augustus →
3.5.0+dfsg-2 →
armhf → 2022-11-23 05:06:07
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| augustus 3.5.0+dfsg-2 (armhf) Wed, 23 Nov 2022 04:05:02 +0000 |
+==============================================================================+
Package: augustus
Version: 3.5.0+dfsg-2
Source Version: 3.5.0+dfsg-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-2b111524-a8f8-48da-8c77-87fec0350536' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/augustus-IMRRR0/resolver-NzhayI' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.4 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.3 MB]
Fetched 27.7 MB in 14s (1983 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'augustus' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/augustus.git
Please use:
git clone https://salsa.debian.org/med-team/augustus.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 152 MB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main augustus 3.5.0+dfsg-2 (dsc) [2347 B]
Get:2 http://172.17.4.1/private bookworm-staging/main augustus 3.5.0+dfsg-2 (tar) [152 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main augustus 3.5.0+dfsg-2 (diff) [19.9 kB]
Fetched 152 MB in 18s (8265 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/augustus-IMRRR0/augustus-3.5.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/augustus-IMRRR0' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| 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, build-essential, fakeroot
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, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [474 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [559 B]
Fetched 1990 B in 0s (37.6 kB/s)
Reading package lists...
Reading package lists...
Install main 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 libperl5.34 perl-modules-5.34
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdextrautils
ca-certificates chrpath cpp-12 debhelper default-libmysqlclient-dev
dh-autoreconf dh-strip-nondeterminism dwz file g++-12 gcc-12 gcc-12-base
gettext gettext-base groff-base icu-devtools intltool-debian libamd2
libarchive-zip-perl libasan8 libatomic1 libbamtools-dev libbamtools2.5.2
libblas-dev libblas3 libboost-iostreams-dev libboost-iostreams1.74-dev
libboost-iostreams1.74.0 libboost-regex1.74-dev libboost-regex1.74.0
libboost-serialization-dev libboost-serialization1.74-dev
libboost-serialization1.74.0 libboost1.74-dev libbrotli1 libbsd0 libbtf1
libbz2-dev libcamd2 libcc1-0 libccolamd2 libcholmod3 libcolamd2
libcurl3-gnutls libcurl4-gnutls-dev libcxsparse3 libdebhelper-perl
libdeflate-dev libdeflate0 libedit2 libelf1 libexpat1
libfile-stripnondeterminism-perl libgcc-12-dev libgcc-s1 libgfortran5
libgomp1 libgsl-dev libgsl27 libgslcblas0 libhts-dev libhts3 libhtscodecs2
libicu-dev libicu72 libklu1 liblapack-dev liblapack3 libldl2
liblpsolve55-dev liblzma-dev liblzma5 libmagic-mgc libmagic1 libmariadb-dev
libmariadb-dev-compat libmariadb3 libmd0 libmetis5 libmongoose2 libmpdec3
libmysql++-dev libmysql++3v5 libncurses-dev libncurses5-dev libncurses6
libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.10-minimal
libpython3.10-stdlib librbio2 librtmp1 libruby libruby3.0 libsliplu1
libspqr2 libsqlite3-0 libsqlite3-dev libssh2-1 libssl-dev libssl3
libstdc++-12-dev libstdc++6 libsub-override-perl libsuitesparse-dev
libsuitesparseconfig5 libtool libubsan1 libuchardet0 libumfpack5 libxml2
libyaml-0-2 m4 man-db mariadb-common media-types mysql-common openssl
po-debconf python3 python3-minimal python3.10 python3.10-minimal rake ruby
ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick
ruby-xmlrpc ruby3.0 rubygems-integration samtools xz-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc gcc-12-locales cpp-12-doc
dh-make gcc-12-doc gettext-doc libasprintf-dev libgettextpo-dev groff
libbamtools-doc liblapack-doc libboost1.74-doc libboost-atomic1.74-dev
libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev
libboost-contract1.74-dev libboost-coroutine1.74-dev
libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-locale1.74-dev libboost-log1.74-dev
libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev
libboost-numpy1.74-dev libboost-program-options1.74-dev
libboost-python1.74-dev libboost-random1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev
librtmp-dev libssh2-1-dev pkg-config gsl-ref-psdoc | gsl-doc-pdf
| gsl-doc-info | gsl-ref-html icu-doc liblzma-doc libmysql++-doc ncurses-doc
sqlite3-doc libssl-doc libstdc++-12-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv python3.10-venv
python3.10-doc binfmt-support ri ruby-dev bundler cwltool
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 libmd0 libmetis5
libmongoose2 libmpdec3 libmysql++-dev libmysql++3v5 libncurses-dev
libncurses5-dev libncurses6 libnghttp2-14 libpipeline1 libpsl5
libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib librbio2
librtmp1 libruby libruby3.0 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 python3.10 python3.10-minimal rake ruby ruby-asciidoctor
ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.0
rubygems-integration samtools sbuild-build-depends-main-dummy zlib1g-dev
The following packages will be upgraded:
cpp-12 g++-12 gcc-12 gcc-12-base libasan8 libatomic1 libcc1-0 libgcc-12-dev
libgcc-s1 libgomp1 liblzma5 libsqlite3-0 libssl3 libstdc++-12-dev libstdc++6
libubsan1 xz-utils
17 upgraded, 128 newly installed, 0 to remove and 49 not upgraded.
Need to get 109 MB of archives.
