augustus →
3.3.1+dfsg-2 →
armhf → 2018-09-16 05:16:14
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| augustus 3.3.1+dfsg-2 (armhf) Sun, 16 Sep 2018 04:40:18 +0000 |
+==============================================================================+
Package: augustus
Version: 3.3.1+dfsg-2
Source Version: 3.3.1+dfsg-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-4787b44a-0acc-4b79-aa75-d580d3541b7f' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.0 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.8 MB]
Fetched 23.8 MB in 27s (898 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 64.3 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main augustus 3.3.1+dfsg-2 (dsc) [2300 B]
Get:2 http://172.17.0.1/private buster-staging/main augustus 3.3.1+dfsg-2 (tar) [64.2 MB]
Get:3 http://172.17.0.1/private buster-staging/main augustus 3.3.1+dfsg-2 (diff) [15.7 kB]
Fetched 64.3 MB in 6s (10.1 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/augustus-f0FpJ0/augustus-3.3.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/augustus-f0FpJ0' 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-X3Modg/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-X3Modg/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-X3Modg/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-X3Modg/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-X3Modg/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-X3Modg/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-X3Modg/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-X3Modg/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (3125 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libssl1.1 openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 71 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-X3Modg/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13964 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 (>= 11), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbam-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, asciidoctor
Filtered Build-Depends: debhelper (>= 11), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbam-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, asciidoctor
dpkg-deb: building package 'sbuild-build-depends-augustus-dummy' in '/<<BUILDDIR>>/resolver-X3Modg/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-X3Modg/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-X3Modg/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-X3Modg/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-X3Modg/apt_archive ./ Sources [562 B]
Get:5 copy:/<<BUILDDIR>>/resolver-X3Modg/apt_archive ./ Packages [645 B]
Fetched 2540 B in 1s (3638 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install augustus build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
dbus dbus-user-session e2fsprogs-l10n libnss-systemd libpam-systemd
systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdmainutils bzip2
debhelper dh-autoreconf dh-strip-nondeterminism dwz file gcc-7-base gettext
gettext-base gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base icu-devtools
intltool-debian libamd2 libarchive-zip-perl libbam-dev libbamtools-dev
libbamtools2.5.1 libblas-dev libblas3 libboost-iostreams-dev
libboost-iostreams1.62-dev libboost-iostreams1.62.0 libboost-regex1.62-dev
libboost-regex1.62.0 libboost1.62-dev libbsd0 libbtf1 libbz2-1.0 libbz2-dev
libcamd2 libccolamd2 libcholmod3 libcolamd2 libcroco3 libcurl3-gnutls
libcxsparse3 libelf1 libfile-stripnondeterminism-perl libfreetype6
libgfortran4 libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin
libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgraphblas2
libgraphite2-3 libgraphite2-dev libgsl-dev libgsl23 libgslcblas0
libgssapi-krb5-2 libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0
libharfbuzz0b libhts-dev libhts2 libicu-dev libicu-le-hb-dev libicu-le-hb0
libicu60 libk5crypto3 libkeyutils1 libklu1 libkrb5-3 libkrb5support0
liblapack-dev liblapack3 libldl2 liblpsolve55-dev liblzma-dev libmagic-mgc
libmagic1 libmetis5 libmongoose2 libmpdec2 libncurses-dev libncurses5-dev
libnghttp2-14 libpcre16-3 libpcre3 libpcre3-dev libpcre32-3 libpcrecpp0v5
libpipeline1 libpsl5 libpython3-stdlib libpython3.6-minimal
libpython3.6-stdlib librbio2 librtmp1 libruby2.5 libsigsegv2 libspqr2
libsqlite3-dev libssh2-1 libsuitesparse-dev libsuitesparseconfig5
libtimedate-perl libtool libumfpack5 libxml2 libyaml-0-2 lzma-dev m4 man-db
mime-support pkg-config po-debconf python3 python3-distutils python3-lib2to3
python3-minimal python3.6 python3.6-minimal rake ruby ruby-asciidoctor
ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert
ruby-test-unit ruby-xmlrpc ruby2.5 rubygems-integration zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation bzip2-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev
groff libbamtools-doc liblapack-doc libboost1.62-doc libboost-atomic1.62-dev
libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev
libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev
libboost-filesystem1.62-dev libboost-graph1.62-dev
libboost-graph-parallel1.62-dev libboost-locale1.62-dev libboost-log1.62-dev
libboost-math1.62-dev libboost-mpi1.62-dev libboost-mpi-python1.62-dev
libboost-program-options1.62-dev libboost-python1.62-dev
libboost-random1.62-dev libboost-serialization1.62-dev
libboost-signals1.62-dev libboost-system1.62-dev libboost-test1.62-dev
libboost-thread1.62-dev libboost-timer1.62-dev libboost-type-erasure1.62-dev
libboost-wave1.62-dev libboost1.62-tools-dev libmpfrc++-dev libntl-dev
libglib2.0-doc libgraphite2-utils gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info
| gsl-ref-html krb5-doc krb5-user icu-doc liblzma-doc ncurses-doc
sqlite3-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc
apparmor less www-browser libmail-box-perl python3-doc python3-tk
python3-venv python3.6-venv python3.6-doc binfmt-support ri ruby-dev bundler
Recommended packages:
curl | wget | lynx bzip2-doc libarchive-cpio-perl shared-mime-info
