augustus →
3.5.0+dfsg-4 →
armhf → 2023-11-20 05:39:27
sbuild (Debian sbuild) 0.85.0 (04 January 2023) on test2023
+==============================================================================+
| augustus 3.5.0+dfsg-4 (armhf) Mon, 20 Nov 2023 05:26:23 +0000 |
+==============================================================================+
Package: augustus
Version: 3.5.0+dfsg-4
Source Version: 3.5.0+dfsg-4
Distribution: trixie-staging
Machine Architecture: arm64
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-bf3bb577-5169-4984-b4f0-9bfbec4bbdf7' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/augustus-2dHr85/resolver-PUhY1k' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.2 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [14.9 MB]
Fetched 29.2 MB in 5s (5542 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'augustus' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/augustus.git
Please use:
git clone https://salsa.debian.org/med-team/augustus.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 152 MB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main augustus 3.5.0+dfsg-4 (dsc) [2347 B]
Get:2 http://172.17.4.1/private trixie-staging/main augustus 3.5.0+dfsg-4 (tar) [152 MB]
Get:3 http://172.17.4.1/private trixie-staging/main augustus 3.5.0+dfsg-4 (diff) [20.3 kB]
Fetched 152 MB in 17s (8776 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/augustus-2dHr85/augustus-3.5.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/augustus-2dHr85' 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 [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [854 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [886 B]
Fetched 2349 B in 0s (0 B/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 additional packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdextrautils bsdutils
ca-certificates chrpath debhelper default-libmysqlclient-dev dh-autoreconf
dh-strip-nondeterminism dpkg-dev dwz file gettext gettext-base groff-base
icu-devtools intltool-debian libamd3 libarchive-zip-perl libbamtools-dev
libbamtools2.5.2 libblas-dev libblas3 libblkid1 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 libbtf2 libbz2-dev libcamd3 libccolamd3 libcholmod4
libcolamd3 libcurl3-gnutls libcurl4-gnutls-dev libcxsparse4
libdebhelper-perl libdeflate-dev libdeflate0 libdpkg-perl libedit2 libelf1
libexpat1 libfile-stripnondeterminism-perl libgfortran5 libgsl-dev libgsl27
libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu-dev libicu72 libklu2
liblapack-dev liblapack3 libldl3 liblpsolve55-dev liblzma-dev libmagic-mgc
libmagic1 libmariadb-dev libmariadb-dev-compat libmariadb3 libmongoose3
libmount1 libmysql++-dev libmysql++3v5 libncurses-dev libncurses6
libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.11-minimal
libpython3.11-stdlib librbio4 librtmp1 libruby libruby3.1 libsmartcols1
libspex2 libspqr4 libsqlite3-0 libsqlite3-dev libssh2-1 libssl-dev
libsub-override-perl libsuitesparse-dev libsuitesparseconfig7 libtool
libuchardet0 libumfpack6 libuuid1 libxml2 libyaml-0-2 m4 man-db
mariadb-common media-types mount mysql-common openssl po-debconf python3
python3-minimal python3.11 python3.11-minimal rake ruby ruby-asciidoctor
ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.1
rubygems-integration samtools sensible-utils util-linux zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make debian-keyring
gettext-doc libasprintf-dev libgettextpo-dev groff libbamtools-doc
liblapack-doc libboost1.74-doc libboost-atomic1.74-dev
libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev
libboost-contract1.74-dev libboost-coroutine1.74-dev
libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-locale1.74-dev libboost-log1.74-dev
libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev
libboost-numpy1.74-dev libboost-program-options1.74-dev
libboost-python1.74-dev libboost-random1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev
libssh2-1-dev pkg-config git bzr gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info
| gsl-ref-html icu-doc liblzma-doc cryptsetup-bin libmysql++-doc ncurses-doc
sqlite3-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
m4-doc apparmor less www-browser nfs-common libmail-box-perl python3-doc
python3-tk python3-venv python3.11-venv python3.11-doc binfmt-support ri
ruby-dev bundler cwltool dosfstools kbd util-linux-extra util-linux-locales
Recommended packages:
libalgorithm-merge-perl curl | wget | lynx bzip2-doc libfile-fcntllock-perl
libarchive-cpio-perl libgpm2 publicsuffix libgraphblas-dev libltdl-dev
uuid-runtime 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 libamd3 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 libbtf2 libbz2-dev libcamd3 libccolamd3 libcholmod4
libcolamd3 libcurl3-gnutls libcurl4-gnutls-dev libcxsparse4
libdebhelper-perl libdeflate-dev libdeflate0 libedit2 libelf1 libexpat1
libfile-stripnondeterminism-perl libgfortran5 libgsl-dev libgsl27
libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu-dev libicu72 libklu2
liblapack-dev liblapack3 libldl3 liblpsolve55-dev liblzma-dev libmagic-mgc
libmagic1 libmariadb-dev libmariadb-dev-compat libmariadb3 libmongoose3
libmysql++-dev libmysql++3v5 libncurses-dev libncurses6 libnghttp2-14
libpipeline1 libpsl5 libpython3-stdlib libpython3.11-minimal
libpython3.11-stdlib librbio4 librtmp1 libruby libruby3.1 libspex2 libspqr4
libsqlite3-dev libssh2-1 libssl-dev libsub-override-perl libsuitesparse-dev
libsuitesparseconfig7 libtool libuchardet0 libumfpack6 libxml2 libyaml-0-2
m4 man-db mariadb-common media-types mysql-common openssl po-debconf python3
python3-minimal python3.11 python3.11-minimal rake ruby ruby-asciidoctor
ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.1
rubygems-integration samtools sbuild-build-depends-main-dummy sensible-utils
zlib1g-dev
The following packages will be upgraded:
bsdutils dpkg-dev libblkid1 libdpkg-perl libmount1 libsmartcols1
libsqlite3-0 libuuid1 mount util-linux
10 upgraded, 125 newly installed, 0 to remove and 19 not upgraded.
1 not fully installed or removed.
Need to get 75.0 MB/77.1 MB of archives.
After this operation, 404 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [984 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf mount armhf 2.39.2-6 [134 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf bsdutils armhf 1:2.39.2-6 [86.5 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf util-linux armhf 2.39.2-6 [1110 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-minimal armhf 3.11.6-3 [800 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-2 [76.8 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf python3.11-minimal armhf 3.11.6-3 [1674 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf python3-minimal armhf 3.11.4-5 [26.2 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf media-types all 10.1.0 [26.9 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf libsqlite3-0 armhf 3.44.0-1 [762 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf libuuid1 armhf 2.39.2-6 [28.1 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-stdlib armhf 3.11.6-3 [1679 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf python3.11 armhf 3.11.6-3 [586 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf libpython3-stdlib armhf 3.11.4-5 [9200 B]
Get:15 http://172.17.4.1/private trixie-staging/main armhf python3 armhf 3.11.4-5 [26.2 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf libblkid1 armhf 2.39.2-6 [145 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf libmount1 armhf 2.39.2-6 [167 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf libsmartcols1 armhf 2.39.2-6 [102 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.2-6 [81.2 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-1 [1358 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf sensible-utils all 0.0.20 [19.3 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf openssl armhf 3.0.11-1 [1367 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf ca-certificates all 20230311 [153 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-13 [156 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf rubygems-integration all 1.18 [6704 B]
Get:32 http://172.17.4.1/private trixie-staging/main armhf rake all 13.0.6-3 [83.9 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf ruby-net-telnet all 0.2.0-1 [13.1 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf ruby-webrick all 1.8.1-1 [51.4 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf ruby-xmlrpc all 0.3.2-2 [24.4 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf libruby armhf 1:3.1 [4968 B]
Get:37 http://172.17.4.1/private trixie-staging/main armhf ruby-sdbm armhf 1.0.0-5+rpi1 [15.9 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libbsd0 armhf 0.11.7-4 [111 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libedit2 armhf 3.1-20230828-1 [76.0 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf libncurses6 armhf 6.4+20231016-1 [80.0 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libyaml-0-2 armhf 0.2.5-1 [44.6 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf libruby3.1 armhf 3.1.2-7 [5011 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf ruby3.1 armhf 3.1.2-7 [663 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf ruby-rubygems all 3.4.20-1 [309 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf ruby armhf 1:3.1 [5868 B]