After this operation, 407 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [980 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libcc1-0 armhf 12.2.0-9+rpi1 [32.2 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libgomp1 armhf 12.2.0-9+rpi1 [95.4 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf libatomic1 armhf 12.2.0-9+rpi1 [8224 B]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libasan8 armhf 12.2.0-9+rpi1 [2089 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf libubsan1 armhf 12.2.0-9+rpi1 [861 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf gcc-12-base armhf 12.2.0-9+rpi1 [37.2 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libstdc++6 armhf 12.2.0-9+rpi1 [504 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf g++-12 armhf 12.2.0-9+rpi1 [7913 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libstdc++-12-dev armhf 12.2.0-9+rpi1 [2025 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libgcc-12-dev armhf 12.2.0-9+rpi1 [725 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf gcc-12 armhf 12.2.0-9+rpi1 [14.2 MB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf cpp-12 armhf 12.2.0-9+rpi1 [7156 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libgcc-s1 armhf 12.2.0-9+rpi1 [36.1 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libssl3 armhf 3.0.7-1 [1614 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-minimal armhf 3.10.8-3 [769 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.5.0-1 [77.2 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf python3.10-minimal armhf 3.10.8-3 [1478 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.10.6-1 [38.7 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf media-types all 8.0.0 [33.4 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf liblzma5 armhf 5.2.7-0.1 [170 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libsqlite3-0 armhf 3.40.0-1 [723 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-stdlib armhf 3.10.8-3 [1597 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf python3.10 armhf 3.10.8-3 [506 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.10.6-1 [21.7 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.10.6-1 [38.2 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-1.1 [78.2 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.1-1 [1341 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf openssl armhf 3.0.7-1 [1349 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf ca-certificates all 20211016 [156 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-9 [171 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf xz-utils armhf 5.2.7-0.1 [328 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf rubygems-integration all 1.18 [6704 B]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf rake all 13.0.6-3 [83.9 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf ruby-net-telnet all 0.1.1-2.1 [12.7 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf ruby-webrick all 1.7.0-4 [50.9 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf ruby-xmlrpc all 0.3.2-2 [24.4 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf ruby-sdbm armhf 1.0.0-5 [13.4 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-2 [28.6 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.7-1 [112 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20221030-1 [76.1 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libyaml-0-2 armhf 0.2.5-1 [44.6 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libruby3.0 armhf 3.0.4-8 [5136 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf ruby3.0 armhf 3.0.4-8 [683 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libruby armhf 1:3.0+3.1 [11.3 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf ruby-rubygems all 3.3.15-1 [293 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf ruby armhf 1:3.0+3.1 [12.2 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf ruby-asciidoctor all 2.0.17-1 [209 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf asciidoctor all 2.0.17-1 [85.8 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-9 [510 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.10.1 [79.9 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libicu72 armhf 72.1-2 [9008 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.1 [570 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-9 [1220 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.10.1 [940 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf mysql-common all 5.8+1.0.8 [7528 B]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf mariadb-common all 1:10.6.10-1 [37.2 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libmariadb3 armhf 1:10.6.10-1+b2 [147 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libssl-dev armhf 3.0.7-1 [2095 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4.1 [183 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libmariadb-dev armhf 1:10.6.10-1+b2 [237 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libmariadb-dev-compat armhf 1:10.6.10-1+b2 [19.7 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf default-libmysqlclient-dev armhf 1.0.8 [3980 B]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf icu-devtools armhf 72.1-2 [175 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libsuitesparseconfig5 armhf 1:5.12.0+dfsg-2 [23.6 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libamd2 armhf 1:5.12.0+dfsg-2 [30.2 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libbamtools2.5.2 armhf 2.5.2+dfsg-2 [127 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libbamtools-dev armhf 2.5.2+dfsg-2 [183 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.10.1-2 [109 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libblas-dev armhf 3.10.1-2 [114 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-17+b1 [9508 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libboost-regex1.74.0 armhf 1.74.0-17+b1 [420 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf libicu-dev armhf 72.1-2 [9962 kB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf libboost-regex1.74-dev armhf 1.74.0-17+b1 [525 kB]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf libboost-iostreams1.74.0 armhf 1.74.0-17+b1 [235 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf libboost-iostreams1.74-dev armhf 1.74.0-17+b1 [245 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf libboost-iostreams-dev armhf 1.74.0.3+b4 [4592 B]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf libboost-serialization1.74.0 armhf 1.74.0-17+b1 [296 kB]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf libboost-serialization1.74-dev armhf 1.74.0-17+b1 [362 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf libboost-serialization-dev armhf 1.74.0.3+b4 [4832 B]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf libbtf1 armhf 1:5.12.0+dfsg-2 [24.1 kB]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf libbz2-dev armhf 1.0.8-5+b2 [26.8 kB]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf libcamd2 armhf 1:5.12.0+dfsg-2 [30.7 kB]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf libccolamd2 armhf 1:5.12.0+dfsg-2 [31.7 kB]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf libcolamd2 armhf 1:5.12.0+dfsg-2 [28.3 kB]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.2.0-9+rpi1 [238 kB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.1-2 [1587 kB]
Get:112 http://172.17.4.1/private bookworm-staging/main armhf libmetis5 armhf 5.1.0.dfsg-7 [133 kB]
Get:113 http://172.17.4.1/private bookworm-staging/main armhf libcholmod3 armhf 1:5.12.0+dfsg-2 [212 kB]
Get:114 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.50.0-1 [65.0 kB]
Get:115 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:116 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:117 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:118 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.86.0-2 [318 kB]
Get:119 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.86.0-2 [394 kB]
Get:120 http://172.17.4.1/private bookworm-staging/main armhf libcxsparse3 armhf 1:5.12.0+dfsg-2 [52.1 kB]
Get:121 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.14-1 [50.9 kB]
Get:122 http://172.17.4.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.14-1 [48.1 kB]
Get:123 http://172.17.4.1/private bookworm-staging/main armhf libgslcblas0 armhf 2.7.1+dfsg-3 [81.4 kB]
Get:124 http://172.17.4.1/private bookworm-staging/main armhf libgsl27 armhf 2.7.1+dfsg-3 [758 kB]
Get:125 http://172.17.4.1/private bookworm-staging/main armhf libgsl-dev armhf 2.7.1+dfsg-3 [958 kB]
Get:126 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.3.0-4 [59.5 kB]
Get:127 http://172.17.4.1/private bookworm-staging/main armhf libhts3 armhf 1.16+ds-3 [367 kB]
Get:128 http://172.17.4.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.7-0.1 [228 kB]
Get:129 http://172.17.4.1/private bookworm-staging/main armhf libhts-dev armhf 1.16+ds-3 [1479 kB]
Get:130 http://172.17.4.1/private bookworm-staging/main armhf libklu1 armhf 1:5.12.0+dfsg-2 [51.8 kB]
Get:131 http://172.17.4.1/private bookworm-staging/main armhf liblapack-dev armhf 3.10.1-2 [2847 kB]
Get:132 http://172.17.4.1/private bookworm-staging/main armhf libldl2 armhf 1:5.12.0+dfsg-2 [23.8 kB]
Get:133 http://172.17.4.1/private bookworm-staging/main armhf libmongoose2 armhf 1:5.12.0+dfsg-2 [43.8 kB]
Get:134 http://172.17.4.1/private bookworm-staging/main armhf libumfpack5 armhf 1:5.12.0+dfsg-2 [128 kB]
Get:135 http://172.17.4.1/private bookworm-staging/main armhf librbio2 armhf 1:5.12.0+dfsg-2 [32.9 kB]
Get:136 http://172.17.4.1/private bookworm-staging/main armhf libspqr2 armhf 1:5.12.0+dfsg-2 [68.2 kB]
Get:137 http://172.17.4.1/private bookworm-staging/main armhf libsliplu1 armhf 1:5.12.0+dfsg-2 [49.5 kB]
Get:138 http://172.17.4.1/private bookworm-staging/main armhf libsuitesparse-dev armhf 1:5.12.0+dfsg-2 [614 kB]
Get:139 http://172.17.4.1/private bookworm-staging/main armhf liblpsolve55-dev armhf 5.5.2.5-2 [349 kB]
Get:140 http://172.17.4.1/private bookworm-staging/main armhf libmysql++3v5 armhf 3.2.5-2.1 [144 kB]
Get:141 http://172.17.4.1/private bookworm-staging/main armhf libmysql++-dev armhf 3.2.5-2.1 [150 kB]
Get:142 http://172.17.4.1/private bookworm-staging/main armhf libncurses-dev armhf 6.3+20220423-2 [289 kB]
Get:143 http://172.17.4.1/private bookworm-staging/main armhf libncurses5-dev armhf 6.3+20220423-2 [940 B]
Get:144 http://172.17.4.1/private bookworm-staging/main armhf libsqlite3-dev armhf 3.40.0-1 [892 kB]
Get:145 http://172.17.4.1/private bookworm-staging/main armhf samtools armhf 1.16.1-1 [559 kB]
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Setting up dh-autoreconf (20) ...