xdg-user-dirs krb5-locales publicsuffix libltdl-dev libmail-sendmail-perl
zip fonts-lato libjs-jquery
The following NEW packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gcc-7-base gettext
gettext-base gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base icu-devtools
intltool-debian libamd2 libarchive-zip-perl libbam-dev libbamtools-dev
libbamtools2.5.1 libblas-dev libblas3 libboost-iostreams-dev
libboost-iostreams1.62-dev libboost-iostreams1.62.0 libboost-regex1.62-dev
libboost-regex1.62.0 libboost1.62-dev libbsd0 libbtf1 libbz2-dev libcamd2
libccolamd2 libcholmod3 libcolamd2 libcroco3 libcurl3-gnutls libcxsparse3
libelf1 libfile-stripnondeterminism-perl libfreetype6 libgfortran4
libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin libglib2.0-data
libglib2.0-dev libglib2.0-dev-bin libgraphblas2 libgraphite2-3
libgraphite2-dev libgsl-dev libgsl23 libgslcblas0 libgssapi-krb5-2
libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b
libhts-dev libhts2 libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60
libk5crypto3 libkeyutils1 libklu1 libkrb5-3 libkrb5support0 liblapack-dev
liblapack3 libldl2 liblpsolve55-dev liblzma-dev libmagic-mgc libmagic1
libmetis5 libmongoose2 libmpdec2 libncurses-dev libncurses5-dev
libnghttp2-14 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5
libpipeline1 libpsl5 libpython3-stdlib libpython3.6-minimal
libpython3.6-stdlib librbio2 librtmp1 libruby2.5 libsigsegv2 libspqr2
libsqlite3-dev libssh2-1 libsuitesparse-dev libsuitesparseconfig5
libtimedate-perl libtool libumfpack5 libxml2 libyaml-0-2 lzma-dev m4 man-db
mime-support pkg-config po-debconf python3 python3-distutils python3-lib2to3
python3-minimal python3.6 python3.6-minimal rake ruby ruby-asciidoctor
ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert
ruby-test-unit ruby-xmlrpc ruby2.5 rubygems-integration
sbuild-build-depends-augustus-dummy zlib1g-dev
The following packages will be upgraded:
bzip2 libbz2-1.0 libpcre3
3 upgraded, 135 newly installed, 0 to remove and 68 not upgraded.
Need to get 69.2 MB/70.8 MB of archives.
After this operation, 354 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-X3Modg/apt_archive ./ sbuild-build-depends-augustus-dummy 0.invalid.0 [928 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-2 [1161 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libpython3.6-minimal armhf 3.6.6-1 [565 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf python3.6-minimal armhf 3.6.6-1 [1383 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.6.5-3 [36.2 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.61 [37.1 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf bzip2 armhf 1.0.6-9 [46.1 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libbz2-1.0 armhf 1.0.6-9 [43.0 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libpython3.6-stdlib armhf 3.6.6-1 [1638 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf python3.6 armhf 3.6.6-1 [234 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.6.5-3 [19.7 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.6.5-3 [24.1 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libpcre3 armhf 2:8.39-11+rpi1 [313 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-7 [117 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9.3 [12.2 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf rubygems-integration all 1.11 [4994 B]
Get:25 http://172.17.0.1/private buster-staging/main armhf rake all 12.3.1-3 [66.9 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf ruby-did-you-mean all 1.2.1-1 [14.4 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf ruby-minitest all 5.11.3-1 [54.8 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf ruby-power-assert all 1.1.1-1 [10.9 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf ruby-test-unit all 3.2.8-1 [72.4 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf ruby-xmlrpc all 0.3.0-2 [23.7 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libyaml-0-2 armhf 0.2.1-1 [38.8 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libruby2.5 armhf 2.5.1-5 [3126 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf ruby2.5 armhf 2.5.1-5 [384 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf ruby armhf 1:2.5.1 [11.3 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf ruby-asciidoctor all 1.5.7.1-1 [183 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf asciidoctor armhf 1.5.7.1-1 [63.9 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-1.1 [771 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-7 [434 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-4 [547 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.042-1 [20.1 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.042-1 [12.1 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.12-1 [69.1 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.8.8-2+rpi1 [860 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-7 [1218 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.5 [981 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libgirepository-1.0-1 armhf 1.56.1-1 [77.6 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf gir1.2-glib-2.0 armhf 1.56.1-1 [142 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-gobject0 armhf 1.8.8-2+rpi1 [648 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf gir1.2-harfbuzz-0.0 armhf 1.8.8-2+rpi1 [655 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 60.2-6 [166 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libsuitesparseconfig5 armhf 1:5.3.0+dfsg-1 [20.3 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libamd2 armhf 1:5.3.0+dfsg-1 [26.9 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libbam-dev armhf 0.1.19-4 [111 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-3 [128 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libbamtools-dev armhf 2.5.1+dfsg-3 [21.8 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-19 [191 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-1 [103 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.8.0-1 [111 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-8 [7003 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.62.0 armhf 1.62.0+dfsg-8 [233 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-icu0 armhf 1.8.8-2+rpi1 [641 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libglib2.0-data all 2.56.1-2 [2671 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libglib2.0-bin armhf 2.56.1-2 [1694 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf python3-lib2to3 all 3.6.6-1 [79.1 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf python3-distutils all 3.6.6-1 [144 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev-bin armhf 2.56.1-2 [1733 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-11+rpi1 [234 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-11+rpi1 [227 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-11+rpi1 [150 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-11+rpi1 [565 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev armhf 2.56.1-2 [2807 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf libgraphite2-dev armhf 1.3.12-1 [22.6 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-dev armhf 1.8.8-2+rpi1 [930 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb-dev armhf 1.0.3+git161113-5 [28.3 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 60.2-6 [8643 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.62-dev armhf 1.62.0+dfsg-8 [327 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62.0 armhf 1.62.0+dfsg-8 [49.3 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62-dev armhf 1.62.0+dfsg-8 [58.8 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams-dev armhf 1.62.0.1+b8 [3694 B]
Get:97 http://172.17.0.1/private buster-staging/main armhf libbtf1 armhf 1:5.3.0+dfsg-1 [20.8 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-9 [27.7 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf libcamd2 armhf 1:5.3.0+dfsg-1 [27.5 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf libccolamd2 armhf 1:5.3.0+dfsg-1 [28.1 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf libcolamd2 armhf 1:5.3.0+dfsg-1 [25.0 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-1 [1518 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf libmetis5 armhf 5.1.0.dfsg-5 [131 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf libcholmod3 armhf 1:5.3.0+dfsg-1 [215 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.32.0-1 [71.7 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-1 [52.5 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.61.0-1 [281 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf libcxsparse3 armhf 1:5.3.0+dfsg-1 [48.5 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf libgraphblas2 armhf 1:5.3.0+dfsg-1 [392 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf libgslcblas0 armhf 2.5+dfsg-5 [78.8 kB]
Get:113 http://172.17.0.1/private buster-staging/main armhf libgsl23 armhf 2.5+dfsg-5 [703 kB]
Get:114 http://172.17.0.1/private buster-staging/main armhf libgsl-dev armhf 2.5+dfsg-5 [894 kB]
Get:115 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.7-2 [259 kB]
Get:116 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.7-2 [329 kB]
Get:117 http://172.17.0.1/private buster-staging/main armhf libklu1 armhf 1:5.3.0+dfsg-1 [48.4 kB]
Get:118 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.8.0-1 [1577 kB]
Get:119 http://172.17.0.1/private buster-staging/main armhf libldl2 armhf 1:5.3.0+dfsg-1 [20.6 kB]
Get:120 http://172.17.0.1/private buster-staging/main armhf libmongoose2 armhf 1:5.3.0+dfsg-1 [40.6 kB]
Get:121 http://172.17.0.1/private buster-staging/main armhf libumfpack5 armhf 1:5.3.0+dfsg-1 [126 kB]
Get:122 http://172.17.0.1/private buster-staging/main armhf librbio2 armhf 1:5.3.0+dfsg-1 [29.4 kB]
Get:123 http://172.17.0.1/private buster-staging/main armhf libspqr2 armhf 1:5.3.0+dfsg-1 [65.0 kB]
Get:124 http://172.17.0.1/private buster-staging/main armhf libsuitesparse-dev armhf 1:5.3.0+dfsg-1 [942 kB]
Get:125 http://172.17.0.1/private buster-staging/main armhf liblpsolve55-dev armhf 5.5.0.15-4 [350 kB]
Get:126 http://172.17.0.1/private buster-staging/main armhf libncurses-dev armhf 6.1+20180714-1 [279 kB]
Get:127 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1+20180714-1 [940 B]
Get:128 http://172.17.0.1/private buster-staging/main armhf libsqlite3-dev armhf 3.24.0-1 [655 kB]
Get:129 http://172.17.0.1/private buster-staging/main armhf lzma-dev all 9.22-2.1 [44.7 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up liblapack3:armhf (3.8.0-1) ...
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Setting up libklu1:armhf (1:5.3.0+dfsg-1) ...
Setting up libcholmod3:armhf (1:5.3.0+dfsg-1) ...
Setting up gir1.2-harfbuzz-0.0:armhf (1.8.8-2+rpi1) ...
Setting up libkrb5-3:armhf (1.16-2) ...
Setting up python3-lib2to3 (3.6.6-1) ...
Setting up python3-distutils (3.6.6-1) ...
Setting up libspqr2:armhf (1:5.3.0+dfsg-1) ...
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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 libglib2.0-dev-bin (2.56.1-2) ...
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Setting up libgssapi-krb5-2:armhf (1.16-2) ...
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Setting up libicu60:armhf (60.2-6) ...
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Setting up dh-autoreconf (19) ...
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Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up dh-strip-nondeterminism (0.042-1) ...
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Setting up gettext (0.19.8.1-7) ...
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Setting up ruby2.5 (2.5.1-5) ...
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Setting up libboost-iostreams1.62-dev:armhf (1.62.0+dfsg-8) ...
Setting up libboost-iostreams-dev:armhf (1.62.0.1+b8) ...
Setting up ruby (1:2.5.1) ...
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Setting up sbuild-build-depends-augustus-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-5+rpi1) ...
