augustus →
3.4.0+dfsg2-3 →
armhf → 2021-10-01 04:37:32
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| augustus 3.4.0+dfsg2-3 (armhf) Fri, 01 Oct 2021 02:57:56 +0000 |
+==============================================================================+
Package: augustus
Version: 3.4.0+dfsg2-3
Source Version: 3.4.0+dfsg2-3
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-e22f7f3f-3769-4e9d-81a3-954ef3a32dc0' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.8 MB in 25s (1016 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 bookworm-staging/main augustus 3.4.0+dfsg2-3 (dsc) [2355 B]
Get:2 http://172.17.0.1/private bookworm-staging/main augustus 3.4.0+dfsg2-3 (tar) [148 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main augustus 3.4.0+dfsg2-3 (diff) [19.2 kB]
Fetched 148 MB in 14s (10.2 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/augustus-p9hpZ2/augustus-3.4.0+dfsg2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/augustus-p9hpZ2' 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-GrRE5n/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-GrRE5n/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-GrRE5n/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-GrRE5n/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-GrRE5n/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-GrRE5n/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-GrRE5n/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-GrRE5n/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2791 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 22 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-GrRE5n/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (22.4 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12484 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-GrRE5n/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-GrRE5n/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-GrRE5n/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-GrRE5n/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-GrRE5n/apt_archive ./ Sources [600 B]
Get:5 copy:/<<BUILDDIR>>/resolver-GrRE5n/apt_archive ./ Packages [683 B]
Fetched 2616 B in 1s (3515 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdextrautils
ca-certificates debhelper default-libmysqlclient-dev dh-autoreconf
dh-strip-nondeterminism dwz file gcc-11-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 libbsd0 libbtf1 libbz2-dev libcamd2 libcc1-0 libccolamd2
libcholmod3 libcolamd2 libcurl3-gnutls libcurl4-gnutls-dev libcxsparse3
libdebhelper-perl libdeflate-dev libdeflate0 libedit2 libelf1 libexpat1
libffi8 libfile-stripnondeterminism-perl libgcc-s1 libgfortran5 libgomp1
libgraphblas5 libgsl-dev libgsl25 libgslcblas0 libhts-dev libhts3
libhtscodecs2 libicu-dev libicu67 libklu1 liblapack-dev liblapack3 libldl2
liblpsolve55-dev liblzma-dev libmagic-mgc libmagic1 libmariadb-dev
libmariadb-dev-compat libmariadb3 libmd0 libmetis5 libmongoose2 libmpdec3
libmysql++-dev libmysql++3v5 libncurses-dev libncurses5-dev libncurses6
libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.9-minimal
libpython3.9-stdlib librbio2 librtmp1 libruby2.7 libsigsegv2 libsliplu1
libspqr2 libsqlite3-dev libssh2-1 libssl-dev libstdc++6 libsub-override-perl
libsuitesparse-dev libsuitesparseconfig5 libtool libubsan1 libuchardet0
libumfpack5 libxml2 libyaml-0-2 lzma-dev m4 man-db mariadb-common
media-types mysql-common openssl po-debconf python3 python3-minimal
python3.9 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 sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libbamtools-doc liblapack-doc
libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev
libboost-container1.74-dev libboost-context1.74-dev
libboost-contract1.74-dev libboost-coroutine1.74-dev
libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-locale1.74-dev libboost-log1.74-dev
libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev
libboost-numpy1.74-dev libboost-program-options1.74-dev
libboost-python1.74-dev libboost-random1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev
librtmp-dev libssh2-1-dev pkg-config gsl-ref-psdoc | gsl-doc-pdf
| gsl-doc-info | gsl-ref-html icu-doc liblzma-doc libmysql++-doc ncurses-doc
sqlite3-doc libssl-doc 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 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 bsdextrautils
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 libbsd0 libbtf1 libbz2-dev libcamd2 libccolamd2 libcholmod3
libcolamd2 libcurl3-gnutls libcurl4-gnutls-dev libcxsparse3
libdebhelper-perl libdeflate-dev libdeflate0 libedit2 libelf1 libexpat1
libffi8 libfile-stripnondeterminism-perl libgfortran5 libgraphblas5
libgsl-dev libgsl25 libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu-dev
libicu67 libklu1 liblapack-dev liblapack3 libldl2 liblpsolve55-dev
liblzma-dev libmagic-mgc libmagic1 libmariadb-dev libmariadb-dev-compat
libmariadb3 libmd0 libmetis5 libmongoose2 libmpdec3 libmysql++-dev
libmysql++3v5 libncurses-dev libncurses5-dev libncurses6 libnghttp2-14
libpipeline1 libpsl5 libpython3-stdlib libpython3.9-minimal
libpython3.9-stdlib librbio2 librtmp1 libruby2.7 libsigsegv2 libsliplu1
libspqr2 libsqlite3-dev libssh2-1 libssl-dev libsub-override-perl
libsuitesparse-dev libsuitesparseconfig5 libtool libuchardet0 libumfpack5
libxml2 libyaml-0-2 lzma-dev m4 man-db mariadb-common media-types
mysql-common openssl po-debconf python3 python3-minimal python3.9
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
sensible-utils zlib1g-dev
The following packages will be upgraded:
gcc-11-base libasan6 libatomic1 libcc1-0 libgcc-s1 libgomp1 libstdc++6
libubsan1
8 upgraded, 132 newly installed, 0 to remove and 14 not upgraded.
Need to get 89.7 MB of archives.
After this operation, 692 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-GrRE5n/apt_archive ./ sbuild-build-depends-augustus-dummy 0.invalid.0 [968 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-1 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libasan6 armhf 11.2.0-7+rpi1 [1944 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf libubsan1 armhf 11.2.0-7+rpi1 [797 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libgomp1 armhf 11.2.0-7+rpi1 [88.1 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf gcc-11-base armhf 11.2.0-7+rpi1 [205 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf libgcc-s1 armhf 11.2.0-7+rpi1 [36.2 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libcc1-0 armhf 11.2.0-7+rpi1 [37.7 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libatomic1 armhf 11.2.0-7+rpi1 [8188 B]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf libstdc++6 armhf 11.2.0-7+rpi1 [465 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-minimal armhf 3.9.7-4+rpi1 [794 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.1-2 [80.3 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf python3.9-minimal armhf 3.9.7-4+rpi1 [1632 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf media-types all 4.0.0 [30.3 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf libffi8 armhf 3.4.2-2 [21.2 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-stdlib armhf 3.9.7-4+rpi1 [1618 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf python3.9 armhf 3.9.7-4+rpi1 [480 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf python3 armhf 3.9.2-3 [37.9 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf openssl armhf 1.1.1l-1 [815 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf ca-certificates all 20210119 [158 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf rubygems-integration all 1.18 [6704 B]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf rake all 13.0.3-1 [84.7 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf ruby-minitest all 5.13.0-1 [57.3 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf ruby-power-assert all 1.1.7-2 [11.5 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf ruby-test-unit all 3.3.9-1 [86.1 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf ruby-xmlrpc all 0.3.0-2 [23.7 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf libmd0 armhf 1.0.3-3 [27.2 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.3-1 [103 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20210910-1 [81.2 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libyaml-0-2 armhf 0.2.2-1 [40.0 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf libruby2.7 armhf 2.7.4-1+b1 [3902 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf ruby2.7 armhf 2.7.4-1+b1 [747 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf ruby-rubygems all 3.2.27-1 [272 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf ruby armhf 1:2.7+2 [11.7 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf ruby-asciidoctor all 2.0.16-1 [210 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf asciidoctor all 2.0.16-1 [87.5 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.4-2 [819 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:60 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:61 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:62 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:63 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:64 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:65 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:66 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:67 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:68 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:69 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:70 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:71 http://172.17.0.1/private bookworm-staging/main armhf mysql-common all 5.8+1.0.7 [7464 B]
Get:72 http://172.17.0.1/private bookworm-staging/main armhf mariadb-common all 1:10.5.12-1 [36.3 kB]
Get:73 http://172.17.0.1/private bookworm-staging/main armhf libmariadb3 armhf 1:10.5.12-1 [160 kB]
Get:74 http://172.17.0.1/private bookworm-staging/main armhf libssl-dev armhf 1.1.1l-1 [1581 kB]
Get:75 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:76 http://172.17.0.1/private bookworm-staging/main armhf libmariadb-dev armhf 1:10.5.12-1 [169 kB]
Get:77 http://172.17.0.1/private bookworm-staging/main armhf libmariadb-dev-compat armhf 1:10.5.12-1 [35.1 kB]
Get:78 http://172.17.0.1/private bookworm-staging/main armhf default-libmysqlclient-dev armhf 1.0.7 [3936 B]
Get:79 http://172.17.0.1/private bookworm-staging/main armhf icu-devtools armhf 67.1-7 [172 kB]
Get:80 http://172.17.0.1/private bookworm-staging/main armhf libsuitesparseconfig5 armhf 1:5.10.1+dfsg-2 [23.2 kB]
Get:81 http://172.17.0.1/private bookworm-staging/main armhf libamd2 armhf 1:5.10.1+dfsg-2 [29.7 kB]
Get:82 http://172.17.0.1/private bookworm-staging/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-9 [135 kB]
Get:83 http://172.17.0.1/private bookworm-staging/main armhf libbamtools-dev armhf 2.5.1+dfsg-9 [179 kB]
Get:84 http://172.17.0.1/private bookworm-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
Get:85 http://172.17.0.1/private bookworm-staging/main armhf libblas-dev armhf 3.9.0-3 [113 kB]
Get:86 http://172.17.0.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-9 [9534 kB]
Get:87 http://172.17.0.1/private bookworm-staging/main armhf libboost-regex1.74.0 armhf 1.74.0-9 [448 kB]
Get:88 http://172.17.0.1/private bookworm-staging/main armhf libicu-dev armhf 67.1-7 [9228 kB]
Get:89 http://172.17.0.1/private bookworm-staging/main armhf libboost-regex1.74-dev armhf 1.74.0-9 [553 kB]
Get:90 http://172.17.0.1/private bookworm-staging/main armhf libboost-iostreams1.74.0 armhf 1.74.0-9 [260 kB]