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127 added, 0 removed; done.
Setting up libcamd2:armhf (1:5.12.0+dfsg-2) ...
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Not building database; man-db/auto-update is not 'true'.
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Setting up rake (13.0.6-3) ...
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Setting up libruby:armhf (1:3.0+3.1) ...
Setting up ruby (1:3.0+3.1) ...
Setting up ruby-asciidoctor (2.0.17-1) ...
Setting up asciidoctor (2.0.17-1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up ruby-sdbm:armhf (1.0.0-5) ...
Setting up ruby-rubygems (3.3.15-1) ...
Processing triggers for libc-bin (2.35-2+rpi1) ...
Processing triggers for ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.39-6+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-9+rpi1 gcc-12_12.2.0-9+rpi1 libc6-dev_2.35-2+rpi1 libstdc++-12-dev_12.2.0-9+rpi1 libstdc++6_12.2.0-9+rpi1 linux-libc-dev_5.19.6-1+rpi1
Package versions: adduser_3.129 apt_2.5.3 asciidoctor_2.0.17-1 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-9 autotools-dev_20220109.1 base-files_12.3+rpi1 base-passwd_3.6.1 bash_5.2~rc2-2 binutils_2.39-6+rpi1 binutils-arm-linux-gnueabihf_2.39-6+rpi1 binutils-common_2.39-6+rpi1 bsdextrautils_2.38.1-1.1 bsdutils_1:2.38.1-1.1 build-essential_12.9 bzip2_1.0.8-5+b2 ca-certificates_20211016 chrpath_0.16-2 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-9+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.10.1 debianutils_5.7-0.3 default-libmysqlclient-dev_1.0.8 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dirmngr_2.2.39-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-9+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-9+rpi1 gcc-12-base_12.2.0-9+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_0.21-9 gettext-base_0.21-9 gnupg_2.2.39-1 gnupg-l10n_2.2.39-1 gnupg-utils_2.2.39-1 gpg_2.2.39-1 gpg-agent_2.2.39-1 gpg-wks-client_2.2.39-1 gpg-wks-server_2.2.39-1 gpgconf_2.2.39-1 gpgsm_2.2.39-1 gpgv_2.2.39-1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 hostname_3.23 icu-devtools_72.1-2 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20211215-1 krb5-locales_1.20-1 libacl1_2.3.1-1 libamd2_1:5.12.0+dfsg-2 libapt-pkg6.0_2.5.3 libarchive-zip-perl_1.68-1 libasan8_12.2.0-9+rpi1 libassuan0_2.5.5-4 libatomic1_12.2.0-9+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbamtools-dev_2.5.2+dfsg-2 libbamtools2.5.2_2.5.2+dfsg-2 libbinutils_2.39-6+rpi1 libblas-dev_3.10.1-2 libblas3_3.10.1-2 libblkid1_2.38.1-1.1 libboost-iostreams-dev_1.74.0.3+b4 libboost-iostreams1.74-dev_1.74.0-17+b1 libboost-iostreams1.74.0_1.74.0-17+b1 libboost-regex1.74-dev_1.74.0-17+b1 libboost-regex1.74.0_1.74.0-17+b1 libboost-serialization-dev_1.74.0.3+b4 libboost-serialization1.74-dev_1.74.0-17+b1 libboost-serialization1.74.0_1.74.0-17+b1 libboost1.74-dev_1.74.0-17+b1 libbrotli1_1.0.9-2+b2 libbsd0_0.11.7-1 libbtf1_1:5.12.0+dfsg-2 libbz2-1.0_1.0.8-5+b2 libbz2-dev_1.0.8-5+b2 libc-bin_2.35-2+rpi1 libc-dev-bin_2.35-2+rpi1 libc6_2.35-2+rpi1 libc6-dev_2.35-2+rpi1 libcamd2_1:5.12.0+dfsg-2 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_12.2.0-9+rpi1 libccolamd2_1:5.12.0+dfsg-2 libcholmod3_1:5.12.0+dfsg-2 libcolamd2_1:5.12.0+dfsg-2 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libctf-nobfd0_2.39-6+rpi1 libctf0_2.39-6+rpi1 libcurl3-gnutls_7.86.0-2 libcurl4-gnutls-dev_7.86.0-2 libcxsparse3_1:5.12.0+dfsg-2 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264 libdebhelper-perl_13.10.1 libdeflate-dev_1.14-1 libdeflate0_1.14-1 libdpkg-perl_1.21.9+rpi1 libedit2_3.1-20221030-1 libelf1_0.187-2+rpi2 libexpat1_2.5.0-1 libext2fs2_1.46.6~rc1-1 libfakeroot_1.29-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-12-dev_12.2.0-9+rpi1 libgcc-s1_12.2.0-9+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_12.2.0-9+rpi1 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-2 libgomp1_12.2.0-9+rpi1 libgpg-error0_1.45-2 libgsl-dev_2.7.1+dfsg-3 libgsl27_2.7.1+dfsg-3 libgslcblas0_2.7.1+dfsg-3 libgssapi-krb5-2_1.20-1 libhogweed6_3.8.1-2 libhts-dev_1.16+ds-3 libhts3_1.16+ds-3 libhtscodecs2_1.3.0-4 libicu-dev_72.1-2 libicu72_72.1-2 libidn2-0_2.3.3-1 libisl23_0.25-1 libk5crypto3_1.20-1 libkeyutils1_1.6.3-1 libklu1_1:5.12.0+dfsg-2 libkrb5-3_1.20-1 libkrb5support0_1.20-1 libksba8_1.6.0-3 liblapack-dev_3.10.1-2 liblapack3_3.10.1-2 libldap-2.5-0_2.5.13+dfsg-2+rpi1 libldl2_1:5.12.0+dfsg-2 liblpsolve55-dev_5.5.2.5-2 liblz4-1_1.9.4-1+rpi1 liblzma-dev_5.2.7-0.1 liblzma5_5.2.7-0.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmariadb-dev_1:10.6.10-1+b2 libmariadb-dev-compat_1:10.6.10-1+b2 libmariadb3_1:10.6.10-1+b2 libmd0_1.0.4-2 libmetis5_5.1.0.dfsg-7 libmongoose2_1:5.12.0+dfsg-2 libmount1_2.38.1-1.1 libmpc3_1.2.1-2 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libmysql++-dev_3.2.5-2.1 libmysql++3v5_3.2.5-2.1 libncurses-dev_6.3+20220423-2 libncurses5-dev_6.3+20220423-2 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnghttp2-14_1.50.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-5 libpam-modules-bin_1.5.2-5 libpam-runtime_1.5.2-5 libpam0g_1.5.2-5 libpcre2-8-0_10.40-1+b2 libpcre3_2:8.39-14 libperl5.32_5.32.1-6 libperl5.34_5.34.0-5 libperl5.36_5.36.0-4 libpipeline1_1.5.7-1 libpsl5_0.21.0-1.2 libpython3-stdlib_3.10.6-1 libpython3.10-minimal_3.10.8-3 libpython3.10-stdlib_3.10.8-3 librbio2_1:5.12.0+dfsg-2 libreadline8_8.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libruby_1:3.0+3.1 libruby3.0_3.0.4-8 libsasl2-2_2.1.28+dfsg-8 libsasl2-modules-db_2.1.28+dfsg-8 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol1_3.1-1 libsepol2_3.4-2 libsliplu1_1:5.12.0+dfsg-2 libsmartcols1_2.38.1-1.1 libspqr2_1:5.12.0+dfsg-2 libsqlite3-0_3.40.0-1 libsqlite3-dev_3.40.0-1 libss2_1.46.6~rc1-1 libssh2-1_1.10.0-3+b1 libssl-dev_3.0.7-1 libssl1.1_1.1.1o-1 libssl3_3.0.7-1 libstdc++-12-dev_12.2.0-9+rpi1 libstdc++6_12.2.0-9+rpi1 libsub-override-perl_0.09-4 libsuitesparse-dev_1:5.12.0+dfsg-2 libsuitesparseconfig5_1:5.12.0+dfsg-2 libsystemd0_251.5-1+rpi1 libtasn1-6_4.19.0-2 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-4 libubsan1_12.2.0-9+rpi1 libuchardet0_0.0.7-1 libudev1_251.5-1+rpi1 libumfpack5_1:5.12.0+dfsg-2 libunistring2_1.0-2 libuuid1_2.38.1-1.1 libxml2_2.9.14+dfsg-1.1 libxxhash0_0.8.1-1 libyaml-0-2_0.2.5-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.6-1+rpi1 login_1:4.12.3+dfsg1-1 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 m4_1.4.19-1 make_4.3-4.1 man-db_2.11.1-1 mariadb-common_1:10.6.10-1 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mount_2.38.1-1.1 mysql-common_5.8+1.0.8 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 openssl_3.0.7-1 passwd_1:4.12.3+dfsg1-1 patch_2.7.6-7 perl_5.36.0-4 perl-base_5.36.0-4 perl-modules-5.32_5.32.1-6 perl-modules-5.34_5.34.0-5 perl-modules-5.36_5.36.0-4 pinentry-curses_1.2.0-2 po-debconf_1.0.21+nmu1 python3_3.10.6-1 python3-minimal_3.10.6-1 python3.10_3.10.8-3 python3.10-minimal_3.10.8-3 rake_13.0.6-3 raspbian-archive-keyring_20120528.2 readline-common_8.2-1 rpcsvc-proto_1.4.2-4 ruby_1:3.0+3.1 ruby-asciidoctor_2.0.17-1 ruby-net-telnet_0.1.1-2.1 ruby-rubygems_3.3.15-1 ruby-sdbm_1.0.0-5 ruby-webrick_1.7.0-4 ruby-xmlrpc_0.3.2-2 ruby3.0_3.0.4-8 rubygems-integration_1.18 samtools_1.16.1-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.31 sysvinit-utils_3.05-6 tar_1.34+dfsg-1 tzdata_2022d-1 util-linux_2.38.1-1.1 util-linux-extra_2.38.1-1.1 xz-utils_5.2.7-0.1 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: augustus
