:04 +0000 |
+==============================================================================+
Package: augustus
Version: 3.5.0+dfsg-3
Source Version: 3.5.0+dfsg-3
Distribution: trixie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/trixie-staging-armhf-sbuild-cf6c6d3a-3d91-4462-ac21-a41143b90f84' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.1 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [14.6 MB]
Fetched 28.7 MB in 10s (2741 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/trixie-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 152 MB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main augustus 3.5.0+dfsg-3 (dsc) [2347 B]
Get:2 http://172.17.4.1/private trixie-staging/main augustus 3.5.0+dfsg-3 (tar) [152 MB]
Get:3 http://172.17.4.1/private trixie-staging/main augustus 3.5.0+dfsg-3 (diff) [20.1 kB]
Fetched 152 MB in 20s (7514 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/augustus-rBvNCI/augustus-3.5.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/augustus-rBvNCI' 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-tSQqVW/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-tSQqVW/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-tSQqVW/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-tSQqVW/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-tSQqVW/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-tSQqVW/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-tSQqVW/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-tSQqVW/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (9925 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 sgml-base util-linux-extra
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 3 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-tSQqVW/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 (71.9 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11775 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, libhts-dev, libncurses5-dev, libboost-serialization-dev, libssl-dev, libmysql++-dev, asciidoctor, python3, samtools, chrpath
Filtered Build-Depends: debhelper-compat (= 13), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbz2-dev, libhts-dev, libncurses5-dev, libboost-serialization-dev, libssl-dev, libmysql++-dev, asciidoctor, python3, samtools, chrpath
dpkg-deb: building package 'sbuild-build-depends-augustus-dummy' in '/<<BUILDDIR>>/resolver-tSQqVW/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-tSQqVW/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-tSQqVW/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-tSQqVW/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-tSQqVW/apt_archive ./ Sources [601 B]
Get:5 copy:/<<BUILDDIR>>/resolver-tSQqVW/apt_archive ./ Packages [683 B]
Fetched 2617 B in 0s (13.0 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 sgml-base util-linux-extra
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdextrautils
ca-certificates chrpath debhelper default-libmysqlclient-dev dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
icu-devtools intltool-debian libamd2 libarchive-zip-perl 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 libcurl3-gnutls libcurl4-gnutls-dev libcxsparse3
libdebhelper-perl libdeflate-dev libdeflate0 libedit2 libelf1 libexpat1
libfile-stripnondeterminism-perl libgfortran5 libgsl-dev libgsl27
libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu-dev libicu72 libklu1
liblapack-dev liblapack3 libldl2 liblpsolve55-dev liblzma-dev libmagic-mgc
libmagic1 libmariadb-dev libmariadb-dev-compat libmariadb3 libmetis5
libmongoose2 libmysql++-dev libmysql++3v5 libncurses-dev libncurses6
libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.11-minimal
libpython3.11-stdlib librbio2 librtmp1 libruby libruby3.1 libsliplu1
libspqr2 libsqlite3-dev libssh2-1 libssl-dev libsub-override-perl
libsuitesparse-dev libsuitesparseconfig5 libtool libuchardet0 libumfpack5
libxml2 libyaml-0-2 m4 man-db mariadb-common media-types mysql-common
openssl po-debconf python3 python3-minimal python3.11 python3.11-minimal
rake ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-sdbm
ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration samtools zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make 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 libidn-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 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor
less www-browser libmail-box-perl python3-doc python3-tk python3-venv
python3.11-venv python3.11-doc binfmt-support ri ruby-dev bundler cwltool
Recommended packages:
curl | wget | lynx bzip2-doc libarchive-cpio-perl libgpm2 publicsuffix
libgraphblas-dev libltdl-dev libmail-sendmail-perl zip fonts-lato
libjs-jquery
The following NEW packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdextrautils
ca-certificates chrpath debhelper default-libmysqlclient-dev dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
icu-devtools intltool-debian libamd2 libarchive-zip-perl 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 libcurl3-gnutls libcurl4-gnutls-dev libcxsparse3
libdebhelper-perl libdeflate-dev libdeflate0 libedit2 libelf1 libexpat1
libfile-stripnondeterminism-perl libgfortran5 libgsl-dev libgsl27
libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu-dev libicu72 libklu1
liblapack-dev liblapack3 libldl2 liblpsolve55-dev liblzma-dev libmagic-mgc
libmagic1 libmariadb-dev libmariadb-dev-compat libmariadb3 libmetis5
libmongoose2 libmysql++-dev libmysql++3v5 libncurses-dev libncurses6
libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.11-minimal
libpython3.11-stdlib librbio2 librtmp1 libruby libruby3.1 libsliplu1
libspqr2 libsqlite3-dev libssh2-1 libssl-dev libsub-override-perl
libsuitesparse-dev libsuitesparseconfig5 libtool libuchardet0 libumfpack5
libxml2 libyaml-0-2 m4 man-db mariadb-common media-types mysql-common
openssl po-debconf python3 python3-minimal python3.11 python3.11-minimal
rake ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-sdbm
ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration samtools
sbuild-build-depends-augustus-dummy zlib1g-dev
0 upgraded, 125 newly installed, 0 to remove and 3 not upgraded.
Need to get 71.2 MB of archives.
After this operation, 402 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-tSQqVW/apt_archive ./ sbuild-build-depends-augustus-dummy 0.invalid.0 [968 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-minimal armhf 3.11.5-3 [800 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-2 [76.8 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf python3.11-minimal armhf 3.11.5-3 [1676 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf python3-minimal armhf 3.11.4-5 [26.2 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf media-types all 10.1.0 [26.9 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-stdlib armhf 3.11.5-3 [1675 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf python3.11 armhf 3.11.5-3 [582 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf libpython3-stdlib armhf 3.11.4-5 [9200 B]
Get:10 http://172.17.4.1/private trixie-staging/main armhf python3 armhf 3.11.4-5 [26.2 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.22.4-10 [774 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.2-1 [80.5 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.11.2-3 [1342 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf openssl armhf 3.0.10-1 [1368 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf ca-certificates all 20230311 [153 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-12 [156 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf rubygems-integration all 1.18 [6704 B]
Get:23 http://172.17.4.1/private trixie-staging/main armhf rake all 13.0.6-3 [83.9 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf ruby-net-telnet all 0.2.0-1 [13.1 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf ruby-webrick all 1.8.1-1 [51.4 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf ruby-xmlrpc all 0.3.2-2 [24.4 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libruby armhf 1:3.1 [4968 B]