Get:91 http://172.17.0.1/private bookworm-staging/main armhf libboost-iostreams1.74-dev armhf 1.74.0-9 [269 kB]
Get:92 http://172.17.0.1/private bookworm-staging/main armhf libboost-iostreams-dev armhf 1.74.0.3+b1 [4588 B]
Get:93 http://172.17.0.1/private bookworm-staging/main armhf libboost-serialization1.74.0 armhf 1.74.0-9 [319 kB]
Get:94 http://172.17.0.1/private bookworm-staging/main armhf libboost-serialization1.74-dev armhf 1.74.0-9 [388 kB]
Get:95 http://172.17.0.1/private bookworm-staging/main armhf libboost-serialization-dev armhf 1.74.0.3+b1 [4832 B]
Get:96 http://172.17.0.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:97 http://172.17.0.1/private bookworm-staging/main armhf libbtf1 armhf 1:5.10.1+dfsg-2 [23.6 kB]
Get:98 http://172.17.0.1/private bookworm-staging/main armhf libbz2-dev armhf 1.0.8-4 [28.0 kB]
Get:99 http://172.17.0.1/private bookworm-staging/main armhf libcamd2 armhf 1:5.10.1+dfsg-2 [30.3 kB]
Get:100 http://172.17.0.1/private bookworm-staging/main armhf libccolamd2 armhf 1:5.10.1+dfsg-2 [31.3 kB]
Get:101 http://172.17.0.1/private bookworm-staging/main armhf libcolamd2 armhf 1:5.10.1+dfsg-2 [27.9 kB]
Get:102 http://172.17.0.1/private bookworm-staging/main armhf libgfortran5 armhf 11.2.0-7+rpi1 [235 kB]
Get:103 http://172.17.0.1/private bookworm-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:104 http://172.17.0.1/private bookworm-staging/main armhf libmetis5 armhf 5.1.0.dfsg-7 [133 kB]
Get:105 http://172.17.0.1/private bookworm-staging/main armhf libcholmod3 armhf 1:5.10.1+dfsg-2 [212 kB]
Get:106 http://172.17.0.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:107 http://172.17.0.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:108 http://172.17.0.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:109 http://172.17.0.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-2 [161 kB]
Get:110 http://172.17.0.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.74.0-1.3 [301 kB]
Get:111 http://172.17.0.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3 [375 kB]
Get:112 http://172.17.0.1/private bookworm-staging/main armhf libcxsparse3 armhf 1:5.10.1+dfsg-2 [51.8 kB]
Get:113 http://172.17.0.1/private bookworm-staging/main armhf libdeflate0 armhf 1.7-2 [44.1 kB]
Get:114 http://172.17.0.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.7-2 [40.5 kB]
Get:115 http://172.17.0.1/private bookworm-staging/main armhf libgraphblas5 armhf 1:5.10.1+dfsg-2 [8852 kB]
Get:116 http://172.17.0.1/private bookworm-staging/main armhf libgslcblas0 armhf 2.6+dfsg-2 [79.5 kB]
Get:117 http://172.17.0.1/private bookworm-staging/main armhf libgsl25 armhf 2.6+dfsg-2 [753 kB]
Get:118 http://172.17.0.1/private bookworm-staging/main armhf libgsl-dev armhf 2.6+dfsg-2 [950 kB]
Get:119 http://172.17.0.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.1.1-3 [49.8 kB]
Get:120 http://172.17.0.1/private bookworm-staging/main armhf libhts3 armhf 1.13+ds-2 [339 kB]
Get:121 http://172.17.0.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2 [219 kB]
Get:122 http://172.17.0.1/private bookworm-staging/main armhf libhts-dev armhf 1.13+ds-2 [4049 kB]
Get:123 http://172.17.0.1/private bookworm-staging/main armhf libklu1 armhf 1:5.10.1+dfsg-2 [51.5 kB]
Get:124 http://172.17.0.1/private bookworm-staging/main armhf liblapack-dev armhf 3.9.0-3 [2980 kB]
Get:125 http://172.17.0.1/private bookworm-staging/main armhf libldl2 armhf 1:5.10.1+dfsg-2 [23.4 kB]
Get:126 http://172.17.0.1/private bookworm-staging/main armhf libmongoose2 armhf 1:5.10.1+dfsg-2 [43.5 kB]
Get:127 http://172.17.0.1/private bookworm-staging/main armhf libumfpack5 armhf 1:5.10.1+dfsg-2 [129 kB]
Get:128 http://172.17.0.1/private bookworm-staging/main armhf librbio2 armhf 1:5.10.1+dfsg-2 [32.3 kB]
Get:129 http://172.17.0.1/private bookworm-staging/main armhf libspqr2 armhf 1:5.10.1+dfsg-2 [67.9 kB]
Get:130 http://172.17.0.1/private bookworm-staging/main armhf libsliplu1 armhf 1:5.10.1+dfsg-2 [49.0 kB]
Get:131 http://172.17.0.1/private bookworm-staging/main armhf libsuitesparse-dev armhf 1:5.10.1+dfsg-2 [8229 kB]
Get:132 http://172.17.0.1/private bookworm-staging/main armhf liblpsolve55-dev armhf 5.5.2.5-2 [349 kB]
Get:133 http://172.17.0.1/private bookworm-staging/main armhf libmysql++3v5 armhf 3.2.5-2 [146 kB]
Get:134 http://172.17.0.1/private bookworm-staging/main armhf libmysql++-dev armhf 3.2.5-2 [149 kB]
Get:135 http://172.17.0.1/private bookworm-staging/main armhf libncurses6 armhf 6.2+20201114-4 [79.7 kB]
Get:136 http://172.17.0.1/private bookworm-staging/main armhf libncurses-dev armhf 6.2+20201114-4 [288 kB]
Get:137 http://172.17.0.1/private bookworm-staging/main armhf libncurses5-dev armhf 6.2+20201114-4 [940 B]
Get:138 http://172.17.0.1/private bookworm-staging/main armhf libsqlite3-dev armhf 3.36.0-2 [873 kB]
Get:139 http://172.17.0.1/private bookworm-staging/main armhf lzma-dev all 9.22-2.2 [44.8 kB]
Get:140 http://172.17.0.1/private bookworm-staging/main armhf samtools armhf 1.13-2 [525 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 89.7 MB in 9s (10.3 MB/s)
Selecting previously unselected package bsdextrautils.
(Reading database ... 12484 files and directories currently installed.)
Preparing to unpack .../bsdextrautils_2.37.2-1_armhf.deb ...
Unpacking bsdextrautils (2.37.2-1) ...
Preparing to unpack .../libasan6_11.2.0-7+rpi1_armhf.deb ...
Unpacking libasan6:armhf (11.2.0-7+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libubsan1_11.2.0-7+rpi1_armhf.deb ...
Unpacking libubsan1:armhf (11.2.0-7+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libgomp1_11.2.0-7+rpi1_armhf.deb ...
Unpacking libgomp1:armhf (11.2.0-7+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../gcc-11-base_11.2.0-7+rpi1_armhf.deb ...
Unpacking gcc-11-base:armhf (11.2.0-7+rpi1) over (11.2.0-4+rpi1) ...
Setting up gcc-11-base:armhf (11.2.0-7+rpi1) ...
(Reading database ... 12515 files and directories currently installed.)
Preparing to unpack .../libgcc-s1_11.2.0-7+rpi1_armhf.deb ...
Unpacking libgcc-s1:armhf (11.2.0-7+rpi1) over (11.2.0-4+rpi1) ...
Setting up libgcc-s1:armhf (11.2.0-7+rpi1) ...
(Reading database ... 12515 files and directories currently installed.)
Preparing to unpack .../libcc1-0_11.2.0-7+rpi1_armhf.deb ...
Unpacking libcc1-0:armhf (11.2.0-7+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libatomic1_11.2.0-7+rpi1_armhf.deb ...
Unpacking libatomic1:armhf (11.2.0-7+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libstdc++6_11.2.0-7+rpi1_armhf.deb ...
Unpacking libstdc++6:armhf (11.2.0-7+rpi1) over (11.2.0-4+rpi1) ...
Setting up libstdc++6:armhf (11.2.0-7+rpi1) ...
Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 12515 files and directories currently installed.)
Preparing to unpack .../0-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../1-groff-base_1.22.4-7_armhf.deb ...
Unpacking groff-base (1.22.4-7) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../2-libpipeline1_1.5.3-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.3-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../3-man-db_2.9.4-2_armhf.deb ...
Unpacking man-db (2.9.4-2) ...
Selecting previously unselected package libpython3.9-minimal:armhf.
Preparing to unpack .../4-libpython3.9-minimal_3.9.7-4+rpi1_armhf.deb ...
Unpacking libpython3.9-minimal:armhf (3.9.7-4+rpi1) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../5-libexpat1_2.4.1-2_armhf.deb ...
Unpacking libexpat1:armhf (2.4.1-2) ...
Selecting previously unselected package python3.9-minimal.
Preparing to unpack .../6-python3.9-minimal_3.9.7-4+rpi1_armhf.deb ...
Unpacking python3.9-minimal (3.9.7-4+rpi1) ...
Setting up libpython3.9-minimal:armhf (3.9.7-4+rpi1) ...
Setting up libexpat1:armhf (2.4.1-2) ...
Setting up python3.9-minimal (3.9.7-4+rpi1) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 13351 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.9.2-3_armhf.deb ...
Unpacking python3-minimal (3.9.2-3) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_4.0.0_all.deb ...
Unpacking media-types (4.0.0) ...
Selecting previously unselected package libffi8:armhf.
Preparing to unpack .../2-libffi8_3.4.2-2_armhf.deb ...
Unpacking libffi8:armhf (3.4.2-2) ...
Selecting previously unselected package libmpdec3:armhf.
Preparing to unpack .../3-libmpdec3_2.5.1-2+rpi1_armhf.deb ...
Unpacking libmpdec3:armhf (2.5.1-2+rpi1) ...
Selecting previously unselected package libpython3.9-stdlib:armhf.
Preparing to unpack .../4-libpython3.9-stdlib_3.9.7-4+rpi1_armhf.deb ...
Unpacking libpython3.9-stdlib:armhf (3.9.7-4+rpi1) ...
Selecting previously unselected package python3.9.
Preparing to unpack .../5-python3.9_3.9.7-4+rpi1_armhf.deb ...
Unpacking python3.9 (3.9.7-4+rpi1) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../6-libpython3-stdlib_3.9.2-3_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.9.2-3) ...
Setting up python3-minimal (3.9.2-3) ...
Selecting previously unselected package python3.
(Reading database ... 13754 files and directories currently installed.)
Preparing to unpack .../000-python3_3.9.2-3_armhf.deb ...
Unpacking python3 (3.9.2-3) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../001-sensible-utils_0.0.17_all.deb ...
Unpacking sensible-utils (0.0.17) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../002-libmagic-mgc_1%3a5.39-3_armhf.deb ...
Unpacking libmagic-mgc (1:5.39-3) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../003-libmagic1_1%3a5.39-3_armhf.deb ...
Unpacking libmagic1:armhf (1:5.39-3) ...
Selecting previously unselected package file.
Preparing to unpack .../004-file_1%3a5.39-3_armhf.deb ...
Unpacking file (1:5.39-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../005-gettext-base_0.21-4_armhf.deb ...
Unpacking gettext-base (0.21-4) ...
Selecting previously unselected package openssl.
Preparing to unpack .../006-openssl_1.1.1l-1_armhf.deb ...
Unpacking openssl (1.1.1l-1) ...
Selecting previously unselected package ca-certificates.
Preparing to unpack .../007-ca-certificates_20210119_all.deb ...
Unpacking ca-certificates (20210119) ...
Selecting previously unselected package rubygems-integration.
Preparing to unpack .../008-rubygems-integration_1.18_all.deb ...
Unpacking rubygems-integration (1.18) ...
Selecting previously unselected package rake.
Preparing to unpack .../009-rake_13.0.3-1_all.deb ...
Unpacking rake (13.0.3-1) ...
Selecting previously unselected package ruby-minitest.
Preparing to unpack .../010-ruby-minitest_5.13.0-1_all.deb ...
Unpacking ruby-minitest (5.13.0-1) ...
Selecting previously unselected package ruby-net-telnet.
Preparing to unpack .../011-ruby-net-telnet_0.1.1-2_all.deb ...
Unpacking ruby-net-telnet (0.1.1-2) ...
Selecting previously unselected package ruby-power-assert.
Preparing to unpack .../012-ruby-power-assert_1.1.7-2_all.deb ...
Unpacking ruby-power-assert (1.1.7-2) ...
Selecting previously unselected package ruby-test-unit.
Preparing to unpack .../013-ruby-test-unit_3.3.9-1_all.deb ...
Unpacking ruby-test-unit (3.3.9-1) ...
Selecting previously unselected package ruby-xmlrpc.
Preparing to unpack .../014-ruby-xmlrpc_0.3.0-2_all.deb ...
Unpacking ruby-xmlrpc (0.3.0-2) ...
Selecting previously unselected package libmd0:armhf.
Preparing to unpack .../015-libmd0_1.0.3-3_armhf.deb ...
Unpacking libmd0:armhf (1.0.3-3) ...
Selecting previously unselected package libbsd0:armhf.
Preparing to unpack .../016-libbsd0_0.11.3-1_armhf.deb ...
Unpacking libbsd0:armhf (0.11.3-1) ...
Selecting previously unselected package libedit2:armhf.
Preparing to unpack .../017-libedit2_3.1-20210910-1_armhf.deb ...
Unpacking libedit2:armhf (3.1-20210910-1) ...
Selecting previously unselected package libyaml-0-2:armhf.