Binary: augustus, augustus-data, augustus-doc
Architecture: any all
Version: 3.5.0+dfsg-2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Sascha Steinbiss <satta@debian.org>
Homepage: https://bioinf.uni-greifswald.de/augustus/
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/augustus
Vcs-Git: https://salsa.debian.org/med-team/augustus.git
Testsuite: autopkgtest
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
Package-List:
augustus deb science optional arch=any
augustus-data deb science optional arch=all
augustus-doc deb doc optional arch=all
Checksums-Sha1:
a926ee500e46fc39c81376be09bbcca055b8a8ad 151813456 augustus_3.5.0+dfsg.orig.tar.xz
94f8380e1b95690ab6321e1579d90e7f7cbcd44c 19920 augustus_3.5.0+dfsg-2.debian.tar.xz
Checksums-Sha256:
30a2a5200e7201a28383bebb98350eab9e043e38d0f7b825a1c8a614a6e68dc8 151813456 augustus_3.5.0+dfsg.orig.tar.xz
2249cb77873071a191813ca9d4e828877aba1ae59ece01f237f0d942edd99ccb 19920 augustus_3.5.0+dfsg-2.debian.tar.xz
Files:
11cc56baea3047c128e2da42f7cf9dd0 151813456 augustus_3.5.0+dfsg.orig.tar.xz
ace135cf933aba3ec77fa12654ee84d2 19920 augustus_3.5.0+dfsg-2.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.NWx20G3d/trustedkeys.kbx': General error
gpgv: Signature made Sun Nov 20 23:29:04 2022 UTC
gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./augustus_3.5.0+dfsg-2.dsc
dpkg-source: info: extracting augustus in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking augustus_3.5.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking augustus_3.5.0+dfsg-2.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
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=f89ee6850c51463faed427366eb0b008
JOURNAL_STREAM=8:31299
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-2b111524-a8f8-48da-8c77-87fec0350536
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c13331
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package augustus
dpkg-buildpackage: info: source version 3.5.0+dfsg-2
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 '/<<PKGBUILDDIR>>'
/usr/bin/make -C auxprogs/bam2hints clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/bam2hints'
rm -f bam2hints.o bam2hints ../../bin/bam2hints
make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/homGeneMapping clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping'
cd src; make clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping/src'
rm -f homGeneMapping gene.o genome.o sqliteDB.o
rm -f ../../../bin/homGeneMapping
make[3]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping/src'
if [ -n /usr/bin/python3 ] ; then cd ../../tests/short && ./execute_test.py --clean homGeneMapping ; fi
make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping'
/usr/bin/make -C auxprogs/joingenes clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/joingenes'
rm -f *.o joingenes ../../bin/joingenes
make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/joingenes'
/usr/bin/make -C auxprogs/aln2wig clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/aln2wig'
rm -f aln2wig aln2wig.o ../../bin/aln2wig
make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2wig clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/compileSpliceCands clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/compileSpliceCands'
rm -f compileSpliceCands *.o ../../bin/compileSpliceCands
make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/filterBam'
(cd src; make clean;)
make[3]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
mkdir -p bin
/usr/bin/make -C auxprogs/aln2wig
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/aln2wig'
cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -ansi -pedantic -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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 '/<<PKGBUILDDIR>>/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2hints
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/bam2hints'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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 '/<<PKGBUILDDIR>>/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/bam2wig
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/bam2wig'
cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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 '/<<PKGBUILDDIR>>/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/compileSpliceCands
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/compileSpliceCands'
cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -pedantic -ansi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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:540:14: note: in a call to allocation function ‘malloc’ declared here
540 | 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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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 '/<<PKGBUILDDIR>>/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/filterBam/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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 '/<<PKGBUILDDIR>>/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/filterBam'
/usr/bin/make -C auxprogs/homGeneMapping/src
make[2]: Entering directory '/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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 '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping/src'
/usr/bin/make -C auxprogs/joingenes
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/joingenes'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++0x -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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 '/<<PKGBUILDDIR>>/auxprogs/joingenes'