Get:46 http://172.17.4.1/private trixie-staging/main armhf ruby-asciidoctor all 2.0.20-1 [212 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf asciidoctor all 2.0.20-1 [87.7 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-13 [496 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.8 [82.1 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:59 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:61 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:63 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:65 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-13 [1201 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:68 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.8 [956 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf mysql-common all 5.8+1.1.0 [6636 B]
Get:70 http://172.17.4.1/private trixie-staging/main armhf mariadb-common all 1:10.11.3-1+rpi1 [24.1 kB]
Get:71 http://172.17.4.1/private trixie-staging/main armhf libmariadb3 armhf 1:10.11.3-1+rpi1 [154 kB]
Get:72 http://172.17.4.1/private trixie-staging/main armhf libssl-dev armhf 3.0.11-1 [2105 kB]
Get:73 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-3 [901 kB]
Get:74 http://172.17.4.1/private trixie-staging/main armhf libmariadb-dev armhf 1:10.11.3-1+rpi1 [247 kB]
Get:75 http://172.17.4.1/private trixie-staging/main armhf libmariadb-dev-compat armhf 1:10.11.3-1+rpi1 [22.9 kB]
Get:76 http://172.17.4.1/private trixie-staging/main armhf default-libmysqlclient-dev armhf 1.1.0 [3092 B]
Get:77 http://172.17.4.1/private trixie-staging/main armhf icu-devtools armhf 72.1-4 [174 kB]
Get:78 http://172.17.4.1/private trixie-staging/main armhf libsuitesparseconfig7 armhf 1:7.2.2+dfsg-1 [19.1 kB]
Get:79 http://172.17.4.1/private trixie-staging/main armhf libamd3 armhf 1:7.2.2+dfsg-1 [36.8 kB]
Get:80 http://172.17.4.1/private trixie-staging/main armhf libbamtools2.5.2 armhf 2.5.2+dfsg-4 [126 kB]
Get:81 http://172.17.4.1/private trixie-staging/main armhf libbamtools-dev armhf 2.5.2+dfsg-4 [182 kB]
Get:82 http://172.17.4.1/private trixie-staging/main armhf libblas3 armhf 3.11.0-2 [100.0 kB]
Get:83 http://172.17.4.1/private trixie-staging/main armhf libblas-dev armhf 3.11.0-2 [106 kB]
Get:84 http://172.17.4.1/private trixie-staging/main armhf libboost1.74-dev armhf 1.74.0+ds1-23 [9511 kB]
Get:85 http://172.17.4.1/private trixie-staging/main armhf libboost-regex1.74.0 armhf 1.74.0+ds1-23 [421 kB]
Get:86 http://172.17.4.1/private trixie-staging/main armhf libicu-dev armhf 72.1-4 [9956 kB]
Get:87 http://172.17.4.1/private trixie-staging/main armhf libboost-regex1.74-dev armhf 1.74.0+ds1-23 [526 kB]
Get:88 http://172.17.4.1/private trixie-staging/main armhf libboost-iostreams1.74.0 armhf 1.74.0+ds1-23 [236 kB]
Get:89 http://172.17.4.1/private trixie-staging/main armhf libboost-iostreams1.74-dev armhf 1.74.0+ds1-23 [245 kB]
Get:90 http://172.17.4.1/private trixie-staging/main armhf libboost-iostreams-dev armhf 1.74.0.3+b4 [4592 B]
Get:91 http://172.17.4.1/private trixie-staging/main armhf libboost-serialization1.74.0 armhf 1.74.0+ds1-23 [296 kB]
Get:92 http://172.17.4.1/private trixie-staging/main armhf libboost-serialization1.74-dev armhf 1.74.0+ds1-23 [363 kB]
Get:93 http://172.17.4.1/private trixie-staging/main armhf libboost-serialization-dev armhf 1.74.0.3+b4 [4832 B]
Get:94 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.0.9-2+b3 [258 kB]
Get:95 http://172.17.4.1/private trixie-staging/main armhf libbtf2 armhf 1:7.2.2+dfsg-1 [21.5 kB]
Get:96 http://172.17.4.1/private trixie-staging/main armhf libbz2-dev armhf 1.0.8-5+b2 [26.8 kB]
Get:97 http://172.17.4.1/private trixie-staging/main armhf libcamd3 armhf 1:7.2.2+dfsg-1 [35.4 kB]
Get:98 http://172.17.4.1/private trixie-staging/main armhf libccolamd3 armhf 1:7.2.2+dfsg-1 [37.1 kB]
Get:99 http://172.17.4.1/private trixie-staging/main armhf libcolamd3 armhf 1:7.2.2+dfsg-1 [29.6 kB]
Get:100 http://172.17.4.1/private trixie-staging/main armhf libgfortran5 armhf 13.2.0-5+rpi1 [247 kB]
Get:101 http://172.17.4.1/private trixie-staging/main armhf liblapack3 armhf 3.11.0-2 [1624 kB]
Get:102 http://172.17.4.1/private trixie-staging/main armhf libcholmod4 armhf 1:7.2.2+dfsg-1 [427 kB]
Get:103 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.58.0-1 [61.7 kB]
Get:104 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:105 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:106 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-2 [195 kB]
Get:107 http://172.17.4.1/private trixie-staging/main armhf libcurl3-gnutls armhf 8.4.0-2+rpi1 [358 kB]
Get:108 http://172.17.4.1/private trixie-staging/main armhf libcurl4-gnutls-dev armhf 8.4.0-2+rpi1 [441 kB]
Get:109 http://172.17.4.1/private trixie-staging/main armhf libcxsparse4 armhf 1:7.2.2+dfsg-1 [74.4 kB]
Get:110 http://172.17.4.1/private trixie-staging/main armhf libdeflate0 armhf 1.18-1 [38.3 kB]
Get:111 http://172.17.4.1/private trixie-staging/main armhf libdeflate-dev armhf 1.18-1 [45.8 kB]
Get:112 http://172.17.4.1/private trixie-staging/main armhf libgslcblas0 armhf 2.7.1+dfsg-6 [79.3 kB]
Get:113 http://172.17.4.1/private trixie-staging/main armhf libgsl27 armhf 2.7.1+dfsg-6 [753 kB]
Get:114 http://172.17.4.1/private trixie-staging/main armhf libgsl-dev armhf 2.7.1+dfsg-6 [965 kB]
Get:115 http://172.17.4.1/private trixie-staging/main armhf libhtscodecs2 armhf 1.5.2-1 [60.0 kB]
Get:116 http://172.17.4.1/private trixie-staging/main armhf libhts3 armhf 1.18+ds-1 [380 kB]
Get:117 http://172.17.4.1/private trixie-staging/main armhf liblzma-dev armhf 5.4.4-0.1 [269 kB]
Get:118 http://172.17.4.1/private trixie-staging/main armhf libhts-dev armhf 1.18+ds-1 [1539 kB]
Get:119 http://172.17.4.1/private trixie-staging/main armhf libklu2 armhf 1:7.2.2+dfsg-1 [76.4 kB]
Get:120 http://172.17.4.1/private trixie-staging/main armhf liblapack-dev armhf 3.11.0-2 [3007 kB]
Get:121 http://172.17.4.1/private trixie-staging/main armhf libldl3 armhf 1:7.2.2+dfsg-1 [20.3 kB]
Get:122 http://172.17.4.1/private trixie-staging/main armhf libmongoose3 armhf 1:7.2.2+dfsg-1 [43.3 kB]
Get:123 http://172.17.4.1/private trixie-staging/main armhf libumfpack6 armhf 1:7.2.2+dfsg-1 [251 kB]
Get:124 http://172.17.4.1/private trixie-staging/main armhf librbio4 armhf 1:7.2.2+dfsg-1 [36.5 kB]
Get:125 http://172.17.4.1/private trixie-staging/main armhf libspqr4 armhf 1:7.2.2+dfsg-1 [122 kB]
Get:126 http://172.17.4.1/private trixie-staging/main armhf libspex2 armhf 1:7.2.2+dfsg-1 [43.6 kB]
Get:127 http://172.17.4.1/private trixie-staging/main armhf libsuitesparse-dev armhf 1:7.2.2+dfsg-1 [1146 kB]
Get:128 http://172.17.4.1/private trixie-staging/main armhf liblpsolve55-dev armhf 5.5.2.5-2+b1 [358 kB]
Get:129 http://172.17.4.1/private trixie-staging/main armhf libmysql++3v5 armhf 3.2.5-2.1 [144 kB]
Get:130 http://172.17.4.1/private trixie-staging/main armhf libmysql++-dev armhf 3.2.5-2.1 [150 kB]
Get:131 http://172.17.4.1/private trixie-staging/main armhf libncurses-dev armhf 6.4+20231016-1 [290 kB]
Get:132 http://172.17.4.1/private trixie-staging/main armhf libsqlite3-dev armhf 3.44.0-1 [937 kB]
Get:133 http://172.17.4.1/private trixie-staging/main armhf samtools armhf 1.18-1 [587 kB]
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Setting up libhtscodecs2:armhf (1.5.2-1) ...
Setting up media-types (10.1.0) ...
Setting up libpipeline1:armhf (1.5.7-1) ...
Setting up mysql-common (5.8+1.1.0) ...
update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode
Setting up libpsl5:armhf (0.21.2-1+b1) ...
Setting up libboost1.74-dev:armhf (1.74.0+ds1-23) ...
Setting up libicu72:armhf (72.1-4) ...
Setting up bsdextrautils (2.39.2-6) ...
Setting up libgslcblas0:armhf (2.7.1+dfsg-6) ...
Setting up libmagic-mgc (1:5.45-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libyaml-0-2:armhf (0.2.5-1) ...
Setting up libboost-iostreams1.74.0:armhf (1.74.0+ds1-23) ...
Setting up libpython3.11-stdlib:armhf (3.11.6-3) ...
Setting up libdebhelper-perl (13.11.8) ...
Setting up libbrotli1:armhf (1.0.9-2+b3) ...
Setting up libcxsparse4:armhf (1:7.2.2+dfsg-1) ...
Setting up libnghttp2-14:armhf (1.58.0-1) ...
Setting up libmagic1:armhf (1:5.45-2) ...
Setting up libdeflate0:armhf (1.18-1) ...
Setting up gettext-base (0.21-13) ...
Setting up libgsl27:armhf (2.7.1+dfsg-6) ...
Setting up m4 (1.4.19-4) ...
Setting up libldl3:armhf (1:7.2.2+dfsg-1) ...
Setting up file (1:5.45-2) ...
Setting up mariadb-common (1:10.11.3-1+rpi1) ...
update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode
Setting up libbtf2:armhf (1:7.2.2+dfsg-1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libblas3:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libsqlite3-dev:armhf (3.44.0-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.4+20231016-1) ...
Setting up ruby-net-telnet (0.2.0-1) ...
Setting up libboost-regex1.74.0:armhf (1.74.0+ds1-23) ...
Setting up libssl-dev:armhf (3.0.11-1) ...
Setting up autopoint (0.21-13) ...
Setting up icu-devtools (72.1-4) ...
Setting up libmariadb3:armhf (1:10.11.3-1+rpi1) ...
Setting up libmysql++3v5:armhf (3.2.5-2.1) ...
Setting up libbamtools2.5.2:armhf (2.5.2+dfsg-4) ...
Setting up libdpkg-perl (1.22.1+rpi1) ...
Setting up libgfortran5:armhf (13.2.0-5+rpi1) ...
Setting up autoconf (2.71-3) ...
Setting up ruby-webrick (1.8.1-1) ...
Setting up liblzma-dev:armhf (5.4.4-0.1) ...
Setting up libboost-serialization1.74.0:armhf (1.74.0+ds1-23) ...
Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-3) ...
Setting up mount (2.39.2-6) ...
Setting up sensible-utils (0.0.20) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsuitesparseconfig7:armhf (1:7.2.2+dfsg-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libssh2-1:armhf (1.11.0-2) ...