Preparing to unpack .../018-libyaml-0-2_0.2.2-1_armhf.deb ...
Unpacking libyaml-0-2:armhf (0.2.2-1) ...
Selecting previously unselected package libruby2.7:armhf.
Preparing to unpack .../019-libruby2.7_2.7.4-1+b1_armhf.deb ...
Unpacking libruby2.7:armhf (2.7.4-1+b1) ...
Selecting previously unselected package ruby2.7.
Preparing to unpack .../020-ruby2.7_2.7.4-1+b1_armhf.deb ...
Unpacking ruby2.7 (2.7.4-1+b1) ...
Selecting previously unselected package ruby-rubygems.
Preparing to unpack .../021-ruby-rubygems_3.2.27-1_all.deb ...
Unpacking ruby-rubygems (3.2.27-1) ...
Selecting previously unselected package ruby.
Preparing to unpack .../022-ruby_1%3a2.7+2_armhf.deb ...
Unpacking ruby (1:2.7+2) ...
Selecting previously unselected package ruby-asciidoctor.
Preparing to unpack .../023-ruby-asciidoctor_2.0.16-1_all.deb ...
Unpacking ruby-asciidoctor (2.0.16-1) ...
Selecting previously unselected package asciidoctor.
Preparing to unpack .../024-asciidoctor_2.0.16-1_all.deb ...
Unpacking asciidoctor (2.0.16-1) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../025-libsigsegv2_2.13-1_armhf.deb ...
Unpacking libsigsegv2:armhf (2.13-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../026-m4_1.4.18-5_armhf.deb ...
Unpacking m4 (1.4.18-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../027-autoconf_2.71-2_all.deb ...
Unpacking autoconf (2.71-2) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../028-autotools-dev_20180224.1+nmu1_all.deb ...
Unpacking autotools-dev (20180224.1+nmu1) ...
Selecting previously unselected package automake.
Preparing to unpack .../029-automake_1%3a1.16.4-2_all.deb ...
Unpacking automake (1:1.16.4-2) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../030-autopoint_0.21-4_all.deb ...
Unpacking autopoint (0.21-4) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../031-libdebhelper-perl_13.5.2_all.deb ...
Unpacking libdebhelper-perl (13.5.2) ...
Selecting previously unselected package libtool.
Preparing to unpack .../032-libtool_2.4.6-15_all.deb ...
Unpacking libtool (2.4.6-15) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../033-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../034-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../035-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../036-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../037-dh-strip-nondeterminism_1.12.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.12.0-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../038-libelf1_0.185-2_armhf.deb ...
Unpacking libelf1:armhf (0.185-2) ...
Selecting previously unselected package dwz.
Preparing to unpack .../039-dwz_0.14-1_armhf.deb ...
Unpacking dwz (0.14-1) ...
Selecting previously unselected package libicu67:armhf.
Preparing to unpack .../040-libicu67_67.1-7_armhf.deb ...
Unpacking libicu67:armhf (67.1-7) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../041-libxml2_2.9.12+dfsg-5_armhf.deb ...
Unpacking libxml2:armhf (2.9.12+dfsg-5) ...
Selecting previously unselected package gettext.
Preparing to unpack .../042-gettext_0.21-4_armhf.deb ...
Unpacking gettext (0.21-4) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../043-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../044-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../045-debhelper_13.5.2_all.deb ...
Unpacking debhelper (13.5.2) ...
Selecting previously unselected package mysql-common.
Preparing to unpack .../046-mysql-common_5.8+1.0.7_all.deb ...
Unpacking mysql-common (5.8+1.0.7) ...
Selecting previously unselected package mariadb-common.
Preparing to unpack .../047-mariadb-common_1%3a10.5.12-1_all.deb ...
Unpacking mariadb-common (1:10.5.12-1) ...
Selecting previously unselected package libmariadb3:armhf.
Preparing to unpack .../048-libmariadb3_1%3a10.5.12-1_armhf.deb ...
Unpacking libmariadb3:armhf (1:10.5.12-1) ...
Selecting previously unselected package libssl-dev:armhf.
Preparing to unpack .../049-libssl-dev_1.1.1l-1_armhf.deb ...
Unpacking libssl-dev:armhf (1.1.1l-1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../050-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Selecting previously unselected package libmariadb-dev.
Preparing to unpack .../051-libmariadb-dev_1%3a10.5.12-1_armhf.deb ...
Unpacking libmariadb-dev (1:10.5.12-1) ...
Selecting previously unselected package libmariadb-dev-compat:armhf.
Preparing to unpack .../052-libmariadb-dev-compat_1%3a10.5.12-1_armhf.deb ...
Unpacking libmariadb-dev-compat:armhf (1:10.5.12-1) ...
Selecting previously unselected package default-libmysqlclient-dev:armhf.
Preparing to unpack .../053-default-libmysqlclient-dev_1.0.7_armhf.deb ...
Unpacking default-libmysqlclient-dev:armhf (1.0.7) ...
Selecting previously unselected package icu-devtools.
Preparing to unpack .../054-icu-devtools_67.1-7_armhf.deb ...
Unpacking icu-devtools (67.1-7) ...
Selecting previously unselected package libsuitesparseconfig5:armhf.
Preparing to unpack .../055-libsuitesparseconfig5_1%3a5.10.1+dfsg-2_armhf.deb ...
Unpacking libsuitesparseconfig5:armhf (1:5.10.1+dfsg-2) ...
Selecting previously unselected package libamd2:armhf.
Preparing to unpack .../056-libamd2_1%3a5.10.1+dfsg-2_armhf.deb ...
Unpacking libamd2:armhf (1:5.10.1+dfsg-2) ...
Selecting previously unselected package libbamtools2.5.1:armhf.
Preparing to unpack .../057-libbamtools2.5.1_2.5.1+dfsg-9_armhf.deb ...
Unpacking libbamtools2.5.1:armhf (2.5.1+dfsg-9) ...
Selecting previously unselected package libbamtools-dev:armhf.
Preparing to unpack .../058-libbamtools-dev_2.5.1+dfsg-9_armhf.deb ...
Unpacking libbamtools-dev:armhf (2.5.1+dfsg-9) ...
Selecting previously unselected package libblas3:armhf.
Preparing to unpack .../059-libblas3_3.9.0-3_armhf.deb ...
Unpacking libblas3:armhf (3.9.0-3) ...
Selecting previously unselected package libblas-dev:armhf.
Preparing to unpack .../060-libblas-dev_3.9.0-3_armhf.deb ...
Unpacking libblas-dev:armhf (3.9.0-3) ...
Selecting previously unselected package libboost1.74-dev:armhf.
Preparing to unpack .../061-libboost1.74-dev_1.74.0-9_armhf.deb ...
Unpacking libboost1.74-dev:armhf (1.74.0-9) ...
Selecting previously unselected package libboost-regex1.74.0:armhf.
Preparing to unpack .../062-libboost-regex1.74.0_1.74.0-9_armhf.deb ...
Unpacking libboost-regex1.74.0:armhf (1.74.0-9) ...
Selecting previously unselected package libicu-dev:armhf.
Preparing to unpack .../063-libicu-dev_67.1-7_armhf.deb ...
Unpacking libicu-dev:armhf (67.1-7) ...
Selecting previously unselected package libboost-regex1.74-dev:armhf.
Preparing to unpack .../064-libboost-regex1.74-dev_1.74.0-9_armhf.deb ...
Unpacking libboost-regex1.74-dev:armhf (1.74.0-9) ...
Selecting previously unselected package libboost-iostreams1.74.0:armhf.
Preparing to unpack .../065-libboost-iostreams1.74.0_1.74.0-9_armhf.deb ...
Unpacking libboost-iostreams1.74.0:armhf (1.74.0-9) ...
Selecting previously unselected package libboost-iostreams1.74-dev:armhf.
Preparing to unpack .../066-libboost-iostreams1.74-dev_1.74.0-9_armhf.deb ...
Unpacking libboost-iostreams1.74-dev:armhf (1.74.0-9) ...
Selecting previously unselected package libboost-iostreams-dev:armhf.
Preparing to unpack .../067-libboost-iostreams-dev_1.74.0.3+b1_armhf.deb ...
Unpacking libboost-iostreams-dev:armhf (1.74.0.3+b1) ...
Selecting previously unselected package libboost-serialization1.74.0:armhf.
Preparing to unpack .../068-libboost-serialization1.74.0_1.74.0-9_armhf.deb ...
Unpacking libboost-serialization1.74.0:armhf (1.74.0-9) ...
Selecting previously unselected package libboost-serialization1.74-dev:armhf.
Preparing to unpack .../069-libboost-serialization1.74-dev_1.74.0-9_armhf.deb ...
Unpacking libboost-serialization1.74-dev:armhf (1.74.0-9) ...
Selecting previously unselected package libboost-serialization-dev:armhf.
Preparing to unpack .../070-libboost-serialization-dev_1.74.0.3+b1_armhf.deb ...
Unpacking libboost-serialization-dev:armhf (1.74.0.3+b1) ...
Selecting previously unselected package libbrotli1:armhf.
Preparing to unpack .../071-libbrotli1_1.0.9-2+b1_armhf.deb ...
Unpacking libbrotli1:armhf (1.0.9-2+b1) ...
Selecting previously unselected package libbtf1:armhf.
Preparing to unpack .../072-libbtf1_1%3a5.10.1+dfsg-2_armhf.deb ...
Unpacking libbtf1:armhf (1:5.10.1+dfsg-2) ...
Selecting previously unselected package libbz2-dev:armhf.
Preparing to unpack .../073-libbz2-dev_1.0.8-4_armhf.deb ...
Unpacking libbz2-dev:armhf (1.0.8-4) ...
Selecting previously unselected package libcamd2:armhf.
Preparing to unpack .../074-libcamd2_1%3a5.10.1+dfsg-2_armhf.deb ...
Unpacking libcamd2:armhf (1:5.10.1+dfsg-2) ...
Selecting previously unselected package libccolamd2:armhf.
Preparing to unpack .../075-libccolamd2_1%3a5.10.1+dfsg-2_armhf.deb ...
Unpacking libccolamd2:armhf (1:5.10.1+dfsg-2) ...
Selecting previously unselected package libcolamd2:armhf.
Preparing to unpack .../076-libcolamd2_1%3a5.10.1+dfsg-2_armhf.deb ...
Unpacking libcolamd2:armhf (1:5.10.1+dfsg-2) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../077-libgfortran5_11.2.0-7+rpi1_armhf.deb ...
Unpacking libgfortran5:armhf (11.2.0-7+rpi1) ...
Selecting previously unselected package liblapack3:armhf.
Preparing to unpack .../078-liblapack3_3.9.0-3_armhf.deb ...
Unpacking liblapack3:armhf (3.9.0-3) ...
Selecting previously unselected package libmetis5:armhf.
Preparing to unpack .../079-libmetis5_5.1.0.dfsg-7_armhf.deb ...
Unpacking libmetis5:armhf (5.1.0.dfsg-7) ...
Selecting previously unselected package libcholmod3:armhf.
Preparing to unpack .../080-libcholmod3_1%3a5.10.1+dfsg-2_armhf.deb ...
Unpacking libcholmod3:armhf (1:5.10.1+dfsg-2) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../081-libnghttp2-14_1.43.0-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.43.0-1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../082-libpsl5_0.21.0-1.2_armhf.deb ...
Unpacking libpsl5:armhf (0.21.0-1.2) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../083-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../084-libssh2-1_1.10.0-2_armhf.deb ...
Unpacking libssh2-1:armhf (1.10.0-2) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../085-libcurl3-gnutls_7.74.0-1.3_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.74.0-1.3) ...
Selecting previously unselected package libcurl4-gnutls-dev:armhf.
Preparing to unpack .../086-libcurl4-gnutls-dev_7.74.0-1.3_armhf.deb ...
Unpacking libcurl4-gnutls-dev:armhf (7.74.0-1.3) ...