dh_auto_build
make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p bin
mkdir -p bin
cd src && make
cd auxprogs && make
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>/auxprogs'
cd aln2wig; make;
make[4]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/auxprogs/aln2wig'
cd bam2hints; make;
make[4]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/bam2hints'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genbank.o genbank.cc
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/bam2hints'
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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o properties.o properties.cc
cd compileSpliceCands; 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=/<<PKGBUILDDIR>>=. -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 '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/auxprogs/compileSpliceCands'
cd filterBam; make;
make[4]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/filterBam'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src;make)
make[5]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/filterBam/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 '/<<PKGBUILDDIR>>/auxprogs/filterBam/src'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/filterBam'
cd homGeneMapping; make;
make[4]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src; make)
make[5]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping/src'
make[5]: Nothing to be done for 'all'.
make[5]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping/src'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping'
cd joingenes; make;
make[4]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/auxprogs/joingenes'
cd utrrnaseq; make;
make[4]: Entering directory '/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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)
| ^~~~~~~
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>::
| ^~~~~~~~~~~~~~~~~~~
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: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=/<<PKGBUILDDIR>>=. -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<>());
| ~~~~~~~~~~~~~~~
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=/<<PKGBUILDDIR>>=. -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/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=/<<PKGBUILDDIR>>=. -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
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=/<<PKGBUILDDIR>>=. -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/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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o namgene.o namgene.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=/<<PKGBUILDDIR>>=. -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"
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=/<<PKGBUILDDIR>>=. -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"
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>::
| ^~~~~~~~~~~~~~~~~~~
/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 ‘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 ‘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);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o types.o types.cc
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=/<<PKGBUILDDIR>>=. -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 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=/<<PKGBUILDDIR>>=. -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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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=/<<PKGBUILDDIR>>=. -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/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o motif.o motif.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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
Finished building target: utrrnaseq
make[4]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/utrrnaseq'
cd bam2wig; make;
make[4]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/auxprogs/bam2wig'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneticcode.o geneticcode.cc
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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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
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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o hints.o hints.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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o extrinsicinfo.o extrinsicinfo.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());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o projectio.o projectio.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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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<>());
| ~~~~~~~~~~~~~~~
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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrmodel.o utrmodel.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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o merkmal.o merkmal.cc
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>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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>::
| ^~~~~~~~~~~~~~~~~~~
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);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthograph.o orthograph.cc
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>::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 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>::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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o speciesgraph.o speciesgraph.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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonMSA.o codonMSA.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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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=/<<PKGBUILDDIR>>=. -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 file included from /usr/include/c++/12/vector:70,
from ../include/types.hh:36,
from ../include/properties.hh:14,
from ../include/pp_simscore.hh:21,
from pp_simscore.cc:10:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void SS::SimilarityScore::printAlignment()’ at pp_simscore.cc:723:56:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cp -f getSeq ../bin/