Get:28 http://172.17.4.1/private trixie-staging/main armhf ruby-sdbm armhf 1.0.0-5+rpi1 [15.9 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf libbsd0 armhf 0.11.7-4 [111 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf libedit2 armhf 3.1-20230828-1 [76.0 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf libncurses6 armhf 6.4+20230625-2 [79.6 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf libyaml-0-2 armhf 0.2.5-1 [44.6 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf libruby3.1 armhf 3.1.2-7 [5011 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf ruby3.1 armhf 3.1.2-7 [663 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf ruby-rubygems all 3.3.15-2 [293 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf ruby armhf 1:3.1 [5868 B]
Get:37 http://172.17.4.1/private trixie-staging/main armhf ruby-asciidoctor all 2.0.20-1 [212 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf asciidoctor all 2.0.20-1 [87.7 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-13 [496 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.6 [81.9 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:50 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:52 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-12 [1201 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:59 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.6 [952 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf mysql-common all 5.8+1.1.0 [6636 B]
Get:61 http://172.17.4.1/private trixie-staging/main armhf mariadb-common all 1:10.11.3-1+rpi1 [24.1 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf libmariadb3 armhf 1:10.11.3-1+rpi1 [154 kB]
Get:63 http://172.17.4.1/private trixie-staging/main armhf libssl-dev armhf 3.0.10-1 [2100 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-3 [901 kB]
Get:65 http://172.17.4.1/private trixie-staging/main armhf libmariadb-dev armhf 1:10.11.3-1+rpi1 [247 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf libmariadb-dev-compat armhf 1:10.11.3-1+rpi1 [22.9 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf default-libmysqlclient-dev armhf 1.1.0 [3092 B]
Get:68 http://172.17.4.1/private trixie-staging/main armhf icu-devtools armhf 72.1-3 [175 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf libsuitesparseconfig5 armhf 1:5.12.0+dfsg-2 [23.6 kB]
Get:70 http://172.17.4.1/private trixie-staging/main armhf libamd2 armhf 1:5.12.0+dfsg-2 [30.2 kB]
Get:71 http://172.17.4.1/private trixie-staging/main armhf libbamtools2.5.2 armhf 2.5.2+dfsg-4 [126 kB]
Get:72 http://172.17.4.1/private trixie-staging/main armhf libbamtools-dev armhf 2.5.2+dfsg-4 [182 kB]
Get:73 http://172.17.4.1/private trixie-staging/main armhf libblas3 armhf 3.11.0-2 [100.0 kB]
Get:74 http://172.17.4.1/private trixie-staging/main armhf libblas-dev armhf 3.11.0-2 [106 kB]
Get:75 http://172.17.4.1/private trixie-staging/main armhf libboost1.74-dev armhf 1.74.0+ds1-21 [9508 kB]
Get:76 http://172.17.4.1/private trixie-staging/main armhf libboost-regex1.74.0 armhf 1.74.0+ds1-21 [420 kB]
Get:77 http://172.17.4.1/private trixie-staging/main armhf libicu-dev armhf 72.1-3 [9959 kB]
Get:78 http://172.17.4.1/private trixie-staging/main armhf libboost-regex1.74-dev armhf 1.74.0+ds1-21 [525 kB]
Get:79 http://172.17.4.1/private trixie-staging/main armhf libboost-iostreams1.74.0 armhf 1.74.0+ds1-21 [235 kB]
Get:80 http://172.17.4.1/private trixie-staging/main armhf libboost-iostreams1.74-dev armhf 1.74.0+ds1-21 [245 kB]
Get:81 http://172.17.4.1/private trixie-staging/main armhf libboost-iostreams-dev armhf 1.74.0.3+b4 [4592 B]
Get:82 http://172.17.4.1/private trixie-staging/main armhf libboost-serialization1.74.0 armhf 1.74.0+ds1-21 [296 kB]
Get:83 http://172.17.4.1/private trixie-staging/main armhf libboost-serialization1.74-dev armhf 1.74.0+ds1-21 [362 kB]
Get:84 http://172.17.4.1/private trixie-staging/main armhf libboost-serialization-dev armhf 1.74.0.3+b4 [4832 B]
Get:85 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.0.9-2+b3 [258 kB]
Get:86 http://172.17.4.1/private trixie-staging/main armhf libbtf1 armhf 1:5.12.0+dfsg-2 [24.1 kB]
Get:87 http://172.17.4.1/private trixie-staging/main armhf libbz2-dev armhf 1.0.8-5+b2 [26.8 kB]
Get:88 http://172.17.4.1/private trixie-staging/main armhf libcamd2 armhf 1:5.12.0+dfsg-2 [30.7 kB]
Get:89 http://172.17.4.1/private trixie-staging/main armhf libccolamd2 armhf 1:5.12.0+dfsg-2 [31.7 kB]
Get:90 http://172.17.4.1/private trixie-staging/main armhf libcolamd2 armhf 1:5.12.0+dfsg-2 [28.3 kB]
Get:91 http://172.17.4.1/private trixie-staging/main armhf libgfortran5 armhf 12.2.0-14+rpi1 [238 kB]
Get:92 http://172.17.4.1/private trixie-staging/main armhf liblapack3 armhf 3.11.0-2 [1624 kB]
Get:93 http://172.17.4.1/private trixie-staging/main armhf libmetis5 armhf 5.1.0.dfsg-7 [133 kB]
Get:94 http://172.17.4.1/private trixie-staging/main armhf libcholmod3 armhf 1:5.12.0+dfsg-2 [212 kB]
Get:95 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.56.0-1 [60.5 kB]
Get:96 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:97 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:98 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-2 [195 kB]
Get:99 http://172.17.4.1/private trixie-staging/main armhf libcurl3-gnutls armhf 7.88.1-10+rpi1 [337 kB]
Get:100 http://172.17.4.1/private trixie-staging/main armhf libcurl4-gnutls-dev armhf 7.88.1-10+rpi1 [419 kB]
Get:101 http://172.17.4.1/private trixie-staging/main armhf libcxsparse3 armhf 1:5.12.0+dfsg-2 [52.1 kB]
Get:102 http://172.17.4.1/private trixie-staging/main armhf libdeflate0 armhf 1.18-1 [38.3 kB]
Get:103 http://172.17.4.1/private trixie-staging/main armhf libdeflate-dev armhf 1.18-1 [45.8 kB]
Get:104 http://172.17.4.1/private trixie-staging/main armhf libgslcblas0 armhf 2.7.1+dfsg-5 [79.2 kB]
Get:105 http://172.17.4.1/private trixie-staging/main armhf libgsl27 armhf 2.7.1+dfsg-5 [752 kB]
Get:106 http://172.17.4.1/private trixie-staging/main armhf libgsl-dev armhf 2.7.1+dfsg-5 [965 kB]
Get:107 http://172.17.4.1/private trixie-staging/main armhf libhtscodecs2 armhf 1.5.1-1 [61.6 kB]
Get:108 http://172.17.4.1/private trixie-staging/main armhf libhts3 armhf 1.17+ds-1 [374 kB]
Get:109 http://172.17.4.1/private trixie-staging/main armhf liblzma-dev armhf 5.4.4-0.1 [269 kB]
Get:110 http://172.17.4.1/private trixie-staging/main armhf libhts-dev armhf 1.17+ds-1 [1507 kB]
Get:111 http://172.17.4.1/private trixie-staging/main armhf libklu1 armhf 1:5.12.0+dfsg-2 [51.8 kB]
Get:112 http://172.17.4.1/private trixie-staging/main armhf liblapack-dev armhf 3.11.0-2 [3007 kB]
Get:113 http://172.17.4.1/private trixie-staging/main armhf libldl2 armhf 1:5.12.0+dfsg-2 [23.8 kB]
Get:114 http://172.17.4.1/private trixie-staging/main armhf libmongoose2 armhf 1:5.12.0+dfsg-2 [43.8 kB]
Get:115 http://172.17.4.1/private trixie-staging/main armhf libumfpack5 armhf 1:5.12.0+dfsg-2 [128 kB]
Get:116 http://172.17.4.1/private trixie-staging/main armhf librbio2 armhf 1:5.12.0+dfsg-2 [32.9 kB]
Get:117 http://172.17.4.1/private trixie-staging/main armhf libspqr2 armhf 1:5.12.0+dfsg-2 [68.2 kB]
Get:118 http://172.17.4.1/private trixie-staging/main armhf libsliplu1 armhf 1:5.12.0+dfsg-2 [49.5 kB]
Get:119 http://172.17.4.1/private trixie-staging/main armhf libsuitesparse-dev armhf 1:5.12.0+dfsg-2 [614 kB]
Get:120 http://172.17.4.1/private trixie-staging/main armhf liblpsolve55-dev armhf 5.5.2.5-2 [349 kB]
Get:121 http://172.17.4.1/private trixie-staging/main armhf libmysql++3v5 armhf 3.2.5-2.1 [144 kB]
Get:122 http://172.17.4.1/private trixie-staging/main armhf libmysql++-dev armhf 3.2.5-2.1 [150 kB]
Get:123 http://172.17.4.1/private trixie-staging/main armhf libncurses-dev armhf 6.4+20230625-2 [290 kB]
Get:124 http://172.17.4.1/private trixie-staging/main armhf libsqlite3-dev armhf 3.43.1-1 [925 kB]
Get:125 http://172.17.4.1/private trixie-staging/main armhf samtools armhf 1.17-1 [579 kB]
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Setting up libhtscodecs2:armhf (1.5.1-1) ...
