augustus →
3.4.0+dfsg2-2 →
armhf → 2021-01-11 06:53:20
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| augustus 3.4.0+dfsg2-2 (armhf) Mon, 11 Jan 2021 05:36:16 +0000 |
+==============================================================================+
Package: augustus
Version: 3.4.0+dfsg2-2
Source Version: 3.4.0+dfsg2-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-7ee6bc33-4623-4b79-bbce-e8387ed08ef5' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [12.0 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.1 MB]
Fetched 25.1 MB in 11s (2316 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'augustus' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/augustus.git
Please use:
git clone https://salsa.debian.org/med-team/augustus.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 148 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main augustus 3.4.0+dfsg2-2 (dsc) [2355 B]
Get:2 http://172.17.0.1/private bullseye-staging/main augustus 3.4.0+dfsg2-2 (tar) [148 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main augustus 3.4.0+dfsg2-2 (diff) [19.2 kB]
Fetched 148 MB in 26s (5618 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/augustus-8MP9Wp/augustus-3.4.0+dfsg2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/augustus-8MP9Wp' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-FdmxkH/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-FdmxkH/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-FdmxkH/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-FdmxkH/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-FdmxkH/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-FdmxkH/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-FdmxkH/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-FdmxkH/apt_archive ./ Packages [430 B]
Fetched 2106 B in 1s (3108 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
bsdextrautils libpam-cap netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 59 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-FdmxkH/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (42.5 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12379 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, libboost-serialization-dev, libssl-dev, libmysql++-dev, asciidoctor, python3, samtools
Filtered Build-Depends: debhelper-compat (= 13), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, libboost-serialization-dev, libssl-dev, libmysql++-dev, asciidoctor, python3, samtools
dpkg-deb: building package 'sbuild-build-depends-augustus-dummy' in '/<<BUILDDIR>>/resolver-FdmxkH/apt_archive/sbuild-build-depends-augustus-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-augustus-dummy sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-FdmxkH/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-FdmxkH/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-FdmxkH/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-FdmxkH/apt_archive ./ Sources [600 B]
Get:5 copy:/<<BUILDDIR>>/resolver-FdmxkH/apt_archive ./ Packages [679 B]
Fetched 2612 B in 1s (5164 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install augustus build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev ca-certificates cpp-10
debhelper default-libmysqlclient-dev dh-autoreconf dh-strip-nondeterminism
dwz file g++-10 gcc-10 gcc-10-base gettext gettext-base groff-base
icu-devtools intltool-debian libamd2 libarchive-zip-perl libasan6 libatomic1
libbamtools-dev libbamtools2.5.1 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 libbtf1 libbz2-dev libcamd2 libcc1-0 libccolamd2 libcholmod3
libcolamd2 libcurl3-gnutls libcurl4-gnutls-dev libcxsparse3
libdebhelper-perl libdeflate-dev libdeflate0 libelf1 libexpat1
libfile-stripnondeterminism-perl libgcc-10-dev libgcc-s1 libgfortran5
libgnutls30 libgomp1 libgraphblas3 libgsl-dev libgsl25 libgslcblas0
libgssapi-krb5-2 libhts-dev libhts3 libicu-dev libicu67 libk5crypto3
libkeyutils1 libklu1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3
libldl2 liblpsolve55-dev liblzma-dev liblzma5 libmagic-mgc libmagic1
libmariadb-dev libmariadb-dev-compat libmariadb3 libmetis5 libmongoose2
libmysql++-dev libmysql++3v5 libncurses-dev libncurses5-dev libncurses6
libncursesw6 libnghttp2-14 libnsl2 libpipeline1 libpsl5 libpython3-stdlib
libpython3.9-minimal libpython3.9-stdlib librbio2 librtmp1 libruby2.7
libsigsegv2 libsliplu1 libspqr2 libsqlite3-dev libssh2-1 libssl-dev
libssl1.1 libstdc++-10-dev libstdc++6 libsub-override-perl
libsuitesparse-dev libsuitesparseconfig5 libtinfo6 libtirpc-common libtirpc3
libtool libubsan1 libuchardet0 libumfpack5 libxml2 libyaml-0-2 lzma-dev m4
mailcap man-db mariadb-common media-types mime-support mysql-common openssl
po-debconf python3 python3-minimal python3.9 python3.9-minimal rake ruby
ruby-asciidoctor ruby-minitest ruby-net-telnet ruby-power-assert
ruby-rubygems ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration
samtools zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc gcc-10-locales dh-make
gcc-10-doc gettext-doc libasprintf-dev libgettextpo-dev groff
libbamtools-doc liblapack-doc libboost1.74-doc libboost-atomic1.74-dev
libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev
libboost-contract1.74-dev libboost-coroutine1.74-dev
libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-locale1.74-dev libboost-log1.74-dev
libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev
libboost-numpy1.74-dev libboost-program-options1.74-dev
libboost-python1.74-dev libboost-random1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev
librtmp-dev libssh2-1-dev pkg-config gnutls-bin gsl-ref-psdoc | gsl-doc-pdf
| gsl-doc-info | gsl-ref-html krb5-doc krb5-user icu-doc liblzma-doc
libmysql++-doc ncurses-doc sqlite3-doc libssl-doc libstdc++-10-doc
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl python3-doc python3-tk python3-venv
python3.9-venv python3.9-doc binfmt-support ri ruby-dev bundler cwltool
Recommended packages:
curl | wget | lynx bzip2-doc libarchive-cpio-perl krb5-locales libgpm2
publicsuffix libltdl-dev libmail-sendmail-perl zip fonts-lato libjs-jquery
The following NEW packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev ca-certificates
debhelper default-libmysqlclient-dev dh-autoreconf dh-strip-nondeterminism
dwz file gettext gettext-base groff-base icu-devtools intltool-debian
libamd2 libarchive-zip-perl libbamtools-dev libbamtools2.5.1 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 libbtf1 libbz2-dev
libcamd2 libccolamd2 libcholmod3 libcolamd2 libcurl3-gnutls
libcurl4-gnutls-dev libcxsparse3 libdebhelper-perl libdeflate-dev
libdeflate0 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5
libgraphblas3 libgsl-dev libgsl25 libgslcblas0 libgssapi-krb5-2 libhts-dev
libhts3 libicu-dev libicu67 libk5crypto3 libkeyutils1 libklu1 libkrb5-3
libkrb5support0 liblapack-dev liblapack3 libldl2 liblpsolve55-dev
liblzma-dev libmagic-mgc libmagic1 libmariadb-dev libmariadb-dev-compat
libmariadb3 libmetis5 libmongoose2 libmysql++-dev libmysql++3v5
libncurses-dev libncurses5-dev libncurses6 libnghttp2-14 libnsl2
libpipeline1 libpsl5 libpython3-stdlib libpython3.9-minimal
libpython3.9-stdlib librbio2 librtmp1 libruby2.7 libsigsegv2 libsliplu1
libspqr2 libsqlite3-dev libssh2-1 libssl-dev libssl1.1 libsub-override-perl
libsuitesparse-dev libsuitesparseconfig5 libtirpc-common libtirpc3 libtool
libuchardet0 libumfpack5 libxml2 libyaml-0-2 lzma-dev m4 mailcap man-db
mariadb-common media-types mime-support mysql-common openssl po-debconf
python3 python3-minimal python3.9 python3.9-minimal rake ruby
ruby-asciidoctor ruby-minitest ruby-net-telnet ruby-power-assert
ruby-rubygems ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration
samtools sbuild-build-depends-augustus-dummy zlib1g-dev
The following packages will be upgraded:
cpp-10 g++-10 gcc-10 gcc-10-base libasan6 libatomic1 libcc1-0 libgcc-10-dev
libgcc-s1 libgnutls30 libgomp1 liblzma5 libncursesw6 libstdc++-10-dev
libstdc++6 libtinfo6 libubsan1
17 upgraded, 135 newly installed, 0 to remove and 42 not upgraded.
Need to get 116 MB of archives.