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
cp -f pp_simScore ../bin/
In file included from /usr/include/c++/12/vector:70,
from ../include/types.hh:36,
from etraining.cc:9:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘static void CRF::compareWeights(Parameters*, std::vector<T>&, std::vector<V>&, int) [with U = double; V = double]’ at ../include/merkmal.hh:277:27:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cp -f etraining ../bin/
cp -f fastBlockSearch ../bin/
cp -f augustus ../bin/
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
asciidoctor -a docdate='' -b manpage --destination-dir=debian/mansrc/ mansrc/*adoc
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p bin
mkdir -p bin
cd src && make
cd auxprogs && make
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs'
cd aln2wig; make;
make[3]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/auxprogs/aln2wig'
cd bam2hints; make;
make[3]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/auxprogs/bam2hints'
cd compileSpliceCands; make;
make[3]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/auxprogs/compileSpliceCands'
cd filterBam; make;
make[3]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/filterBam'
make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src;make)
make[4]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/filterBam/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
mkdir -p ../../../bin
mv filterBam ../../../bin/filterBam
make[4]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/filterBam/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/filterBam'
cd homGeneMapping; make;
make[3]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping'
make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src; make)
make[4]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping/src'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping'
cd joingenes; make;
make[3]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/auxprogs/joingenes'
cd utrrnaseq; make;
make[3]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/utrrnaseq'
make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
mkdir -p build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/utrrnaseq'
cd bam2wig; make;
make[3]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/auxprogs/bam2wig'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/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) ... ok
test_hints_MPE (examples.test_examples.TestExamples) ... ok
test_training_new_species (examples.test_examples.TestExamples) ... ok
test_ab_initio_prediction (examples.test_examples.TestExamples) ... ok
test_format_and_error_out (examples.test_examples.TestExamples) ... ok
test_cgp (examples.test_examples.TestExamples) ... ok
test_cgp_sqlite (examples.test_examples.TestExamples) ... ok
test_cgp_sqlite_hints (examples.test_examples.TestExamples) ... ok
----------------------------------------------------------------------
Ran 8 tests in 1462.652s
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) ... ok
test_bam2hints_pipes (auxprogs.bam2hints.test_bam2hints.TestBam2Hints) ... ok
----------------------------------------------------------------------
Ran 2 tests in 0.372s
OK
cd tests/short && ./execute_test.py --html bam2wig
test_bam2wig (auxprogs.bam2wig.test_bam2wig.TestBam2Wig) ... ok
test_bam2wig_region (auxprogs.bam2wig.test_bam2wig.TestBam2Wig) ... ok
----------------------------------------------------------------------
Ran 2 tests in 0.255s
OK
cd tests/short && ./execute_test.py --html filterbam
test_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_no_minId_no_minCover (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_no_minId (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_no_minCover (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_minCover99 (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_uniqThresh (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_best (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_noIntrons (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_noIntrons_insertLimit (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_not_paired (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_paired (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_pairwiseAlignments_2 (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_paired_maxIntronLen (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_paired_pairBedFile (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_commonGeneFile (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_calmd_seq_with_equalsigns_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_calmd_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_calmd_seq_with_equalsigns_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_calmd_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_calmd_seq_with_equalsigns_best (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_calmd_best (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_calmd_seq_with_equalsigns_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
test_calmd_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam) ... ok
----------------------------------------------------------------------
Ran 25 tests in 3.865s
OK
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
chrpath -d debian/*/usr/bin/bam2hints
chrpath -d debian/*/usr/bin/filterBam
dh_install
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installchangelogs -k docs/HISTORY.TXT
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
debian/rules override_dh_compress
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_compress -Xtutorial
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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/load2sqlitedb contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/load2db contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: 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/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/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/augustus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/pp_simScore contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/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/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/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/bam2hints contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/joingenes 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/load2sqlitedb debian/augustus/usr/bin/aln2wig debian/augustus/usr/bin/load2db debian/augustus/usr/bin/bam2wig debian/augustus/usr/bin/prepareAlign debian/augustus/usr/bin/etraining debian/augustus/usr/bin/filterBam debian/augustus/usr/bin/compileSpliceCands debian/augustus/usr/bin/augustus debian/augustus/usr/bin/pp_simScore debian/augustus/usr/bin/fastBlockSearch debian/augustus/usr/bin/getSeq debian/augustus/usr/bin/homGeneMapping debian/augustus/usr/bin/bam2hints debian/augustus/usr/bin/joingenes 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-2_armhf.deb'.