Setting up media-types (10.1.0) ...
Setting up libpipeline1:armhf (1.5.7-1) ...
Setting up mysql-common (5.8+1.1.0) ...
update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode
Setting up libpsl5:armhf (0.21.2-1+b1) ...
Setting up libboost1.74-dev:armhf (1.74.0+ds1-21) ...
Setting up libicu72:armhf (72.1-3) ...
Setting up bsdextrautils (2.39.2-1) ...
Setting up libgslcblas0:armhf (2.7.1+dfsg-5) ...
Setting up libmagic-mgc (1:5.45-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libyaml-0-2:armhf (0.2.5-1) ...
Setting up libboost-iostreams1.74.0:armhf (1.74.0+ds1-21) ...
Setting up libpython3.11-stdlib:armhf (3.11.5-3) ...
Setting up libdebhelper-perl (13.11.6) ...
Setting up libbrotli1:armhf (1.0.9-2+b3) ...
Setting up libldl2:armhf (1:5.12.0+dfsg-2) ...
Setting up libnghttp2-14:armhf (1.56.0-1) ...
Setting up libmagic1:armhf (1:5.45-2) ...
Setting up libdeflate0:armhf (1.18-1) ...
Setting up gettext-base (0.21-12) ...
Setting up libgsl27:armhf (2.7.1+dfsg-5) ...
Setting up m4 (1.4.19-4) ...
Setting up libmetis5:armhf (5.1.0.dfsg-7) ...
Setting up file (1:5.45-2) ...
Setting up libbtf1:armhf (1:5.12.0+dfsg-2) ...
Setting up mariadb-common (1:10.11.3-1+rpi1) ...
update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode
Setting up autotools-dev (20220109.1) ...
Setting up libblas3:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libsqlite3-dev:armhf (3.43.1-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.4+20230625-2) ...
Setting up ruby-net-telnet (0.2.0-1) ...
Setting up libboost-regex1.74.0:armhf (1.74.0+ds1-21) ...
Setting up libssl-dev:armhf (3.0.10-1) ...
Setting up autopoint (0.21-13) ...
Setting up icu-devtools (72.1-3) ...
Setting up libmariadb3:armhf (1:10.11.3-1+rpi1) ...
Setting up libmysql++3v5:armhf (3.2.5-2.1) ...
Setting up libbamtools2.5.2:armhf (2.5.2+dfsg-4) ...
Setting up libgfortran5:armhf (12.2.0-14+rpi1) ...
Setting up autoconf (2.71-3) ...
Setting up ruby-webrick (1.8.1-1) ...
Setting up liblzma-dev:armhf (5.4.4-0.1) ...
Setting up libboost-serialization1.74.0:armhf (1.74.0+ds1-21) ...
Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-3) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libssh2-1:armhf (1.11.0-2) ...
Setting up libcxsparse3:armhf (1:5.12.0+dfsg-2) ...
Setting up openssl (3.0.10-1) ...
Setting up libbsd0:armhf (0.11.7-4) ...
Setting up libdeflate-dev:armhf (1.18-1) ...
Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up libicu-dev:armhf (72.1-3) ...
Setting up ruby-xmlrpc (0.3.2-2) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
Setting up libsuitesparseconfig5:armhf (1:5.12.0+dfsg-2) ...
Setting up chrpath (0.16-2) ...
Setting up libblas-dev:armhf (3.11.0-2) ...
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 libpython3-stdlib:armhf (3.11.4-5) ...
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 (1.13.1-1) ...
Setting up libamd2:armhf (1:5.12.0+dfsg-2) ...
Setting up python3.11 (3.11.5-3) ...
Setting up liblapack3:armhf (3.11.0-2) ...
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 (6.4+20230625-2) ...
Setting up gettext (0.21-12) ...
Setting up libgsl-dev (2.7.1+dfsg-5) ...
Setting up libcolamd2:armhf (1:5.12.0+dfsg-2) ...
Setting up libtool (2.4.7-7) ...
Setting up libedit2:armhf (3.1-20230828-1) ...
Setting up libcurl3-gnutls:armhf (7.88.1-10+rpi1) ...
Setting up python3 (3.11.4-5) ...
Setting up libcurl4-gnutls-dev:armhf (7.88.1-10+rpi1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libsliplu1:armhf (1:5.12.0+dfsg-2) ...
Setting up dh-autoreconf (20) ...
Setting up ca-certificates (20230311) ...
Updating certificates in /etc/ssl/certs...
140 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-4) ...
Setting up liblapack-dev:armhf (3.11.0-2) ...
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 libboost-serialization1.74-dev:armhf (1.74.0+ds1-21) ...
Setting up libmariadb-dev (1:10.11.3-1+rpi1) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up libboost-regex1.74-dev:armhf (1.74.0+ds1-21) ...
Setting up groff-base (1.22.4-10) ...
Setting up libklu1:armhf (1:5.12.0+dfsg-2) ...
Setting up libccolamd2:armhf (1:5.12.0+dfsg-2) ...
Setting up libcholmod3:armhf (1:5.12.0+dfsg-2) ...
Setting up libmariadb-dev-compat (1:10.11.3-1+rpi1) ...
Setting up libspqr2:armhf (1:5.12.0+dfsg-2) ...
Setting up libhts3:armhf (1.17+ds-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhts-dev:armhf (1.17+ds-1) ...
Setting up rubygems-integration (1.18) ...
Setting up man-db (2.11.2-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up samtools (1.17-1) ...
Setting up libboost-iostreams1.74-dev:armhf (1.74.0+ds1-21) ...
Setting up libumfpack5:armhf (1:5.12.0+dfsg-2) ...
Setting up libboost-serialization-dev:armhf (1.74.0.3+b4) ...
Setting up default-libmysqlclient-dev:armhf (1.1.0) ...
Setting up libsuitesparse-dev:armhf (1:5.12.0+dfsg-2) ...
Setting up debhelper (13.11.6) ...
Setting up libboost-iostreams-dev:armhf (1.74.0.3+b4) ...
Setting up libmysql++-dev:armhf (3.2.5-2.1) ...
Setting up liblpsolve55-dev (5.5.2.5-2) ...
Setting up libruby:armhf (1:3.1) ...
Setting up ruby-rubygems (3.3.15-2) ...
Setting up ruby (1:3.1) ...
Setting up ruby-asciidoctor (2.0.20-1) ...
Setting up rake (13.0.6-3) ...
Setting up asciidoctor (2.0.20-1) ...
Setting up ruby-sdbm:armhf (1.0.0-5+rpi1) ...
Setting up libruby3.1:armhf (3.1.2-7) ...
Setting up sbuild-build-depends-augustus-dummy (0.invalid.0) ...
Setting up ruby3.1 (3.1.2-7) ...
Processing triggers for libc-bin (2.36-9+rpi1+deb12u1) ...
Processing triggers for ca-certificates (20230311) ...