Setting up openssl (3.0.11-1) ...
Setting up libbsd0:armhf (0.11.7-4) ...
Setting up libdeflate-dev:armhf (1.18-1) ...
Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up libicu-dev:armhf (72.1-4) ...
Setting up ruby-xmlrpc (0.3.2-2) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
Setting up chrpath (0.16-2) ...
Setting up libblas-dev:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up libpython3-stdlib:armhf (3.11.4-5) ...
Setting up libbz2-dev:armhf (1.0.8-5+b2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up python3.11 (3.11.6-3) ...
Setting up liblapack3:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libncurses-dev:armhf (6.4+20231016-1) ...
Setting up gettext (0.21-13) ...
Setting up libgsl-dev (2.7.1+dfsg-6) ...
Setting up libamd3:armhf (1:7.2.2+dfsg-1) ...
Setting up libtool (2.4.7-7) ...
Setting up libcolamd3:armhf (1:7.2.2+dfsg-1) ...
Setting up libedit2:armhf (3.1-20230828-1) ...
Setting up libcurl3-gnutls:armhf (8.4.0-2+rpi1) ...
Setting up python3 (3.11.4-5) ...
Setting up libcurl4-gnutls-dev:armhf (8.4.0-2+rpi1) ...
Setting up libcamd3:armhf (1:7.2.2+dfsg-1) ...
Setting up libmongoose3:armhf (1:7.2.2+dfsg-1) ...
Setting up dpkg-dev (1.22.1+rpi1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up ca-certificates (20230311) ...
Updating certificates in /etc/ssl/certs...
140 added, 0 removed; done.
Setting up librbio4:armhf (1:7.2.2+dfsg-1) ...
Setting up libbamtools-dev:armhf (2.5.2+dfsg-4) ...
Setting up liblapack-dev:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libccolamd3:armhf (1:7.2.2+dfsg-1) ...
Setting up libboost-serialization1.74-dev:armhf (1.74.0+ds1-23) ...
Setting up libmariadb-dev (1:10.11.3-1+rpi1) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up libboost-regex1.74-dev:armhf (1.74.0+ds1-23) ...
Setting up groff-base (1.23.0-3) ...
Setting up libcholmod4:armhf (1:7.2.2+dfsg-1) ...
Setting up libmariadb-dev-compat (1:10.11.3-1+rpi1) ...
Setting up libhts3:armhf (1.18+ds-1) ...
Setting up libspex2:armhf (1:7.2.2+dfsg-1) ...
Setting up libspqr4:armhf (1:7.2.2+dfsg-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhts-dev:armhf (1.18+ds-1) ...
Setting up rubygems-integration (1.18) ...
Setting up man-db (2.12.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up samtools (1.18-1) ...
Setting up libboost-iostreams1.74-dev:armhf (1.74.0+ds1-23) ...
Setting up libklu2:armhf (1:7.2.2+dfsg-1) ...
Setting up libboost-serialization-dev:armhf (1.74.0.3+b4) ...
Setting up libumfpack6:armhf (1:7.2.2+dfsg-1) ...
Setting up default-libmysqlclient-dev:armhf (1.1.0) ...
Setting up libsuitesparse-dev:armhf (1:7.2.2+dfsg-1) ...
Setting up debhelper (13.11.8) ...
Setting up libboost-iostreams-dev:armhf (1.74.0.3+b4) ...
Setting up libmysql++-dev:armhf (3.2.5-2.1) ...
Setting up liblpsolve55-dev (5.5.2.5-2+b1) ...
Setting up libruby:armhf (1:3.1) ...
Setting up ruby-rubygems (3.4.20-1) ...
Setting up ruby (1:3.1) ...
Setting up ruby-asciidoctor (2.0.20-1) ...
Setting up rake (13.0.6-3) ...
Setting up asciidoctor (2.0.20-1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up ruby-sdbm:armhf (1.0.0-5+rpi1) ...
Setting up libruby3.1:armhf (3.1.2-7) ...
Setting up ruby3.1 (3.1.2-7) ...
Processing triggers for libc-bin (2.37-12+rpi2) ...
Processing triggers for ca-certificates (20230311) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.47-v8+ #1 SMP PREEMPT Fri Sep 1 07:05:33 BST 2023 arm64 (aarch64)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc-12_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 libc6-dev_2.37-12+rpi2 libstdc++-12-dev_12.3.0-10+rpi1 libstdc++-13-dev_13.2.0-5+rpi1 libstdc++6_13.2.0-5+rpi1 linux-libc-dev_6.5.6-1+rpi1
Package versions: adduser_3.137 apt_2.7.6 asciidoctor_2.0.20-1 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.2 bash_5.2.15-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.2-6 bsdutils_1:2.39.2-6 build-essential_12.9 bzip2_1.0.8-5+b2 ca-certificates_20230311 chrpath_0.16-2 coreutils_9.1-1 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-10+rpi1 cpp-13_13.2.0-5+rpi1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.8 debianutils_5.14 default-libmysqlclient-dev_1.1.0 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.1+rpi1 dpkg-dev_1.22.1+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.1-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc_4:13.2.0-1+rpi1 gcc-10-base_10.4.0-7+rpi1 gcc-12_12.3.0-10+rpi1 gcc-12-base_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 gcc-13-base_13.2.0-5+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_0.21-13 gettext-base_0.21-13 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu1 icu-devtools_72.1-4 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libamd3_1:7.2.2+dfsg-1 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libasan8_13.2.0-5+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-5+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbamtools-dev_2.5.2+dfsg-4 libbamtools2.5.2_2.5.2+dfsg-4 libbinutils_2.41-6+rpi1 libblas-dev_3.11.0-2 libblas3_3.11.0-2 libblkid1_2.39.2-6 libboost-iostreams-dev_1.74.0.3+b4 libboost-iostreams1.74-dev_1.74.0+ds1-23 libboost-iostreams1.74.0_1.74.0+ds1-23 libboost-regex1.74-dev_1.74.0+ds1-23 libboost-regex1.74.0_1.74.0+ds1-23 libboost-serialization-dev_1.74.0.3+b4 libboost-serialization1.74-dev_1.74.0+ds1-23 libboost-serialization1.74.0_1.74.0+ds1-23 libboost1.74-dev_1.74.0+ds1-23 libbrotli1_1.0.9-2+b3 libbsd0_0.11.7-4 libbtf2_1:7.2.2+dfsg-1 libbz2-1.0_1.0.8-5+b2 libbz2-dev_1.0.8-5+b2 libc-bin_2.37-12+rpi2 libc-dev-bin_2.37-12+rpi2 libc6_2.37-12+rpi2 libc6-dev_2.37-12+rpi2 libcamd3_1:7.2.2+dfsg-1 libcap-ng0_0.8.3-1+b1 libcap2_1:2.66-4 libcc1-0_13.2.0-5+rpi1 libccolamd3_1:7.2.2+dfsg-1 libcholmod4_1:7.2.2+dfsg-1 libcolamd3_1:7.2.2+dfsg-1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libcurl3-gnutls_8.4.0-2+rpi1 libcurl4-gnutls-dev_8.4.0-2+rpi1 libcxsparse4_1:7.2.2+dfsg-1 libdb5.3_5.3.28+dfsg2-2 libdebconfclient0_0.271 libdebhelper-perl_13.11.8 libdeflate-dev_1.18-1 libdeflate0_1.18-1 libdpkg-perl_1.22.1+rpi1 libedit2_3.1-20230828-1 libelf1_0.188-2.1+rpi1 libexpat1_2.5.0-2 libext2fs2_1.47.0-2 libfakeroot_1.32.1-1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-10+rpi1 libgcc-13-dev_13.2.0-5+rpi1 libgcc-s1_13.2.0-5+rpi1 libgcrypt20_1.10.2-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_13.2.0-5+rpi1 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.1-4 libgomp1_13.2.0-5+rpi1 libgpg-error0_1.47-2 libgsl-dev_2.7.1+dfsg-6 libgsl27_2.7.1+dfsg-6 libgslcblas0_2.7.1+dfsg-6 libgssapi-krb5-2_1.20.1-4 libhogweed6_3.9.1-2 libhts-dev_1.18+ds-1 libhts3_1.18+ds-1 libhtscodecs2_1.5.2-1 libicu-dev_72.1-4 libicu72_72.1-4 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libk5crypto3_1.20.1-4 libkeyutils1_1.6.3-2 libklu2_1:7.2.2+dfsg-1 libkrb5-3_1.20.1-4 libkrb5support0_1.20.1-4 libksba8_1.6.4-2 liblapack-dev_3.11.0-2 liblapack3_3.11.0-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 libldl3_1:7.2.2+dfsg-1 liblocale-gettext-perl_1.07-6 liblpsolve55-dev_5.5.2.5-2+b1 liblz4-1_1.9.4-1+rpi1+b1 liblzma-dev_5.4.4-0.1 liblzma5_5.4.4-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmariadb-dev_1:10.11.3-1+rpi1 libmariadb-dev-compat_1:10.11.3-1+rpi1 libmariadb3_1:10.11.3-1+rpi1 libmd0_1.1.0-1 libmongoose3_1:7.2.2+dfsg-1 libmount1_2.39.2-6 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libmysql++-dev_3.2.5-2.1 libmysql++3v5_3.2.5-2.1 libncurses-dev_6.4+20231016-1 libncurses6_6.4+20231016-1 libncursesw6_6.4+20231016-1 libnettle8_3.9.1-2 libnghttp2-14_1.58.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.25.0-5 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpcre2-8-0_10.42-4 libperl5.36_5.36.0-9 libpipeline1_1.5.7-1 libpsl5_0.21.2-1+b1 libpython3-stdlib_3.11.4-5 libpython3.11-minimal_3.11.6-3 libpython3.11-stdlib_3.11.6-3 librbio4_1:7.2.2+dfsg-1 libreadline8_8.2-1.3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libruby_1:3.1 libruby3.1_3.1.2-7 libsasl2-2_2.1.28+dfsg1-3 libsasl2-modules-db_2.1.28+dfsg1-3 libseccomp2_2.5.4-1+rpi1+b1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol2_3.5-1 libsframe1_2.41-6+rpi1 libsmartcols1_2.39.2-6 libspex2_1:7.2.2+dfsg-1 libspqr4_1:7.2.2+dfsg-1 libsqlite3-0_3.44.0-1 libsqlite3-dev_3.44.0-1 libss2_1.47.0-2 libssh2-1_1.11.0-2 libssl-dev_3.0.11-1 libssl3_3.0.11-1 libstdc++-12-dev_12.3.0-10+rpi1 libstdc++-13-dev_13.2.0-5+rpi1 libstdc++6_13.2.0-5+rpi1 libsub-override-perl_0.09-4 libsuitesparse-dev_1:7.2.2+dfsg-1 libsuitesparseconfig7_1:7.2.2+dfsg-1 libsystemd0_254.5-1+rpi1 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11 libtext-iconv-perl_1.7-8 libtinfo6_6.4+20231016-1 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-7 libubsan1_13.2.0-5+rpi1 libuchardet0_0.0.7-1 libudev1_254.5-1+rpi1 libumfpack6_1:7.2.2+dfsg-1 libunistring5_1.1-2 libuuid1_2.39.2-6 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libyaml-0-2_0.2.5-1 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-1 mariadb-common_1:10.11.3-1+rpi1 mawk_1.3.4.20230808-1 media-types_10.1.0 mount_2.39.2-6 mysql-common_5.8+1.1.0 ncurses-base_6.4+20231016-1 ncurses-bin_6.4+20231016-1 openssl_3.0.11-1 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.36.0-9 perl-base_5.36.0-9 perl-modules-5.36_5.36.0-9 pinentry-curses_1.2.1-1 po-debconf_1.0.21+nmu1 python3_3.11.4-5 python3-minimal_3.11.4-5 python3.11_3.11.6-3 python3.11-minimal_3.11.6-3 rake_13.0.6-3 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 ruby_1:3.1 ruby-asciidoctor_2.0.20-1 ruby-net-telnet_0.2.0-1 ruby-rubygems_3.4.20-1 ruby-sdbm_1.0.0-5+rpi1 ruby-webrick_1.8.1-1 ruby-xmlrpc_0.3.2-2 ruby3.1_3.1.2-7 rubygems-integration_1.18 samtools_1.18-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sysvinit-utils_3.08-3 tar_1.34+dfsg-1.2 tzdata_2023c-10 usr-is-merged_37 util-linux_2.39.2-6 xz-utils_5.4.4-0.1 zlib1g_1:1.2.13.dfsg-3 zlib1g-dev_1:1.2.13.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----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-4
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
6a69caecfd6f16557523333e175bf2a0bbdba35d 20256 augustus_3.5.0+dfsg-4.debian.tar.xz
Checksums-Sha256:
30a2a5200e7201a28383bebb98350eab9e043e38d0f7b825a1c8a614a6e68dc8 151813456 augustus_3.5.0+dfsg.orig.tar.xz
dec840e8add73afe43b19f279a5ae9b75d0bf55a2c9036217e1500866d59e68f 20256 augustus_3.5.0+dfsg-4.debian.tar.xz
Files:
11cc56baea3047c128e2da42f7cf9dd0 151813456 augustus_3.5.0+dfsg.orig.tar.xz
5968a6a5d5744790b18d5b75f961f648 20256 augustus_3.5.0+dfsg-4.debian.tar.xz
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gpgv: Signature made Sat Nov 18 08:11:16 2023 UTC
gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./augustus_3.5.0+dfsg-4.dsc: no acceptable signature found
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-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying search_config_path
dpkg-source: info: applying set_installdir
dpkg-source: info: applying interpreter_paths.patch
dpkg-source: info: applying switch_cgp_testing_off.patch
dpkg-source: info: applying disable-compare.patch
dpkg-source: info: applying s390x-disable-filterbam-tests.patch
dpkg-source: info: applying cstdint.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
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
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=124
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-bf3bb577-5169-4984-b4f0-9bfbec4bbdf7
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -mRaspbian pi5 test autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package augustus
dpkg-buildpackage: info: source version 3.5.0+dfsg-4
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'
/usr/bin/make -C auxprogs/utrrnaseq clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/utrrnaseq'
rm -rf build/test *.gff
rm -rf 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 build/Compute_UTRs.d build/Coord_Transform.d build/Genomic_Data.d build/Splice_Sites.d build/Supporting_Methods.d build/Test.d build/UTRs.d build/main.d build utrrnaseq
make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/utrrnaseq'
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 tests -name "*.sam.bam" | xargs -r rm
find auxprogs -name "*.o" | xargs -r rm
rm -rf tests/short/examples/results \
tests/short/auxprogs/bam2hints/tmp/ \
tests/short/auxprogs/bam2hints/result_files/ \
tests/short/auxprogs/filterbam/result_files/
rm -f auxprogs/utrrnaseq/Debug/utrrnaseq \
src/augustus \
src/cxxflags \
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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -I/usr/include/bamtools -c bam2hints.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -c compileSpliceCands.c
compileSpliceCands.c: In function ‘getChromosome’:
compileSpliceCands.c:226:9: warning: this decimal constant is unsigned only in ISO C90
226 | s = malloc(3500000000);
| ^
compileSpliceCands.c:216:9: warning: ‘__builtin_strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
216 | strncat(checkstring,chromosomename,strlen(chromosomename));
| ^
compileSpliceCands.c:216:9: note: length computed here
216 | strncat(checkstring,chromosomename,strlen(chromosomename));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compileSpliceCands.c:226:13: warning: argument 1 value ‘3500000000’ exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
226 | s = malloc(3500000000);
| ^~~~~~~~~~~~~~~~~~
In file included from compileSpliceCands.c:14:
/usr/include/stdlib.h:553:14: note: in a call to allocation function ‘malloc’ declared here
553 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
| ^~~~~~
compileSpliceCands.c: In function ‘parseLine’:
compileSpliceCands.c:292:9: warning: ‘__builtin_strncpy’ specified bound 256 equals destination size [-Wstringop-truncation]
292 | strncpy(d->name,tokens[0],LINEBUFFER);
| ^
compileSpliceCands.c: In function ‘parseList’:
compileSpliceCands.c:333:69: warning: ‘left’ may be used uninitialized [-Wmaybe-uninitialized]
333 | isCandidate = ((right->averageCoverage>=left->averageCoverage*threshold) ||
| ~~~~^~~~~~~~~~~~~~~~~
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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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.
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/bam2hints'
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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genbank.o genbank.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o properties.o properties.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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++/13/map:62,