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_2.31.1-2+rpi1 dpkg-dev_1.19.0.5 g++-8_8.1.0-12+rpi1 gcc-8_8.1.0-12+rpi1 libc6-dev_2.27-5+rpi1 libstdc++-8-dev_8.1.0-12+rpi1 libstdc++6_8.1.0-12+rpi1 linux-libc-dev_4.16.16-2+rpi1
Package versions: adduser_3.117 apt_1.6.3 asciidoctor_1.5.7.1-1 autoconf_2.69-11 automake_1:1.16.1-1.1 autopoint_0.19.8.1-7 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-2+rpi1 binutils-arm-linux-gnueabihf_2.31.1-2+rpi1 binutils-common_2.31.1-2+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:8.1.0-1+rpi1 cpp-8_8.1.0-12+rpi1 dash_0.5.8-2.10 dbus_1.12.10-1 dbus-user-session_1.12.10-1 debconf_1.5.69 debhelper_11.3.5 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dirmngr_2.2.9-1+rpi1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.3-1 e2fsprogs_1.44.3-1 e2fsprogs-l10n_1.44.3-1 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20171230-2 g++_4:8.1.0-1+rpi1 g++-8_8.1.0-12+rpi1 gcc_4:8.1.0-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.4.0-18+rpi1 gcc-7-base_7.3.0-19 gcc-8_8.1.0-12+rpi1 gcc-8-base_8.1.0-12+rpi1 gettext_0.19.8.1-7 gettext-base_0.19.8.1-7 gir1.2-glib-2.0_1.56.1-1 gir1.2-harfbuzz-0.0_1.8.8-2+rpi1 gnupg_2.2.9-1+rpi1 gnupg-l10n_2.2.9-1+rpi1 gnupg-utils_2.2.9-1+rpi1 gpg_2.2.9-1+rpi1 gpg-agent_2.2.9-1+rpi1 gpg-wks-client_2.2.9-1+rpi1 gpg-wks-server_2.2.9-1+rpi1 gpgconf_2.2.9-1+rpi1 gpgsm_2.2.9-1+rpi1 gpgv_2.2.9-1+rpi1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2 hostname_3.20 icu-devtools_60.2-6 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-1 libacl1_2.2.52-3 libamd2_1:5.3.0+dfsg-1 libapparmor1_2.13-8 libapt-pkg5.0_1.6.3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.1.0-12+rpi1 libassuan0_2.5.1-2 libatomic1_8.1.0-12+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbam-dev_0.1.19-4 libbamtools-dev_2.5.1+dfsg-3 libbamtools2.5.1_2.5.1+dfsg-3 libbinutils_2.31.1-2+rpi1 libblas-dev_3.8.0-1 libblas3_3.8.0-1 libblkid1_2.32.1-0.1 libboost-iostreams-dev_1.62.0.1+b8 libboost-iostreams1.62-dev_1.62.0+dfsg-8 libboost-iostreams1.62.0_1.62.0+dfsg-8 libboost-regex1.62-dev_1.62.0+dfsg-8 libboost-regex1.62.0_1.62.0+dfsg-8 libboost1.62-dev_1.62.0+dfsg-8 libbsd0_0.9.1-1 libbtf1_1:5.3.0+dfsg-1 libbz2-1.0_1.0.6-9 libbz2-dev_1.0.6-9 libc-bin_2.27-5+rpi1 libc-dev-bin_2.27-5+rpi1 libc6_2.27-5+rpi1 libc6-dev_2.27-5+rpi1 libcamd2_1:5.3.0+dfsg-1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-12+rpi1 libccolamd2_1:5.3.0+dfsg-1 libcholmod3_1:5.3.0+dfsg-1 libcolamd2_1:5.3.0+dfsg-1 libcom-err2_1.44.3-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.61.0-1 libcxsparse3_1:5.3.0+dfsg-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.10-1 libdebconfclient0_0.244 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.92-1+rpi1 libdrm2_2.4.92-1+rpi1 libelf1_0.170-0.5 libexpat1_2.2.5-3 libext2fs2_1.44.3-1 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libfreetype6_2.8.1-2 libgcc-8-dev_8.1.0-12+rpi1 libgcc1_1:8.1.0-12+rpi1 libgcrypt20_1.8.3-1 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgfortran4_7.3.0-19 libgirepository-1.0-1_1.56.1-1 libglib2.0-0_2.56.1-2 libglib2.0-bin_2.56.1-2 libglib2.0-data_2.56.1-2 libglib2.0-dev_2.56.1-2 libglib2.0-dev-bin_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.19-1 libgomp1_8.1.0-12+rpi1 libgpg-error0_1.32-1 libgraphblas2_1:5.3.0+dfsg-1 libgraphite2-3_1.3.12-1 libgraphite2-dev_1.3.12-1 libgsl-dev_2.5+dfsg-5 libgsl23_2.5+dfsg-5 libgslcblas0_2.5+dfsg-5 libgssapi-krb5-2_1.16-2 libharfbuzz-dev_1.8.8-2+rpi1 libharfbuzz-gobject0_1.8.8-2+rpi1 libharfbuzz-icu0_1.8.8-2+rpi1 libharfbuzz0b_1.8.8-2+rpi1 libhogweed4_3.4-1 libhts-dev_1.7-2 libhts2_1.7-2 libicu-dev_60.2-6 libicu-le-hb-dev_1.0.3+git161113-5 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-2.2 libip4tc0_1.6.2-1.1 libisl19_0.20-1 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libklu1_1:5.3.0+dfsg-1 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 liblapack-dev_3.8.0-1 liblapack3_3.8.0-1 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 libldl2_1:5.3.0+dfsg-1 liblocale-gettext-perl_1.07-3+b2 liblpsolve55-dev_5.5.0.15-4 liblz4-1_1.8.2-1+rpi1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmetis5_5.1.0.dfsg-5 libmongoose2_1:5.3.0+dfsg-1 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-1 libncurses-dev_6.1+20180714-1 libncurses5_6.1+20180714-1 libncurses5-dev_6.1+20180714-1 libncurses6_6.1+20180714-1 libncursesw5_6.1+20180714-1 libncursesw6_6.1+20180714-1 libnettle6_3.4-1 libnghttp2-14_1.32.0-1 libnpth0_1.6-1 libnss-systemd_239-7 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_239-7 libpam0g_1.1.8-3.7 libpcre16-3_2:8.39-11+rpi1 libpcre3_2:8.39-11+rpi1 libpcre3-dev_2:8.39-11+rpi1 libpcre32-3_2:8.39-11+rpi1 libpcrecpp0v5_2:8.39-11+rpi1 libperl5.26_5.26.2-7 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libpsl5_0.20.2-1 libpython3-stdlib_3.6.5-3 libpython3.6-minimal_3.6.6-1 libpython3.6-stdlib_3.6.6-1 librbio2_1:5.3.0+dfsg-1 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libruby2.5_2.5.1-5 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32.1-0.1 libspqr2_1:5.3.0+dfsg-1 libsqlite3-0_3.24.0-1 libsqlite3-dev_3.24.0-1 libss2_1.44.3-1 libssh2-1_1.8.0-2 libssl1.1_1.1.0h-4 libstdc++-8-dev_8.1.0-12+rpi1 libstdc++6_8.1.0-12+rpi1 libsuitesparse-dev_1:5.3.0+dfsg-1 libsuitesparseconfig5_1:5.3.0+dfsg-1 libsystemd0_239-7 libtasn1-6_4.13-3 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180714-1 libtinfo6_6.1+20180714-1 libtool_2.4.6-4 libubsan1_8.1.0-12+rpi1 libudev1_239-7 libumfpack5_1:5.3.0+dfsg-1 libunistring2_0.9.10-1 libuuid1_2.32.1-0.1 libxml2_2.9.4+dfsg1-7 libyaml-0-2_0.2.1-1 libzstd1_1.3.4+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.16.16-2+rpi1 login_1:4.5-1.1 