dpkg-deb: building package 'augustus' in '../augustus_3.5.0+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=any -O../augustus_3.5.0+dfsg-2_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> -O../augustus_3.5.0+dfsg-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2022-11-23T05:05:50Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
augustus_3.5.0+dfsg-2_armhf.changes:
------------------------------------
Format: 1.8
Date: Mon, 21 Nov 2022 00:11:53 +0100
Source: augustus
Binary: augustus augustus-dbgsym
Architecture: armhf
Version: 3.5.0+dfsg-2
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
augustus - gene prediction in eukaryotic genomes
Changes:
augustus (3.5.0+dfsg-2) unstable; urgency=medium
.
* Skip filterBam auxprogs test on s390x.
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Checksums-Sha256:
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Files:
adcf94b6d8740807b56fc4b0b90bfe3f 37795312 debug optional augustus-dbgsym_3.5.0+dfsg-2_armhf.deb
477ab1b049756bd41785c2eacbdbff94 8440 science optional augustus_3.5.0+dfsg-2_armhf.buildinfo
8338e374a5d86ef2935ec8c42dc7ed28 1524840 science optional augustus_3.5.0+dfsg-2_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: augustus
Binary: augustus augustus-dbgsym
Architecture: armhf
Version: 3.5.0+dfsg-2
Checksums-Md5:
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Checksums-Sha1:
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Checksums-Sha256:
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Wed, 23 Nov 2022 05:05:47 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
asciidoctor (= 2.0.17-1),
autoconf (= 2.71-2),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-9),
autotools-dev (= 20220109.1),
base-files (= 12.3+rpi1),
base-passwd (= 3.6.1),
bash (= 5.2~rc2-2),
binutils (= 2.39-6+rpi1),
binutils-arm-linux-gnueabihf (= 2.39-6+rpi1),
binutils-common (= 2.39-6+rpi1),
bsdextrautils (= 2.38.1-1.1),
bsdutils (= 1:2.38.1-1.1),
build-essential (= 12.9),
bzip2 (= 1.0.8-5+b2),
ca-certificates (= 20211016),
chrpath (= 0.16-2),
coreutils (= 9.1-1),
cpp (= 4:12.2.0-1+rpi1),
cpp-12 (= 12.2.0-9+rpi1),
dash (= 0.5.11+git20210903+057cd650a4ed-9),
debconf (= 1.5.79),
debhelper (= 13.10.1),
debianutils (= 5.7-0.3),
default-libmysqlclient-dev (= 1.0.8),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.0-1),
diffutils (= 1:3.8-1),
dpkg (= 1.21.9+rpi1),
dpkg-dev (= 1.21.9+rpi1),
dwz (= 0.14+20220924-2),
file (= 1:5.41-4),
findutils (= 4.9.0-3),
g++ (= 4:12.2.0-1+rpi1),
g++-12 (= 12.2.0-9+rpi1),
gcc (= 4:12.2.0-1+rpi1),
gcc-12 (= 12.2.0-9+rpi1),
gcc-12-base (= 12.2.0-9+rpi1),
gettext (= 0.21-9),
gettext-base (= 0.21-9),
grep (= 3.7-1),
groff-base (= 1.22.4-8),
gzip (= 1.12-1),
hostname (= 3.23),
icu-devtools (= 72.1-2),
init-system-helpers (= 1.64),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-1),
libamd2 (= 1:5.12.0+dfsg-2),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 12.2.0-9+rpi1),
libatomic1 (= 12.2.0-9+rpi1),
libattr1 (= 1:2.5.1-1),
libaudit-common (= 1:3.0.7-1.1),
libaudit1 (= 1:3.0.7-1.1),
libbamtools-dev (= 2.5.2+dfsg-2),
libbamtools2.5.2 (= 2.5.2+dfsg-2),
libbinutils (= 2.39-6+rpi1),
libblas-dev (= 3.10.1-2),
libblas3 (= 3.10.1-2),
libblkid1 (= 2.38.1-1.1),
libboost-iostreams-dev (= 1.74.0.3+b4),
libboost-iostreams1.74-dev (= 1.74.0-17+b1),
libboost-iostreams1.74.0 (= 1.74.0-17+b1),
libboost-regex1.74-dev (= 1.74.0-17+b1),
libboost-regex1.74.0 (= 1.74.0-17+b1),
libboost-serialization-dev (= 1.74.0.3+b4),
libboost-serialization1.74-dev (= 1.74.0-17+b1),
libboost-serialization1.74.0 (= 1.74.0-17+b1),
libboost1.74-dev (= 1.74.0-17+b1),
libbrotli1 (= 1.0.9-2+b2),
libbsd0 (= 0.11.7-1),
libbtf1 (= 1:5.12.0+dfsg-2),
libbz2-1.0 (= 1.0.8-5+b2),
libbz2-dev (= 1.0.8-5+b2),
libc-bin (= 2.35-2+rpi1),
libc-dev-bin (= 2.35-2+rpi1),
libc6 (= 2.35-2+rpi1),
libc6-dev (= 2.35-2+rpi1),
libcamd2 (= 1:5.12.0+dfsg-2),
libcap-ng0 (= 0.8.3-1),
libcap2 (= 1:2.44-1),
libcc1-0 (= 12.2.0-9+rpi1),
libccolamd2 (= 1:5.12.0+dfsg-2),
libcholmod3 (= 1:5.12.0+dfsg-2),
libcolamd2 (= 1:5.12.0+dfsg-2),
libcom-err2 (= 1.46.6~rc1-1),
libcrypt-dev (= 1:4.4.28-2),
libcrypt1 (= 1:4.4.28-2),
libctf-nobfd0 (= 2.39-6+rpi1),
libctf0 (= 2.39-6+rpi1),
libcurl3-gnutls (= 7.86.0-2),
libcurl4-gnutls-dev (= 7.86.0-2),
libcxsparse3 (= 1:5.12.0+dfsg-2),
libdb5.3 (= 5.3.28+dfsg1-0.10),
libdebconfclient0 (= 0.264),
libdebhelper-perl (= 13.10.1),
libdeflate-dev (= 1.14-1),
libdeflate0 (= 1.14-1),
libdpkg-perl (= 1.21.9+rpi1),
libedit2 (= 3.1-20221030-1),
libelf1 (= 0.187-2+rpi2),
libexpat1 (= 2.5.0-1),
libffi8 (= 3.4.2-4),
libfile-stripnondeterminism-perl (= 1.13.0-1),
libgcc-12-dev (= 12.2.0-9+rpi1),
libgcc-s1 (= 12.2.0-9+rpi1),
libgcrypt20 (= 1.10.1-2+b2),
libgdbm-compat4 (= 1.23-3),
libgdbm6 (= 1.23-3),
libgfortran5 (= 12.2.0-9+rpi1),
libgmp10 (= 2:6.2.1+dfsg1-1.1),
libgnutls30 (= 3.7.8-2),
libgomp1 (= 12.2.0-9+rpi1),
libgpg-error0 (= 1.45-2),
libgsl-dev (= 2.7.1+dfsg-3),
libgsl27 (= 2.7.1+dfsg-3),
libgslcblas0 (= 2.7.1+dfsg-3),
libgssapi-krb5-2 (= 1.20-1),
libhogweed6 (= 3.8.1-2),
libhts-dev (= 1.16+ds-3),
libhts3 (= 1.16+ds-3),
libhtscodecs2 (= 1.3.0-4),
libicu-dev (= 72.1-2),
libicu72 (= 72.1-2),
libidn2-0 (= 2.3.3-1),
libisl23 (= 0.25-1),
libk5crypto3 (= 1.20-1),
libkeyutils1 (= 1.6.3-1),
libklu1 (= 1:5.12.0+dfsg-2),
libkrb5-3 (= 1.20-1),
libkrb5support0 (= 1.20-1),
liblapack-dev (= 3.10.1-2),
liblapack3 (= 3.10.1-2),
libldap-2.5-0 (= 2.5.13+dfsg-2+rpi1),
libldl2 (= 1:5.12.0+dfsg-2),
liblpsolve55-dev (= 5.5.2.5-2),
liblz4-1 (= 1.9.4-1+rpi1),
liblzma-dev (= 5.2.7-0.1),
liblzma5 (= 5.2.7-0.1),
libmagic-mgc (= 1:5.41-4),
libmagic1 (= 1:5.41-4),
libmariadb-dev (= 1:10.6.10-1+b2),
libmariadb-dev-compat (= 1:10.6.10-1+b2),
libmariadb3 (= 1:10.6.10-1+b2),
libmd0 (= 1.0.4-2),
libmetis5 (= 5.1.0.dfsg-7),
libmongoose2 (= 1:5.12.0+dfsg-2),
libmount1 (= 2.38.1-1.1),
libmpc3 (= 1.2.1-2),
libmpdec3 (= 2.5.1-2+rpi1),
libmpfr6 (= 4.1.0-3),
libmysql++-dev (= 3.2.5-2.1),
libmysql++3v5 (= 3.2.5-2.1),
libncurses-dev (= 6.3+20220423-2),
libncurses5-dev (= 6.3+20220423-2),