from src/Compute_UTRs.hpp:14,
from src/Compute_UTRs.cpp:8:
/usr/include/c++/13/bits/stl_tree.h: In 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++/13/bits/stl_tree.h:2210:5: 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
2210 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/Compute_UTRs.cpp: In function ‘void compute_UTRs(std::string)’:
src/Compute_UTRs.cpp:142:18: warning: ‘chrom_pos’ may be used uninitialized [-Wmaybe-uninitialized]
142 | unsigned chrom_pos; //position for fixedStep only
| ^~~~~~~~~
src/Compute_UTRs.cpp:251:69: warning: ‘step’ may be used uninitialized [-Wmaybe-uninitialized]
251 | for (int i = 0; i < (int)step; ++i) {
| ^~~~~~~~~
src/Compute_UTRs.cpp:143:18: note: ‘step’ was declared here
143 | unsigned step; //Step for fixedStep only
| ^~~~
In file included from /usr/include/c++/13/vector:66,
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++/13/bits/stl_vector.h:1126:41: warning: ‘idx_former_scaff’ may be used uninitialized [-Wmaybe-uninitialized]
1126 | 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;
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/map:62,
from ../include/types.hh:39,
from ../include/geneticcode.hh:12,
from ../include/pp_profile.hh:16,
from pp_profile.cc:11:
/usr/include/c++/13/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++/13/bits/stl_tree.h:2458:7: 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
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -fstack-clash-protection -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++/13/bits/refwrap.h:39,
from /usr/include/c++/13/vector:68,
from src/flex_vec.hpp:8,
from src/Coord_Transform.cpp:5:
/usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/bits/stl_function.h:1438:
/usr/include/c++/13/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++/13/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++/13/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++/13/backward/binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
In file included from /usr/include/c++/13/vector:72,
from ../include/types.hh:36:
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<PP::Column>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
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++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PP::Column*, std::vector<PP::Column> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
src/Coord_Transform.cpp: In constructor ‘Coord_Transform::Coord_Transform(unsigned int, int, unsigned int, unsigned int, unsigned int, unsigned int, std::vector<Genomic_Data::Intron>*)’:
src/Coord_Transform.cpp:148:70: warning: ‘skip_end’ may be used uninitialized [-Wmaybe-uninitialized]
148 | if (skip_start*dir > 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
| ^~~~~~~~
/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type ‘std::vector<LLDouble>::iterator’ changed in GCC 7.1
529 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<LLDouble>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
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 -fstack-clash-protection -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"
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++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1289 | _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++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1289 | _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++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1034 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/map:63:
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++/13/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | 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++/13/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<LLDouble>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
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++/13/bits/stl_vector.h:1296:21,
inlined from ‘bool PP::Block::initThresholds()’ at pp_profile.cc:257:30:
/usr/include/c++/13/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++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1034 | _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++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1289 | _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++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1034 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<PP::Block>::iterator’ changed in GCC 7.1
445 | 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++/13/bits/stl_vector.h:1296:21,
inlined from ‘void PP::Profile::parse_stream(std::istream&)’ at pp_profile.cc:682:29:
/usr/include/c++/13/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++/13/map:62,
from ../include/types.hh:39,
from ../include/properties.hh:14,
from properties.cc:8:
/usr/include/c++/13/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++/13/bits/stl_tree.h:2210:5: 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
2210 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/stl_tree.h:2458:7: 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
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/map:63:
/usr/include/c++/13/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++/13/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | 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++/13/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | 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 -fstack-clash-protection -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++/13/vector:72,
from ../include/types.hh:36:
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ changed in GCC 7.1
445 | 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++/13/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++/13/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++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::nullptr_t}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ changed in GCC 7.1
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ changed in GCC 7.1
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ changed in GCC 7.1
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: 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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_scoring.o pp_scoring.cc
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double&}; _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 = double&; BasicJsonType = nlohmann::basic_json<>]’ at ../include/json.hpp:5479:58,
inlined from ‘bool nlohmann::detail::json_sax_dom_parser<BasicJsonType>::number_float(number_float_t, const string_t&) [with BasicJsonType = nlohmann::basic_json<>]’ at ../include/json.hpp:5379:21,
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:10382:29:
/usr/include/c++/13/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 = {std::nullptr_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 = std::nullptr_t; BasicJsonType = nlohmann::basic_json<>]’ at ../include/json.hpp:5479:58,
inlined from ‘bool nlohmann::detail::json_sax_dom_parser<BasicJsonType>::null() [with BasicJsonType = nlohmann::basic_json<>]’ at ../include/json.hpp:5355:21,
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:10401:29:
/usr/include/c++/13/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 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 int&; BasicJsonType = nlohmann::basic_json<>]’ at ../include/json.hpp:5479:58,
inlined from ‘bool nlohmann::detail::json_sax_dom_parser<BasicJsonType>::number_integer(number_integer_t) [with BasicJsonType = nlohmann::basic_json<>]’ at ../include/json.hpp:5367:21,
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:10419:29:
/usr/include/c++/13/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 = {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++/13/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++/13/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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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++/13/vector:72,
from ../include/types.hh:36,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<PP::BonusProbEntry>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/map:62,
from ../include/types.hh:39:
/usr/include/c++/13/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++/13/bits/stl_tree.h:2210:5: 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
2210 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/stl_tree.h:2458:7: 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
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/stl_tree.h:2458:7: 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
/usr/include/c++/13/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++/13/bits/stl_tree.h:2503:5: 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
2503 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_tree.h:2503:5: 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++/13/bits/stl_map.h:1139:26,
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++/13/bits/stl_tree.h:1239:21: 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
1239 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/map:63:
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++/13/bits/stl_map.h:927:45: 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
927 | return _M_t._M_emplace_hint_unique(__position,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
928 | 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++/13/bits/stl_map.h:927:45: 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
927 | return _M_t._M_emplace_hint_unique(__position,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
928 | std::forward<_Pair>(__x));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/stl_tree.h:2521:19: 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
2521 | _M_erase_aux(__p.first, __p.second);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
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++/13/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | 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++/13/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | 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++/13/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | 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++/13/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | 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++/13/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from statemodel.cc:8:
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<Ancestor>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Ancestor}; _Tp = Ancestor; _Alloc = std::allocator<Ancestor>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Ancestor; _Alloc = std::allocator<Ancestor>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘void StateModel::initPredecessors(Matrix<LLDouble>&, int)’ at statemodel.cc:45:24:
/usr/include/c++/13/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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -fstack-clash-protection -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++/13/vector:66:
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++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PP::BonusProbEntry*, std::vector<PP::BonusProbEntry> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __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 PP::BonusProbType::mergeIntoSubmap(int, ViterbiSubmapType&, SubstateIdMap*)’ at pp_scoring.cc:310:16:
/usr/include/c++/13/bits/stl_map.h:927:45: 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
927 | return _M_t._M_emplace_hint_unique(__position,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
928 | 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++/13/bits/stl_map.h:1139:26,
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++/13/bits/stl_tree.h:1239:21: 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
1239 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]’,
inlined from ‘bool ViterbiSubmapType::setMax(SubstateId, Double, ViterbiSubmapType*) const’ at ../include/vitmatrix.hh:428:52,
inlined from ‘virtual void PP::SingleTargetExonScorer::exportSubstates(ViterbiSubmapType&)’ at pp_scoring.cc:806:18,
inlined from ‘virtual void PP::SingleTargetExonScorer::exportSubstates(ViterbiSubmapType&)’ at pp_scoring.cc:791:6:
/usr/include/c++/13/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | 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++/13/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | 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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o types.o types.cc
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 -fstack-clash-protection -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++/13/bits/stl_map.h:1139:26,
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++/13/bits/stl_tree.h:1239:21: 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
1239 | _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++/13/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | 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++/13/string:49,
from src/Genomic_Data.hpp:8,
from src/UTRs.cpp:5:
/usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/stl_function.h:1438:
/usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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 -fstack-clash-protection -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++/13/bits/stl_algo.h:61,
from /usr/include/c++/13/algorithm:61,
from ../include/types.hh:38,
from types.cc:8:
/usr/include/c++/13/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++/13/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++/13/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++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1792 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1812 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
/usr/include/c++/13/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++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1932 | 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++/13/bits/stl_algo.h:4861:18,
inlined from ‘Double quantile(const std::vector<LLDouble>&, float)’ at types.cc:513:12:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __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++/13/bits/stl_algo.h:1950:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >]’ at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from ‘Double quantile(const std::vector<LLDouble>&, float)’ at types.cc:513:12:
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from ../include/types.hh:36:
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/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++/13/bits/stl_vector.h:1296:21,
inlined from ‘static void Constant::init()’ at types.cc:356:21:
/usr/include/c++/13/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++/13/bits/stl_vector.h:1296:21,
inlined from ‘static void Constant::init()’ at types.cc:363:21:
/usr/include/c++/13/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++/13/bits/stl_vector.h:1296:21,
inlined from ‘static void Constant::init()’ at types.cc:370:17:
/usr/include/c++/13/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 -fstack-clash-protection -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++/13/vector:72,
from src/Genomic_Data.hpp:9:
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
445 | 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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o motif.o motif.cc
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++/13/bits/stl_vector.h:1296:21,
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++/13/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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algo.h:61,
from /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1812 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/13/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++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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++/13/vector:72,
from ../include/matrix.hh:12,
from ../include/motif.hh:12,
from motif.cc:10:
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<LLDouble>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
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++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/13/list:66,
from ../include/vitmatrix.hh:17,
from ../include/pp_scoring.hh:16,
from ../include/gene.hh:13:
/usr/include/c++/13/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++/13/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++/13/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 -fstack-clash-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o extrinsicinfo.o extrinsicinfo.cc
In file included from /usr/include/c++/13/vector:72,
from ../include/matrix.hh:12,
from ../include/motif.hh:12:
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
445 | 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++/13/bits/stl_vector.h:1296:21,
inlined from ‘void examineBaseCountOfGeneSeq(AnnoSequence*)’ at gene.cc:3432:22:
/usr/include/c++/13/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++/13/bits/stl_algo.h:4861:18,
inlined from ‘void examineBaseCountOfGeneSeq(AnnoSequence*)’ at gene.cc:3441:14:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __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++/13/bits/stl_algo.h:1950:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]’ at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from ‘void examineBaseCountOfGeneSeq(AnnoSequence*)’ at gene.cc:3441:14:
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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++/13/bits/list.tcc:267:5,
inlined from ‘static StatePath* StatePath::condenseStatePath(StatePath*)’ at gene.cc:995:37:
/usr/include/c++/13/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++/13/bits/list.tcc:267:5,
inlined from ‘Gene::Gene(const Gene&)’ at gene.cc:1391:28:
/usr/include/c++/13/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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o projectio.o projectio.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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++/13/map:62,
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++/13/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++/13/bits/stl_tree.h:2458:7: 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
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/map:63:
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++/13/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | 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++/13/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | 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:1241:16:
/usr/include/c++/13/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | 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++/13/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | 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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrmodel.o utrmodel.cc
In file included from /usr/include/c++/13/map:62,
from ../include/types.hh:39,
from ../include/hints.hh:12,
from ../include/extrinsicinfo.hh:15,
from extrinsicinfo.cc:10:
/usr/include/c++/13/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++/13/bits/stl_tree.h:2210:5: 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
2210 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/algorithm:61,
from ../include/types.hh:38:
/usr/include/c++/13/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++/13/bits/stl_algo.h:5383:5: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
5383 | __set_difference(_InputIterator1 __first1, _InputIterator1 __last1,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:5383:5: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:5383:5: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:5383:5: 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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o merkmal.o merkmal.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++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:5448:46: 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++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:5448:46: 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++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:5448:46: 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++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:5448:46: 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++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:5448:46: 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++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:5448:46: 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++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:5448:46: 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++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:5448:46: 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++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:5448:46: 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++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:5448:46: 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++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:5448:46: 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++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<Feature>’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:5448:46: 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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o vitmatrix.o vitmatrix.cc
In file included from /usr/include/c++/13/vector:72,
from ../include/types.hh:36,
from ../include/vitmatrix.hh:12,
from vitmatrix.cc:10:
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<ViterbiSubmapType>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/map:62,
from ../include/types.hh:39:
/usr/include/c++/13/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++/13/bits/stl_tree.h:2210:5: 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
2210 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/stl_tree.h:2458:7: 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
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/map:63:
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++/13/bits/stl_map.h:927:45: 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
927 | return _M_t._M_emplace_hint_unique(__position,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
928 | std::forward<_Pair>(__x));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/stl_tree.h:2458:7: 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
2458 | _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++/13/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | 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++/13/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/stl_tree.h:2503:5: 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
2503 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_tree.h:2503:5: 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++/13/bits/stl_map.h:1139:26,
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++/13/bits/stl_tree.h:1239:21: 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
1239 | _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++/13/bits/stl_map.h:1139:26,
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++/13/bits/stl_tree.h:1239:21: 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
1239 | _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++/13/bits/stl_map.h:1119:26,
inlined from ‘int ViterbiSubmapType::eraseUnneededSubstate(SubstateId)’ at vitmatrix.cc:103:18:
/usr/include/c++/13/bits/stl_tree.h:2521:19: 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
2521 | _M_erase_aux(__p.first, __p.second);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<ViterbiEntryType>::iterator’ changed in GCC 7.1
445 | 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++/13/bits/stl_vector.h:1296:21,
inlined from ‘void ViterbiColumnType::addState(int, signed char)’ at vitmatrix.cc:289:14:
/usr/include/c++/13/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++/13/vector:66:
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++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ViterbiSubmapType*, std::vector<ViterbiSubmapType> >’ changed in GCC 7.1
1289 | _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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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++/13/bits/stl_algo.h:61,
from /usr/include/c++/13/algorithm:61,
from ../include/types.hh:38,
from ../include/merkmal.hh:14,
from merkmal.cc:10:
/usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1792 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1812 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
/usr/include/c++/13/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++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1812 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
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++/13/bits/stl_algo.h:4861:18,
inlined from ‘static std::vector<double> CRF::capOutliers(std::vector<double>)’ at merkmal.cc:841:11:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __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++/13/bits/stl_algo.h:1950:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]’ at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from ‘static std::vector<double> CRF::capOutliers(std::vector<double>)’ at merkmal.cc:841:11:
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from ../include/types.hh:36:
/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
529 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<LLDouble>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/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 file included from /usr/include/c++/13/vector:66:
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++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1034 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
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++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
445 | 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++/13/bits/stl_vector.h:1296:21,
inlined from ‘AugustusGraph::AugustusGraph(std::__cxx11::list<Status>*, const char*)’ at ../include/graph.hh:344:25:
/usr/include/c++/13/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 -fstack-clash-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exoncand.o exoncand.cc
/usr/include/c++/13/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++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1932 | 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++/13/bits/stl_algo.h:4861:18,
inlined from ‘void BinnedMMGroup::trainBins(int)’ at merkmal.cc:111:14:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __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++/13/bits/stl_algo.h:1950:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<LLDouble*, vector<LLDouble> >]’ at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from ‘void BinnedMMGroup::trainBins(int)’ at merkmal.cc:111:14:
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1864 | 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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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++/13/vector:72,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from ../include/ncmodel.hh:11,
from ncmodel.cc:8:
/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type ‘std::vector<LLDouble>::iterator’ changed in GCC 7.1
529 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
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++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1034 | _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 -fstack-clash-protection -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++/13/vector:72,
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++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<hints>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algo.h:61,
from /usr/include/c++/13/algorithm:61,
from ../include/types.hh:38,
from ../include/geneticcode.hh:12,
from contTimeMC.cc:10:
/usr/include/c++/13/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++/13/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,
| ^~~~~~~~~~~~~
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++/13/bits/stl_vector.h:1296:21,