After this operation, 205 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-FdmxkH/apt_archive ./ sbuild-build-depends-augustus-dummy 0.invalid.0 [968 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libubsan1 armhf 10.2.1-3+rpi1 [746 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf gcc-10-base armhf 10.2.1-3+rpi1 [201 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libgcc-s1 armhf 10.2.1-3+rpi1 [36.0 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libgomp1 armhf 10.2.1-3+rpi1 [83.7 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libatomic1 armhf 10.2.1-3+rpi1 [8212 B]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libasan6 armhf 10.2.1-3+rpi1 [1986 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf cpp-10 armhf 10.2.1-3+rpi1 [6687 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libcc1-0 armhf 10.2.1-3+rpi1 [38.3 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf g++-10 armhf 10.2.1-3+rpi1 [7337 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf gcc-10 armhf 10.2.1-3+rpi1 [13.4 MB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libgcc-10-dev armhf 10.2.1-3+rpi1 [683 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libstdc++-10-dev armhf 10.2.1-3+rpi1 [1752 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libstdc++6 armhf 10.2.1-3+rpi1 [409 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1i-1 [1272 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-minimal armhf 3.9.1-1+rpi1 [789 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-1 [73.3 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf python3.9-minimal armhf 3.9.1-1+rpi1 [1625 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.9.1-1 [37.8 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf media-types all 1.1.0 [19.0 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf mailcap all 3.68 [31.6 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.66 [10.9 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf liblzma5 armhf 5.2.5-1.0 [158 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libtinfo6 armhf 6.2+20201114-2 [328 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libncursesw6 armhf 6.2+20201114-2 [105 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.18.3-4 [62.3 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.18.3-4 [108 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.18.3-4 [315 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.18.3-4 [142 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libtirpc-common all 1.3.1-1 [13.4 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libtirpc3 armhf 1.3.1-1 [71.2 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libnsl2 armhf 1.3.0-2 [33.2 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-stdlib armhf 3.9.1-1+rpi1 [1654 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf python3.9 armhf 3.9.1-1+rpi1 [461 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.9.1-1 [21.0 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.9.1-1 [64.1 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libgnutls30 armhf 3.7.0-5 [1275 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.21-3 [170 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf openssl armhf 1.1.1i-1 [813 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates all 20200601 [158 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf rubygems-integration all 1.17.3 [6448 B]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf rake all 13.0.1-4 [84.7 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf ruby-minitest all 5.13.0-1 [57.3 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf ruby-power-assert all 1.1.7-1 [11.4 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf ruby-test-unit all 3.3.5-1 [85.3 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf ruby-xmlrpc all 0.3.0-2 [23.7 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libyaml-0-2 armhf 0.2.2-1 [40.0 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libruby2.7 armhf 2.7.2-3 [3837 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf ruby2.7 armhf 2.7.2-3 [683 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf ruby-rubygems all 3.2.0~rc.2-6 [275 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf ruby armhf 1:2.7+2 [11.7 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf ruby-asciidoctor all 2.0.10-2 [201 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf asciidoctor all 2.0.10-2 [77.7 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-3 [32.4 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.21-3 [509 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3.1 [188 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182-2 [162 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13+20201015-2 [162 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-5 [8288 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.21-3 [1214 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.3.1 [1010 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf mysql-common all 5.8+1.0.6 [7360 B]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf mariadb-common all 1:10.5.8-3 [35.6 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libmariadb3 armhf 1:10.5.8-3 [159 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libssl-dev armhf 1.1.1i-1 [1575 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libmariadb-dev armhf 1:10.5.8-3 [168 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libmariadb-dev-compat armhf 1:10.5.8-3 [34.4 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf default-libmysqlclient-dev armhf 1.0.6 [3816 B]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf icu-devtools armhf 67.1-5 [172 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libsuitesparseconfig5 armhf 1:5.8.1+dfsg-2 [22.6 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libamd2 armhf 1:5.8.1+dfsg-2 [29.3 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-7+b1 [135 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libbamtools-dev armhf 2.5.1+dfsg-7+b1 [179 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-3 [113 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libboost1.74-dev armhf 1.74.0-3 [9532 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libboost-regex1.74.0 armhf 1.74.0-3 [447 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libicu-dev armhf 67.1-5 [9227 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libboost-regex1.74-dev armhf 1.74.0-3 [553 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams1.74.0 armhf 1.74.0-3 [259 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams1.74-dev armhf 1.74.0-3 [269 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams-dev armhf 1.74.0.3 [4316 B]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libboost-serialization1.74.0 armhf 1.74.0-3 [319 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf libboost-serialization1.74-dev armhf 1.74.0-3 [388 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf libboost-serialization-dev armhf 1.74.0.3 [4560 B]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf libbtf1 armhf 1:5.8.1+dfsg-2 [23.2 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-4 [28.0 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf libcamd2 armhf 1:5.8.1+dfsg-2 [29.8 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf libccolamd2 armhf 1:5.8.1+dfsg-2 [30.5 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf libcolamd2 armhf 1:5.8.1+dfsg-2 [27.4 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.2.1-3+rpi1 [231 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf libmetis5 armhf 5.1.0.dfsg-7 [133 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf libcholmod3 armhf 1:5.8.1+dfsg-2 [212 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.42.0-1 [66.7 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.9.0-2 [141 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.74.0-1 [301 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf libcurl4-gnutls-dev armhf 7.74.0-1 [375 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf libcxsparse3 armhf 1:5.8.1+dfsg-2 [51.6 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.7-1 [44.0 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf libdeflate-dev armhf 1.7-1 [40.3 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf libgraphblas3 armhf 1:5.8.1+dfsg-2 [4826 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf libgslcblas0 armhf 2.6+dfsg-2 [79.5 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf libgsl25 armhf 2.6+dfsg-2 [753 kB]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf libgsl-dev armhf 2.6+dfsg-2 [950 kB]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.11-2 [318 kB]
Get:133 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.5-1.0 [219 kB]
Get:134 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.11-2 [4495 kB]
Get:135 http://172.17.0.1/private bullseye-staging/main armhf libklu1 armhf 1:5.8.1+dfsg-2 [51.1 kB]
Get:136 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-3 [2980 kB]
Get:137 http://172.17.0.1/private bullseye-staging/main armhf libldl2 armhf 1:5.8.1+dfsg-2 [23.0 kB]
Get:138 http://172.17.0.1/private bullseye-staging/main armhf libmongoose2 armhf 1:5.8.1+dfsg-2 [43.3 kB]
Get:139 http://172.17.0.1/private bullseye-staging/main armhf libumfpack5 armhf 1:5.8.1+dfsg-2 [127 kB]
Get:140 http://172.17.0.1/private bullseye-staging/main armhf librbio2 armhf 1:5.8.1+dfsg-2 [31.9 kB]
Get:141 http://172.17.0.1/private bullseye-staging/main armhf libspqr2 armhf 1:5.8.1+dfsg-2 [68.7 kB]
Get:142 http://172.17.0.1/private bullseye-staging/main armhf libsliplu1 armhf 1:5.8.1+dfsg-2 [48.1 kB]
Get:143 http://172.17.0.1/private bullseye-staging/main armhf libsuitesparse-dev armhf 1:5.8.1+dfsg-2 [5224 kB]
Get:144 http://172.17.0.1/private bullseye-staging/main armhf liblpsolve55-dev armhf 5.5.2.5-2 [349 kB]
Get:145 http://172.17.0.1/private bullseye-staging/main armhf libmysql++3v5 armhf 3.2.5-2 [146 kB]
Get:146 http://172.17.0.1/private bullseye-staging/main armhf libmysql++-dev armhf 3.2.5-2 [149 kB]
Get:147 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20201114-2 [79.9 kB]
Get:148 http://172.17.0.1/private bullseye-staging/main armhf libncurses-dev armhf 6.2+20201114-2 [288 kB]
Get:149 http://172.17.0.1/private bullseye-staging/main armhf libncurses5-dev armhf 6.2+20201114-2 [936 B]
Get:150 http://172.17.0.1/private bullseye-staging/main armhf libsqlite3-dev armhf 3.34.0-1 [852 kB]
Get:151 http://172.17.0.1/private bullseye-staging/main armhf lzma-dev all 9.22-2.2 [44.8 kB]
Get:152 http://172.17.0.1/private bullseye-staging/main armhf samtools armhf 1.11-1 [502 kB]
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Setting up libubsan1:armhf (10.2.1-3+rpi1) ...
Setting up libboost-serialization1.74.0:armhf (1.74.0-3) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.9.0-2) ...
Setting up libcxsparse3:armhf (1:5.8.1+dfsg-2) ...
Setting up libkrb5-3:armhf (1.18.3-4) ...
Setting up openssl (1.1.1i-1) ...
Setting up libdeflate-dev:armhf (1.7-1) ...
Setting up mailcap (3.68) ...
Setting up libelf1:armhf (0.182-2) ...
Setting up libicu-dev:armhf (67.1-5) ...
Setting up ruby-xmlrpc (0.3.0-2) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.3) ...
Setting up libsuitesparseconfig5:armhf (1:5.8.1+dfsg-2) ...
Setting up libcc1-0:armhf (10.2.1-3+rpi1) ...
Setting up cpp-10 (10.2.1-3+rpi1) ...
Setting up libblas-dev:armhf (3.9.0-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up librbio2:armhf (1:5.8.1+dfsg-2) ...
Setting up libbz2-dev:armhf (1.0.8-4) ...
Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
Setting up libamd2:armhf (1:5.8.1+dfsg-2) ...
Setting up libgraphblas3:armhf (1:5.8.1+dfsg-2) ...
Setting up liblapack3:armhf (3.9.0-3) ...
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 (6.2+20201114-2) ...
Setting up gettext (0.21-3) ...
Setting up libgsl-dev (2.6+dfsg-2) ...
Setting up mime-support (3.66) ...