Selecting previously unselected package libcxsparse3:armhf.
Preparing to unpack .../087-libcxsparse3_1%3a5.10.1+dfsg-2_armhf.deb ...
Unpacking libcxsparse3:armhf (1:5.10.1+dfsg-2) ...
Selecting previously unselected package libdeflate0:armhf.
Preparing to unpack .../088-libdeflate0_1.7-2_armhf.deb ...
Unpacking libdeflate0:armhf (1.7-2) ...
Selecting previously unselected package libdeflate-dev:armhf.
Preparing to unpack .../089-libdeflate-dev_1.7-2_armhf.deb ...
Unpacking libdeflate-dev:armhf (1.7-2) ...
Selecting previously unselected package libgraphblas5:armhf.
Preparing to unpack .../090-libgraphblas5_1%3a5.10.1+dfsg-2_armhf.deb ...
Unpacking libgraphblas5:armhf (1:5.10.1+dfsg-2) ...
Selecting previously unselected package libgslcblas0:armhf.
Preparing to unpack .../091-libgslcblas0_2.6+dfsg-2_armhf.deb ...
Unpacking libgslcblas0:armhf (2.6+dfsg-2) ...
Selecting previously unselected package libgsl25:armhf.
Preparing to unpack .../092-libgsl25_2.6+dfsg-2_armhf.deb ...
Unpacking libgsl25:armhf (2.6+dfsg-2) ...
Selecting previously unselected package libgsl-dev.
Preparing to unpack .../093-libgsl-dev_2.6+dfsg-2_armhf.deb ...
Unpacking libgsl-dev (2.6+dfsg-2) ...
Selecting previously unselected package libhtscodecs2:armhf.
Preparing to unpack .../094-libhtscodecs2_1.1.1-3_armhf.deb ...
Unpacking libhtscodecs2:armhf (1.1.1-3) ...
Selecting previously unselected package libhts3:armhf.
Preparing to unpack .../095-libhts3_1.13+ds-2_armhf.deb ...
Unpacking libhts3:armhf (1.13+ds-2) ...
Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../096-liblzma-dev_5.2.5-2_armhf.deb ...
Unpacking liblzma-dev:armhf (5.2.5-2) ...
Selecting previously unselected package libhts-dev:armhf.
Preparing to unpack .../097-libhts-dev_1.13+ds-2_armhf.deb ...
Unpacking libhts-dev:armhf (1.13+ds-2) ...
Selecting previously unselected package libklu1:armhf.
Preparing to unpack .../098-libklu1_1%3a5.10.1+dfsg-2_armhf.deb ...
Unpacking libklu1:armhf (1:5.10.1+dfsg-2) ...
Selecting previously unselected package liblapack-dev:armhf.
Preparing to unpack .../099-liblapack-dev_3.9.0-3_armhf.deb ...
Unpacking liblapack-dev:armhf (3.9.0-3) ...
Selecting previously unselected package libldl2:armhf.
Preparing to unpack .../100-libldl2_1%3a5.10.1+dfsg-2_armhf.deb ...
Unpacking libldl2:armhf (1:5.10.1+dfsg-2) ...
Selecting previously unselected package libmongoose2:armhf.
Preparing to unpack .../101-libmongoose2_1%3a5.10.1+dfsg-2_armhf.deb ...
Unpacking libmongoose2:armhf (1:5.10.1+dfsg-2) ...
Selecting previously unselected package libumfpack5:armhf.
Preparing to unpack .../102-libumfpack5_1%3a5.10.1+dfsg-2_armhf.deb ...
Unpacking libumfpack5:armhf (1:5.10.1+dfsg-2) ...
Selecting previously unselected package librbio2:armhf.
Preparing to unpack .../103-librbio2_1%3a5.10.1+dfsg-2_armhf.deb ...
Unpacking librbio2:armhf (1:5.10.1+dfsg-2) ...
Selecting previously unselected package libspqr2:armhf.
Preparing to unpack .../104-libspqr2_1%3a5.10.1+dfsg-2_armhf.deb ...
Unpacking libspqr2:armhf (1:5.10.1+dfsg-2) ...
Selecting previously unselected package libsliplu1:armhf.
Preparing to unpack .../105-libsliplu1_1%3a5.10.1+dfsg-2_armhf.deb ...
Unpacking libsliplu1:armhf (1:5.10.1+dfsg-2) ...
Selecting previously unselected package libsuitesparse-dev:armhf.
Preparing to unpack .../106-libsuitesparse-dev_1%3a5.10.1+dfsg-2_armhf.deb ...
Unpacking libsuitesparse-dev:armhf (1:5.10.1+dfsg-2) ...
Selecting previously unselected package liblpsolve55-dev.
Preparing to unpack .../107-liblpsolve55-dev_5.5.2.5-2_armhf.deb ...
Unpacking liblpsolve55-dev (5.5.2.5-2) ...
Selecting previously unselected package libmysql++3v5:armhf.
Preparing to unpack .../108-libmysql++3v5_3.2.5-2_armhf.deb ...
Unpacking libmysql++3v5:armhf (3.2.5-2) ...
Selecting previously unselected package libmysql++-dev:armhf.
Preparing to unpack .../109-libmysql++-dev_3.2.5-2_armhf.deb ...
Unpacking libmysql++-dev:armhf (3.2.5-2) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../110-libncurses6_6.2+20201114-4_armhf.deb ...
Unpacking libncurses6:armhf (6.2+20201114-4) ...
Selecting previously unselected package libncurses-dev:armhf.
Preparing to unpack .../111-libncurses-dev_6.2+20201114-4_armhf.deb ...
Unpacking libncurses-dev:armhf (6.2+20201114-4) ...
Selecting previously unselected package libncurses5-dev:armhf.
Preparing to unpack .../112-libncurses5-dev_6.2+20201114-4_armhf.deb ...
Unpacking libncurses5-dev:armhf (6.2+20201114-4) ...
Selecting previously unselected package libsqlite3-dev:armhf.
Preparing to unpack .../113-libsqlite3-dev_3.36.0-2_armhf.deb ...
Unpacking libsqlite3-dev:armhf (3.36.0-2) ...
Selecting previously unselected package lzma-dev.
Preparing to unpack .../114-lzma-dev_9.22-2.2_all.deb ...
Unpacking lzma-dev (9.22-2.2) ...
Selecting previously unselected package samtools.
Preparing to unpack .../115-samtools_1.13-2_armhf.deb ...
Unpacking samtools (1.13-2) ...
Selecting previously unselected package sbuild-build-depends-augustus-dummy.
Preparing to unpack .../116-sbuild-build-depends-augustus-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-augustus-dummy (0.invalid.0) ...
Setting up libhtscodecs2:armhf (1.1.1-3) ...
Setting up media-types (4.0.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up mysql-common (5.8+1.0.7) ...
update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up libboost1.74-dev:armhf (1.74.0-9) ...
Setting up bsdextrautils (2.37.2-1) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-7) ...
Setting up libgslcblas0:armhf (2.6+dfsg-2) ...
Setting up ruby-power-assert (1.1.7-2) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libgsl25:armhf (2.6+dfsg-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libyaml-0-2:armhf (0.2.2-1) ...
Setting up libboost-iostreams1.74.0:armhf (1.74.0-9) ...
Setting up libdebhelper-perl (13.5.2) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libldl2:armhf (1:5.10.1+dfsg-2) ...
Setting up libnghttp2-14:armhf (1.43.0-1) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up libdeflate0:armhf (1.7-2) ...
Setting up gettext-base (0.21-4) ...
Setting up libmetis5:armhf (5.1.0.dfsg-7) ...
Setting up file (1:5.39-3) ...
Setting up libgomp1:armhf (11.2.0-7+rpi1) ...
Setting up libbtf1:armhf (1:5.10.1+dfsg-2) ...
Setting up libasan6:armhf (11.2.0-7+rpi1) ...
Setting up ruby-minitest (5.13.0-1) ...
Setting up mariadb-common (1:10.5.12-1) ...
update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libblas3:armhf (3.9.0-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libsqlite3-dev:armhf (3.36.0-2) ...
Setting up ruby-test-unit (3.3.9-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.2+20201114-4) ...
Setting up ruby-net-telnet (0.1.1-2) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up libboost-regex1.74.0:armhf (1.74.0-9) ...
Setting up libbamtools2.5.1:armhf (2.5.1+dfsg-9) ...
Setting up libssl-dev:armhf (1.1.1l-1) ...
Setting up libatomic1:armhf (11.2.0-7+rpi1) ...
Setting up autopoint (0.21-4) ...
Setting up icu-devtools (67.1-7) ...
Setting up libmariadb3:armhf (1:10.5.12-1) ...
Setting up libmysql++3v5:armhf (3.2.5-2) ...
Setting up libgfortran5:armhf (11.2.0-7+rpi1) ...
Setting up liblzma-dev:armhf (5.2.5-2) ...
Setting up libubsan1:armhf (11.2.0-7+rpi1) ...
Setting up libboost-serialization1.74.0:armhf (1.74.0-9) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libffi8:armhf (3.4.2-2) ...
Setting up libmd0:armhf (1.0.3-3) ...
Setting up sensible-utils (0.0.17) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libmpdec3:armhf (2.5.1-2+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.10.0-2) ...
Setting up libcxsparse3:armhf (1:5.10.1+dfsg-2) ...
Setting up openssl (1.1.1l-1) ...
Setting up libbsd0:armhf (0.11.3-1) ...
Setting up libdeflate-dev:armhf (1.7-2) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up libicu-dev:armhf (67.1-7) ...
Setting up ruby-xmlrpc (0.3.0-2) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up libsuitesparseconfig5:armhf (1:5.10.1+dfsg-2) ...
Setting up libcc1-0:armhf (11.2.0-7+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 (1:5.10.1+dfsg-2) ...
Setting up libpython3.9-stdlib:armhf (3.9.7-4+rpi1) ...
Setting up libpython3-stdlib:armhf (3.9.2-3) ...
Setting up libbz2-dev:armhf (1.0.8-4) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-1) ...
Setting up libamd2:armhf (1:5.10.1+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+20201114-4) ...
Setting up gettext (0.21-4) ...
Setting up libgsl-dev (2.6+dfsg-2) ...
Setting up libcolamd2:armhf (1:5.10.1+dfsg-2) ...
Setting up libtool (2.4.6-15) ...
Setting up libedit2:armhf (3.1-20210910-1) ...
Setting up m4 (1.4.18-5) ...
Setting up libcurl3-gnutls:armhf (7.74.0-1.3) ...
Setting up libcurl4-gnutls-dev:armhf (7.74.0-1.3) ...
Setting up libgraphblas5:armhf (1:5.10.1+dfsg-2) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libsliplu1:armhf (1:5.10.1+dfsg-2) ...
Setting up ca-certificates (20210119) ...
Updating certificates in /etc/ssl/certs...
129 added, 0 removed; done.
Setting up libcamd2:armhf (1:5.10.1+dfsg-2) ...
Setting up libmongoose2:armhf (1:5.10.1+dfsg-2) ...
Setting up libbamtools-dev:armhf (2.5.1+dfsg-9) ...
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 lzma-dev (9.22-2.2) ...
Setting up autoconf (2.71-2) ...
Setting up libboost-serialization1.74-dev:armhf (1.74.0-9) ...
Setting up libmariadb-dev (1:10.5.12-1) ...
Setting up dh-strip-nondeterminism (1.12.0-1) ...
Setting up dwz (0.14-1) ...
Setting up libboost-regex1.74-dev:armhf (1.74.0-9) ...
Setting up groff-base (1.22.4-7) ...
Setting up libklu1:armhf (1:5.10.1+dfsg-2) ...
Setting up libccolamd2:armhf (1:5.10.1+dfsg-2) ...
Setting up libncurses5-dev:armhf (6.2+20201114-4) ...
Setting up libcholmod3:armhf (1:5.10.1+dfsg-2) ...
Setting up python3.9 (3.9.7-4+rpi1) ...