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_2.40-2+rpi2 dpkg-dev_1.21.22+rpi1 g++-12_12.2.0-14+rpi1 gcc-12_12.2.0-14+rpi1 libc6-dev_2.36-9+rpi1+deb12u1 libstdc++-12-dev_12.2.0-14+rpi1 libstdc++6_12.2.0-14+rpi1 linux-libc-dev_6.1.38-1+rpi1
Package versions: adduser_3.137 apt_2.7.3 asciidoctor_2.0.20-1 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.1 bash_5.2.15-2 binutils_2.40-2+rpi2 binutils-arm-linux-gnueabihf_2.40-2+rpi2 binutils-common_2.40-2+rpi2 bsdextrautils_2.39.2-1 bsdutils_1:2.39.2-1 build-essential_12.9 bzip2_1.0.8-5+b2 ca-certificates_20230311 chrpath_0.16-2 coreutils_9.1-1 cpp_4:12.2.0-3+rpi1 cpp-12_12.2.0-14+rpi1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.6 debianutils_5.13 default-libmysqlclient-dev_1.1.0 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dirmngr_2.2.40-1.1 dpkg_1.21.22+rpi1 dpkg-dev_1.21.22+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.1-1 file_1:5.45-2 findutils_4.9.0-4 g++_4:12.2.0-3+rpi1 g++-12_12.2.0-14+rpi1 gcc_4:12.2.0-3+rpi1 gcc-12_12.2.0-14+rpi1 gcc-12-base_12.2.0-14+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_0.21-12 gettext-base_0.21-12 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.8-5 groff-base_1.22.4-10 gzip_1.12-1 hostname_3.23+nmu1 icu-devtools_72.1-3 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-3 libacl1_2.3.1-3 libamd2_1:5.12.0+dfsg-2 libapt-pkg6.0_2.7.3 libarchive-zip-perl_1.68-1 libasan8_12.2.0-14+rpi1 libassuan0_2.5.6-1 libatomic1_12.2.0-14+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbamtools-dev_2.5.2+dfsg-4 libbamtools2.5.2_2.5.2+dfsg-4 libbinutils_2.40-2+rpi2 libblas-dev_3.11.0-2 libblas3_3.11.0-2 libblkid1_2.39.2-1 libboost-iostreams-dev_1.74.0.3+b4 libboost-iostreams1.74-dev_1.74.0+ds1-21 libboost-iostreams1.74.0_1.74.0+ds1-21 libboost-regex1.74-dev_1.74.0+ds1-21 libboost-regex1.74.0_1.74.0+ds1-21 libboost-serialization-dev_1.74.0.3+b4 libboost-serialization1.74-dev_1.74.0+ds1-21 libboost-serialization1.74.0_1.74.0+ds1-21 libboost1.74-dev_1.74.0+ds1-21 libbrotli1_1.0.9-2+b3 libbsd0_0.11.7-4 libbtf1_1:5.12.0+dfsg-2 libbz2-1.0_1.0.8-5+b2 libbz2-dev_1.0.8-5+b2 libc-bin_2.36-9+rpi1+deb12u1 libc-dev-bin_2.36-9+rpi1+deb12u1 libc6_2.36-9+rpi1+deb12u1 libc6-dev_2.36-9+rpi1+deb12u1 libcamd2_1:5.12.0+dfsg-2 libcap-ng0_0.8.3-1+b1 libcap2_1:2.66-4 libcap2-bin_1:2.66-4 libcc1-0_12.2.0-14+rpi1 libccolamd2_1:5.12.0+dfsg-2 libcholmod3_1:5.12.0+dfsg-2 libcolamd2_1:5.12.0+dfsg-2 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.40-2+rpi2 libctf0_2.40-2+rpi2 libcurl3-gnutls_7.88.1-10+rpi1 libcurl4-gnutls-dev_7.88.1-10+rpi1 libcxsparse3_1:5.12.0+dfsg-2 libdb5.3_5.3.28+dfsg2-2 libdebconfclient0_0.270 libdebhelper-perl_13.11.6 libdeflate-dev_1.18-1 libdeflate0_1.18-1 libdpkg-perl_1.21.22+rpi1 libedit2_3.1-20230828-1 libelf1_0.188-2.1+rpi1 libexpat1_2.5.0-2 libext2fs2_1.47.0-2 libfakeroot_1.32.1-1 libffi8_3.4.4-1 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.2.0-14+rpi1 libgcc-s1_12.2.0-14+rpi1 libgcrypt20_1.10.2-2 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_12.2.0-14+rpi1 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.1-4 libgomp1_12.2.0-14+rpi1 libgpg-error0_1.47-2 libgsl-dev_2.7.1+dfsg-5 libgsl27_2.7.1+dfsg-5 libgslcblas0_2.7.1+dfsg-5 libgssapi-krb5-2_1.20.1-3 libhogweed6_3.9.1-2 libhts-dev_1.17+ds-1 libhts3_1.17+ds-1 libhtscodecs2_1.5.1-1 libicu-dev_72.1-3 libicu72_72.1-3 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libk5crypto3_1.20.1-3 libkeyutils1_1.6.3-2 libklu1_1:5.12.0+dfsg-2 libkrb5-3_1.20.1-3 libkrb5support0_1.20.1-3 libksba8_1.6.3-2 liblapack-dev_3.11.0-2 liblapack3_3.11.0-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 libldl2_1:5.12.0+dfsg-2 liblpsolve55-dev_5.5.2.5-2 liblz4-1_1.9.4-1+rpi1+b1 liblzma-dev_5.4.4-0.1 liblzma5_5.4.4-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmariadb-dev_1:10.11.3-1+rpi1 libmariadb-dev-compat_1:10.11.3-1+rpi1 libmariadb3_1:10.11.3-1+rpi1 libmd0_1.1.0-1 libmetis5_5.1.0.dfsg-7 libmongoose2_1:5.12.0+dfsg-2 libmount1_2.39.2-1 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libmysql++-dev_3.2.5-2.1 libmysql++3v5_3.2.5-2.1 libncurses-dev_6.4+20230625-2 libncurses6_6.4+20230625-2 libncursesw6_6.4+20230625-2 libnettle8_3.9.1-2 libnghttp2-14_1.56.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.0-4 libpam-cap_1:2.66-4 libpam-modules_1.5.2-7 libpam-modules-bin_1.5.2-7 libpam-runtime_1.5.2-7 libpam0g_1.5.2-7 libpcre2-8-0_10.42-4 libpcre3_2:8.39-15 libperl5.36_5.36.0-7 libpipeline1_1.5.7-1 libpsl5_0.21.2-1+b1 libpython3-stdlib_3.11.4-5 libpython3.11-minimal_3.11.5-3 libpython3.11-stdlib_3.11.5-3 librbio2_1:5.12.0+dfsg-2 libreadline8_8.2-1.3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libruby_1:3.1 libruby3.1_3.1.2-7 libsasl2-2_2.1.28+dfsg1-3 libsasl2-modules-db_2.1.28+dfsg1-3 libseccomp2_2.5.4-1+rpi1+b1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.4-1+b2 libsepol1_3.1-1 libsepol2_3.5-1 libsliplu1_1:5.12.0+dfsg-2 libsmartcols1_2.39.2-1 libspqr2_1:5.12.0+dfsg-2 libsqlite3-0_3.43.1-1 libsqlite3-dev_3.43.1-1 libss2_1.47.0-2 libssh2-1_1.11.0-2 libssl-dev_3.0.10-1 libssl1.1_1.1.1o-1 libssl3_3.0.10-1 libstdc++-12-dev_12.2.0-14+rpi1 libstdc++6_12.2.0-14+rpi1 libsub-override-perl_0.09-4 libsuitesparse-dev_1:5.12.0+dfsg-2 libsuitesparseconfig5_1:5.12.0+dfsg-2 libsystemd0_252.12-1~deb12u1+rpi1 libtasn1-6_4.19.0-3 libtext-glob-perl_0.11-3 libtinfo6_6.4+20230625-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-7 libubsan1_12.2.0-14+rpi1 libuchardet0_0.0.7-1 libudev1_252.12-1~deb12u1+rpi1 libumfpack5_1:5.12.0+dfsg-2 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.2-1 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.1-1 libyaml-0-2_0.2.5-1 libzstd1_1.5.5+dfsg2-1 linux-libc-dev_6.1.38-1+rpi1 login_1:4.13+dfsg1-1 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.11.2-3 mariadb-common_1:10.11.3-1+rpi1 mawk_1.3.4.20230808-1 media-types_10.1.0 mount_2.39.2-1 mysql-common_5.8+1.1.0 nano_7.2-1 ncurses-base_6.4+20230625-2 ncurses-bin_6.4+20230625-2 netbase_6.4 openssl_3.0.10-1 passwd_1:4.13+dfsg1-1 patch_2.7.6-7 perl_5.36.0-7 perl-base_5.36.0-7 perl-modules-5.36_5.36.0-9 pinentry-curses_1.2.1-1 po-debconf_1.0.21+nmu1 python3_3.11.4-5 python3-minimal_3.11.4-5 python3.11_3.11.5-3 python3.11-minimal_3.11.5-3 rake_13.0.6-3 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 ruby_1:3.1 ruby-asciidoctor_2.0.20-1 ruby-net-telnet_0.2.0-1 ruby-rubygems_3.3.15-2 ruby-sdbm_1.0.0-5+rpi1 ruby-webrick_1.8.1-1 ruby-xmlrpc_0.3.2-2 ruby3.1_3.1.2-7 rubygems-integration_1.18 samtools_1.17-1 sbuild-build-depends-augustus-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sgml-base_1.31 sysvinit-utils_3.07-1 tar_1.34+dfsg-1.2 tzdata_2023c-10 usrmerge_37 util-linux_2.39.2-1 util-linux-extra_2.39.2-1 xz-utils_5.4.4-0.1 zlib1g_1:1.2.13.dfsg-3 zlib1g-dev_1:1.2.13.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: Signature made Sat Jun 17 16:49:52 2023 UTC
gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./augustus_3.5.0+dfsg-3.dsc: no acceptable signature found
dpkg-source: info: extracting augustus in /<<BUILDDIR>>/augustus-3.5.0+dfsg
dpkg-source: info: unpacking augustus_3.5.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking augustus_3.5.0+dfsg-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
dpkg-source: info: applying s390x-disable-filterbam-tests.patch
dpkg-source: info: applying cstdint.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-cf6c6d3a-3d91-4462-ac21-a41143b90f84
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package augustus
dpkg-buildpackage: info: source version 3.5.0+dfsg-3
dpkg-buildpackage: info: source distribution unstable
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-3.5.0+dfsg'
/usr/bin/make -C auxprogs/bam2hints clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/bam2hints'