Setting up libcolamd2:armhf (1:5.8.1+dfsg-2) ...
Setting up libtool (2.4.6-14) ...
Setting up libgcc-10-dev:armhf (10.2.1-3+rpi1) ...
Setting up m4 (1.4.18-4) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libsliplu1:armhf (1:5.8.1+dfsg-2) ...
Setting up ca-certificates (20200601) ...
Updating certificates in /etc/ssl/certs...
126 added, 0 removed; done.
Setting up libcamd2:armhf (1:5.8.1+dfsg-2) ...
Setting up libmongoose2:armhf (1:5.8.1+dfsg-2) ...
Setting up libbamtools-dev:armhf (2.5.1+dfsg-7+b1) ...
Setting up liblapack-dev:armhf (3.9.0-3) ...
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 libgssapi-krb5-2:armhf (1.18.3-4) ...
Setting up gcc-10 (10.2.1-3+rpi1) ...
Setting up lzma-dev (9.22-2.2) ...
Setting up autoconf (2.69-14) ...
Setting up libmariadb-dev (1:10.5.8-3) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13+20201015-2) ...
Setting up groff-base (1.22.4-5) ...
Setting up libklu1:armhf (1:5.8.1+dfsg-2) ...
Setting up libccolamd2:armhf (1:5.8.1+dfsg-2) ...
Setting up libncurses5-dev:armhf (6.2+20201114-2) ...
Setting up libcholmod3:armhf (1:5.8.1+dfsg-2) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libtirpc3:armhf (1.3.1-1) ...
Setting up libmariadb-dev-compat:armhf (1:10.5.8-3) ...
Setting up libspqr2:armhf (1:5.8.1+dfsg-2) ...
Setting up libstdc++-10-dev:armhf (10.2.1-3+rpi1) ...
Setting up libboost1.74-dev:armhf (1.74.0-3) ...
Setting up g++-10 (10.2.1-3+rpi1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libcurl3-gnutls:armhf (7.74.0-1) ...
Setting up rubygems-integration (1.17.3) ...
Setting up libcurl4-gnutls-dev:armhf (7.74.0-1) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libumfpack5:armhf (1:5.8.1+dfsg-2) ...
Setting up libboost-serialization1.74-dev:armhf (1.74.0-3) ...
Setting up libboost-regex1.74-dev:armhf (1.74.0-3) ...
Setting up libnsl2:armhf (1.3.0-2) ...
Setting up libpython3.9-stdlib:armhf (3.9.1-1+rpi1) ...
Setting up libpython3-stdlib:armhf (3.9.1-1) ...
Setting up default-libmysqlclient-dev:armhf (1.0.6) ...
Setting up libhts3:armhf (1.11-2) ...
Setting up libsuitesparse-dev:armhf (1:5.8.1+dfsg-2) ...
Setting up libhts-dev:armhf (1.11-2) ...
Setting up samtools (1.11-1) ...
Setting up libmysql++-dev:armhf (3.2.5-2) ...
Setting up libboost-iostreams1.74-dev:armhf (1.74.0-3) ...
Setting up libboost-serialization-dev:armhf (1.74.0.3) ...
Setting up liblpsolve55-dev (5.5.2.5-2) ...
Setting up python3.9 (3.9.1-1+rpi1) ...
Setting up python3 (3.9.1-1) ...
Setting up libboost-iostreams-dev:armhf (1.74.0.3) ...
Setting up rake (13.0.1-4) ...
Setting up ruby-rubygems (3.2.0~rc.2-6) ...
Setting up libruby2.7:armhf (2.7.2-3) ...
Setting up dh-autoreconf (19) ...
Setting up ruby2.7 (2.7.2-3) ...
Setting up debhelper (13.3.1) ...
Setting up ruby (1:2.7+2) ...
Setting up ruby-asciidoctor (2.0.10-2) ...
Setting up asciidoctor (2.0.10-2) ...
Setting up sbuild-build-depends-augustus-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-5+rpi1) ...
Processing triggers for ca-certificates (20200601) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.35.1-5+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.1-3+rpi1 gcc-10_10.2.1-3+rpi1 libc6-dev_2.31-3+rpi1 libstdc++-10-dev_10.2.1-3+rpi1 libstdc++6_10.2.1-3+rpi1 linux-libc-dev_5.9.6-1+rpi1+b1
Package versions: adduser_3.118 apt_2.1.12 asciidoctor_2.0.10-2 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-3 autotools-dev_20180224.1+nmu1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1-1 binutils_2.35.1-5+rpi1 binutils-arm-linux-gnueabihf_2.35.1-5+rpi1 binutils-common_2.35.1-5+rpi1 bsdextrautils_2.36.1-2 bsdutils_1:2.36.1-2 build-essential_12.8 bzip2_1.0.8-4 ca-certificates_20200601 coreutils_8.32-4 cpp_4:10.2.0-1+rpi1 cpp-10_10.2.1-3+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.74 debhelper_13.3.1 debianutils_4.11.2 default-libmysqlclient-dev_1.0.6 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13+20201015-2 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1.1 fdisk_2.36.1-2 file_1:5.39-3 findutils_4.7.0+git20201010-2 g++_4:10.2.0-1+rpi1 g++-10_10.2.1-3+rpi1 gcc_4:10.2.0-1+rpi1 gcc-10_10.2.1-3+rpi1 gcc-10-base_10.2.1-3+rpi1 gettext_0.21-3 gettext-base_0.21-3 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 icu-devtools_67.1-5 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 libacl1_2.2.53-8 libamd2_1:5.8.1+dfsg-2 libapt-pkg6.0_2.1.12 libarchive-zip-perl_1.68-1 libasan6_10.2.1-3+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-3+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3.1 libaudit1_1:2.8.5-3.1+b1 libbamtools-dev_2.5.1+dfsg-7+b1 libbamtools2.5.1_2.5.1+dfsg-7+b1 libbinutils_2.35.1-5+rpi1 libblas-dev_3.9.0-3 libblas3_3.9.0-3 libblkid1_2.36.1-2 libboost-iostreams-dev_1.74.0.3 libboost-iostreams1.74-dev_1.74.0-3 libboost-iostreams1.74.0_1.74.0-3 libboost-regex1.74-dev_1.74.0-3 libboost-regex1.74.0_1.74.0-3 libboost-serialization-dev_1.74.0.3 libboost-serialization1.74-dev_1.74.0-3 libboost-serialization1.74.0_1.74.0-3 libboost1.74-dev_1.74.0-3 libbrotli1_1.0.9-2+b1 libbtf1_1:5.8.1+dfsg-2 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.31-5+rpi1 libc-dev-bin_2.31-3+rpi1 libc6_2.31-3+rpi1 libc6-dev_2.31-3+rpi1 libcamd2_1:5.8.1+dfsg-2 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_10.2.1-3+rpi1 libccolamd2_1:5.8.1+dfsg-2 libcholmod3_1:5.8.1+dfsg-2 libcolamd2_1:5.8.1+dfsg-2 libcom-err2_1.45.6-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-5+rpi1 libctf0_2.35.1-5+rpi1 libcurl3-gnutls_7.74.0-1 libcurl4-gnutls-dev_7.74.0-1 libcxsparse3_1:5.8.1+dfsg-2 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.255+b1 libdebhelper-perl_13.3.1 libdeflate-dev_1.7-1 libdeflate0_1.7-1 libdpkg-perl_1.20.5+rpi1 libelf1_0.182-2 libexpat1_2.2.10-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1.1 libfdisk1_2.36.1-2 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.1-3+rpi1 libgcc-s1_10.2.1-3+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libgfortran5_10.2.1-3+rpi1 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.0-5 libgomp1_10.2.1-3+rpi1 libgpg-error0_1.38-2 libgraphblas3_1:5.8.1+dfsg-2 libgsl-dev_2.6+dfsg-2 libgsl25_2.6+dfsg-2 libgslcblas0_2.6+dfsg-2 libgssapi-krb5-2_1.18.3-4 libhogweed6_3.6-2 libhts-dev_1.11-2 libhts3_1.11-2 libicu-dev_67.1-5 libicu67_67.1-5 libidn2-0_2.3.0-4 libisl23_0.23-1 libk5crypto3_1.18.3-4 libkeyutils1_1.6.1-2 libklu1_1:5.8.1+dfsg-2 libkrb5-3_1.18.3-4 libkrb5support0_1.18.3-4 libksba8_1.5.0-2 liblapack-dev_3.9.0-3 liblapack3_3.9.0-3 libldap-2.4-2_2.4.56+dfsg-1+rpi1+b1 libldap-common_2.4.56+dfsg-1+rpi1 libldl2_1:5.8.1+dfsg-2 liblpsolve55-dev_5.5.2.5-2 liblz4-1_1.9.2-2 liblzma-dev_5.2.5-1.0 liblzma5_5.2.5-1.0 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmariadb-dev_1:10.5.8-3 libmariadb-dev-compat_1:10.5.8-3 libmariadb3_1:10.5.8-3 libmetis5_5.1.0.dfsg-7 libmongoose2_1:5.8.1+dfsg-2 libmount1_2.36.1-2 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libmysql++-dev_3.2.5-2 libmysql++3v5_3.2.5-2 libncurses-dev_6.2+20201114-2 libncurses5-dev_6.2+20201114-2 libncurses6_6.2+20201114-2 libncursesw6_6.2+20201114-2 libnettle8_3.6-2 libnghttp2-14_1.42.0-1 libnpth0_1.6-3 libnsl2_1.3.0-2 libp11-kit0_0.23.21-2 libpam-cap_1:2.44-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.0-5 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.1 libpython3-stdlib_3.9.1-1 libpython3.9-minimal_3.9.1-1+rpi1 libpython3.9-stdlib_3.9.1-1+rpi1 librbio2_1:5.8.1+dfsg-2 libreadline8_8.1-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libruby2.7_2.7.2-3 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.0-3+rpi1 libselinux1_3.1-2+b1 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.12-3 libsliplu1_1:5.8.1+dfsg-2 libsmartcols1_2.36.1-2 libspqr2_1:5.8.1+dfsg-2 libsqlite3-0_3.34.0-1 libsqlite3-dev_3.34.0-1 libss2_1.45.6-1 libssh2-1_1.9.0-2 libssl-dev_1.1.1i-1 libssl1.1_1.1.1i-1 libstdc++-10-dev_10.2.1-3+rpi1 libstdc++6_10.2.1-3+rpi1 libsub-override-perl_0.09-2 libsuitesparse-dev_1:5.8.1+dfsg-2 libsuitesparseconfig5_1:5.8.1+dfsg-2 libsystemd0_246.6-4+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-14 libubsan1_10.2.1-3+rpi1 libuchardet0_0.0.7-1 libudev1_246.6-4+rpi1 libumfpack5_1:5.8.1+dfsg-2 libunistring2_0.9.10-4 libuuid1_2.36.1-2 libxml2_2.9.10+dfsg-6.3 libyaml-0-2_0.2.2-1 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.9.6-1+rpi1+b1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 lzma-dev_9.22-2.2 m4_1.4.18-4 mailcap_3.68 make_4.3-4 man-db_2.9.3-2 mariadb-common_1:10.5.8-3 mawk_1.3.4.20200120-2 media-types_1.1.0 mime-support_3.66 mount_2.36.1-2 mysql-common_5.8+1.0.6 ncurses-base_6.2+20201114-1 ncurses-bin_6.2+20201114-1 netbase_6.2 openssl_1.1.1i-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.32.0-5 perl-base_5.32.0-5 perl-modules-5.32_5.32.0-6 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 python3_3.9.1-1 python3-minimal_3.9.1-1 python3.9_3.9.1-1+rpi1 python3.9-minimal_3.9.1-1+rpi1 rake_13.0.1-4 raspbian-archive-keyring_20120528.2 readline-common_8.1-1 ruby_1:2.7+2 ruby-asciidoctor_2.0.10-2 ruby-minitest_5.13.0-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.7-1 ruby-rubygems_3.2.0~rc.2-6 ruby-test-unit_3.3.5-1 ruby-xmlrpc_0.3.0-2 ruby2.7_2.7.2-3 rubygems-integration_1.17.3 samtools_1.11-1 sbuild-build-depends-augustus-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-5 tar_1.32+dfsg-1+rpi1 tzdata_2020d-1 util-linux_2.36.1-2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.oFlQJ4Q4/trustedkeys.kbx': General error
gpgv: Signature made Sun Jan 3 15:35:33 2021 UTC
gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./augustus_3.4.0+dfsg2-2.dsc
dpkg-source: info: extracting augustus in /<<BUILDDIR>>/augustus-3.4.0+dfsg2
dpkg-source: info: unpacking augustus_3.4.0+dfsg2.orig.tar.xz
dpkg-source: info: unpacking augustus_3.4.0+dfsg2-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying search_config_path
dpkg-source: info: applying set_installdir
dpkg-source: info: applying interpreter_paths.patch
dpkg-source: info: applying switch_cgp_testing_off.patch
dpkg-source: info: applying disable-compare.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-7ee6bc33-4623-4b79-bbce-e8387ed08ef5
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package augustus
dpkg-buildpackage: info: source version 3.4.0+dfsg2-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
/usr/bin/make -C auxprogs/bam2hints clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2hints'
rm -f bam2hints.o bam2hints ../../bin/bam2hints
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/homGeneMapping clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping'
cd src; make clean
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src'
rm -f homGeneMapping gene.o genome.o sqliteDB.o
rm -f ../../../bin/homGeneMapping
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src'
cd ../..; tests/auxprogs/homGeneMapping/test_homGeneMapping.py --clean
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping'
/usr/bin/make -C auxprogs/joingenes clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/joingenes'
rm -rf *.o joingenes; rm -rf ../../bin/joingenes
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/joingenes'
/usr/bin/make -C auxprogs/aln2wig clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/aln2wig'
rm -f aln2wig aln2wig.o; rm -f ../../bin/aln2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2wig clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2wig'
rm -f bam2wig bam2wig.o bam2wig
rm -f ../../bin/bam2wig
cd ../..; tests/auxprogs/bam2wig/test_bam2wig.py --clean