Setting up automake (1:1.16.4-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libmariadb-dev-compat:armhf (1:10.5.12-1) ...
Setting up libspqr2:armhf (1:5.10.1+dfsg-2) ...
Setting up libhts3:armhf (1.13+ds-2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhts-dev:armhf (1.13+ds-2) ...
Setting up python3 (3.9.2-3) ...
Setting up rubygems-integration (1.18) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up samtools (1.13-2) ...
Setting up libboost-iostreams1.74-dev:armhf (1.74.0-9) ...
Setting up dh-autoreconf (20) ...
Setting up libumfpack5:armhf (1:5.10.1+dfsg-2) ...
Setting up libboost-serialization-dev:armhf (1.74.0.3+b1) ...
Setting up default-libmysqlclient-dev:armhf (1.0.7) ...
Setting up libsuitesparse-dev:armhf (1:5.10.1+dfsg-2) ...
Setting up debhelper (13.5.2) ...
Setting up libboost-iostreams-dev:armhf (1.74.0.3+b1) ...
Setting up libmysql++-dev:armhf (3.2.5-2) ...
Setting up liblpsolve55-dev (5.5.2.5-2) ...
Setting up ruby (1:2.7+2) ...
Setting up ruby-asciidoctor (2.0.16-1) ...
Setting up rake (13.0.3-1) ...
Setting up asciidoctor (2.0.16-1) ...
Setting up ruby-rubygems (3.2.27-1) ...
Setting up libruby2.7:armhf (2.7.4-1+b1) ...
Setting up sbuild-build-depends-augustus-dummy (0.invalid.0) ...
Setting up ruby2.7 (2.7.4-1+b1) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
Processing triggers for ca-certificates (20210119) ...
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 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-9+rpi1 gcc-10_10.3.0-9+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-7+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 asciidoctor_2.0.16-1 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-1 bsdutils_1:2.37.2-1 build-essential_12.9 bzip2_1.0.8-4 ca-certificates_20210119 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-9+rpi1 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 default-libmysqlclient-dev_1.0.7 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-9+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-9+rpi1 gcc-10-base_10.3.0-9+rpi1 gcc-11-base_11.2.0-7+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 icu-devtools_67.1-7 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libamd2_1:5.10.1+dfsg-2 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libasan6_11.2.0-7+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-7+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbamtools-dev_2.5.1+dfsg-9 libbamtools2.5.1_2.5.1+dfsg-9 libbinutils_2.37-5+rpi1 libblas-dev_3.9.0-3 libblas3_3.9.0-3 libblkid1_2.37.2-1 libboost-iostreams-dev_1.74.0.3+b1 libboost-iostreams1.74-dev_1.74.0-9 libboost-iostreams1.74.0_1.74.0-9 libboost-regex1.74-dev_1.74.0-9 libboost-regex1.74.0_1.74.0-9 libboost-serialization-dev_1.74.0.3+b1 libboost-serialization1.74-dev_1.74.0-9 libboost-serialization1.74.0_1.74.0-9 libboost1.74-dev_1.74.0-9 libbrotli1_1.0.9-2+b1 libbsd0_0.11.3-1 libbtf1_1:5.10.1+dfsg-2 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcamd2_1:5.10.1+dfsg-2 libcap-ng0_0.7.9-2.2+b1 libcc1-0_11.2.0-7+rpi1 libccolamd2_1:5.10.1+dfsg-2 libcholmod3_1:5.10.1+dfsg-2 libcolamd2_1:5.10.1+dfsg-2 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libcurl3-gnutls_7.74.0-1.3 libcurl4-gnutls-dev_7.74.0-1.3 libcxsparse3_1:5.10.1+dfsg-2 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdeflate-dev_1.7-2 libdeflate0_1.7-2 libdpkg-perl_1.20.9+rpi1 libedit2_3.1-20210910-1 libelf1_0.185-2 libexpat1_2.4.1-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libffi8_3.4.2-2 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.3.0-9+rpi1 libgcc-s1_11.2.0-7+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgfortran5_11.2.0-7+rpi1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-7+rpi1 libgpg-error0_1.42-3 libgraphblas5_1:5.10.1+dfsg-2 libgsl-dev_2.6+dfsg-2 libgsl25_2.6+dfsg-2 libgslcblas0_2.6+dfsg-2 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libhts-dev_1.13+ds-2 libhts3_1.13+ds-2 libhtscodecs2_1.1.1-3 libicu-dev_67.1-7 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.23-1 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libklu1_1:5.10.1+dfsg-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 liblapack-dev_3.9.0-3 liblapack3_3.9.0-3 libldap-2.4-2_2.4.59+dfsg-1 libldl2_1:5.10.1+dfsg-2 liblocale-gettext-perl_1.07-4+b1 liblpsolve55-dev_5.5.2.5-2 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmariadb-dev_1:10.5.12-1 libmariadb-dev-compat_1:10.5.12-1 libmariadb3_1:10.5.12-1 libmd0_1.0.3-3 libmetis5_5.1.0.dfsg-7 libmongoose2_1:5.10.1+dfsg-2 libmount1_2.37.2-1 libmpc3_1.2.0-1 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libmysql++-dev_3.2.5-2 libmysql++3v5_3.2.5-2 libncurses-dev_6.2+20201114-4 libncurses5-dev_6.2+20201114-4 libncurses6_6.2+20201114-4 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-2 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-5 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.2 libpython3-stdlib_3.9.2-3 libpython3.9-minimal_3.9.7-4+rpi1 libpython3.9-stdlib_3.9.7-4+rpi1 librbio2_1:5.10.1+dfsg-2 libreadline8_8.1-2 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libruby2.7_2.7.4-1+b1 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsliplu1_1:5.10.1+dfsg-2 libsmartcols1_2.37.2-1 libspqr2_1:5.10.1+dfsg-2 libsqlite3-0_3.36.0-2 libsqlite3-dev_3.36.0-2 libss2_1.46.4-1 libssh2-1_1.10.0-2 libssl-dev_1.1.1l-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-7+rpi1 libsub-override-perl_0.09-2 libsuitesparse-dev_1:5.10.1+dfsg-2 libsuitesparseconfig5_1:5.10.1+dfsg-2 libsystemd0_247.9-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-7+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libumfpack5_1:5.10.1+dfsg-2 libunistring2_0.9.10-6 libuuid1_2.37.2-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libyaml-0-2_0.2.2-1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 lzma-dev_9.22-2.2 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mariadb-common_1:10.5.12-1 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.37.2-1 mysql-common_5.8+1.0.7 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 openssl_1.1.1l-1 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 python3_3.9.2-3 python3-minimal_3.9.2-3 python3.9_3.9.7-4+rpi1 python3.9-minimal_3.9.7-4+rpi1 rake_13.0.3-1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 ruby_1:2.7+2 ruby-asciidoctor_2.0.16-1 ruby-minitest_5.13.0-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.7-2 ruby-rubygems_3.2.27-1 ruby-test-unit_3.3.9-1 ruby-xmlrpc_0.3.0-2 ruby2.7_2.7.4-1+b1 rubygems-integration_1.18 samtools_1.13-2 sbuild-build-depends-augustus-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.37.2-1 xz-utils_5.2.5-2 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.tOoCpd3v/trustedkeys.kbx': General error
gpgv: Signature made Tue Sep 28 20:37:41 2021 UTC
gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./augustus_3.4.0+dfsg2-3.dsc
dpkg-source: info: extracting augustus in /<<BUILDDIR>>/augustus-3.4.0+dfsg2
dpkg-source: info: unpacking augustus_3.4.0+dfsg2.orig.tar.xz
dpkg-source: info: unpacking augustus_3.4.0+dfsg2-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying search_config_path
dpkg-source: info: applying set_installdir
dpkg-source: info: applying interpreter_paths.patch
dpkg-source: info: applying switch_cgp_testing_off.patch
dpkg-source: info: applying disable-compare.patch
Check disc 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=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-e22f7f3f-3769-4e9d-81a3-954ef3a32dc0
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package augustus
dpkg-buildpackage: info: source version 3.4.0+dfsg2-3
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
/usr/bin/make -C auxprogs/bam2hints clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2hints'
rm -f bam2hints.o bam2hints ../../bin/bam2hints
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/homGeneMapping clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping'
cd src; make clean
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src'
rm -f homGeneMapping gene.o genome.o sqliteDB.o
rm -f ../../../bin/homGeneMapping
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src'
cd ../..; tests/auxprogs/homGeneMapping/test_homGeneMapping.py --clean
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping'
/usr/bin/make -C auxprogs/joingenes clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/joingenes'
rm -rf *.o joingenes; rm -rf ../../bin/joingenes
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/joingenes'
/usr/bin/make -C auxprogs/aln2wig clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/aln2wig'
rm -f aln2wig aln2wig.o; rm -f ../../bin/aln2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2wig clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2wig'
rm -f bam2wig bam2wig.o bam2wig
rm -f ../../bin/bam2wig
cd ../..; tests/auxprogs/bam2wig/test_bam2wig.py --clean
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/compileSpliceCands clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands'
rm -f compileSpliceCands compileSpliceCands.o ../../bin/compileSpliceCands list.o
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam'
(cd src; make clean;)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src'
rm -f *~ filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o
rm -f filterBam
rm -f ../../../bin/filterBam
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam'
rm -rf bin
rm -f debian/*substvars
rm -f debian/mansrc/*.1
find . -name "__pycache__" | xargs -r rm -r
find src -name "*.o" | xargs -r rm
find auxprogs -name "*.o" | xargs -r rm
rm -f auxprogs/utrrnaseq/Debug/utrrnaseq src/augustus src/etraining src/fastBlockSearch src/getSeq src/load2db src/load2sqlitedb src/pp_simScore src/prepareAlign
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
mkdir -p bin
/usr/bin/make -C auxprogs/aln2wig
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/aln2wig'
cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -ansi -pedantic -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -c aln2wig.c
In file included from /usr/include/string.h:519,
from aln2wig.c:15:
In function 'strncpy',
inlined from 'main' at aln2wig.c:454:6:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation]
91 | 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:91:10: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation]
91 | 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:91:10: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation]
91 | 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:91:10: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -Wall -Wno-sign-compare -ansi -pedantic -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o aln2wig aln2wig.o
mkdir -p ../../bin
cp aln2wig ../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2hints
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2hints'
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c bam2hints.cc -o bam2hints.o -I/usr/include/bamtools
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o bam2hints bam2hints.o -lbamtools -lz
mkdir -p ../../bin
cp bam2hints ../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/bam2wig
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2wig'
cc -Wall -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bam2wig.c -o bam2wig.o -I/usr/include/htslib
bam2wig.c: In function 'main':
bam2wig.c:172:14: 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 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now bam2wig.o -o bam2wig -lhts -lz -lpthread
mkdir -p ../../bin
cp bam2wig ../../bin/bam2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/compileSpliceCands
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands'
cc -Wall -pedantic -ansi -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compileSpliceCands.c
compileSpliceCands.c: In function 'getChromosome':
compileSpliceCands.c:226:2: warning: this decimal constant is unsigned only in ISO C90
226 | s = malloc(3500000000);
| ^
In file included from /usr/include/string.h:519,
from compileSpliceCands.c:12:
In function 'strncat',
inlined from 'getChromosome' at compileSpliceCands.c:216:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:122:10: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=]
122 | 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:519,
from compileSpliceCands.c:12:
In function 'strncpy',
inlined from 'parseLine' at compileSpliceCands.c:292:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation]
91 | 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 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o list.o list.c
cc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o compileSpliceCands compileSpliceCands.o list.o
cp compileSpliceCands ../../bin/compileSpliceCands
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src'
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c filterBam.cc -o filterBam.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/MatePairs.cc -o MatePairs.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/getReferenceName.cc -o getReferenceName.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/initOptions.cc -o initOptions.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/SingleAlignment.cc -o SingleAlignment.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/printElapsedTime.cc -o printElapsedTime.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumMandIOperations.cc -o sumMandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumDandIOperations.cc -o sumDandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/PairednessCoverage.cc -o PairednessCoverage.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz
filterBam compiled with BAMTOOLS=/usr/include/bamtools
mkdir -p ../../../bin
mv filterBam ../../../bin/filterBam
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam'
/usr/bin/make -C auxprogs/homGeneMapping/src
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src'
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -o gene.o gene.cc -I../include
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -o genome.o genome.cc -I../include
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -o sqliteDB.o sqliteDB.cc -I../include
g++ -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wl,-z,relro -Wl,-z,now -o homGeneMapping main.cc gene.o genome.o sqliteDB.o -I../include -lsqlite3
mkdir -p ../../../bin/
cp homGeneMapping ../../../bin/homGeneMapping
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src'
/usr/bin/make -C auxprogs/joingenes
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/joingenes'
g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 joingenes.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 jg_transcript.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 jg_ios.cpp
In file included from /usr/include/string.h:519,
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:91:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation]
91 | 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:91:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation]
91 | 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:91:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound 300 equals destination size [-Wstringop-truncation]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now joingenes.o jg_transcript.o jg_ios.o -o joingenes
mkdir -p ../../bin/
cp joingenes ../../bin/
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/joingenes'
dh_auto_build
make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
mkdir -p bin
cd src && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o genbank.o genbank.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o properties.o properties.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_profile.o pp_profile.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_hitseq.o pp_hitseq.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_scoring.o pp_scoring.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/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:2195:5: 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
2195 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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>::
| ^~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o statemodel.o statemodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/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/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:2526:5: 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
2526 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h:2526:5: 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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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:2195:5: 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
2195 | _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:1247:14: 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
1247 | _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:2460:7: 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
2460 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h: In member function 'void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)':
/usr/include/c++/10/bits/stl_tree.h:2544:19: 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
2544 | _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:2544:19: 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
2544 | _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:2544:19: 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
2544 | _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:2544:19: 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
2544 | _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:2544:19: 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
2544 | _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<>());
| ~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o namgene.o namgene.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
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:1247:14: 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
1247 | _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:1247:14: 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
1247 | _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 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o types.o types.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o gene.o gene.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o evaluation.o evaluation.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/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:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1824 | __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:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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:1844:5: 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: 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:1667:5: 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:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1942 | 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:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: 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, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1896 | 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:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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:1844:5: 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:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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:1950:5: 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:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o motif.o motif.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o 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 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o hints.o hints.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