rm -f bam2hints.o bam2hints ../../bin/bam2hints
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/homGeneMapping clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/homGeneMapping'
cd src; make clean
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src'
rm -f homGeneMapping gene.o genome.o sqliteDB.o
rm -f ../../../bin/homGeneMapping
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src'
if [ -n /usr/bin/python3 ] ; then cd ../../tests/short && ./execute_test.py --clean homGeneMapping ; fi
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/homGeneMapping'
/usr/bin/make -C auxprogs/joingenes clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/joingenes'
rm -f *.o joingenes ../../bin/joingenes
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/joingenes'
/usr/bin/make -C auxprogs/aln2wig clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/aln2wig'
rm -f aln2wig aln2wig.o ../../bin/aln2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2wig clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/bam2wig'
rm -f bam2wig.o bam2wig
rm -f ../../bin/bam2wig
if [ -n /usr/bin/python3 ] ; then cd ../../tests/short && ./execute_test.py --clean bam2wig ; fi
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/compileSpliceCands clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands'
rm -f compileSpliceCands *.o ../../bin/compileSpliceCands
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/filterBam'
(cd src; make clean;)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/filterBam/src'
rm -f *~ filterBam.o initOptions.o printElapsedTime.o MatePairs.o PairednessCoverage.o BamToolsAccess.o
rm -f filterBam
rm -f ../../../bin/filterBam
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/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-3.5.0+dfsg'
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-3.5.0+dfsg'
mkdir -p bin
/usr/bin/make -C auxprogs/aln2wig
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/aln2wig'
cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -ansi -pedantic -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c aln2wig.c
cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -ansi -pedantic -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o aln2wig aln2wig.o
mkdir -p ../../bin
cp -f aln2wig ../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2hints
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/bam2hints'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/bamtools -c bam2hints.cc
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++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-rpath,/usr/lib -I/usr/include/bamtools -o bam2hints bam2hints.o -lbamtools -lz
mkdir -p ../../bin
cp -f bam2hints ../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/bam2wig
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/bam2wig'
cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/htslib -I/usr/local/include/htslib/ -c bam2wig.c
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 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o bam2wig bam2wig.o -lhts -lz -lpthread
mkdir -p ../../bin
cp -f bam2wig ../../bin/bam2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/compileSpliceCands
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands'
cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -pedantic -ansi -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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:553:14: note: in a call to allocation function 'malloc' declared here
553 | 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 -Wall -pedantic -ansi -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o list.o list.c
cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -pedantic -ansi -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o compileSpliceCands compileSpliceCands.o list.o
cp -f compileSpliceCands ../../bin/compileSpliceCands
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/filterBam/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c filterBam.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c functions/initOptions.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c functions/printElapsedTime.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c functions/MatePairs.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c functions/PairednessCoverage.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c BamToolsAccess.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-rpath,/usr/lib -o filterBam filterBam.o initOptions.o printElapsedTime.o MatePairs.o PairednessCoverage.o BamToolsAccess.o -lbamtools -lz
mkdir -p ../../../bin
mv filterBam ../../../bin/filterBam
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/filterBam'
/usr/bin/make -C auxprogs/homGeneMapping/src
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -c gene.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -c genome.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -c sqliteDB.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -o homGeneMapping main.cc gene.o genome.o sqliteDB.o -lsqlite3
mkdir -p ../../../bin/
cp -f homGeneMapping ../../../bin/homGeneMapping
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src'
/usr/bin/make -C auxprogs/joingenes
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/joingenes'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++0x -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c joingenes.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++0x -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c jg_transcript.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++0x -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c jg_ios.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++0x -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o joingenes joingenes.o jg_transcript.o jg_ios.o
mkdir -p ../../bin/
cp -f joingenes ../../bin/
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/joingenes'
dh_auto_build
make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg'
mkdir -p bin
mkdir -p bin
cd src && make
cd auxprogs && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs'
cd aln2wig; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/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-3.5.0+dfsg/auxprogs/aln2wig'
cd bam2hints; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/bam2hints'
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-3.5.0+dfsg/auxprogs/bam2hints'
cd compileSpliceCands; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands'
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-3.5.0+dfsg/auxprogs/compileSpliceCands'
cd filterBam; make;
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genbank.o genbank.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o properties.o properties.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_profile.o pp_profile.cc
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/filterBam'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src;make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/filterBam/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-rpath,/usr/lib -o filterBam filterBam.o initOptions.o printElapsedTime.o MatePairs.o PairednessCoverage.o BamToolsAccess.o -lbamtools -lz
mkdir -p ../../../bin
mv filterBam ../../../bin/filterBam
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/filterBam/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/filterBam'
cd homGeneMapping; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/homGeneMapping'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src; make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src'
make[5]: Nothing to be done for 'all'.