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/compileSpliceCands clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands'
rm -f compileSpliceCands compileSpliceCands.o ../../bin/compileSpliceCands list.o
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam'
(cd src; make clean;)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src'
rm -f *~ filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o
rm -f filterBam
rm -f ../../../bin/filterBam
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam'
rm -rf bin
rm -f debian/*substvars
rm -f debian/mansrc/*.1
find . -name "__pycache__" | xargs -r rm -r
find src -name "*.o" | xargs -r rm
find auxprogs -name "*.o" | xargs -r rm
rm -f auxprogs/utrrnaseq/Debug/utrrnaseq src/augustus src/etraining src/fastBlockSearch src/getSeq src/load2db src/load2sqlitedb src/pp_simScore src/prepareAlign
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
mkdir -p bin
/usr/bin/make -C auxprogs/aln2wig
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/aln2wig'
cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -ansi -pedantic -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -c aln2wig.c
In file included from /usr/include/string.h:495,
from aln2wig.c:15:
In function 'strncpy',
inlined from 'main' at aln2wig.c:454:6:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncpy',
inlined from 'main' at aln2wig.c:460:6:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncpy',
inlined from 'main' at aln2wig.c:327:6:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncpy',
inlined from 'main' at aln2wig.c:334:6:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -Wall -Wno-sign-compare -ansi -pedantic -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o aln2wig aln2wig.o
mkdir -p ../../bin
cp aln2wig ../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2hints
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2hints'
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c bam2hints.cc -o bam2hints.o -I/usr/include/bamtools
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o bam2hints bam2hints.o -lbamtools -lz
mkdir -p ../../bin
cp bam2hints ../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/bam2wig
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2wig'
cc -Wall -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bam2wig.c -o bam2wig.o -I/usr/include/htslib
bam2wig.c: In function 'main':
bam2wig.c:172:14: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
172 | printf("%ld %d\n", pos+1, coverage);
| ~~^ ~~~~~
| | |
| long int hts_pos_t {aka long long int}
| %lld
cc -Wall -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now bam2wig.o -o bam2wig -lhts -lz -lpthread
mkdir -p ../../bin
cp bam2wig ../../bin/bam2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/compileSpliceCands
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands'
cc -Wall -pedantic -ansi -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compileSpliceCands.c
compileSpliceCands.c: In function 'getChromosome':
compileSpliceCands.c:226:2: warning: this decimal constant is unsigned only in ISO C90
226 | s = malloc(3500000000);
| ^
In file included from /usr/include/string.h:495,
from compileSpliceCands.c:12:
In function 'strncat',
inlined from 'getChromosome' at compileSpliceCands.c:216:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:10: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compileSpliceCands.c: In function 'getChromosome':
compileSpliceCands.c:216:2: note: length computed here
216 | strncat(checkstring,chromosomename,strlen(chromosomename));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compileSpliceCands.c:226:6: warning: argument 1 value '3500000000' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
226 | s = malloc(3500000000);
| ^~~~~~~~~~~~~~~~~~
In file included from compileSpliceCands.c:14:
/usr/include/stdlib.h:539:14: note: in a call to allocation function 'malloc' declared here
539 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
| ^~~~~~
In file included from /usr/include/string.h:495,
from compileSpliceCands.c:12:
In function 'strncpy',
inlined from 'parseLine' at compileSpliceCands.c:292:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compileSpliceCands.c: In function 'parseList':
compileSpliceCands.c:350:36: warning: 'left' may be used uninitialized in this function [-Wmaybe-uninitialized]
350 | findPossibleSpliceSites(left->name,actualChromosome,left->startPos,left->endPos,right->startPos,right->endPos,left->strand,right->strand);
| ~~~~^~~~~~
compileSpliceCands.c: In function 'main':
compileSpliceCands.c:563:3: warning: 'chromosomeLength' may be used uninitialized in this function [-Wmaybe-uninitialized]
563 | parseList(&L,actualChromosome,chromosomeLength,oldname,maxSpliceSiteDiff,threshold,maxIntronLength);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o list.o list.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o compileSpliceCands compileSpliceCands.o list.o
cp compileSpliceCands ../../bin/compileSpliceCands
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src'
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c filterBam.cc -o filterBam.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/MatePairs.cc -o MatePairs.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/getReferenceName.cc -o getReferenceName.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/initOptions.cc -o initOptions.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/SingleAlignment.cc -o SingleAlignment.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/printElapsedTime.cc -o printElapsedTime.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumMandIOperations.cc -o sumMandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumDandIOperations.cc -o sumDandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/PairednessCoverage.cc -o PairednessCoverage.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz
filterBam compiled with BAMTOOLS=/usr/include/bamtools
mkdir -p ../../../bin
mv filterBam ../../../bin/filterBam
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam'
/usr/bin/make -C auxprogs/homGeneMapping/src
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src'
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -o gene.o gene.cc -I../include
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -o genome.o genome.cc -I../include
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -o sqliteDB.o sqliteDB.cc -I../include
g++ -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wl,-z,relro -Wl,-z,now -o homGeneMapping main.cc gene.o genome.o sqliteDB.o -I../include -lsqlite3
mkdir -p ../../../bin/
cp homGeneMapping ../../../bin/homGeneMapping
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src'
/usr/bin/make -C auxprogs/joingenes
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/joingenes'
g++ -c -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 joingenes.cpp
g++ -c -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 jg_transcript.cpp
g++ -c -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 jg_ios.cpp
In file included from /usr/include/string.h:495,
from jg_transcript.h:5,
from jg_ios.cpp:1:
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'void load(std::unordered_map<std::__cxx11::basic_string<char>, Gene*>&, std::string&, int&, std::unordered_map<std::__cxx11::basic_string<char>, bool>&, Properties&)' at jg_ios.cpp:251:14:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'void load(std::unordered_map<std::__cxx11::basic_string<char>, Gene*>&, std::string&, int&, std::unordered_map<std::__cxx11::basic_string<char>, bool>&, Properties&)' at jg_ios.cpp:79:14:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'void load(std::unordered_map<std::__cxx11::basic_string<char>, Gene*>&, std::string&, int&, std::unordered_map<std::__cxx11::basic_string<char>, bool>&, Properties&)' at jg_ios.cpp:148:9:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound 300 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now joingenes.o jg_transcript.o jg_ios.o -o joingenes
mkdir -p ../../bin/
cp joingenes ../../bin/
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/joingenes'
dh_auto_build
make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
mkdir -p bin
cd src && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o genbank.o genbank.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o properties.o properties.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_profile.o pp_profile.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_hitseq.o pp_hitseq.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_scoring.o pp_scoring.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:36,
from ../include/geneticcode.hh:12,
from ../include/pp_profile.hh:16,
from pp_profile.cc:11:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PP::Column&}; _Tp = PP::Column; _Alloc = std::allocator<PP::Column>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<PP::Column>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/types.hh:36,
from ../include/geneticcode.hh:12,
from ../include/pp_profile.hh:16,
from pp_profile.cc:11:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'PP::Block::Block(PP::DistanceType, const std::vector<std::__cxx11::basic_string<char> >&, std::string)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PP::Column*, std::vector<PP::Column> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:36,
from ../include/geneticcode.hh:12,
from ../include/pp_profile.hh:16,
from pp_profile.cc:11:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'bool PP::Block::_ZN2PP5Block14initThresholdsEv.part.0()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/types.hh:36,
from ../include/geneticcode.hh:12,
from ../include/pp_profile.hh:16,
from pp_profile.cc:11:
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:36,
from ../include/geneticcode.hh:12,
from ../include/pp_profile.hh:16,
from pp_profile.cc:11:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {PP::Block}; _Tp = PP::Block; _Alloc = std::allocator<PP::Block>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<PP::Block>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void PP::Profile::parse_stream(std::istream&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PP::Block*, std::vector<PP::Block> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:39,
from ../include/geneticcode.hh:12,
from ../include/pp_profile.hh:16,
from pp_profile.cc:11:
/usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _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++/10/bits/stl_tree.h:2193:5: 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
2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/types.hh:36,
from ../include/geneticcode.hh:12,
from ../include/pp_profile.hh:16,
from pp_profile.cc:11:
/usr/include/c++/10/bits/stl_vector.h: In member function 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map<int, LLDouble>*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/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++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PP::BonusProbEntry&}; _Tp = PP::BonusProbEntry; _Alloc = std::allocator<PP::BonusProbEntry>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<PP::BonusProbEntry>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/10/bits/stl_tree.h:2524:5: 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
2524 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h:2524:5: 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 file included from /usr/include/c++/10/vector:67,