lsb-base_9.20170808+rpi1 lzma-dev_9.22-2.1 m4_1.4.18-1 make_4.2.1-1.2 makedev_2.3.1-93 man-db_2.8.4-2 mawk_1.3.3-17 mime-support_3.61 mount_2.32.1-0.1 multiarch-support_2.27-5+rpi1 nano_2.9.8-1 ncurses-base_6.1+20180714-1 ncurses-bin_6.1+20180714-1 netbase_5.4 openssl_1.1.0h-4 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.26.2-7 perl-base_5.26.2-7 perl-modules-5.26_5.26.2-7 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 python3_3.6.5-3 python3-distutils_3.6.6-1 python3-lib2to3_3.6.6-1 python3-minimal_3.6.5-3 python3.6_3.6.6-1 python3.6-minimal_3.6.6-1 rake_12.3.1-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 ruby_1:2.5.1 ruby-asciidoctor_1.5.7.1-1 ruby-did-you-mean_1.2.1-1 ruby-minitest_5.11.3-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.1-1 ruby-test-unit_3.2.8-1 ruby-xmlrpc_0.3.0-2 ruby2.5_2.5.1-5 rubygems-integration_1.11 sbuild-build-depends-augustus-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 systemd_239-7 systemd-sysv_239-7 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 udev_239-7 util-linux_2.32.1-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Sep 13 14:02:22 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./augustus_3.3.1+dfsg-2.dsc
dpkg-source: info: extracting augustus in /<<BUILDDIR>>/augustus-3.3.1+dfsg
dpkg-source: info: unpacking augustus_3.3.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking augustus_3.3.1+dfsg-2.debian.tar.xz
dpkg-source: info: applying search_config_path
dpkg-source: info: applying set_installdir
dpkg-source: info: applying keep_cflags
dpkg-source: info: applying buildflags.patch
dpkg-source: info: applying spelling.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=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-4787b44a-0acc-4b79-aa75-d580d3541b7f
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package augustus
dpkg-buildpackage: info: source version 3.3.1+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build augustus-3.3.1+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
/usr/bin/make -C auxprogs/bam2hints clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2hints'
rm -f bam2hints.o bam2hints ../../bin/bam2hints
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/homGeneMapping clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping'
(cd src; make clean; cd ../bin; rm -f homGeneMapping; cd ../../../bin; rm -f homGeneMapping)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping/src'
rm -f homGeneMapping gene.o genome.o
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping/src'
/bin/sh: 1: cd: can't cd to ../../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping'
/usr/bin/make -C auxprogs/joingenes clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/joingenes'
rm -rf *o joingenes; rm -rf ../../bin/joingenes
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/joingenes'
/usr/bin/make -C auxprogs/aln2wig clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/aln2wig'
rm -f aln2wig aln2wig.o; rm -f ../../bin/aln2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2wig clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2wig'
rm -f bam2wig bam2wig.o
rm -f ../../bin/bam2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/checkTargetSortedness clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/checkTargetSortedness'
rm -f *.o checkTargetSortedness
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/checkTargetSortedness'
/usr/bin/make -C auxprogs/compileSpliceCands clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/compileSpliceCands'
rm -f compileSpliceCands compileSpliceCands.o ../../bin/compileSpliceCands list.o
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam'
(cd src; make clean;)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/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 ../../../bin/filterBam
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam'
rm -rf bin
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
dh_clean
debian/rules build-arch
dh build-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-3.3.1+dfsg'
mkdir -p bin
/usr/bin/make -C auxprogs/aln2wig
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/aln2wig'
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -O2 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -c aln2wig.c
gcc -Wall -Wno-sign-compare -ansi -pedantic -O2 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o aln2wig aln2wig.o;
cp aln2wig ../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2hints
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2hints'
g++ -Wall -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c bam2hints.cc -o bam2hints.o -I/usr/include/bamtools
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o bam2hints bam2hints.o -lbamtools -lz
cp bam2hints ../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/bam2wig
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2wig'
cc -Wall -O2 -I/usr/include/samtools/ -I. -I/usr/include/htslib/ -I/usr/include/bcftools/ -I/usr/include/tabix/ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c bam2wig.c -o bam2wig.o
cc -Wall -O2 -I/usr/include/samtools/ -I. -I/usr/include/htslib/ -I/usr/include/bcftools/ -I/usr/include/tabix/ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now bam2wig.o -o bam2wig /usr/lib/libbam.a -lhts -lcurses -lm -lz -lpthread -lbz2 -llzma
cp bam2wig ../../bin/bam2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/checkTargetSortedness
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/checkTargetSortedness'
cc -g -Wall -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c checkTargetSortedness.c -o checkTargetSortedness.o -I/usr/include/samtools -I.