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 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o extrinsicinfo.o extrinsicinfo.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/string.h:519,
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:91:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation]
91 | 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 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o projectio.o projectio.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o intronmodel.o intronmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o exonmodel.o exonmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/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:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: 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, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1896 | 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 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o igenicmodel.o igenicmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/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:2195:5: 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
2195 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o 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 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o merkmal.o merkmal.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o vitmatrix.o vitmatrix.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In 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:2195:5: 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
2195 | _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:5375:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5375 | __set_difference(_InputIterator1 __first1, _InputIterator1 __last1,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:5375:5: 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:5375:5: 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:5375:5: 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:2526:5: 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
2526 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h:2526:5: 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:1247:14: 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
1247 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h:1247:14: 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
1247 | _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:2544:19: 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
2544 | _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:2195:5: 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
2195 | _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:2460:7: 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
2460 | _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<>());
| ~~~~~~~~~~~~~~~
/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:5440:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5440 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5440:46: 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:5440:46: 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:5440:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5440 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5440:46: 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:5440:46: 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:5440:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5440 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5440:46: 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:5440:46: 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:5440:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5440 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5440:46: 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:5440:46: 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:5440:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5440 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5440:46: 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:5440:46: 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:5440:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5440 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5440:46: 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:5440:46: 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:5440:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5440 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5440:46: 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:5440:46: 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:5440:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5440 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5440:46: 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:5440:46: 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:5440:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5440 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5440:46: 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:5440:46: 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:5440:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5440 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5440:46: 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:5440:46: 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:5440:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5440 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5440:46: 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:5440:46: 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:5440:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5440 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5440:46: 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:5440:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o 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:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1824 | __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:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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:1950:5: 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:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o mea.o mea.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
/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:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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 static member function 'static std::vector<double> CRF::capOutliers(std::vector<double>)':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: 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, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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>::
| ^~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o graph.o graph.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
/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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o meaPath.o meaPath.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o exoncand.o exoncand.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
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:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: 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:1667:5: 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:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1942 | 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:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: 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, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o randseqaccess.o randseqaccess.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o fasta.o fasta.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o ncmodel.o ncmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o parser/parse.o parser/parse.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o scanner/lex.o scanner/lex.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o genomicMSA.o genomicMSA.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o geneMSA.o geneMSA.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/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 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o contTimeMC.o contTimeMC.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/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:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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:1844:5: 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:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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:1950:5: 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:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __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: 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:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: 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, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1896 | 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o codonevo.o codonevo.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
/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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o compgenepred.o compgenepred.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/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);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o phylotree.o phylotree.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/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>::
| ^~~~~~~~~~~~~~~~~~~
/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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o orthograph.o orthograph.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o orthoexon.o orthoexon.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
/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);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o alignment.o alignment.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
/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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o speciesgraph.o speciesgraph.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o codonMSA.o codonMSA.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o train_logReg_param.o train_logReg_param.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o tokenizer.o tokenizer.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o sqliteDB.o sqliteDB.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o commontrain.o commontrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o igenictrain.o igenictrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o introntrain.o introntrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o exontrain.o exontrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o utrtrain.o utrtrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o dummy.o dummy.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
In file included from /usr/include/c++/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: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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc
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>::
| ^~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++
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 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o pp_simScore pp_simscore.cc fasta.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
cp prepareAlign ../bin/
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o load2db load2db.cc fasta.o hints.o types.o properties.o lldouble.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o getSeq getSeq.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o load2sqlitedb load2sqlitedb.cc fasta.o hints.o types.o properties.o lldouble.o sqliteDB.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
cp load2sqlitedb ../bin/
echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
In file included from /usr/include/c++/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>::
| ^~~~~~~~~~~~~~~~~~~
/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 load2db ../bin/
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
cp getSeq ../bin/
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3
cp pp_simScore ../bin/
In file included from /usr/include/c++/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 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz
filterBam compiled with BAMTOOLS=/usr/include/bamtools
mkdir -p ../../../bin
mv filterBam ../../../bin/filterBam
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/filterBam'
cd homGeneMapping; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src; make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src'
make[5]: Nothing to be done for 'all'.
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping'
cd joingenes; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/joingenes'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/joingenes'
cd utrrnaseq/Debug; make all;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2/auxprogs/utrrnaseq/Debug'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
Building file: ../src/Compute_UTRs.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Compute_UTRs.d" -MT"src/Compute_UTRs.o" -o "src/Compute_UTRs.o" "../src/Compute_UTRs.cpp"
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:5658:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
5658 | inline min_element(_ForwardIterator __first, _ForwardIterator __last)
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:5658:12: 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:5667:43: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
5667 | 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:5636:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
5636 | __min_element(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:5636:5: 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:5643:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
5643 | 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:2291:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
2291 | __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 3544.162s
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 0.692s
OK
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
create-stamp debian/debhelper-build-stamp
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
mkdir -p debian/augustus/usr/bin
install bin/* debian/augustus/usr/bin
install auxprogs/bam2wig/bam2wig \
debian/augustus/usr/bin
install auxprogs/compileSpliceCands/compileSpliceCands \
debian/augustus/usr/bin
install auxprogs/homGeneMapping/src/homGeneMapping \
debian/augustus/usr/bin
install auxprogs/joingenes/joingenes \
debian/augustus/usr/bin
mkdir -p debian/augustus/usr/share/augustus
cp -r scripts debian/augustus/usr/share/augustus
chmod -R -x debian/augustus/usr/share/augustus/scripts/*
rm -rf debian/augustus/usr/share/augustus/scripts/*.patch \
debian/augustus/usr/share/augustus/scripts/executeTestCGP.py \
debian/augustus/usr/share/augustus/scripts/*.txt
chmod +x debian/augustus/usr/share/augustus/scripts/checkUTR \
debian/augustus/usr/share/augustus/scripts/*.pl*
mkdir -p debian/augustus-doc/usr/share/doc/augustus
cp README* debian/augustus-doc/usr/share/doc/augustus
cp docs/*.txt debian/augustus-doc/usr/share/doc/augustus
cp docs/RUNNING* debian/augustus-doc/usr/share/doc/augustus
cp docs/README* debian/augustus-doc/usr/share/doc/augustus
cp docs/EXONCAND-MSAS-CGP.md \
debian/augustus-doc/usr/share/doc/augustus
cp -r docs/tutorial \
debian/augustus-doc/usr/share/doc/augustus
cp -r docs/tutorial-cgp \
debian/augustus-doc/usr/share/doc/augustus
mkdir -p debian/augustus-data/usr/share/augustus
cp -r config debian/augustus-data/usr/share/augustus
find debian/augustus-data/usr/share/augustus \
-type f -exec chmod -x {} \;
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_installchangelogs -k docs/HISTORY.TXT
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
debian/rules override_dh_compress
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_compress -Xtutorial
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.4.0+dfsg2'
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/augustus/usr/bin/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/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/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/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/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/augustus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/pp_simScore contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/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/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/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/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/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/filterBam debian/augustus/usr/bin/compileSpliceCands debian/augustus/usr/bin/joingenes debian/augustus/usr/bin/bam2hints debian/augustus/usr/bin/bam2wig debian/augustus/usr/bin/etraining debian/augustus/usr/bin/fastBlockSearch debian/augustus/usr/bin/aln2wig debian/augustus/usr/bin/augustus debian/augustus/usr/bin/pp_simScore debian/augustus/usr/bin/getSeq debian/augustus/usr/bin/prepareAlign debian/augustus/usr/bin/load2db debian/augustus/usr/bin/homGeneMapping 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+dfsg2-3_armhf.deb'.
dpkg-deb: building package 'augustus' in '../augustus_3.4.0+dfsg2-3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../augustus_3.4.0+dfsg2-3_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-10-01T04:37:07Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
augustus_3.4.0+dfsg2-3_armhf.changes:
-------------------------------------
Format: 1.8
Date: Tue, 28 Sep 2021 22:14:24 +0200
Source: augustus
Binary: augustus augustus-dbgsym
Architecture: armhf
Version: 3.4.0+dfsg2-3
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
augustus - gene prediction in eukaryotic genomes
Changes:
augustus (3.4.0+dfsg2-3) unstable; urgency=medium
.
* Fix watchfile to work with recent GitHub link structure.
Checksums-Sha1:
554ea59cba6b318607143963c549c8bd56414c51 34510444 augustus-dbgsym_3.4.0+dfsg2-3_armhf.deb
d16e6e1709c841ef6e63247bd659811a6e58c218 8416 augustus_3.4.0+dfsg2-3_armhf.buildinfo
b1c628f13e97ed2d9f1aab4c62ca238d997793c1 1445904 augustus_3.4.0+dfsg2-3_armhf.deb
Checksums-Sha256:
d87aa94456ce1018643a1f27d6669c18ce645b16be7cb9cfb07e92a85c57bc67 34510444 augustus-dbgsym_3.4.0+dfsg2-3_armhf.deb
1ffd04e308ae4a74d0aa1af59af5462ef3b505f51df4ece524c7ca952334008d 8416 augustus_3.4.0+dfsg2-3_armhf.buildinfo
c3c9a5c4a11a475336c053a2827418cef6d877849935c9f6e84e065da381aacd 1445904 augustus_3.4.0+dfsg2-3_armhf.deb
Files:
82cf90c204796ffb4d339ada92d77df5 34510444 debug optional augustus-dbgsym_3.4.0+dfsg2-3_armhf.deb
09b1368437a100c6cd5033726f8adc05 8416 science optional augustus_3.4.0+dfsg2-3_armhf.buildinfo
fbfd83c6b8e576e2752fc1edb9083200 1445904 science optional augustus_3.4.0+dfsg2-3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
augustus-dbgsym_3.4.0+dfsg2-3_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 34510444 bytes: control archive=1288 bytes.