from ../include/types.hh:36,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void PP::MultiTargetExonScorer::initBonusProbs(PP::BonusProbType&, int, int)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PP::BonusProbEntry*, std::vector<PP::BonusProbEntry> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o statemodel.o statemodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/10/bits/stl_tree.h:2193:5: 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
2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h: In member function 'void PP::SubstateModel::scoreAssOrRDss(ViterbiSubmapType&, bool, int, const Double&)':
/usr/include/c++/10/bits/stl_tree.h:1245:14: 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
1245 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/10/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>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o namgene.o namgene.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
/usr/include/c++/10/bits/stl_tree.h: In member function 'void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)':
/usr/include/c++/10/bits/stl_tree.h:2542:19: 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
2542 | _M_erase_aux(__p.first, __p.second);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_tree.h:2542:19: 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
2542 | _M_erase_aux(__p.first, __p.second);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_tree.h:2542:19: 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
2542 | _M_erase_aux(__p.first, __p.second);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_tree.h:2542:19: 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
2542 | _M_erase_aux(__p.first, __p.second);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_tree.h:2542:19: 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
2542 | _M_erase_aux(__p.first, __p.second);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_tree.h: In member function 'virtual void PP::MultiTargetExonScorer::postProcessing(const Double&)':
/usr/include/c++/10/bits/stl_tree.h:1245:14: 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
1245 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_map.h: In member function 'virtual void PP::SingleTargetExonScorer::exportSubstates(ViterbiSubmapType&)':
/usr/include/c++/10/bits/stl_map.h:501:37: 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
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h: In member function 'void PP::MultiTargetExonScorer::updateBonusProbs(PP::Position, const Double&)':
/usr/include/c++/10/bits/stl_map.h:501:37: 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
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_tree.h: In member function 'virtual void PP::MultiTargetExonScorer::scoreInternal(ViterbiColumnType&, int, const Double&)':
/usr/include/c++/10/bits/stl_tree.h:1245:14: 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
1245 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o types.o types.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o gene.o gene.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/10/vector:72,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from statemodel.cc:8:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Ancestor}; _Tp = Ancestor; _Alloc = std::allocator<Ancestor>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Ancestor>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Ancestor>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void StateModel::initPredecessors(Matrix<LLDouble>&, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Ancestor*, std::vector<Ancestor> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:38,
from types.cc:8:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Distance = int; _Tp = LLDouble; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:38,
from types.cc:8:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:36,
from types.cc:8:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o evaluation.o evaluation.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void Constant::init()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:38,
from types.cc:8:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1662 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1937 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'Double quantile(const std::vector<LLDouble>&, float)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from ../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++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
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++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o motif.o motif.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/10/vector:72,
from ../include/matrix.hh:12,
from ../include/motif.hh:12,
from motif.cc:10:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from ../include/matrix.hh:12,
from ../include/motif.hh:12,
from motif.cc:10:
/usr/include/c++/10/bits/stl_vector.h: In member function 'Double Motif::getProbThreshold(double, int)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o geneticcode.o geneticcode.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o hints.o hints.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o extrinsicinfo.o extrinsicinfo.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../include/types.hh:34,
from ../include/hints.hh:12,
from hints.cc:10:
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'std::istream& operator>>(std::istream&, Feature&)' at hints.cc:82:9:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o projectio.o projectio.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o intronmodel.o intronmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o exonmodel.o exonmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/10/vector:72,
from ../include/matrix.hh:12,
from ../include/motif.hh:12,
from ../include/gene.hh:12,
from gene.cc:8:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void examineBaseCountOfGeneSeq(AnnoSequence*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
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++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/list:64,
from ../include/vitmatrix.hh:17,
from ../include/pp_scoring.hh:16,
from ../include/gene.hh:13,
from gene.cc:8:
/usr/include/c++/10/bits/list.tcc: In member function 'std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::insert(std::__cxx11::list<_Tp, _Alloc>::const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::_List_const_iterator<PP::Match>; <template-parameter-2-2> = void; _Tp = PP::Match; _Alloc = std::allocator<PP::Match>]':
/usr/include/c++/10/bits/list.tcc:133:7: note: parameter passing for argument of type 'std::__cxx11::list<PP::Match>::const_iterator' changed in GCC 7.1
133 | list<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/list.tcc:133:7: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
/usr/include/c++/10/bits/list.tcc:133:7: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
/usr/include/c++/10/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++/10/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++/10/bits/list.tcc:308:7: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
/usr/include/c++/10/bits/list.tcc:320:17: note: parameter passing for argument of type 'std::__cxx11::list<PP::Match>::const_iterator' changed in GCC 7.1
320 | insert(__last1, __first2, __last2);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/list.tcc:320:17: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
/usr/include/c++/10/bits/list.tcc: In copy constructor 'Gene::Gene(const Gene&)':
/usr/include/c++/10/bits/list.tcc:286:22: 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());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/list.tcc: In static member function 'static StatePath* StatePath::condenseStatePath(StatePath*)':
/usr/include/c++/10/bits/list.tcc:286:22: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
286 | _M_assign_dispatch(__x.begin(), __x.end(), __false_type());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o igenicmodel.o igenicmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from ../include/statemodel.hh:13,
from ../include/intronmodel.hh:11,
from intronmodel.cc:8:
/usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _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++/10/bits/stl_tree.h:2193:5: 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
2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o utrmodel.o utrmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o merkmal.o merkmal.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o vitmatrix.o vitmatrix.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:39,
from ../include/hints.hh:12,
from ../include/extrinsicinfo.hh:15,
from extrinsicinfo.cc:10:
/usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/10/bits/stl_tree.h:2193:5: 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
2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:38,
from ../include/hints.hh:12,
from ../include/extrinsicinfo.hh:15,
from extrinsicinfo.cc:10:
/usr/include/c++/10/bits/stl_algo.h: In function '_OutputIterator std::__set_difference(_InputIterator1, _InputIterator1, _InputIterator2, _InputIterator2, _OutputIterator, _Compare) [with _InputIterator1 = std::_Rb_tree_const_iterator<Feature>; _InputIterator2 = std::_Rb_tree_const_iterator<Feature>; _OutputIterator = std::insert_iterator<std::set<Feature> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:5370:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5370 | __set_difference(_InputIterator1 __first1, _InputIterator1 __last1,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:5370:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5370:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5370:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In member function 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)':
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5435 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5435 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5435 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5435 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5435 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5435 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5435 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5435 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5435 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5435 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5435 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5435 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5435:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:36,
from ../include/vitmatrix.hh:12,
from vitmatrix.cc:10:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ViterbiSubmapType&}; _Tp = ViterbiSubmapType; _Alloc = std::allocator<ViterbiSubmapType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<ViterbiSubmapType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from vitmatrix.cc:10:
/usr/include/c++/10/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/10/bits/stl_tree.h:2524:5: 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
2524 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h:2524:5: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
/usr/include/c++/10/bits/stl_tree.h: In member function 'void ViterbiSubmapType::useMaximum(Double&)':