libncurses6 (= 6.3+20220423-2),
libncursesw6 (= 6.3+20220423-2),
libnettle8 (= 3.8.1-2),
libnghttp2-14 (= 1.50.0-1),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libp11-kit0 (= 0.24.1-1),
libpam-modules (= 1.5.2-5),
libpam-modules-bin (= 1.5.2-5),
libpam-runtime (= 1.5.2-5),
libpam0g (= 1.5.2-5),
libpcre2-8-0 (= 10.40-1+b2),
libpcre3 (= 2:8.39-14),
libperl5.36 (= 5.36.0-4),
libpipeline1 (= 1.5.7-1),
libpsl5 (= 0.21.0-1.2),
libpython3-stdlib (= 3.10.6-1),
libpython3.10-minimal (= 3.10.8-3),
libpython3.10-stdlib (= 3.10.8-3),
librbio2 (= 1:5.12.0+dfsg-2),
libreadline8 (= 8.2-1),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libruby (= 1:3.0+3.1),
libruby3.0 (= 3.0.4-8),
libsasl2-2 (= 2.1.28+dfsg-8),
libsasl2-modules-db (= 2.1.28+dfsg-8),
libseccomp2 (= 2.5.4-1+rpi1),
libselinux1 (= 3.4-1),
libsliplu1 (= 1:5.12.0+dfsg-2),
libsmartcols1 (= 2.38.1-1.1),
libspqr2 (= 1:5.12.0+dfsg-2),
libsqlite3-0 (= 3.40.0-1),
libsqlite3-dev (= 3.40.0-1),
libssh2-1 (= 1.10.0-3+b1),
libssl-dev (= 3.0.7-1),
libssl3 (= 3.0.7-1),
libstdc++-12-dev (= 12.2.0-9+rpi1),
libstdc++6 (= 12.2.0-9+rpi1),
libsub-override-perl (= 0.09-4),
libsuitesparse-dev (= 1:5.12.0+dfsg-2),
libsuitesparseconfig5 (= 1:5.12.0+dfsg-2),
libsystemd0 (= 251.5-1+rpi1),
libtasn1-6 (= 4.19.0-2),
libtinfo6 (= 6.3+20220423-2),
libtirpc-common (= 1.3.3+ds-1),
libtirpc-dev (= 1.3.3+ds-1),
libtirpc3 (= 1.3.3+ds-1),
libtool (= 2.4.7-4),
libubsan1 (= 12.2.0-9+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 251.5-1+rpi1),
libumfpack5 (= 1:5.12.0+dfsg-2),
libunistring2 (= 1.0-2),
libuuid1 (= 2.38.1-1.1),
libxml2 (= 2.9.14+dfsg-1.1),
libyaml-0-2 (= 0.2.5-1),
libzstd1 (= 1.5.2+dfsg-1),
linux-libc-dev (= 5.19.6-1+rpi1),
login (= 1:4.12.3+dfsg1-1),
m4 (= 1.4.19-1),
make (= 4.3-4.1),
man-db (= 2.11.1-1),
mariadb-common (= 1:10.6.10-1),
mawk (= 1.3.4.20200120-3.1),
media-types (= 8.0.0),
mysql-common (= 5.8+1.0.8),
ncurses-base (= 6.3+20220423-2),
ncurses-bin (= 6.3+20220423-2),
openssl (= 3.0.7-1),
patch (= 2.7.6-7),
perl (= 5.36.0-4),
perl-base (= 5.36.0-4),
perl-modules-5.36 (= 5.36.0-4),
po-debconf (= 1.0.21+nmu1),
python3 (= 3.10.6-1),
python3-minimal (= 3.10.6-1),
python3.10 (= 3.10.8-3),
python3.10-minimal (= 3.10.8-3),
rake (= 13.0.6-3),
readline-common (= 8.2-1),
rpcsvc-proto (= 1.4.2-4),
ruby (= 1:3.0+3.1),
ruby-asciidoctor (= 2.0.17-1),
ruby-net-telnet (= 0.1.1-2.1),
ruby-rubygems (= 3.3.15-1),
ruby-sdbm (= 1.0.0-5),
ruby-webrick (= 1.7.0-4),
ruby-xmlrpc (= 0.3.2-2),
ruby3.0 (= 3.0.4-8),
rubygems-integration (= 1.18),
samtools (= 1.16.1-1),
sed (= 4.8-1),
sensible-utils (= 0.0.17),
sgml-base (= 1.31),
sysvinit-utils (= 3.05-6),
tar (= 1.34+dfsg-1),
util-linux (= 2.38.1-1.1),
util-linux-extra (= 2.38.1-1.1),
xz-utils (= 5.2.7-0.1),
zlib1g (= 1:1.2.11.dfsg-4.1),
zlib1g-dev (= 1:1.2.11.dfsg-4.1)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1668985913"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
augustus-dbgsym_3.5.0+dfsg-2_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 37795312 bytes: control archive=1296 bytes.
960 bytes, 12 lines control
1678 bytes, 16 lines md5sums
Package: augustus-dbgsym
Source: augustus
Version: 3.5.0+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 38640
Depends: augustus (= 3.5.0+dfsg-2)
Section: debug
Priority: optional
Description: debug symbols for augustus
Build-Ids: 0c8984f1246e07925346444cbf1c9bcecb4df571 1b1fe54b0698ce272b2b783108a1c2485d28b67c 1bcd5243526173f3ee4718427b091aa29e7ebc9c 25c1f5dfb08ab391b1a45fb72035f1fafbc4b16d 415cc61ea2d9eeabb91002cf91568b2b516ae2e0 45613ac643f51fb8a871f5a230e549e4b68fb445 6d85b043dc6272e5fd41127b87b425e41cca2fff 7130149940a8d093fda862553286f1e4ee6f1889 7516364c48599aab36d7f7fc74bd794643eca789 81dd73cde9742decc11f0023b0293e9fefc216f6 869f1e351a084dce02bdd54f70c422ab6bc0d619 8849606ec97644f540e85196c418fd04419531d1 9f18f003f92ac71ed5188ecb327b1f5a76f33650 c1d4625a68e062ede14425e702c9fbdce3df293e de092e612906f292e024b622102d85a4e9fe17d5
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drwxr-xr-x root/root 0 2022-11-20 23:11 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2022-11-20 23:11 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 5518576 2022-11-20 23:11 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/augustus.debug
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drwxr-xr-x root/root 0 2022-11-20 23:11 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-11-20 23:11 ./usr/share/doc/augustus-dbgsym -> augustus
augustus_3.5.0+dfsg-2_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 1524840 bytes: control archive=5052 bytes.
1524 bytes, 23 lines control
10549 bytes, 141 lines md5sums
Package: augustus
Version: 3.5.0+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 9373
Depends: libbamtools2.5.2 (>= 2.5.2+dfsg), libboost-iostreams1.74.0 (>= 1.74.0), libc6 (>= 2.34), libcolamd2 (>= 1:4.5.2), libgcc-s1 (>= 3.5), libgsl27 (>= 2.7.1), libhts3 (>= 1.10), libmariadb3 (>= 3.0.0), libmysql++3v5 (>= 3.2.5-1~), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 11), augustus-data
Recommends: samtools
Suggests: cdbfasta, diamond-aligner, libfile-which-perl, libparallel-forkmanager-perl, libyaml-perl, libdbd-mysql-perl, python3-biopython
Section: science
Priority: optional
Homepage: https://bioinf.uni-greifswald.de/augustus/
Description: gene prediction in eukaryotic genomes
AUGUSTUS is a software for gene prediction in eukaryotic genomic sequences
that is based on a generalized hidden Markov model (HMM), a probabilistic
model of a sequence and its gene structure. After learning gene structures
from a reference annotation, AUGUSTUS uses the HMM to recognize genes in a new
sequence and annotates it with the regions of identified genes. External hints,
e.g. from RNA sequencing, EST or protein alignments etc. can be used to guide
and improve the gene finding process. The result is the set of most likely gene
structures that comply with all given user constraints, if such gene
structures exist.
AUGUSTUS already includes prebuilt HMMs for many species, as well as scripts
to train custom models using annotated genomes.
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 1568676
Build-Time: 2530
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 1020
Job: augustus_3.5.0+dfsg-2
Machine Architecture: armhf
Package: augustus
Package-Time: 3648
Source-Version: 3.5.0+dfsg-2
Space: 1568676
Status: successful
Version: 3.5.0+dfsg-2
--------------------------------------------------------------------------------
Finished at 2022-11-23T05:05:50Z
Build needed 01:00:48, 1568676k disk space