962 bytes, 12 lines control
1678 bytes, 16 lines md5sums
Package: augustus-dbgsym
Source: augustus
Version: 3.4.0+dfsg2-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 35489
Depends: augustus (= 3.4.0+dfsg2-3)
Section: debug
Priority: optional
Description: debug symbols for augustus
Build-Ids: 186551031852378feb07401f662dfc2af93eec1d 1cc46ea9ff037423815fcefbc4455aaf4e8e8cb7 2ae13768a14c7138e42cf186075fd92d9487b061 547687127b735613aad0f460bda3415b1809a803 644eb6a18aefe7445d3a58b9ad9d498117d22bd0 66efac23588c87aa0cd3c5c779aaa4c53c7afb77 8139c3c4918ed21e5864f2b9f00ec43d74ead00b 8a20383903ee81dbded80d4137364570a4072609 9643d6a9cfa12c915d6863043d10a7ba8c3c7870 9d6b432e667ceae7e1239bfdc5b1025248867e90 b8abd5cf49856f763875584d3f0ff6ae1f14f61e c4b1ffcf811c99288b028c3e0c548ed37317150e c84365fc614d12f07d1652ec9f2268068bf8c5e2 cfbc20bf8453a5ef1b343ad725ba151c885f9273 f098c32a647e1f4b262ef349a20ea6970eacb794
drwxr-xr-x root/root 0 2021-09-28 20:14 ./
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/.build-id/18/
-rw-r--r-- root/root 7998604 2021-09-28 20:14 ./usr/lib/debug/.build-id/18/6551031852378feb07401f662dfc2af93eec1d.debug
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/.build-id/1c/
-rw-r--r-- root/root 13596 2021-09-28 20:14 ./usr/lib/debug/.build-id/1c/c46ea9ff037423815fcefbc4455aaf4e8e8cb7.debug
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/.build-id/2a/
-rw-r--r-- root/root 8179740 2021-09-28 20:14 ./usr/lib/debug/.build-id/2a/e13768a14c7138e42cf186075fd92d9487b061.debug
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/.build-id/54/
-rw-r--r-- root/root 780756 2021-09-28 20:14 ./usr/lib/debug/.build-id/54/7687127b735613aad0f460bda3415b1809a803.debug
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/.build-id/64/
-rw-r--r-- root/root 1038692 2021-09-28 20:14 ./usr/lib/debug/.build-id/64/4eb6a18aefe7445d3a58b9ad9d498117d22bd0.debug
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/.build-id/66/
-rw-r--r-- root/root 741056 2021-09-28 20:14 ./usr/lib/debug/.build-id/66/efac23588c87aa0cd3c5c779aaa4c53c7afb77.debug
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/.build-id/81/
-rw-r--r-- root/root 8952656 2021-09-28 20:14 ./usr/lib/debug/.build-id/81/39c3c4918ed21e5864f2b9f00ec43d74ead00b.debug
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/.build-id/8a/
-rw-r--r-- root/root 610448 2021-09-28 20:14 ./usr/lib/debug/.build-id/8a/20383903ee81dbded80d4137364570a4072609.debug
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/.build-id/96/
-rw-r--r-- root/root 123932 2021-09-28 20:14 ./usr/lib/debug/.build-id/96/43d6a9cfa12c915d6863043d10a7ba8c3c7870.debug
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/.build-id/9d/
-rw-r--r-- root/root 125724 2021-09-28 20:14 ./usr/lib/debug/.build-id/9d/6b432e667ceae7e1239bfdc5b1025248867e90.debug
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/.build-id/b8/
-rw-r--r-- root/root 1144884 2021-09-28 20:14 ./usr/lib/debug/.build-id/b8/abd5cf49856f763875584d3f0ff6ae1f14f61e.debug
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/.build-id/c4/
-rw-r--r-- root/root 19212 2021-09-28 20:14 ./usr/lib/debug/.build-id/c4/b1ffcf811c99288b028c3e0c548ed37317150e.debug
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/.build-id/c8/
-rw-r--r-- root/root 1096112 2021-09-28 20:14 ./usr/lib/debug/.build-id/c8/4365fc614d12f07d1652ec9f2268068bf8c5e2.debug
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/.build-id/cf/
-rw-r--r-- root/root 13340 2021-09-28 20:14 ./usr/lib/debug/.build-id/cf/bc20bf8453a5ef1b343ad725ba151c885f9273.debug
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/.build-id/f0/
-rw-r--r-- root/root 895776 2021-09-28 20:14 ./usr/lib/debug/.build-id/f0/98c32a647e1f4b262ef349a20ea6970eacb794.debug
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 4569416 2021-09-28 20:14 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/augustus.debug
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/share/
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-09-28 20:14 ./usr/share/doc/augustus-dbgsym -> augustus
augustus_3.4.0+dfsg2-3_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 1445904 bytes: control archive=4964 bytes.
1522 bytes, 23 lines control
10306 bytes, 138 lines md5sums
Package: augustus
Version: 3.4.0+dfsg2-3
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 2021-09-28 20:14 ./
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/bin/
-rwxr-xr-x root/root 9820 2021-09-28 20:14 ./usr/bin/aln2wig
-rwxr-xr-x root/root 2038588 2021-09-28 20:14 ./usr/bin/augustus
-rwxr-xr-x root/root 26676 2021-09-28 20:14 ./usr/bin/bam2hints
-rwxr-xr-x root/root 9820 2021-09-28 20:14 ./usr/bin/bam2wig
-rwxr-xr-x root/root 13916 2021-09-28 20:14 ./usr/bin/compileSpliceCands
-rwxr-xr-x root/root 2186044 2021-09-28 20:14 ./usr/bin/etraining
-rwxr-xr-x root/root 221188 2021-09-28 20:14 ./usr/bin/fastBlockSearch
-rwxr-xr-x root/root 149164 2021-09-28 20:14 ./usr/bin/filterBam
-rwxr-xr-x root/root 2018252 2021-09-28 20:14 ./usr/bin/getSeq
-rwxr-xr-x root/root 124784 2021-09-28 20:14 ./usr/bin/homGeneMapping
-rwxr-xr-x root/root 132752 2021-09-28 20:14 ./usr/bin/joingenes
-rwxr-xr-x root/root 167716 2021-09-28 20:14 ./usr/bin/load2db
-rwxr-xr-x root/root 155476 2021-09-28 20:14 ./usr/bin/load2sqlitedb
-rwxr-xr-x root/root 233436 2021-09-28 20:14 ./usr/bin/pp_simScore
-rwxr-xr-x root/root 26276 2021-09-28 20:14 ./usr/bin/prepareAlign
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/share/
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/share/augustus/
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/share/augustus/scripts/
-rw-r--r-- root/root 12674 2021-09-28 20:14 ./usr/share/augustus/scripts/README.autoAug
-rw-r--r-- root/root 12247 2021-09-28 20:14 ./usr/share/augustus/scripts/SplicedAlignment.pm
-rwxr-xr-x root/root 20552 2021-09-28 20:14 ./usr/share/augustus/scripts/aa2nonred.pl
-rwxr-xr-x root/root 3510 2021-09-28 20:14 ./usr/share/augustus/scripts/add_name_to_gff3.pl
-rw-r--r-- root/root 24576 2021-09-28 20:14 ./usr/share/augustus/scripts/augustify.py
-rwxr-xr-x root/root 3022 2021-09-28 20:14 ./usr/share/augustus/scripts/augustus2browser.pl
-rwxr-xr-x root/root 389 2021-09-28 20:14 ./usr/share/augustus/scripts/augustus2gbrowse.pl
-rwxr-xr-x root/root 54522 2021-09-28 20:14 ./usr/share/augustus/scripts/autoAug.pl
-rwxr-xr-x root/root 23383 2021-09-28 20:14 ./usr/share/augustus/scripts/autoAugPred.pl
-rwxr-xr-x root/root 45628 2021-09-28 20:14 ./usr/share/augustus/scripts/autoAugTrain.pl
-rw-r--r-- root/root 12830 2021-09-28 20:14 ./usr/share/augustus/scripts/bamToWig.py
-rwxr-xr-x root/root 3370 2021-09-28 20:14 ./usr/share/augustus/scripts/bedgraph2wig.pl
-rwxr-xr-x root/root 4724 2021-09-28 20:14 ./usr/share/augustus/scripts/blat2gbrowse.pl
-rwxr-xr-x root/root 32708 2021-09-28 20:14 ./usr/share/augustus/scripts/blat2hints.pl
-rwxr-xr-x root/root 11321 2021-09-28 20:14 ./usr/share/augustus/scripts/block2prfl.pl
-rwxr-xr-x root/root 2233 2021-09-28 20:14 ./usr/share/augustus/scripts/cegma2gff.pl
-rwxr-xr-x root/root 3843 2021-09-28 20:14 ./usr/share/augustus/scripts/checkParamArchive.pl
-rwxr-xr-x root/root 1151 2021-09-28 20:14 ./usr/share/augustus/scripts/checkUTR
-rwxr-xr-x root/root 535 2021-09-28 20:14 ./usr/share/augustus/scripts/cleanDOSfasta.pl
-rwxr-xr-x root/root 7558 2021-09-28 20:14 ./usr/share/augustus/scripts/clusterAndSplitGenes.pl
-rwxr-xr-x root/root 1653 2021-09-28 20:14 ./usr/share/augustus/scripts/compare_masking.pl
-rwxr-xr-x root/root 2364 2021-09-28 20:14 ./usr/share/augustus/scripts/computeFlankingRegion.pl
-rwxr-xr-x root/root 7247 2021-09-28 20:14 ./usr/share/augustus/scripts/createAugustusJoblist.pl
-rwxr-xr-x root/root 3244 2021-09-28 20:14 ./usr/share/augustus/scripts/del_from_prfl.pl
-rwxr-xr-x root/root 9675 2021-09-28 20:14 ./usr/share/augustus/scripts/evalCGP.pl
-rwxr-xr-x root/root 13247 2021-09-28 20:14 ./usr/share/augustus/scripts/eval_dualdecomp.pl
-rwxr-xr-x root/root 3397 2021-09-28 20:14 ./usr/share/augustus/scripts/eval_multi_gtf.pl
-rwxr-xr-x root/root 3043 2021-09-28 20:14 ./usr/share/augustus/scripts/exonerate2hints.pl
-rwxr-xr-x root/root 1301 2021-09-28 20:14 ./usr/share/augustus/scripts/exoniphyDb2hints.pl
-rw-r--r-- root/root 4617 2021-09-28 20:14 ./usr/share/augustus/scripts/extractAnno.py
-rwxr-xr-x root/root 507 2021-09-28 20:14 ./usr/share/augustus/scripts/extractTranscriptEnds.pl
-rwxr-xr-x root/root 446 2021-09-28 20:14 ./usr/share/augustus/scripts/filter-ppx.pl
-rwxr-xr-x root/root 850 2021-09-28 20:14 ./usr/share/augustus/scripts/filterGenes.pl
-rwxr-xr-x root/root 1071 2021-09-28 20:14 ./usr/share/augustus/scripts/filterGenesIn.pl