cc -g -Wall -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now checkTargetSortedness.o -o checkTargetSortedness -lbam -lcurses -lm -lz -lpthread
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/checkTargetSortedness'
/usr/bin/make -C auxprogs/compileSpliceCands
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/compileSpliceCands'
cc -Wall -pedantic -ansi -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -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
s = malloc(3500000000);
^
compileSpliceCands.c:226:6: warning: argument 1 value '3500000000' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
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
extern void *malloc (size_t __size) __THROW __attribute_malloc__ __wur;
^~~~~~
compileSpliceCands.c: In function 'parseList':
compileSpliceCands.c:344:35: warning: 'left' may be used uninitialized in this function [-Wmaybe-uninitialized]
findPossibleSpliceSites(left->name,actualChromosome,left->startPos-maxSpliceSiteDiff,left->endPos+maxSpliceSiteDiff,right->startPos-maxSpliceSiteDiff,right->startPos+maxSpliceSiteDiff,left->strand,right->strand);
~~~~^~~~~~
compileSpliceCands.c: In function 'main':
compileSpliceCands.c:563:3: warning: 'chromosomeLength' may be used uninitialized in this function [-Wmaybe-uninitialized]
parseList(&L,actualChromosome,chromosomeLength,oldname,maxSpliceSiteDiff,threshold,maxIntronLength);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o list.o list.c
cc -o compileSpliceCands compileSpliceCands.o list.o -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now;
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam/src'
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c filterBam.cc -o filterBam.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/MatePairs.cc -o MatePairs.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/getReferenceName.cc -o getReferenceName.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/initOptions.cc -o initOptions.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/SingleAlignment.cc -o SingleAlignment.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/printElapsedTime.cc -o printElapsedTime.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumMandIOperations.cc -o sumMandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumDandIOperations.cc -o sumDandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/PairednessCoverage.cc -o PairednessCoverage.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
mv filterBam ../../../bin/filterBam
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam'
/usr/bin/make -C auxprogs/homGeneMapping/src
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping/src'
g++ -c -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -o gene.o gene.cc -I../include
g++ -c -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -o genome.o genome.cc -I../include
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -o homGeneMapping main.cc gene.o genome.o -I../include -Wl,-z,relro -Wl,-z,now
cp homGeneMapping ../../../bin/homGeneMapping
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping/src'
/usr/bin/make -C auxprogs/joingenes
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/joingenes'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x joingenes.cpp
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x jg_transcript.cpp
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x jg_ios.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x joingenes.o jg_transcript.o jg_ios.o -o joingenes -Wl,-z,relro -Wl,-z,now
cp joingenes ../../bin/
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/joingenes'
dh_auto_build
make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
mkdir -p bin
cd src && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o genbank.o genbank.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o properties.o properties.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_profile.o pp_profile.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_hitseq.o pp_hitseq.cc -I../include
In file included from properties.cc:17:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/pp_profile.hh:21,
from ../include/pp_hitseq.hh:18,
from pp_hitseq.cc:14:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/genbank.hh:19,
from genbank.cc:15:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/pp_profile.hh:21,
from pp_profile.cc:14:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/pp_profile.hh:22,
from ../include/pp_hitseq.hh:18,
from pp_hitseq.cc:14:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
properties.cc: In static member function 'static void Properties::init(int, char**)':
properties.cc:439:27: warning: catching polymorphic type 'struct PropertiesError' by value [-Wcatch-value=]
} catch (PropertiesError e){
^
properties.cc:464:30: warning: catching polymorphic type 'struct PropertiesError' by value [-Wcatch-value=]
} catch (PropertiesError e){
^
In file included from ../include/pp_scoring.hh:21,
from ../include/gene.hh:15,
from ../include/genbank.hh:19,
from genbank.cc:15:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/pp_profile.hh:22,
from pp_profile.cc:14:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from pp_profile.cc:17:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
pp_profile.cc: In member function 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map<int, LLDouble>*)':
pp_profile.cc:328:35: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
pp_profile.cc:339:35: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
pp_profile.cc: In member function 'Double PP::Block::scoreFromScratch(bool, int, int, int) const':
pp_profile.cc:384:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
pp_profile.cc:395:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
In file included from genbank.cc:19:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
genbank.cc: In member function 'AnnoSequence* GBProcessor::getAnnoSequence(GBPositions*)':
genbank.cc:51:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
genbank.cc:58:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
genbank.cc: In member function 'AnnoSequence* GBProcessor::getAnnoSequenceList()':
genbank.cc:312:19: warning: catching polymorphic type 'class GBError' by value [-Wcatch-value=]
} catch (GBError e) {
^
genbank.cc: In constructor 'GBFeature::GBFeature(const char*)':
genbank.cc:490:25: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_scoring.o pp_scoring.cc -I../include
In file included from ../include/pp_scoring.hh:21,
from pp_scoring.cc:14:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/pp_profile.hh:21,
from ../include/pp_hitseq.hh:18,
from ../include/pp_scoring.hh:22,
from pp_scoring.cc:14:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from pp_scoring.cc:17:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from /usr/include/c++/8/vector:69,
from ../include/types.hh:35,
from ../include/geneticcode.hh:17,
from ../include/pp_profile.hh:21,
from pp_profile.cc:14:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<PP::Column>::iterator' {aka '__gnu_cxx::__normal_iterator<PP::Column*, std::vector<PP::Column> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
pp_scoring.cc: In member function 'void PP::SubstateModel::scoreAssOrRDss(ViterbiSubmapType&, bool, int, const Double&)':
pp_scoring.cc:119:15: warning: catching polymorphic type 'class std::out_of_range' by value [-Wcatch-value=]
} catch (out_of_range) {
^~~~~~~~~~~~
pp_scoring.cc: In member function 'void PP::MultiTargetExonScorer::initBonusProbs(PP::BonusProbType&, int, int)':
pp_scoring.cc:271:11: warning: catching polymorphic type 'class std::out_of_range' by value [-Wcatch-value=]