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++/13/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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1812 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/13/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++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1932 | 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++/13/bits/stl_algo.h:4861:18,
inlined from ‘void Evo::setBranchLengths(std::vector<double>, int)’ at contTimeMC.cc:52:9:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __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++/13/bits/stl_algo.h:1950:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]’ at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from ‘void Evo::setBranchLengths(std::vector<double>, int)’ at contTimeMC.cc:52:9:
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from ../include/matrix.hh:12,
from ../include/contTimeMC.hh:13,
from contTimeMC.cc:9:
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
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++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1289 | _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 -fstack-clash-protection -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 -fstack-clash-protection -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++/13/vector:72,
from ../include/types.hh:36,
from ../include/geneticcode.hh:12,
from geneMSA.cc:10:
/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
529 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from ../include/matrix.hh:12,
from ../include/contTimeMC.hh:13,
from ../include/codonevo.hh:11,
from codonevo.cc:9:
/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
529 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
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++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1034 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
445 | 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++/13/bits/stl_vector.h:1296:21,
inlined from ‘void CodonEvo::setOmegas(int)’ at codonevo.cc:42:18:
/usr/include/c++/13/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++/13/bits/stl_vector.h:1296:21,
inlined from ‘void CodonEvo::setOmegas(int)’ at codonevo.cc:43:21:
/usr/include/c++/13/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++/13/bits/stl_vector.h:1296:21,
inlined from ‘void CodonEvo::setOmegas(int)’ at codonevo.cc:45:18:
/usr/include/c++/13/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++/13/bits/stl_vector.h:1296:21,
inlined from ‘void CodonEvo::setOmegas(int)’ at codonevo.cc:48:23:
/usr/include/c++/13/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++/13/bits/stl_vector.h:1296:21,
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++/13/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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
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++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1289 | _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 CodonEvo::setAAPostProbs()’ at codonevo.cc:92:17:
/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1034 | _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 -fstack-clash-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthograph.o orthograph.cc
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void cumValues::addLogliks(std::vector<double>*)’ at ../include/geneMSA.hh:41:21,
inlined from ‘void GeneMSA::computeOmegasEff(std::__cxx11::list<OrthoExon>&, const std::vector<AnnoSequence*>&, PhyloTree*, std::ofstream*)’ at geneMSA.cc:1560:17:
/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1034 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
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++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘AugustusGraph::AugustusGraph(std::__cxx11::list<Status>*, const char*)’ at ../include/graph.hh:344:25:
/usr/include/c++/13/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++/13/vector:72,
from ../include/phylotree.hh:13,
from phylotree.cc:12:
/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
529 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
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++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1034 | _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++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1034 | _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++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1034 | _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++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1034 | _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++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1034 | _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++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1034 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void Treenode::resizeTable(int, double)’ at phylotree.cc:55:17,
inlined from ‘int PhyloTree::fitch(std::vector<int>&, int)’ at phylotree.cc:543:26:
/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1034 | _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++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1034 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
445 | 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++/13/bits/stl_vector.h:1296:21,
inlined from ‘void PhyloTree::getBranchLengths(std::vector<double>&) const’ at phylotree.cc:320:25:
/usr/include/c++/13/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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthoexon.o orthoexon.cc
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++/13/bits/stl_vector.h:1296:21,
inlined from ‘void CompGenePred::runPredictionOrTest()’ at compgenepred.cc:282:23:
/usr/include/c++/13/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++/13/bits/stl_vector.h:1296:21,
inlined from ‘void CompGenePred::runPredictionOrTest()’ at compgenepred.cc:284:41:
/usr/include/c++/13/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++/13/bits/stl_vector.h:1296:21,
inlined from ‘void CompGenePred::runPredictionOrTest()’ at compgenepred.cc:288:27:
/usr/include/c++/13/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++/13/vector:66:
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++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1289 | _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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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++/13/vector:72,
from ../include/types.hh:36,
from ../include/exoncand.hh:13,
from ../include/orthoexon.hh:11,
from orthoexon.cc:10:
/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
529 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
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++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1034 | _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++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1034 | _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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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++/13/vector:72,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from ../include/intronmodel.hh:11,
from introntrain.cc:8:
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<LLDouble>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
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++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1289 | _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++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from ../include/exonmodel.hh:11,
from exontrain.cc:8:
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<LLDouble>::iterator’ changed in GCC 7.1
445 | 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 -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc
In file included from /usr/include/c++/13/vector:66:
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++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1289 | _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++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >’ changed in GCC 7.1
1289 | _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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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/
In file included from /usr/include/c++/13/vector:72,
from ../include/types.hh:36,
from ../include/properties.hh:14,
from ../include/pp_simscore.hh:21,
from pp_simscore.cc:10:
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
445 | 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 -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘void SS::SimilarityScore::printAlignment()’ at pp_simscore.cc:723:56:
/usr/include/c++/13/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 -fstack-clash-protection -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++/13/vector:72,
from ../include/types.hh:36,
from etraining.cc:9:
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
445 | 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++/13/bits/stl_vector.h:1296:21,
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++/13/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 -fstack-clash-protection -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 -fstack-clash-protection -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.test_utr_on) ... ok
test_hints_MPE (examples.test_examples.TestExamples.test_hints_MPE) ... ok
test_training_new_species (examples.test_examples.TestExamples.test_training_new_species) ... ok
test_ab_initio_prediction (examples.test_examples.TestExamples.test_ab_initio_prediction) ... ok
test_format_and_error_out (examples.test_examples.TestExamples.test_format_and_error_out) ... ok
test_cgp (examples.test_examples.TestExamples.test_cgp) ... ok
test_cgp_sqlite (examples.test_examples.TestExamples.test_cgp_sqlite) ... ok
test_cgp_sqlite_hints (examples.test_examples.TestExamples.test_cgp_sqlite_hints) ... ok
----------------------------------------------------------------------
Ran 8 tests in 435.092s
OK
Removing generated test files...
----------------------------------------------------------------------
Executing small test suite
----------------------------------------------------------------------
Creating SQLite database for cgp test cases...
cd tests/short && ./execute_test.py --html bam2hints
test_bam2hints (auxprogs.bam2hints.test_bam2hints.TestBam2Hints.test_bam2hints) ... ok
test_bam2hints_pipes (auxprogs.bam2hints.test_bam2hints.TestBam2Hints.test_bam2hints_pipes) ... ok
----------------------------------------------------------------------
Ran 2 tests in 0.012s
OK
cd tests/short && ./execute_test.py --html bam2wig
test_bam2wig (auxprogs.bam2wig.test_bam2wig.TestBam2Wig.test_bam2wig) ... ok
test_bam2wig_region (auxprogs.bam2wig.test_bam2wig.TestBam2Wig.test_bam2wig_region) ... ok
----------------------------------------------------------------------
Ran 2 tests in 0.014s
OK
cd tests/short && ./execute_test.py --html filterbam
test_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_options) ... ok
test_no_minId_no_minCover (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_minId_no_minCover) ... ok
test_no_minId (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_minId) ... ok
test_no_minCover (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_minCover) ... ok
test_minCover99 (auxprogs.filterbam.test_filterbam.TestFilterBam.test_minCover99) ... ok
test_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam.test_uniq) ... ok
test_uniqThresh (auxprogs.filterbam.test_filterbam.TestFilterBam.test_uniqThresh) ... ok
test_best (auxprogs.filterbam.test_filterbam.TestFilterBam.test_best) ... ok
test_noIntrons (auxprogs.filterbam.test_filterbam.TestFilterBam.test_noIntrons) ... ok
test_noIntrons_insertLimit (auxprogs.filterbam.test_filterbam.TestFilterBam.test_noIntrons_insertLimit) ... ok
test_not_paired (auxprogs.filterbam.test_filterbam.TestFilterBam.test_not_paired) ... ok
test_paired (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired) ... ok
test_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired_pairwiseAlignments) ... ok
test_pairwiseAlignments_2 (auxprogs.filterbam.test_filterbam.TestFilterBam.test_pairwiseAlignments_2) ... ok
test_paired_maxIntronLen (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired_maxIntronLen) ... ok
test_paired_pairBedFile (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired_pairBedFile) ... ok
test_commonGeneFile (auxprogs.filterbam.test_filterbam.TestFilterBam.test_commonGeneFile) ... ok
test_calmd_seq_with_equalsigns_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_no_options) ... ok
test_calmd_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_no_options) ... ok
test_calmd_seq_with_equalsigns_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_uniq) ... ok
test_calmd_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_uniq) ... ok
test_calmd_seq_with_equalsigns_best (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_best) ... ok
test_calmd_best (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_best) ... ok
test_calmd_seq_with_equalsigns_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_paired_pairwiseAlignments) ... ok
test_calmd_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_paired_pairwiseAlignments) ... ok
----------------------------------------------------------------------
Ran 25 tests in 0.477s
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/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/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/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/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/etraining contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/getSeq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/load2db contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/bam2hints contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/homGeneMapping debian/augustus/usr/bin/filterBam debian/augustus/usr/bin/pp_simScore debian/augustus/usr/bin/fastBlockSearch debian/augustus/usr/bin/compileSpliceCands debian/augustus/usr/bin/load2sqlitedb debian/augustus/usr/bin/augustus debian/augustus/usr/bin/etraining debian/augustus/usr/bin/getSeq debian/augustus/usr/bin/load2db debian/augustus/usr/bin/aln2wig debian/augustus/usr/bin/prepareAlign debian/augustus/usr/bin/bam2hints debian/augustus/usr/bin/joingenes debian/augustus/usr/bin/bam2wig were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.5.0+dfsg-4_armhf.deb'.