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/homGeneMapping'
cd joingenes; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/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-3.5.0+dfsg/auxprogs/joingenes'
cd utrrnaseq; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/utrrnaseq'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
mkdir -p build
Building file: src/Compute_UTRs.cpp
Invoking: GCC C++ Compiler: g++
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Compute_UTRs.d" -MT"build/Compute_UTRs.o" -o "build/Compute_UTRs.o" "src/Compute_UTRs.cpp"
In file included from /usr/include/c++/12/map:60,
from src/Compute_UTRs.hpp:14,
from src/Compute_UTRs.cpp:8:
/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>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/Compute_UTRs.cpp: In function 'void compute_UTRs(std::string)':
src/Compute_UTRs.cpp:254:58: warning: 'step' may be used uninitialized [-Wmaybe-uninitialized]
254 | chrom_pos+=step;
| ~~~~~~~~~^~~~~~
src/Compute_UTRs.cpp:143:18: note: 'step' was declared here
143 | unsigned step; //Step for fixedStep only
| ^~~~
src/Compute_UTRs.cpp:254:58: warning: 'chrom_pos' may be used uninitialized [-Wmaybe-uninitialized]
254 | chrom_pos+=step;
| ~~~~~~~~~^~~~~~
src/Compute_UTRs.cpp:142:18: note: 'chrom_pos' was declared here
142 | unsigned chrom_pos; //position for fixedStep only
| ^~~~~~~~~
In file included from /usr/include/c++/12/vector:64,
from src/Genomic_Data.hpp:9,
from src/Compute_UTRs.cpp:5:
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Genomic_Data::Scaff_plus_Gen_Data; _Alloc = std::allocator<Genomic_Data::Scaff_plus_Gen_Data>]',
inlined from 'void compute_UTRs(std::string)' at src/Compute_UTRs.cpp:199:106:
/usr/include/c++/12/bits/stl_vector.h:1124:41: warning: 'idx_former_scaff' may be used uninitialized [-Wmaybe-uninitialized]
1124 | return *(this->_M_impl._M_start + __n);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
src/Compute_UTRs.cpp: In function 'void compute_UTRs(std::string)':
src/Compute_UTRs.cpp:150:18: note: 'idx_former_scaff' was declared here
150 | unsigned idx_former_scaff;
| ^~~~~~~~~~~~~~~~
Finished building: src/Compute_UTRs.cpp
Building file: src/Coord_Transform.cpp
Invoking: GCC C++ Compiler: g++
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Coord_Transform.d" -MT"build/Coord_Transform.o" -o "build/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)
| ^~~~~~~
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:131:54: warning: 'skip_end' may be used uninitialized [-Wmaybe-uninitialized]
131 | i = skip_end + dir;
| ~~~~~~~~~^~~~~
src/Coord_Transform.cpp:65:13: note: 'skip_end' was declared here
65 | int skip_end; //normally end position + W for this next intron
| ^~~~~~~~
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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
Finished building: src/Coord_Transform.cpp
Building file: src/Genomic_Data.cpp
Invoking: GCC C++ Compiler: g++
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Genomic_Data.d" -MT"build/Genomic_Data.o" -o "build/Genomic_Data.o" "src/Genomic_Data.cpp"
/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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:60,
from ../include/types.hh:39,
from ../include/properties.hh:14,
from properties.cc:8:
/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 = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >]':
/usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator' changed in GCC 7.1
2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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 std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::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:
/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 = std::__cxx11::basic_string<char>; _Tp = nlohmann::basic_json<>; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >]':
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::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 = std::__cxx11::basic_string<char>; _Tp = nlohmann::basic_json<>; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >]',
inlined from 'bool nlohmann::detail::json_sax_dom_callback_parser<BasicJsonType>::key(string_t&) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5599:76:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::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 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 = {nlohmann::detail::value_t}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {nlohmann::detail::value_t}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]',
inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser<BasicJsonType>::handle_value(Value&&) [with Value = nlohmann::detail::value_t; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58,
inlined from 'bool nlohmann::detail::json_sax_dom_parser<BasicJsonType>::start_array(std::size_t) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5423:41:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >' 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 = {nlohmann::detail::value_t}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]',
inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser<BasicJsonType>::handle_value(Value&&) [with Value = nlohmann::detail::value_t; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58,
inlined from 'bool nlohmann::detail::json_sax_dom_parser<BasicJsonType>::start_object(std::size_t) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5397:41:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >' 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 = {std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::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 = {long long unsigned int&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator' changed in GCC 7.1
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_hitseq.o pp_hitseq.cc
In file included from /usr/include/c++/12/bits/stl_algobase.h:64,
from /usr/include/c++/12/string:50,
from src/Genomic_Data.hpp:8,
from src/Genomic_Data.cpp:5:
In constructor 'constexpr std::pair<_T1, _T2>::pair(_U1&&, _U2&&) [with _U1 = unsigned int&; _U2 = unsigned int&; typename std::enable_if<(std::_PCC<true, _T1, _T2>::_MoveConstructiblePair<_U1, _U2>() && std::_PCC<true, _T1, _T2>::_ImplicitlyMoveConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = unsigned int]',
inlined from 'constexpr std::pair<typename std::__strip_reference_wrapper<typename std::decay<_Tp>::type>::__type, typename std::__strip_reference_wrapper<typename std::decay<_Tp2>::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = unsigned int&; _T2 = unsigned int&]' at /usr/include/c++/12/bits/stl_pair.h:746:72,
inlined from 'std::vector<std::pair<unsigned int, unsigned int> > lower_case_runs(std::string)' at src/Genomic_Data.cpp:62:19:
/usr/include/c++/12/bits/stl_pair.h:535:11: warning: 'start' may be used uninitialized [-Wmaybe-uninitialized]
535 | : first(std::forward<_U1>(__x)), second(std::forward<_U2>(__y)) { }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/Genomic_Data.cpp: In function 'std::vector<std::pair<unsigned int, unsigned int> > lower_case_runs(std::string)':
src/Genomic_Data.cpp:42:18: note: 'start' was declared here
42 | unsigned start;
| ^~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]',
inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser<BasicJsonType>::handle_value(Value&&) [with Value = std::__cxx11::basic_string<char>&; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58,
inlined from 'bool nlohmann::detail::json_sax_dom_parser<BasicJsonType>::string(string_t&) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5385:21,
inlined from 'bool nlohmann::detail::parser<BasicJsonType, InputAdapterType>::sax_parse_internal(SAX*) [with SAX = nlohmann::detail::json_sax_dom_parser<nlohmann::basic_json<> >; BasicJsonType = nlohmann::basic_json<>; InputAdapterType = nlohmann::detail::input_stream_adapter]' at ../include/json.hpp:10428:29:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >' 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 = {long long unsigned int&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]',
inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser<BasicJsonType>::handle_value(Value&&) [with Value = long long unsigned int&; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58,
inlined from 'bool nlohmann::detail::json_sax_dom_parser<BasicJsonType>::number_unsigned(number_unsigned_t) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5373:21,
inlined from 'bool nlohmann::detail::parser<BasicJsonType, InputAdapterType>::sax_parse_internal(SAX*) [with SAX = nlohmann::detail::json_sax_dom_parser<nlohmann::basic_json<> >; BasicJsonType = nlohmann::basic_json<>; InputAdapterType = nlohmann::detail::input_stream_adapter]' at ../include/json.hpp:10437:29:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_scoring.o pp_scoring.cc
Finished building: src/Genomic_Data.cpp
Building file: src/Splice_Sites.cpp
Invoking: GCC C++ Compiler: g++
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Splice_Sites.d" -MT"build/Splice_Sites.o" -o "build/Splice_Sites.o" "src/Splice_Sites.cpp"
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o statemodel.o statemodel.cc
Finished building: src/Splice_Sites.cpp
Building file: src/Supporting_Methods.cpp
Invoking: GCC C++ Compiler: g++
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Supporting_Methods.d" -MT"build/Supporting_Methods.o" -o "build/Supporting_Methods.o" "src/Supporting_Methods.cpp"
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o namgene.o namgene.cc
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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
Finished building: src/Supporting_Methods.cpp
Building file: src/Test.cpp
Invoking: GCC C++ Compiler: g++
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Test.d" -MT"build/Test.o" -o "build/Test.o" "src/Test.cpp"
/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<>());
| ~~~~~~~~~~~~~~~
Finished building: src/Test.cpp
Building file: src/UTRs.cpp
Invoking: GCC C++ Compiler: g++
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/UTRs.d" -MT"build/UTRs.o" -o "build/UTRs.o" "src/UTRs.cpp"
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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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<>());
| ~~~~~~~~~~~~~~~
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)
| ^~~~~~~
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o types.o types.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o gene.o gene.cc
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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 '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>::
| ^~~~~~~~~~~~~~~~~~~
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o evaluation.o evaluation.cc
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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference 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 boost::assign_detail::call_push_back<C>::operator()(T&&) [with T = double; C = std::vector<double, std::allocator<double> >]' at /usr/include/boost/assign/list_inserter.hpp:91:25,
inlined from 'void boost::assign::list_inserter<Function, Argument>::insert(single_arg_type, T&&) [with T = double; Function = boost::assign_detail::call_push_back<std::vector<double, std::allocator<double> > >; Argument = double]' at /usr/include/boost/assign/list_inserter.hpp:414:20,
inlined from 'boost::assign::list_inserter<Function, Argument>& boost::assign::list_inserter<Function, Argument>::operator()(Ts&& ...) [with Ts = {double}; Function = boost::assign_detail::call_push_back<std::vector<double, std::allocator<double> > >; Argument = double]' at /usr/include/boost/assign/list_inserter.hpp:406:19,
inlined from 'boost::assign::list_inserter<boost::assign_detail::call_push_back<std::vector<_Tp, _Alloc> >, V> boost::assign::operator+=(std::vector<_Tp, _Alloc>&, V2&&) [with V = double; A = std::allocator<double>; V2 = double]' at /usr/include/boost/assign/std/vector.hpp:42:30,
inlined from 'static void UTRs::compute_UTRs(const Genomic_Data::Scaff_plus_Gen_Data&, const std::map<unsigned int, double>&)' at src/UTRs.cpp:382:7:
/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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o motif.o motif.cc
Finished building: src/UTRs.cpp
Building file: src/main.cpp
Invoking: GCC C++ Compiler: g++
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/main.d" -MT"build/main.o" -o "build/main.o" "src/main.cpp"
Finished building: src/main.cpp
Building target: utrrnaseq
Invoking: GCC C++ Linker