/usr/include/c++/10/bits/stl_tree.h:1245:14: 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
1245 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h:1245:14: 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
1245 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h: In member function 'int ViterbiSubmapType::eraseUnneededSubstate(SubstateId)':
/usr/include/c++/10/bits/stl_tree.h:2542:19: 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
2542 | _M_erase_aux(__p.first, __p.second);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:36,
from ../include/vitmatrix.hh:12,
from vitmatrix.cc:10:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {ViterbiEntryType}; _Tp = ViterbiEntryType; _Alloc = std::allocator<ViterbiEntryType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<ViterbiEntryType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void ViterbiColumnType::addState(int, signed char)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ViterbiEntryType*, std::vector<ViterbiEntryType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/types.hh:36,
from ../include/vitmatrix.hh:12,
from vitmatrix.cc:10:
/usr/include/c++/10/bits/stl_vector.h: In member function 'ViterbiSubmapType& ViterbiColumnType::addSubstates(const ViterbiSubmapType&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ViterbiSubmapType*, std::vector<ViterbiSubmapType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from vitmatrix.cc:10:
/usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/10/bits/stl_tree.h:2193:5: 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
2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/10/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++/10/map:61,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:12,
from vitmatrix.cc:10:
/usr/include/c++/10/bits/stl_map.h: In member function 'void ViterbiSubmapType::registerPredecessors()':
/usr/include/c++/10/bits/stl_map.h:501:37: 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
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o lldouble.o lldouble.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:38,
from ../include/merkmal.hh:14,
from merkmal.cc:10:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Distance = int; _Tp = LLDouble; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:38,
from ../include/merkmal.hh:14,
from merkmal.cc:10:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o mea.o mea.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
/usr/include/c++/10/bits/stl_algo.h: In static member function 'static std::vector<double> CRF::capOutliers(std::vector<double>)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o graph.o graph.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:36,
from ../include/merkmal.hh:14,
from merkmal.cc:10:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void Parameters::addMerkmal(Double*, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/types.hh:36,
from ../include/merkmal.hh:14,
from merkmal.cc:10:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:36,
from ../include/merkmal.hh:14,
from merkmal.cc:10:
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void CRF::compareWeights(Parameters*, std::vector<T>&, std::vector<V>&, int) [with U = int; V = double]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void CRF::compareWeights(Parameters*, std::vector<T>&, std::vector<V>&, int) [with U = double; V = double]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/types.hh:36,
from ../include/merkmal.hh:14,
from merkmal.cc:10:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static void CRF::onlineLargeMarginTraining(Parameters*, std::vector<AnnoSequence*>, FeatureCollection&)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/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++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'AugustusGraph::AugustusGraph(std::__cxx11::list<Status>*, const char*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:38,
from ../include/merkmal.hh:14,
from merkmal.cc:10:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1662 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1937 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In member function 'void BinnedMMGroup::trainBins(int)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o meaPath.o meaPath.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o exoncand.o exoncand.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o randseqaccess.o randseqaccess.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o fasta.o fasta.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o ncmodel.o ncmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o parser/parse.o parser/parse.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o scanner/lex.o scanner/lex.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o genomicMSA.o genomicMSA.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o geneMSA.o geneMSA.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/10/vector:72,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from ../include/ncmodel.hh:11,
from ncmodel.cc:8:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from ../include/ncmodel.hh:11,
from ncmodel.cc:8:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void NcModel::computeLengthDistributions()':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o contTimeMC.o contTimeMC.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:38,
from ../include/geneticcode.hh:12,
from contTimeMC.cc:10:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:38,
from ../include/geneticcode.hh:12,
from contTimeMC.cc:10:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/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++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {hints}; _Tp = hints; _Alloc = std::allocator<hints>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<hints>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<hints>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void mysqlpp::Query::storein_sequence(Sequence&, const mysqlpp::SQLTypeAdapter&) [with Sequence = std::vector<hints>]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<hints*, std::vector<hints> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/matrix.hh:12,
from ../include/contTimeMC.hh:13,
from contTimeMC.cc:9:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/matrix.hh:12,
from ../include/contTimeMC.hh:13,
from contTimeMC.cc:9:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void ExonEvo::addBranchLength(double)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/matrix.hh:12,
from ../include/contTimeMC.hh:13,
from contTimeMC.cc:9:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:38,
from ../include/geneticcode.hh:12,
from contTimeMC.cc:10:
/usr/include/c++/10/bits/stl_algo.h: In member function 'void Evo::setBranchLengths(std::vector<double>, int)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/matrix.hh:12,
from ../include/contTimeMC.hh:13,
from contTimeMC.cc:9:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o codonevo.o codonevo.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o compgenepred.o compgenepred.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/10/vector:72,
from ../include/matrix.hh:12,
from ../include/contTimeMC.hh:13,
from ../include/codonevo.hh:11,
from codonevo.cc:9:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/matrix.hh:12,
from ../include/contTimeMC.hh:13,
from ../include/codonevo.hh:11,
from codonevo.cc:9:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void CodonEvo::setPrior(double)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/matrix.hh:12,
from ../include/contTimeMC.hh:13,
from ../include/codonevo.hh:11,
from codonevo.cc:9:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void CodonEvo::setOmegas(int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'double CodonEvo::estOmegaOnSeqTuple(std::vector<std::__cxx11::basic_string<char> >&, PhyloTree*, int&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/matrix.hh:12,
from ../include/contTimeMC.hh:13,
from ../include/codonevo.hh:11,
from codonevo.cc:9:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void CodonEvo::setAAPostProbs()':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:36,
from ../include/geneticcode.hh:12,
from geneMSA.cc:10:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o phylotree.o phylotree.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from ../include/types.hh:36,
from ../include/geneticcode.hh:12,
from geneMSA.cc:10:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void GeneMSA::calcConsScore(std::__cxx11::list<OrthoExon>&, const std::vector<AnnoSequence*>&, std::string)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/phylotree.hh:13,
from phylotree.cc:12:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/phylotree.hh:13,
from phylotree.cc:12:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void Treenode::resizeTable(int, double)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'double PhyloTree::pruningAlgor(std::vector<int>&, Evo*, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'int PhyloTree::fitch(std::vector<int>&, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'double PhyloTree::MAP(std::vector<int>&, std::vector<double>&, Evo*, bool)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/phylotree.hh:13,
from phylotree.cc:12:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void PhyloTree::getBranchLengths(std::vector<double>&) const':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void GeneMSA::computeOmegasEff(std::__cxx11::list<OrthoExon>&, const std::vector<AnnoSequence*>&, PhyloTree*, std::ofstream*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o orthograph.o orthograph.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o orthoexon.o orthoexon.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/10/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++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'AugustusGraph::AugustusGraph(std::__cxx11::list<Status>*, const char*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void CompGenePred::runPredictionOrTest()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:36,
from ../include/exoncand.hh:13,
from ../include/orthoexon.hh:11,
from orthoexon.cc:10:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/types.hh:36,
from ../include/exoncand.hh:13,
from ../include/orthoexon.hh:11,
from orthoexon.cc:10:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void OrthoExon::setOmega(std::vector<double>*, CodonEvo*, bool)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In constructor 'OrthoExon::OrthoExon(int_fast64_t, size_t)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o alignment.o alignment.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o speciesgraph.o speciesgraph.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o codonMSA.o codonMSA.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o train_logReg_param.o train_logReg_param.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o tokenizer.o tokenizer.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o sqliteDB.o sqliteDB.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o commontrain.o commontrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o igenictrain.o igenictrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o introntrain.o introntrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o exontrain.o exontrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o utrtrain.o utrtrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o dummy.o dummy.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/10/vector:72,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from ../include/intronmodel.hh:11,