} catch (out_of_range) {
^~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' {aka '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' {aka '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' {aka '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'bool PP::Block::initThresholds()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../include/types.hh:35,
from ../include/geneticcode.hh:17,
from ../include/pp_profile.hh:21,
from pp_profile.cc:14:
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In constructor 'PP::Block::Block(PP::DistanceType, const std::vector<std::__cxx11::basic_string<char> >&, std::__cxx11::string)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PP::Column*, std::vector<PP::Column> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../include/types.hh:35,
from ../include/vitmatrix.hh:14,
from ../include/pp_scoring.hh:21,
from pp_scoring.cc:14:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<PP::BonusProbEntry>::iterator' {aka '__gnu_cxx::__normal_iterator<PP::BonusProbEntry*, std::vector<PP::BonusProbEntry> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:60,
from ../include/types.hh:38,
from ../include/vitmatrix.hh:14,
from ../include/pp_scoring.hh:21,
from pp_scoring.cc:14:
/usr/include/c++/8/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++/8/bits/stl_tree.h:2500:5: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h:2500:5: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
/usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::size_type std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const _Key&) [with _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/8/bits/stl_tree.h:2518:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
_M_erase_aux(__p.first, __p.second);
^~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../include/types.hh:35,
from ../include/geneticcode.hh:17,
from ../include/pp_profile.hh:21,
from pp_profile.cc:14:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<PP::Block>::iterator' {aka '__gnu_cxx::__normal_iterator<PP::Block*, std::vector<PP::Block> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../include/types.hh:35,
from ../include/vitmatrix.hh:14,
from ../include/pp_scoring.hh:21,
from pp_scoring.cc:14:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void PP::MultiTargetExonScorer::initBonusProbs(PP::BonusProbType&, int, int)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PP::BonusProbEntry*, std::vector<PP::BonusProbEntry> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void PP::Profile::parse_stream(std::istream&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PP::Block*, std::vector<PP::Block> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o statemodel.o statemodel.cc -I../include
In file included from /usr/include/c++/8/map:60,
from ../include/types.hh:38,
from ../include/vitmatrix.hh:14,
from ../include/pp_scoring.hh:21,
from pp_scoring.cc:14:
/usr/include/c++/8/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++/8/bits/stl_tree.h:2146:5: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:60,
from ../include/types.hh:38,
from ../include/geneticcode.hh:17,
from ../include/pp_profile.hh:21,
from pp_profile.cc:14:
/usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, LLDouble>; _KeyOfValue = std::_Select1st<std::pair<const int, LLDouble> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, LLDouble> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, LLDouble>, std::_Select1st<std::pair<const int, LLDouble> >, std::less<int>, std::allocator<std::pair<const int, LLDouble> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, LLDouble> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_tree.h:2411:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h:2411:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
In file included from /usr/include/c++/8/map:61,
from ../include/types.hh:38,
from ../include/vitmatrix.hh:14,
from ../include/pp_scoring.hh:21,
from pp_scoring.cc:14:
/usr/include/c++/8/bits/stl_map.h: In member function 'void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)':
/usr/include/c++/8/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:64,
from ../include/types.hh:35,
from ../include/geneticcode.hh:17,
from ../include/pp_profile.hh:21,
from pp_profile.cc:14:
/usr/include/c++/8/bits/stl_vector.h: In member function 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map<int, LLDouble>*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from ../include/types.hh:38,
from ../include/geneticcode.hh:17,
from ../include/pp_profile.hh:21,
from pp_profile.cc:14:
/usr/include/c++/8/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, LLDouble> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, LLDouble> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from ../include/statemodel.hh:16,
from statemodel.cc:16:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:60,
from ../include/types.hh:38,
from ../include/vitmatrix.hh:14,
from ../include/pp_scoring.hh:21,
from pp_scoring.cc:14:
/usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Arg&&, _NodeGen&) [with _Arg = std::pair<SubstateId, ViterbiSubmapEntry>&; _NodeGen = 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> > >::_Alloc_node; _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++/8/bits/stl_tree.h:2207:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h:2207:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
In file included from ../include/extrinsicinfo.hh:24,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from statemodel.cc:16:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
/usr/include/c++/8/bits/stl_tree.h: In member function 'void PP::SubstateModel::scoreAssOrRDss(ViterbiSubmapType&, bool, int, const Double&)':
/usr/include/c++/8/bits/stl_tree.h:1169:2: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
_M_erase_aux(__first, __last);
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h:1042:65: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
return _M_insert_unique_(__pos, std::forward<_Arg>(__x), __an);
^
/usr/include/c++/8/bits/stl_tree.h:1042:65: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
return _M_insert_unique_(__pos, std::forward<_Arg>(__x), __an);
^
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/extrinsicinfo.hh:25,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from statemodel.cc:16:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from ../include/types.hh:38,
from ../include/vitmatrix.hh:14,
from ../include/pp_scoring.hh:21,
from pp_scoring.cc:14:
/usr/include/c++/8/bits/stl_map.h: In member function 'virtual void PP::SingleTargetExonScorer::exportSubstates(ViterbiSubmapType&)':
/usr/include/c++/8/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/map:60,
from ../include/types.hh:38,
from ../include/vitmatrix.hh:14,
from ../include/pp_scoring.hh:21,
from pp_scoring.cc:14:
/usr/include/c++/8/bits/stl_tree.h: In member function 'void PP::BonusProbType::mergeIntoSubmap(int, ViterbiSubmapType&, SubstateIdMap*)':
/usr/include/c++/8/bits/stl_tree.h:1042:65: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
return _M_insert_unique_(__pos, std::forward<_Arg>(__x), __an);
^
In file included from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from statemodel.cc:16:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h: In member function 'virtual void PP::MultiTargetExonScorer::postProcessing(const Double&)':
/usr/include/c++/8/bits/stl_tree.h:1169:2: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
_M_erase_aux(__first, __last);
^~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o namgene.o namgene.cc -I../include