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o utrrnaseq build/Compute_UTRs.o build/Coord_Transform.o build/Genomic_Data.o build/Splice_Sites.o build/Supporting_Methods.o build/Test.o build/UTRs.o build/main.o
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
Finished building target: utrrnaseq
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/utrrnaseq'
cd bam2wig; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/bam2wig'
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-3.5.0+dfsg/auxprogs/bam2wig'
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs'
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneticcode.o geneticcode.cc
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());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++ -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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o hints.o hints.cc
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:3432:22:
/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:3441:14:
/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:3441:14:
/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++ -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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o extrinsicinfo.o extrinsicinfo.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o projectio.o projectio.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o intronmodel.o intronmodel.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exonmodel.o exonmodel.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenicmodel.o igenicmodel.cc
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:1241:16:
/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:1243:16:
/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:1184:12:
/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:1186:12:
/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 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++ -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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrmodel.o utrmodel.cc
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++ -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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o merkmal.o merkmal.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o vitmatrix.o vitmatrix.cc
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:2518:20:
/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:2524:17:
/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:2537:20:
/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:2558:20:
/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:2564:17:
/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:2576:20:
/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:2596:20:
/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:2602:17:
/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:2614:20:
/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:2642:20:
/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:2648:17:
/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:2660:20:
/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++ -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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o lldouble.o lldouble.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o mea.o mea.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o graph.o graph.cc
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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++ -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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o meaPath.o meaPath.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exoncand.o exoncand.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o randseqaccess.o randseqaccess.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o fasta.o fasta.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o ncmodel.o ncmodel.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o parser/parse.o parser/parse.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o scanner/lex.o scanner/lex.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genomicMSA.o genomicMSA.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneMSA.o geneMSA.cc
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++ -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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o contTimeMC.o contTimeMC.cc
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 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/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:387:17:
/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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonevo.o codonevo.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o compgenepred.o compgenepred.cc
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:1705:21:
/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/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:185:23,
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++ -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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o phylotree.o phylotree.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthograph.o orthograph.cc
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:1560:17:
/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/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: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:252:23:
/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:258:26:
/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:543:26:
/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:550:26:
/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:402:26:
/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:415:26:
/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:320:25:
/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 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:282:23:
/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:284:41:
/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:288:27:
/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:295:26:
/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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthoexon.o orthoexon.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o alignment.o alignment.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o speciesgraph.o speciesgraph.cc
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>::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++ -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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonMSA.o codonMSA.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o train_logReg_param.o train_logReg_param.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o tokenizer.o tokenizer.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o sqliteDB.o sqliteDB.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o commontrain.o commontrain.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenictrain.o igenictrain.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o introntrain.o introntrain.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exontrain.o exontrain.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrtrain.o utrtrain.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o dummy.o dummy.cc
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: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: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>::
| ^~~~~~~~~~~~~~~~~~~
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc
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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o pp_simScore pp_simscore.cc fasta.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
cp -f 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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o load2db load2db.cc fasta.o hints.o types.o properties.o lldouble.o -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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -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 -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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o load2sqlitedb load2sqlitedb.cc fasta.o hints.o types.o properties.o lldouble.o sqliteDB.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
cp -f load2sqlitedb ../bin/
echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -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 -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>::
| ^~~~~~~~~~~~~~~~~~~
cp -f 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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -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 -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
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 -f getSeq ../bin/
cp -f pp_simScore ../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-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -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 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 -f etraining ../bin/
cp -f fastBlockSearch ../bin/
cp -f augustus ../bin/
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/src'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg'
asciidoctor -a docdate='' -b manpage --destination-dir=debian/mansrc/ mansrc/*adoc
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg'
dh_auto_test -a
make -j4 test
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg'
mkdir -p bin
mkdir -p bin
cd src && make
cd auxprogs && make
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs'
cd aln2wig; make;
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/aln2wig'
make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[3]: 'aln2wig' is up to date.
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/aln2wig'
cd bam2hints; make;
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/bam2hints'
make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/bam2hints'
cd compileSpliceCands; make;
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands'
make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands'
cd filterBam; make;
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/filterBam'
make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src;make)
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/filterBam/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-rpath,/usr/lib -o filterBam filterBam.o initOptions.o printElapsedTime.o MatePairs.o PairednessCoverage.o BamToolsAccess.o -lbamtools -lz
echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/src'
mkdir -p ../../../bin
mv filterBam ../../../bin/filterBam
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/filterBam/src'
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/filterBam'
cd homGeneMapping; make;
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/homGeneMapping'
make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src; make)
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src'
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/homGeneMapping'
cd joingenes; make;
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/joingenes'
make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/joingenes'
cd utrrnaseq; make;
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/utrrnaseq'
make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
mkdir -p build
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/utrrnaseq'
cd bam2wig; make;
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/bam2wig'
make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs/bam2wig'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg/auxprogs'
If you run make test on a non-AMD64 architecture or a non-Linux system (like macOS), most tests will run without the --compare option!
cd tests/short && ./execute_test.py examples
test_utr_on (examples.test_examples.TestExamples.test_utr_on) ... ok
test_hints_MPE (examples.test_examples.TestExamples.test_hints_MPE) ... ok
test_training_new_species (examples.test_examples.TestExamples.test_training_new_species) ... ok
test_ab_initio_prediction (examples.test_examples.TestExamples.test_ab_initio_prediction) ... ok
test_format_and_error_out (examples.test_examples.TestExamples.test_format_and_error_out) ... ok
test_cgp (examples.test_examples.TestExamples.test_cgp) ... ok
test_cgp_sqlite (examples.test_examples.TestExamples.test_cgp_sqlite) ... ok
test_cgp_sqlite_hints (examples.test_examples.TestExamples.test_cgp_sqlite_hints) ... ok
----------------------------------------------------------------------
Ran 8 tests in 3402.772s
OK
Removing generated test files...