-rwxr-xr-x root/root 2911 2021-09-28 20:14 ./usr/share/augustus/scripts/filterGenesIn_mRNAname.pl
-rwxr-xr-x root/root 1716 2021-09-28 20:14 ./usr/share/augustus/scripts/filterGenesOut_mRNAname.pl
-rwxr-xr-x root/root 1122 2021-09-28 20:14 ./usr/share/augustus/scripts/filterInFrameStopCodons.pl
-rwxr-xr-x root/root 2923 2021-09-28 20:14 ./usr/share/augustus/scripts/filterMaf.pl
-rwxr-xr-x root/root 17619 2021-09-28 20:14 ./usr/share/augustus/scripts/filterPSL.pl
-rwxr-xr-x root/root 4465 2021-09-28 20:14 ./usr/share/augustus/scripts/filterShrimp.pl
-rwxr-xr-x root/root 2081 2021-09-28 20:14 ./usr/share/augustus/scripts/filterSpliceHints.pl
-rwxr-xr-x root/root 1649 2021-09-28 20:14 ./usr/share/augustus/scripts/findGffNamesInFasta.pl
-rw-r--r-- root/root 39199 2021-09-28 20:14 ./usr/share/augustus/scripts/fix_in_frame_stop_codon_genes.py
-rwxr-xr-x root/root 3632 2021-09-28 20:14 ./usr/share/augustus/scripts/fix_joingenes_gtf.pl
-rwxr-xr-x root/root 3098 2021-09-28 20:14 ./usr/share/augustus/scripts/gbSmallDNA2gff.pl
-rw-r--r-- root/root 8078 2021-09-28 20:14 ./usr/share/augustus/scripts/gbrowse.conf
-rwxr-xr-x root/root 3769 2021-09-28 20:14 ./usr/share/augustus/scripts/gbrowseold2gff3.pl
-rwxr-xr-x root/root 7642 2021-09-28 20:14 ./usr/share/augustus/scripts/getAnnoFasta.pl
-rw-r--r-- root/root 11503 2021-09-28 20:14 ./usr/share/augustus/scripts/getAnnoFastaFromJoingenes.py
-rwxr-xr-x root/root 2038 2021-09-28 20:14 ./usr/share/augustus/scripts/getLinesMatching.pl
-rwxr-xr-x root/root 2138 2021-09-28 20:14 ./usr/share/augustus/scripts/get_loci_from_gb.pl
-rwxr-xr-x root/root 19123 2021-09-28 20:14 ./usr/share/augustus/scripts/gff2gbSmallDNA.pl
-rw-r--r-- root/root 1758 2021-09-28 20:14 ./usr/share/augustus/scripts/gff2ps_mycustom
-rwxr-xr-x root/root 4074 2021-09-28 20:14 ./usr/share/augustus/scripts/gffGetmRNA.pl
-rwxr-xr-x root/root 3109 2021-09-28 20:14 ./usr/share/augustus/scripts/gp2othergp.pl
-rwxr-xr-x root/root 7019 2021-09-28 20:14 ./usr/share/augustus/scripts/gtf2aa.pl
-rwxr-xr-x root/root 9915 2021-09-28 20:14 ./usr/share/augustus/scripts/gtf2bed.pl
-rwxr-xr-x root/root 15592 2021-09-28 20:14 ./usr/share/augustus/scripts/gtf2gff.pl
-rwxr-xr-x root/root 2833 2021-09-28 20:14 ./usr/share/augustus/scripts/gth2gtf.pl
-rwxr-xr-x root/root 12923 2021-09-28 20:14 ./usr/share/augustus/scripts/hal2maf_split.pl
-rw-r--r-- root/root 9809 2021-09-28 20:14 ./usr/share/augustus/scripts/helpMod.pm
-rwxr-xr-x root/root 1427 2021-09-28 20:14 ./usr/share/augustus/scripts/joinPeptides.pl
-rwxr-xr-x root/root 9060 2021-09-28 20:14 ./usr/share/augustus/scripts/join_aug_pred.pl
-rwxr-xr-x root/root 2665 2021-09-28 20:14 ./usr/share/augustus/scripts/join_mult_hints.pl
-rwxr-xr-x root/root 3469 2021-09-28 20:14 ./usr/share/augustus/scripts/maf2conswig.pl
-rwxr-xr-x root/root 468 2021-09-28 20:14 ./usr/share/augustus/scripts/makeMatchLists.pl
-rwxr-xr-x root/root 16749 2021-09-28 20:14 ./usr/share/augustus/scripts/makeUtrTrainingSet.pl
-rwxr-xr-x root/root 1658 2021-09-28 20:14 ./usr/share/augustus/scripts/maskNregions.pl
-rwxr-xr-x root/root 1701 2021-09-28 20:14 ./usr/share/augustus/scripts/merge_masking.pl
-rwxr-xr-x root/root 2490 2021-09-28 20:14 ./usr/share/augustus/scripts/moveParameters.pl
-rwxr-xr-x root/root 20704 2021-09-28 20:14 ./usr/share/augustus/scripts/msa2prfl.pl
-rwxr-xr-x root/root 7720 2021-09-28 20:14 ./usr/share/augustus/scripts/new_species.pl
-rwxr-xr-x root/root 7092 2021-09-28 20:14 ./usr/share/augustus/scripts/opt_init_and_term_probs.pl
-rwxr-xr-x root/root 85334 2021-09-28 20:14 ./usr/share/augustus/scripts/optimize_augustus.pl
-rwxr-xr-x root/root 3606 2021-09-28 20:14 ./usr/share/augustus/scripts/parseSim4Output.pl
-rwxr-xr-x root/root 17132 2021-09-28 20:14 ./usr/share/augustus/scripts/partition_gtf2gb.pl
-rwxr-xr-x root/root 2108 2021-09-28 20:14 ./usr/share/augustus/scripts/pasapolyA2hints.pl
-rwxr-xr-x root/root 3369 2021-09-28 20:14 ./usr/share/augustus/scripts/peptides2alternatives.pl
-rwxr-xr-x root/root 6792 2021-09-28 20:14 ./usr/share/augustus/scripts/peptides2hints.pl
-rwxr-xr-x root/root 2761 2021-09-28 20:14 ./usr/share/augustus/scripts/phastconsDB2hints.pl
-rwxr-xr-x root/root 2330 2021-09-28 20:14 ./usr/share/augustus/scripts/polyA2hints.pl
-rwxr-xr-x root/root 10582 2021-09-28 20:14 ./usr/share/augustus/scripts/prints2prfl.pl
-rwxr-xr-x root/root 8032 2021-09-28 20:14 ./usr/share/augustus/scripts/pslMap.pl
-rwxr-xr-x root/root 1971 2021-09-28 20:14 ./usr/share/augustus/scripts/randomSplit.pl
-rwxr-xr-x root/root 1946 2021-09-28 20:14 ./usr/share/augustus/scripts/retroDB2hints.pl
-rwxr-xr-x root/root 1403 2021-09-28 20:14 ./usr/share/augustus/scripts/rmRedundantHints.pl
-rwxr-xr-x root/root 723 2021-09-28 20:14 ./usr/share/augustus/scripts/runAllSim4.pl
-rwxr-xr-x root/root 4992 2021-09-28 20:14 ./usr/share/augustus/scripts/samMap.pl
-rwxr-xr-x root/root 1159 2021-09-28 20:14 ./usr/share/augustus/scripts/scipiogff2gff.pl
-rwxr-xr-x root/root 2221 2021-09-28 20:14 ./usr/share/augustus/scripts/setStopCodonFreqs.pl
-rwxr-xr-x root/root 1215 2021-09-28 20:14 ./usr/share/augustus/scripts/simpleFastaHeaders.pl
-rwxr-xr-x root/root 2598 2021-09-28 20:14 ./usr/share/augustus/scripts/simplifyFastaHeaders.pl
-rwxr-xr-x root/root 2099 2021-09-28 20:14 ./usr/share/augustus/scripts/splitMfasta.pl
-rwxr-xr-x root/root 861 2021-09-28 20:14 ./usr/share/augustus/scripts/split_wiggle.pl
-rwxr-xr-x root/root 2158 2021-09-28 20:14 ./usr/share/augustus/scripts/summarizeACGTcontent.pl
-rwxr-xr-x root/root 19253 2021-09-28 20:14 ./usr/share/augustus/scripts/transMap2hints.pl
-rwxr-xr-x root/root 1965 2021-09-28 20:14 ./usr/share/augustus/scripts/uniquePeptides.pl
-rwxr-xr-x root/root 2395 2021-09-28 20:14 ./usr/share/augustus/scripts/utrgff2gbrowse.pl
-rw-r--r-- root/root 6352 2021-09-28 20:14 ./usr/share/augustus/scripts/webserver-results.head
-rw-r--r-- root/root 1033 2021-09-28 20:14 ./usr/share/augustus/scripts/webserver-results.tail
-rwxr-xr-x root/root 1602 2021-09-28 20:14 ./usr/share/augustus/scripts/weedMaf.pl
-rwxr-xr-x root/root 5374 2021-09-28 20:14 ./usr/share/augustus/scripts/wig2hints.pl
-rwxr-xr-x root/root 2881 2021-09-28 20:14 ./usr/share/augustus/scripts/wigchoose.pl
-rwxr-xr-x root/root 14137 2021-09-28 20:14 ./usr/share/augustus/scripts/writeResultsPage.pl
-rwxr-xr-x root/root 10061 2021-09-28 20:14 ./usr/share/augustus/scripts/yaml2gff.1.4.pl
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/share/doc/augustus/
lrwxrwxrwx root/root 0 2021-09-28 20:14 ./usr/share/doc/augustus/HISTORY.TXT.gz -> changelog.gz
-rw-r--r-- root/root 1951 2021-09-28 20:14 ./usr/share/doc/augustus/changelog.Debian.gz
-rw-r--r-- root/root 8573 2020-12-11 15:40 ./usr/share/doc/augustus/changelog.gz
-rw-r--r-- root/root 3366 2021-09-28 20:13 ./usr/share/doc/augustus/copyright
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/share/man/
drwxr-xr-x root/root 0 2021-09-28 20:14 ./usr/share/man/man1/
-rw-r--r-- root/root 603 2021-09-28 20:14 ./usr/share/man/man1/aln2wig.1.gz
-rw-r--r-- root/root 1697 2021-09-28 20:14 ./usr/share/man/man1/augustus.1.gz
-rw-r--r-- root/root 1541 2021-09-28 20:14 ./usr/share/man/man1/bam2hints.1.gz
-rw-r--r-- root/root 794 2021-09-28 20:14 ./usr/share/man/man1/bam2wig.1.gz
-rw-r--r-- root/root 842 2021-09-28 20:14 ./usr/share/man/man1/compileSpliceCands.1.gz
-rw-r--r-- root/root 724 2021-09-28 20:14 ./usr/share/man/man1/etraining.1.gz
-rw-r--r-- root/root 1348 2021-09-28 20:14 ./usr/share/man/man1/fastBlockSearch.1.gz
-rw-r--r-- root/root 1756 2021-09-28 20:14 ./usr/share/man/man1/filterBam.1.gz
-rw-r--r-- root/root 1252 2021-09-28 20:14 ./usr/share/man/man1/getSeq.1.gz
-rw-r--r-- root/root 1854 2021-09-28 20:14 ./usr/share/man/man1/homGeneMapping.1.gz
-rw-r--r-- root/root 2044 2021-09-28 20:14 ./usr/share/man/man1/joingenes.1.gz
-rw-r--r-- root/root 1257 2021-09-28 20:14 ./usr/share/man/man1/load2db.1.gz
-rw-r--r-- root/root 1436 2021-09-28 20:14 ./usr/share/man/man1/load2sqlitedb.1.gz
-rw-r--r-- root/root 2296 2021-09-28 20:14 ./usr/share/man/man1/pp_simScore.1.gz
-rw-r--r-- root/root 680 2021-09-28 20:14 ./usr/share/man/man1/prepareAlign.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 1537368
Build-Time: 5186
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 624
Job: augustus_3.4.0+dfsg2-3
Machine Architecture: armhf
Package: augustus
Package-Time: 5951
Source-Version: 3.4.0+dfsg2-3
Space: 1537368
Status: successful
Version: 3.4.0+dfsg2-3
--------------------------------------------------------------------------------
Finished at 2021-10-01T04:37:07Z
Build needed 01:39:11, 1537368k disc space