from introntrain.cc:8:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from ../include/exonmodel.hh:11,
from exontrain.cc:8:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from ../include/intronmodel.hh:11,
from introntrain.cc:8:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void IntronModel::makeDSSProbs()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void IntronModel::buildProbabilities(const AnnoSequence*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from ../include/exonmodel.hh:11,
from exontrain.cc:8:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void ExonModel::buildProbabilities()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1198 | _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 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o pp_simScore pp_simscore.cc fasta.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o load2db load2db.cc fasta.o hints.o types.o properties.o lldouble.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o getSeq getSeq.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
cp prepareAlign ../bin/
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o load2sqlitedb load2sqlitedb.cc fasta.o hints.o types.o properties.o lldouble.o sqliteDB.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
In file included from /usr/include/c++/10/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++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cp load2sqlitedb ../bin/
echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
/usr/include/c++/10/bits/vector.tcc: In member function 'void SS::SimilarityScore::printAlignment()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cp pp_simScore ../bin/
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
cp getSeq ../bin/
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
cp load2db ../bin/
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:36,
from etraining.cc:9:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void CRF::compareWeights(Parameters*, std::vector<T>&, std::vector<V>&, int) [with U = double; V = double]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cp fastBlockSearch ../bin/
cp etraining ../bin/
cp augustus ../bin/
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/src'
cd auxprogs && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs'
cd aln2wig; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/aln2wig'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: 'aln2wig' is up to date.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/aln2wig'
cd bam2hints; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2hints'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: 'bam2hints' is up to date.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2hints'
cd compileSpliceCands; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: 'compileSpliceCands' is up to date.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands'
cd filterBam; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src;make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src'
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz
filterBam compiled with BAMTOOLS=/usr/include/bamtools
mkdir -p ../../../bin
mv filterBam ../../../bin/filterBam
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam'
cd homGeneMapping; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src; make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src'
make[5]: Nothing to be done for 'all'.
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping'
cd joingenes; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/joingenes'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/joingenes'
cd utrrnaseq/Debug; make all;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/utrrnaseq/Debug'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
Building file: ../src/Compute_UTRs.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Compute_UTRs.d" -MT"src/Compute_UTRs.o" -o "src/Compute_UTRs.o" "../src/Compute_UTRs.cpp"
Finished building: ../src/Compute_UTRs.cpp
Building file: ../src/Coord_Transform.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Coord_Transform.d" -MT"src/Coord_Transform.o" -o "src/Coord_Transform.o" "../src/Coord_Transform.cpp"
Finished building: ../src/Coord_Transform.cpp
Building file: ../src/Genomic_Data.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Genomic_Data.d" -MT"src/Genomic_Data.o" -o "src/Genomic_Data.o" "../src/Genomic_Data.cpp"
Finished building: ../src/Genomic_Data.cpp
Building file: ../src/Splice_Sites.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Splice_Sites.d" -MT"src/Splice_Sites.o" -o "src/Splice_Sites.o" "../src/Splice_Sites.cpp"
Finished building: ../src/Splice_Sites.cpp
Building file: ../src/Supporting_Methods.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Supporting_Methods.d" -MT"src/Supporting_Methods.o" -o "src/Supporting_Methods.o" "../src/Supporting_Methods.cpp"
Finished building: ../src/Supporting_Methods.cpp
Building file: ../src/Test.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Test.d" -MT"src/Test.o" -o "src/Test.o" "../src/Test.cpp"
Finished building: ../src/Test.cpp
Building file: ../src/UTRs.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/UTRs.d" -MT"src/UTRs.o" -o "src/UTRs.o" "../src/UTRs.cpp"
../src/UTRs.cpp: In static member function 'static void UTRs::compute_UTRs(const Genomic_Data::Scaff_plus_Gen_Data&, const std::map<unsigned int, double>&)':
../src/UTRs.cpp:387:64: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
387 | vector<double>::iterator jt = min_element(d.begin(), d.end());
| ^
In file included from /usr/include/c++/10/algorithm:62,
from ../src/UTRs.cpp:20:
/usr/include/c++/10/bits/stl_algo.h: In function 'constexpr _FIter std::min_element(_FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >]':
/usr/include/c++/10/bits/stl_algo.h:5653:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
5653 | inline min_element(_ForwardIterator __first, _ForwardIterator __last)
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:5653:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5662:43: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
5662 | return _GLIBCXX_STD_A::__min_element(__first, __last,
| ^
In file included from /usr/include/c++/10/bits/stl_algobase.h:71,
from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from ../src/Genomic_Data.hpp:8,
from ../src/UTRs.cpp:5:
/usr/include/c++/10/bits/predefined_ops.h: In member function 'constexpr bool __gnu_cxx::__ops::_Iter_less_iter::operator()(_Iterator1, _Iterator2) const [with _Iterator1 = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >; _Iterator2 = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >]':
/usr/include/c++/10/bits/predefined_ops.h:42:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
42 | operator()(_Iterator1 __it1, _Iterator2 __it2) const
| ^~~~~~~~
/usr/include/c++/10/bits/predefined_ops.h:42:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from ../src/UTRs.cpp:20:
/usr/include/c++/10/bits/stl_algo.h: In function 'constexpr _ForwardIterator std::__min_element(_ForwardIterator, _ForwardIterator, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:5631:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
5631 | __min_element(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:5631:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5638:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
5638 | if (__comp(__first, __result))
| ~~~~~~^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../src/Genomic_Data.hpp:9,
from ../src/UTRs.cpp:5:
/usr/include/c++/10/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++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:66,
from ../src/Genomic_Data.hpp:9,
from ../src/UTRs.cpp:5:
/usr/include/c++/10/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator<double>]':
/usr/include/c++/10/bits/stl_uninitialized.h:347:2: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
346 | return std::__uninitialized_copy_a
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
347 | (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
348 | _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*; _Tp = double]':
/usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
323 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:325:37: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
325 | { return std::uninitialized_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*]':
/usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
125 | uninitialized_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*]':
/usr/include/c++/10/bits/stl_uninitialized.h:107:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
107 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:107:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:109:27: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
109 | { return std::copy(__first, __last, __result); }
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from ../src/Genomic_Data.hpp:8,
from ../src/UTRs.cpp:5:
/usr/include/c++/10/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator<double*>; _OI = double*]':
/usr/include/c++/10/bits/stl_algobase.h:560:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
560 | copy(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/10/bits/stl_algobase.h:560:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algobase.h:67,
from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from ../src/Genomic_Data.hpp:8,
from ../src/UTRs.cpp:5:
/usr/include/c++/10/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]':
/usr/include/c++/10/bits/stl_iterator.h:2198:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
2198 | __miter_base(move_iterator<_Iterator> __it)
| ^~~~~~~~~~~~
Finished building: ../src/UTRs.cpp
Building file: ../src/main.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/main.d" -MT"src/main.o" -o "src/main.o" "../src/main.cpp"
Finished building: ../src/main.cpp
Building target: utrrnaseq
Invoking: GCC C++ Linker
g++ -o "utrrnaseq" ./src/Compute_UTRs.o ./src/Coord_Transform.o ./src/Genomic_Data.o ./src/Splice_Sites.o ./src/Supporting_Methods.o ./src/Test.o ./src/UTRs.o ./src/main.o
Finished building target: utrrnaseq
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/utrrnaseq/Debug'
cd bam2wig; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2wig'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: 'bam2wig' is up to date.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2wig'
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
asciidoctor -a docdate='' -b manpage --destination-dir=debian/mansrc/ mansrc/*adoc
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_auto_test -a
make -j4 test
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
cd tests/examples && ./testcases.py --html
test_utr_on (__main__.TestAugustus) ... ok
test_hints_MPE (__main__.TestAugustus) ... ok
test_training_new_species (__main__.TestAugustus) ... ok
test_ab_initio_prediction (__main__.TestAugustus) ... ok
test_format_and_error_out (__main__.TestAugustus) ... ok
test_cgp (__main__.TestAugustus) ... ok
test_cgp_sqlite (__main__.TestAugustus) ... ok
test_cgp_sqlite_hints (__main__.TestAugustus) ... ok
----------------------------------------------------------------------
Ran 8 tests in 3356.246s
OK
Removing generated test files...