----------------------------------------------------------------------
Executing small test suite
----------------------------------------------------------------------
Creating SQLite database for cgp test cases...
cd tests/short && ./execute_test.py --html bam2hints
test_bam2hints (auxprogs.bam2hints.test_bam2hints.TestBam2Hints.test_bam2hints) ... ok
test_bam2hints_pipes (auxprogs.bam2hints.test_bam2hints.TestBam2Hints.test_bam2hints_pipes) ... ok
----------------------------------------------------------------------
Ran 2 tests in 0.043s
OK
cd tests/short && ./execute_test.py --html bam2wig
test_bam2wig (auxprogs.bam2wig.test_bam2wig.TestBam2Wig.test_bam2wig) ... ok
test_bam2wig_region (auxprogs.bam2wig.test_bam2wig.TestBam2Wig.test_bam2wig_region) ... ok
----------------------------------------------------------------------
Ran 2 tests in 0.080s
OK
cd tests/short && ./execute_test.py --html filterbam
test_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_options) ... ok
test_no_minId_no_minCover (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_minId_no_minCover) ... ok
test_no_minId (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_minId) ... ok
test_no_minCover (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_minCover) ... ok
test_minCover99 (auxprogs.filterbam.test_filterbam.TestFilterBam.test_minCover99) ... ok
test_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam.test_uniq) ... ok
test_uniqThresh (auxprogs.filterbam.test_filterbam.TestFilterBam.test_uniqThresh) ... ok
test_best (auxprogs.filterbam.test_filterbam.TestFilterBam.test_best) ... ok
test_noIntrons (auxprogs.filterbam.test_filterbam.TestFilterBam.test_noIntrons) ... ok
test_noIntrons_insertLimit (auxprogs.filterbam.test_filterbam.TestFilterBam.test_noIntrons_insertLimit) ... ok
test_not_paired (auxprogs.filterbam.test_filterbam.TestFilterBam.test_not_paired) ... ok
test_paired (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired) ... ok
test_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired_pairwiseAlignments) ... ok
test_pairwiseAlignments_2 (auxprogs.filterbam.test_filterbam.TestFilterBam.test_pairwiseAlignments_2) ... ok
test_paired_maxIntronLen (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired_maxIntronLen) ... ok
test_paired_pairBedFile (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired_pairBedFile) ... ok
test_commonGeneFile (auxprogs.filterbam.test_filterbam.TestFilterBam.test_commonGeneFile) ... ok
test_calmd_seq_with_equalsigns_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_no_options) ... ok
test_calmd_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_no_options) ... ok
test_calmd_seq_with_equalsigns_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_uniq) ... ok
test_calmd_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_uniq) ... ok
test_calmd_seq_with_equalsigns_best (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_best) ... ok
test_calmd_best (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_best) ... ok
test_calmd_seq_with_equalsigns_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_paired_pairwiseAlignments) ... ok
test_calmd_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_paired_pairwiseAlignments) ... ok
----------------------------------------------------------------------
Ran 25 tests in 1.699s
OK
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg'
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-3.5.0+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg'
chrpath -d debian/*/usr/bin/bam2hints
chrpath -d debian/*/usr/bin/filterBam
dh_install
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg'
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg'
dh_installchangelogs -k docs/HISTORY.TXT
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg'
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
debian/rules override_dh_compress
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg'
dh_compress -Xtutorial
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.5.0+dfsg'
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/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/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/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/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/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/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/load2db 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/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/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/bam2hints 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/fastBlockSearch debian/augustus/usr/bin/aln2wig debian/augustus/usr/bin/joingenes debian/augustus/usr/bin/prepareAlign debian/augustus/usr/bin/filterBam debian/augustus/usr/bin/load2sqlitedb debian/augustus/usr/bin/bam2wig debian/augustus/usr/bin/etraining debian/augustus/usr/bin/getSeq debian/augustus/usr/bin/load2db debian/augustus/usr/bin/pp_simScore debian/augustus/usr/bin/homGeneMapping debian/augustus/usr/bin/augustus debian/augustus/usr/bin/bam2hints debian/augustus/usr/bin/compileSpliceCands 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_3.5.0+dfsg-3_armhf.deb'.
dpkg-deb: building package 'augustus' in '../augustus_3.5.0+dfsg-3_armhf.deb'.
dpkg-genbuildinfo --build=any -O../augustus_3.5.0+dfsg-3_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../augustus_3.5.0+dfsg-3_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 2023-09-22T16:16:19Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
augustus_3.5.0+dfsg-3_armhf.changes:
------------------------------------
Format: 1.8
Date: Sat, 17 Jun 2023 18:33:10 +0200
Source: augustus
Binary: augustus augustus-dbgsym
Architecture: armhf
Version: 3.5.0+dfsg-3
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
augustus - gene prediction in eukaryotic genomes
Changes:
augustus (3.5.0+dfsg-3) unstable; urgency=medium
.
* Add patch to fix building with GCC 13.
Addresses: #1037821
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
augustus-dbgsym_3.5.0+dfsg-3_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 37789064 bytes: control archive=1288 bytes.
960 bytes, 12 lines control
1678 bytes, 16 lines md5sums
Package: augustus-dbgsym
Source: augustus
Version: 3.5.0+dfsg-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 38642
Depends: augustus (= 3.5.0+dfsg-3)
Section: debug
Priority: optional
Description: debug symbols for augustus
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drwxr-xr-x root/root 0 2023-06-17 16:33 ./usr/share/doc/
lrwxrwxrwx root/root 0 2023-06-17 16:33 ./usr/share/doc/augustus-dbgsym -> augustus
augustus_3.5.0+dfsg-3_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 1529112 bytes: control archive=5052 bytes.
1528 bytes, 23 lines control
10549 bytes, 141 lines md5sums
Package: augustus
Version: 3.5.0+dfsg-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8941
Depends: libbamtools2.5.2 (>= 2.5.2+dfsg), libboost-iostreams1.74.0 (>= 1.74.0+ds1), libc6 (>= 2.34), libcolamd2 (>= 1:4.5.2), libgcc-s1 (>= 3.5), libgsl27 (>= 2.7.1), libhts3 (>= 1.17), 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.
drwxr-xr-x root/root 0 2023-06-17 16:33 ./
drwxr-xr-x root/root 0 2023-06-17 16:33 ./usr/
drwxr-xr-x root/root 0 2023-06-17 16:33 ./usr/bin/
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drwxr-xr-x root/root 0 2023-06-17 16:33 ./usr/share/doc/
drwxr-xr-x root/root 0 2023-06-17 16:33 ./usr/share/doc/augustus/
lrwxrwxrwx root/root 0 2023-06-17 16:33 ./usr/share/doc/augustus/HISTORY.TXT.gz -> changelog.gz
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-rw-r--r-- root/root 2741 2022-11-06 01:02 ./usr/share/doc/augustus/copyright
drwxr-xr-x root/root 0 2023-06-17 16:33 ./usr/share/man/
drwxr-xr-x root/root 0 2023-06-17 16:33 ./usr/share/man/man1/
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-rw-r--r-- root/root 722 2023-06-17 16:33 ./usr/share/man/man1/etraining.1.gz
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-rw-r--r-- root/root 1251 2023-06-17 16:33 ./usr/share/man/man1/getSeq.1.gz
-rw-r--r-- root/root 1853 2023-06-17 16:33 ./usr/share/man/man1/homGeneMapping.1.gz
-rw-r--r-- root/root 2042 2023-06-17 16:33 ./usr/share/man/man1/joingenes.1.gz
-rw-r--r-- root/root 1255 2023-06-17 16:33 ./usr/share/man/man1/load2db.1.gz
-rw-r--r-- root/root 1434 2023-06-17 16:33 ./usr/share/man/man1/load2sqlitedb.1.gz
-rw-r--r-- root/root 2295 2023-06-17 16:33 ./usr/share/man/man1/pp_simScore.1.gz
-rw-r--r-- root/root 678 2023-06-17 16:33 ./usr/share/man/man1/prepareAlign.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 1568224
Build-Time: 3949
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 620
Job: augustus_3.5.0+dfsg-3
Machine Architecture: armhf
Package: augustus
Package-Time: 4635
Source-Version: 3.5.0+dfsg-3
Space: 1568224
Status: successful
Version: 3.5.0+dfsg-3
--------------------------------------------------------------------------------
Finished at 2023-09-22T16:16:19Z
Build needed 01:17:15, 1568224k disk space