dpkg-deb: building package 'augustus' in '../augustus_3.5.0+dfsg-4_armhf.deb'.
dpkg-genbuildinfo --build=any -O../augustus_3.5.0+dfsg-4_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi5 test autobuilder <root@raspbian.org> -O../augustus_3.5.0+dfsg-4_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2023-11-20T05:39:14Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
augustus_3.5.0+dfsg-4_armhf.changes:
------------------------------------
Format: 1.8
Date: Sat, 18 Nov 2023 08:21:25 +0100
Source: augustus
Binary: augustus augustus-dbgsym
Architecture: armhf
Version: 3.5.0+dfsg-4
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian pi5 test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
augustus - gene prediction in eukaryotic genomes
Closes: 1043915
Changes:
augustus (3.5.0+dfsg-4) unstable; urgency=medium
.
* Ensure multiple builds can be done in same directory.
Done by ensuring the directory is cleaned correctly.
Closes: #1043915
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Files:
382104836d225acac1084aa99396b862 34606648 debug optional augustus-dbgsym_3.5.0+dfsg-4_armhf.deb
ab01bc9991900cb8133cc7f54f05b209 8523 science optional augustus_3.5.0+dfsg-4_armhf.buildinfo
33d49acd359e3ed67bc47e752e342c98 1547352 science optional augustus_3.5.0+dfsg-4_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: augustus
Binary: augustus augustus-dbgsym
Architecture: armhf
Version: 3.5.0+dfsg-4
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: Mon, 20 Nov 2023 05:39:13 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
asciidoctor (= 2.0.20-1),
autoconf (= 2.71-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-13),
autotools-dev (= 20220109.1),
base-files (= 13+rpi1),
base-passwd (= 3.6.2),
bash (= 5.2.15-2),
binutils (= 2.41-6+rpi1),
binutils-arm-linux-gnueabihf (= 2.41-6+rpi1),
binutils-common (= 2.41-6+rpi1),
bsdextrautils (= 2.39.2-6),
bsdutils (= 1:2.39.2-6),
build-essential (= 12.9),
bzip2 (= 1.0.8-5+b2),
ca-certificates (= 20230311),
chrpath (= 0.16-2),
coreutils (= 9.1-1),
cpp (= 4:13.2.0-1+rpi1),
cpp-12 (= 12.3.0-10+rpi1),
cpp-13 (= 13.2.0-5+rpi1),
dash (= 0.5.12-6),
debconf (= 1.5.82),
debhelper (= 13.11.8),
debianutils (= 5.14),
default-libmysqlclient-dev (= 1.1.0),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.1-1),
diffutils (= 1:3.10-1),
dpkg (= 1.22.1+rpi1),
dpkg-dev (= 1.22.1+rpi1),
dwz (= 0.15-1),
file (= 1:5.45-2),
findutils (= 4.9.0-5),
g++ (= 4:13.2.0-1+rpi1),
g++-13 (= 13.2.0-5+rpi1),
gcc (= 4:13.2.0-1+rpi1),
gcc-12 (= 12.3.0-10+rpi1),
gcc-12-base (= 12.3.0-10+rpi1),
gcc-13 (= 13.2.0-5+rpi1),
gcc-13-base (= 13.2.0-5+rpi1),
gettext (= 0.21-13),
gettext-base (= 0.21-13),
grep (= 3.11-3),
groff-base (= 1.23.0-3),
gzip (= 1.12-1),
hostname (= 3.23+nmu1),
icu-devtools (= 72.1-4),
init-system-helpers (= 1.65.2),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-3),
libamd3 (= 1:7.2.2+dfsg-1),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 13.2.0-5+rpi1),
libatomic1 (= 13.2.0-5+rpi1),
libattr1 (= 1:2.5.1-4),
libaudit-common (= 1:3.1.1-1),
libaudit1 (= 1:3.1.1-1),
libbamtools-dev (= 2.5.2+dfsg-4),
libbamtools2.5.2 (= 2.5.2+dfsg-4),
libbinutils (= 2.41-6+rpi1),
libblas-dev (= 3.11.0-2),
libblas3 (= 3.11.0-2),
libblkid1 (= 2.39.2-6),
libboost-iostreams-dev (= 1.74.0.3+b4),
libboost-iostreams1.74-dev (= 1.74.0+ds1-23),
libboost-iostreams1.74.0 (= 1.74.0+ds1-23),
libboost-regex1.74-dev (= 1.74.0+ds1-23),
libboost-regex1.74.0 (= 1.74.0+ds1-23),
libboost-serialization-dev (= 1.74.0.3+b4),
libboost-serialization1.74-dev (= 1.74.0+ds1-23),
libboost-serialization1.74.0 (= 1.74.0+ds1-23),
libboost1.74-dev (= 1.74.0+ds1-23),
libbrotli1 (= 1.0.9-2+b3),
libbsd0 (= 0.11.7-4),
libbtf2 (= 1:7.2.2+dfsg-1),
libbz2-1.0 (= 1.0.8-5+b2),
libbz2-dev (= 1.0.8-5+b2),
libc-bin (= 2.37-12+rpi2),
libc-dev-bin (= 2.37-12+rpi2),
libc6 (= 2.37-12+rpi2),
libc6-dev (= 2.37-12+rpi2),
libcamd3 (= 1:7.2.2+dfsg-1),
libcap-ng0 (= 0.8.3-1+b1),
libcap2 (= 1:2.66-4),
libcc1-0 (= 13.2.0-5+rpi1),
libccolamd3 (= 1:7.2.2+dfsg-1),
libcholmod4 (= 1:7.2.2+dfsg-1),
libcolamd3 (= 1:7.2.2+dfsg-1),
libcom-err2 (= 1.47.0-2),
libcrypt-dev (= 1:4.4.36-2),
libcrypt1 (= 1:4.4.36-2),
libctf-nobfd0 (= 2.41-6+rpi1),
libctf0 (= 2.41-6+rpi1),
libcurl3-gnutls (= 8.4.0-2+rpi1),
libcurl4-gnutls-dev (= 8.4.0-2+rpi1),
libcxsparse4 (= 1:7.2.2+dfsg-1),
libdb5.3 (= 5.3.28+dfsg2-2),
libdebconfclient0 (= 0.271),
libdebhelper-perl (= 13.11.8),
libdeflate-dev (= 1.18-1),
libdeflate0 (= 1.18-1),
libdpkg-perl (= 1.22.1+rpi1),
libedit2 (= 3.1-20230828-1),
libelf1 (= 0.188-2.1+rpi1),
libexpat1 (= 2.5.0-2),
libffi8 (= 3.4.4-1),
libfile-stripnondeterminism-perl (= 1.13.1-1),
libgcc-12-dev (= 12.3.0-10+rpi1),
libgcc-13-dev (= 13.2.0-5+rpi1),
libgcc-s1 (= 13.2.0-5+rpi1),
libgcrypt20 (= 1.10.2-3),
libgdbm-compat4 (= 1.23-3),
libgdbm6 (= 1.23-3),
libgfortran5 (= 13.2.0-5+rpi1),
libgmp10 (= 2:6.3.0+dfsg-2),
libgnutls30 (= 3.8.1-4),
libgomp1 (= 13.2.0-5+rpi1),
libgpg-error0 (= 1.47-2),
libgsl-dev (= 2.7.1+dfsg-6),
libgsl27 (= 2.7.1+dfsg-6),
libgslcblas0 (= 2.7.1+dfsg-6),
libgssapi-krb5-2 (= 1.20.1-4),
libhogweed6 (= 3.9.1-2),
libhts-dev (= 1.18+ds-1),
libhts3 (= 1.18+ds-1),
libhtscodecs2 (= 1.5.2-1),
libicu-dev (= 72.1-4),
libicu72 (= 72.1-4),
libidn2-0 (= 2.3.4-1),
libisl23 (= 0.26-3),
libjansson4 (= 2.14-2),
libk5crypto3 (= 1.20.1-4),
libkeyutils1 (= 1.6.3-2),
libklu2 (= 1:7.2.2+dfsg-1),
libkrb5-3 (= 1.20.1-4),
libkrb5support0 (= 1.20.1-4),
liblapack-dev (= 3.11.0-2),
liblapack3 (= 3.11.0-2),
libldap-2.5-0 (= 2.5.13+dfsg-5+rpi1),
libldl3 (= 1:7.2.2+dfsg-1),
liblpsolve55-dev (= 5.5.2.5-2+b1),
liblz4-1 (= 1.9.4-1+rpi1+b1),
liblzma-dev (= 5.4.4-0.1),
liblzma5 (= 5.4.4-0.1),
libmagic-mgc (= 1:5.45-2),
libmagic1 (= 1:5.45-2),
libmariadb-dev (= 1:10.11.3-1+rpi1),
libmariadb-dev-compat (= 1:10.11.3-1+rpi1),
libmariadb3 (= 1:10.11.3-1+rpi1),
libmd0 (= 1.1.0-1),
libmongoose3 (= 1:7.2.2+dfsg-1),
libmount1 (= 2.39.2-6),
libmpc3 (= 1.3.1-1),
libmpfr6 (= 4.2.1-1),
libmysql++-dev (= 3.2.5-2.1),
libmysql++3v5 (= 3.2.5-2.1),
libncurses-dev (= 6.4+20231016-1),
libncurses6 (= 6.4+20231016-1),
libncursesw6 (= 6.4+20231016-1),
libnettle8 (= 3.9.1-2),
libnghttp2-14 (= 1.58.0-1),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libp11-kit0 (= 0.25.0-5),