----------------------------------------------------------------------
Executing small test suite
----------------------------------------------------------------------
Creating SQLite database for cgp test cases...
tests/auxprogs/bam2wig/test_bam2wig.py --html
test_bam2wig (__main__.TestBam2Wig) ... ok
test_bam2wig_region (__main__.TestBam2Wig) ... ok
----------------------------------------------------------------------
Ran 2 tests in 0.113s
OK
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
create-stamp debian/debhelper-build-stamp
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
mkdir -p debian/augustus/usr/bin
install bin/* debian/augustus/usr/bin
install auxprogs/bam2wig/bam2wig \
debian/augustus/usr/bin
install auxprogs/compileSpliceCands/compileSpliceCands \
debian/augustus/usr/bin
install auxprogs/homGeneMapping/src/homGeneMapping \
debian/augustus/usr/bin
install auxprogs/joingenes/joingenes \
debian/augustus/usr/bin
mkdir -p debian/augustus/usr/share/augustus
cp -r scripts debian/augustus/usr/share/augustus
chmod -R -x debian/augustus/usr/share/augustus/scripts/*
rm -rf debian/augustus/usr/share/augustus/scripts/*.patch \
debian/augustus/usr/share/augustus/scripts/executeTestCGP.py \
debian/augustus/usr/share/augustus/scripts/*.txt
chmod +x debian/augustus/usr/share/augustus/scripts/checkUTR \
debian/augustus/usr/share/augustus/scripts/*.pl*
mkdir -p debian/augustus-doc/usr/share/doc/augustus
cp README* debian/augustus-doc/usr/share/doc/augustus
cp docs/*.txt debian/augustus-doc/usr/share/doc/augustus
cp docs/RUNNING* debian/augustus-doc/usr/share/doc/augustus
cp docs/README* debian/augustus-doc/usr/share/doc/augustus
cp docs/EXONCAND-MSAS-CGP.md \
debian/augustus-doc/usr/share/doc/augustus
cp -r docs/tutorial \
debian/augustus-doc/usr/share/doc/augustus
cp -r docs/tutorial-cgp \
debian/augustus-doc/usr/share/doc/augustus
mkdir -p debian/augustus-data/usr/share/augustus
cp -r config debian/augustus-data/usr/share/augustus
find debian/augustus-data/usr/share/augustus \
-type f -exec chmod -x {} \;
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_installchangelogs -k docs/HISTORY.TXT
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
debian/rules override_dh_compress
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_compress -Xtutorial
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_fixperms -a
dh_missing -a
dh_dwz -a -a
dh_strip -a -a
dh_makeshlibs -a -a
dh_shlibdeps -a -a
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/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/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/filterBam contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/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/augustus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/bam2hints contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/prepareAlign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/joingenes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/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: package could avoid a useless dependency if debian/augustus/usr/bin/etraining debian/augustus/usr/bin/aln2wig debian/augustus/usr/bin/load2db debian/augustus/usr/bin/getSeq debian/augustus/usr/bin/filterBam debian/augustus/usr/bin/compileSpliceCands debian/augustus/usr/bin/homGeneMapping debian/augustus/usr/bin/pp_simScore debian/augustus/usr/bin/augustus debian/augustus/usr/bin/bam2hints debian/augustus/usr/bin/prepareAlign debian/augustus/usr/bin/joingenes debian/augustus/usr/bin/bam2wig debian/augustus/usr/bin/fastBlockSearch debian/augustus/usr/bin/load2sqlitedb were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.4.0+dfsg2-2_armhf.deb'.
dpkg-deb: building package 'augustus' in '../augustus_3.4.0+dfsg2-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../augustus_3.4.0+dfsg2-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-01-11T06:53:12Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
augustus_3.4.0+dfsg2-2_armhf.changes:
-------------------------------------
Format: 1.8
Date: Sun, 03 Jan 2021 16:10:48 +0100
Source: augustus
Binary: augustus augustus-dbgsym
Architecture: armhf
Version: 3.4.0+dfsg2-2
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
augustus - gene prediction in eukaryotic genomes
Changes:
augustus (3.4.0+dfsg2-2) unstable; urgency=medium
.
* Fix dversionmangle to allow for +dfsgX suffixes.
* Run tests without --compare. This hopefully fixes FTBFS due to different
results on different platforms, not matching the reference.
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+------------------------------------------------------------------------------+
| Package contents |
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augustus-dbgsym_3.4.0+dfsg2-2_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 34485792 bytes: control archive=1292 bytes.
962 bytes, 12 lines control
1678 bytes, 16 lines md5sums
Package: augustus-dbgsym
Source: augustus
Version: 3.4.0+dfsg2-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 35403
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Section: debug
Priority: optional
Description: debug symbols for augustus
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drwxr-xr-x root/root 0 2021-01-03 15:10 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-01-03 15:10 ./usr/share/doc/augustus-dbgsym -> augustus
augustus_3.4.0+dfsg2-2_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 1446520 bytes: control archive=4952 bytes.
1522 bytes, 23 lines control
10306 bytes, 138 lines md5sums
Package: augustus
Version: 3.4.0+dfsg2-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8269
Depends: libbamtools2.5.1 (>= 2.5.1+dfsg), libboost-iostreams1.74.0 (>= 1.74.0), libc6 (>= 2.29), libcolamd2 (>= 1:4.5.2), libgcc-s1 (>= 3.5), libgsl25 (>= 2.6), libhts3 (>= 1.10), libmariadb3 (>= 3.0.0), libmysql++3v5 (>= 3.2.5-1~), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 6), augustus-data
Recommends: samtools
Suggests: cdbfasta, diamond-aligner, libfile-which-perl, libparallel-forkmanager-perl, libyaml-perl, libdbd-mysql-perl, python3-biopython
Section: science
Priority: optional
Homepage: https://bioinf.uni-greifswald.de/augustus/
Description: gene prediction in eukaryotic genomes
AUGUSTUS is a software for gene prediction in eukaryotic genomic sequences
that is based on a generalized hidden Markov model (HMM), a probabilistic
model of a sequence and its gene structure. After learning gene structures
from a reference annotation, AUGUSTUS uses the HMM to recognize genes in a new
sequence and annotates it with the regions of identified genes. External hints,
e.g. from RNA sequencing, EST or protein alignments etc. can be used to guide
and improve the gene finding process. The result is the set of most likely gene
structures that comply with all given user constraints, if such gene
structures exist.
AUGUSTUS already includes prebuilt HMMs for many species, as well as scripts
to train custom models using annotated genomes.
drwxr-xr-x root/root 0 2021-01-03 15:10 ./
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drwxr-xr-x root/root 0 2021-01-03 15:10 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-01-03 15:10 ./usr/share/doc/augustus/
lrwxrwxrwx root/root 0 2021-01-03 15:10 ./usr/share/doc/augustus/HISTORY.TXT.gz -> changelog.gz
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-rw-r--r-- root/root 3366 2020-12-28 21:22 ./usr/share/doc/augustus/copyright
drwxr-xr-x root/root 0 2021-01-03 15:10 ./usr/share/man/
drwxr-xr-x root/root 0 2021-01-03 15:10 ./usr/share/man/man1/
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-rw-r--r-- root/root 2287 2021-01-03 15:10 ./usr/share/man/man1/pp_simScore.1.gz
-rw-r--r-- root/root 672 2021-01-03 15:10 ./usr/share/man/man1/prepareAlign.1.gz
+------------------------------------------------------------------------------+
| Post Build |
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+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 1538136
Build-Time: 3899
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 643
Job: augustus_3.4.0+dfsg2-2
Machine Architecture: armhf
Package: augustus
Package-Time: 4616
Source-Version: 3.4.0+dfsg2-2
Space: 1538136
Status: successful
Version: 3.4.0+dfsg2-2
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Finished at 2021-01-11T06:53:12Z
Build needed 01:16:56, 1538136k disk space