libpam-modules (= 1.5.2-9.1),
libpam-modules-bin (= 1.5.2-9.1),
libpam-runtime (= 1.5.2-9.1),
libpam0g (= 1.5.2-9.1),
libpcre2-8-0 (= 10.42-4),
libperl5.36 (= 5.36.0-9),
libpipeline1 (= 1.5.7-1),
libpsl5 (= 0.21.2-1+b1),
libpython3-stdlib (= 3.11.4-5),
libpython3.11-minimal (= 3.11.6-3),
libpython3.11-stdlib (= 3.11.6-3),
librbio4 (= 1:7.2.2+dfsg-1),
libreadline8 (= 8.2-1.3),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libruby (= 1:3.1),
libruby3.1 (= 3.1.2-7),
libsasl2-2 (= 2.1.28+dfsg1-3),
libsasl2-modules-db (= 2.1.28+dfsg1-3),
libseccomp2 (= 2.5.4-1+rpi1+b1),
libselinux1 (= 3.5-1),
libsframe1 (= 2.41-6+rpi1),
libsmartcols1 (= 2.39.2-6),
libspex2 (= 1:7.2.2+dfsg-1),
libspqr4 (= 1:7.2.2+dfsg-1),
libsqlite3-0 (= 3.44.0-1),
libsqlite3-dev (= 3.44.0-1),
libssh2-1 (= 1.11.0-2),
libssl-dev (= 3.0.11-1),
libssl3 (= 3.0.11-1),
libstdc++-12-dev (= 12.3.0-10+rpi1),
libstdc++-13-dev (= 13.2.0-5+rpi1),
libstdc++6 (= 13.2.0-5+rpi1),
libsub-override-perl (= 0.09-4),
libsuitesparse-dev (= 1:7.2.2+dfsg-1),
libsuitesparseconfig7 (= 1:7.2.2+dfsg-1),
libsystemd0 (= 254.5-1+rpi1),
libtasn1-6 (= 4.19.0-3),
libtinfo6 (= 6.4+20231016-1),
libtirpc-common (= 1.3.3+ds-1),
libtirpc-dev (= 1.3.3+ds-1),
libtirpc3 (= 1.3.3+ds-1),
libtool (= 2.4.7-7),
libubsan1 (= 13.2.0-5+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 254.5-1+rpi1),
libumfpack6 (= 1:7.2.2+dfsg-1),
libunistring5 (= 1.1-2),
libuuid1 (= 2.39.2-6),
libxml2 (= 2.9.14+dfsg-1.3),
libyaml-0-2 (= 0.2.5-1),
libzstd1 (= 1.5.5+dfsg2-2),
linux-libc-dev (= 6.5.6-1+rpi1),
login (= 1:4.13+dfsg1-3),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.12.0-1),
mariadb-common (= 1:10.11.3-1+rpi1),
mawk (= 1.3.4.20230808-1),
media-types (= 10.1.0),
mysql-common (= 5.8+1.1.0),
ncurses-base (= 6.4+20231016-1),
ncurses-bin (= 6.4+20231016-1),
openssl (= 3.0.11-1),
patch (= 2.7.6-7),
perl (= 5.36.0-9),
perl-base (= 5.36.0-9),
perl-modules-5.36 (= 5.36.0-9),
po-debconf (= 1.0.21+nmu1),
python3 (= 3.11.4-5),
python3-minimal (= 3.11.4-5),
python3.11 (= 3.11.6-3),
python3.11-minimal (= 3.11.6-3),
rake (= 13.0.6-3),
readline-common (= 8.2-1.3),
rpcsvc-proto (= 1.4.3-1),
ruby (= 1:3.1),
ruby-asciidoctor (= 2.0.20-1),
ruby-net-telnet (= 0.2.0-1),
ruby-rubygems (= 3.4.20-1),
ruby-sdbm (= 1.0.0-5+rpi1),
ruby-webrick (= 1.8.1-1),
ruby-xmlrpc (= 0.3.2-2),
ruby3.1 (= 3.1.2-7),
rubygems-integration (= 1.18),
samtools (= 1.18-1),
sed (= 4.9-1),
sensible-utils (= 0.0.20),
sysvinit-utils (= 3.08-3),
tar (= 1.34+dfsg-1.2),
tzdata (= 2023c-10),
usr-is-merged (= 37),
util-linux (= 2.39.2-6),
xz-utils (= 5.4.4-0.1),
zlib1g (= 1:1.2.13.dfsg-3),
zlib1g-dev (= 1:1.2.13.dfsg-3)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
LC_COLLATE="C.UTF-8"
SOURCE_DATE_EPOCH="1700292085"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
augustus-dbgsym_3.5.0+dfsg-4_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 34606648 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-4
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 35482
Depends: augustus (= 3.5.0+dfsg-4)
Section: debug
Priority: optional
Description: debug symbols for augustus
Build-Ids: 062a49aa733f96385973e2958febb60d32ad099e 28c1fc7d29d7361ee0c640599f2ad125daf8e00e 2d014857566b3331e254dea13fb58016b5f0e5b5 3697315d6ba5accedf44ded973da356d718c91aa 42ee0c322e160136095bc1cc9b847788233ee354 4bb9647024141a7429e66d6168055b4bed553e87 77a7fdf8dd9712db89cddef91aa161c97f47ecee a6f922badf4a06d7455b70e133d5ac2b72071cb6 bb22de0e4889ae5787b9614309a7a87a98f4f9f7 bfc3ed6a3cd60613e2b4215cc45ca8c0f3878d68 c484a85ea2c0f18d79cfa5cc69384b850602b145 dbab2de2ee535af3a9c627a74dc2a6f0307d866b e4c9942d44e9aab8f903d5e443e2cbf01b9f0d66 f57b83de7cc237a3e16912c7835800e22ae0e47e fe6caf0c273d6a98d2944715b201f3a788b75f59
drwxr-xr-x root/root 0 2023-11-18 07:21 ./
drwxr-xr-x root/root 0 2023-11-18 07:21 ./usr/
drwxr-xr-x root/root 0 2023-11-18 07:21 ./usr/lib/
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drwxr-xr-x root/root 0 2023-11-18 07:21 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2023-11-18 07:21 ./usr/lib/debug/.build-id/06/
-rw-r--r-- root/root 19408 2023-11-18 07:21 ./usr/lib/debug/.build-id/06/2a49aa733f96385973e2958febb60d32ad099e.debug
drwxr-xr-x root/root 0 2023-11-18 07:21 ./usr/lib/debug/.build-id/28/
-rw-r--r-- root/root 174196 2023-11-18 07:21 ./usr/lib/debug/.build-id/28/c1fc7d29d7361ee0c640599f2ad125daf8e00e.debug
drwxr-xr-x root/root 0 2023-11-18 07:21 ./usr/lib/debug/.build-id/2d/
-rw-r--r-- root/root 13472 2023-11-18 07:21 ./usr/lib/debug/.build-id/2d/014857566b3331e254dea13fb58016b5f0e5b5.debug
drwxr-xr-x root/root 0 2023-11-18 07:21 ./usr/lib/debug/.build-id/36/
-rw-r--r-- root/root 783908 2023-11-18 07:21 ./usr/lib/debug/.build-id/36/97315d6ba5accedf44ded973da356d718c91aa.debug
drwxr-xr-x root/root 0 2023-11-18 07:21 ./usr/lib/debug/.build-id/42/
-rw-r--r-- root/root 8481844 2023-11-18 07:21 ./usr/lib/debug/.build-id/42/ee0c322e160136095bc1cc9b847788233ee354.debug
drwxr-xr-x root/root 0 2023-11-18 07:21 ./usr/lib/debug/.build-id/4b/
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drwxr-xr-x root/root 0 2023-11-18 07:21 ./usr/lib/debug/.build-id/77/
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augustus_3.5.0+dfsg-4_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 1547352 bytes: control archive=5056 bytes.
1530 bytes, 23 lines control
10549 bytes, 141 lines md5sums
Package: augustus
Version: 3.5.0+dfsg-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 9097
Depends: libbamtools2.5.2 (>= 2.5.2+dfsg), libboost-iostreams1.74.0 (>= 1.74.0+ds1), libc6 (>= 2.34), libcolamd3 (>= 1:7.0.1), libgcc-s1 (>= 3.5), libgsl27 (>= 2.7.1), libhts3 (>= 1.17), libmariadb3 (>= 3.0.0), libmysql++3v5 (>= 3.2.5-1~), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 13.1), 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: 1540272
Build-Time: 658
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 74
Job: augustus_3.5.0+dfsg-4
Machine Architecture: arm64
Package: augustus
Package-Time: 771
Source-Version: 3.5.0+dfsg-4
Space: 1540272
Status: successful
Version: 3.5.0+dfsg-4
--------------------------------------------------------------------------------
Finished at 2023-11-20T05:39:14Z
Build needed 00:12:51, 1540272k disk space