In file included from /usr/include/c++/8/map:61,
from ../include/types.hh:38,
from ../include/vitmatrix.hh:14,
from ../include/pp_scoring.hh:21,
from pp_scoring.cc:14:
/usr/include/c++/8/bits/stl_map.h: In member function 'void PP::MultiTargetExonScorer::updateBonusProbs(PP::Position, const Double&)':
/usr/include/c++/8/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
statemodel.cc: In static member function 'static StateModel* StateModel::newStateModelPtr(const char*)':
statemodel.cc:94:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
statemodel.cc: In member function 'Double SnippetProbs::getElemSeqProb(int, int)':
statemodel.cc:301:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
statemodel.cc:312:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
statemodel.cc: In member function 'void SegProbs::setEmiProbs(std::vector<LLDouble>*, int, int)':
statemodel.cc:427:15: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){
^~~~~~~~~~~~~~~~~~~~~~
statemodel.cc:435:15: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){
^~~~~~~~~~~~~~~~~~~~~~
statemodel.cc: In member function 'Double SegProbs::getSeqProb(int, int)':
statemodel.cc:456:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError) {
^~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o types.o types.cc -I../include
In file included from /usr/include/c++/8/map:60,
from ../include/types.hh:38,
from ../include/vitmatrix.hh:14,
from ../include/pp_scoring.hh:21,
from pp_scoring.cc:14:
/usr/include/c++/8/bits/stl_tree.h: In member function 'virtual void PP::MultiTargetExonScorer::scoreInternal(ViterbiColumnType&, int, const Double&)':
/usr/include/c++/8/bits/stl_tree.h:1169:2: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
_M_erase_aux(__first, __last);
^~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from ../include/types.hh:38,
from ../include/vitmatrix.hh:14,
from ../include/pp_scoring.hh:21,
from pp_scoring.cc:14:
/usr/include/c++/8/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from ../include/extrinsicinfo.hh:24,
from ../include/namgene.hh:15,
from namgene.cc:21:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/extrinsicinfo.hh:25,
from ../include/namgene.hh:15,
from namgene.cc:21:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/pp_scoring.hh:21,
from ../include/gene.hh:15,
from ../include/extrinsicinfo.hh:25,
from ../include/namgene.hh:15,
from namgene.cc:21:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from types.cc:21:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
types.cc: In static member function 'static void Constant::init()':
types.cc:215:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:220:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:225:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:230:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:235:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:240:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:245:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {}
^
types.cc:248:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:254:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:259:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:264:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:269:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:274:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:279:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:284:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:290:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:296:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:301:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:306:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:311:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:316:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:321:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:326:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:331:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:336:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
In file included from ../include/namgene.hh:15,
from namgene.cc:21:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
namgene.cc: In constructor 'NAMGene::NAMGene()':
namgene.cc:116:41: warning: catching polymorphic type 'struct PP::ProfileNotFoundError' by value [-Wcatch-value=]
} catch (PP::ProfileNotFoundError e) {
^
namgene.cc:119:17: warning: catching polymorphic type 'struct PP::ProfileNotFoundError' by value [-Wcatch-value=]
} catch (PP::ProfileNotFoundError) {
^~~~~~~~~~~~~~~~~~~~
namgene.cc:128:12: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {
^~~~~~~~~~~~~~~~
namgene.cc:130:34: warning: catching polymorphic type 'struct PP::ProfileInsigError' by value [-Wcatch-value=]
} catch (PP::ProfileInsigError e) {
^
In file included from /usr/include/c++/8/vector:69,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from statemodel.cc:16:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<Ancestor>::iterator' {aka '__gnu_cxx::__normal_iterator<Ancestor*, std::vector<Ancestor> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void StateModel::initPredecessors(Matrix<LLDouble>&, int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Ancestor*, std::vector<Ancestor> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o gene.o gene.cc -I../include
In file included from /usr/include/c++/8/vector:69,
from ../include/types.hh:35,
from types.cc:18:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from gene.cc:21:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/pp_scoring.hh:21,
from ../include/gene.hh:15,
from gene.cc:21:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/graph.hh:10,
from ../include/mea.hh:5,
from gene.cc:22:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/exonmodel.hh:22,
from ../include/exoncand.hh:27,
from ../include/graph.hh:11,
from ../include/mea.hh:5,
from gene.cc:22:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../include/types.hh:37,
from types.cc:18:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o evaluation.o evaluation.cc -I../include
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from ../include/types.hh:37,
from types.cc:18:
/usr/include/c++/8/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++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../include/types.hh:37,
from types.cc:18:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
__heap_select(_RandomAccessIterator __first,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1933:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
std::__heap_select(__first, __middle, __last, __comp);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'Double quantile(const std::vector<LLDouble>&, float)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o motif.o motif.cc -I../include
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/evaluation.hh:22,
from evaluation.cc:15:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/pp_scoring.hh:21,
from ../include/gene.hh:15,
from ../include/evaluation.hh:22,
from evaluation.cc:15:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
namgene.cc: In member function 'std::__cxx11::list<AltGene>* NAMGene::findGenes(const char*, Strand, bool)':
namgene.cc:864:19: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=]
sprintf(gr, "s%d-", (i+1));
^~~~~~
namgene.cc:864:19: note: directive argument in the range [1, 2147483646]
In file included from /usr/include/stdio.h:862,
from /usr/include/c++/8/cstdio:42,
from /usr/include/c++/8/ext/string_conversions.h:43,
from /usr/include/c++/8/bits/basic_string.h:6391,
from /usr/include/c++/8/string:52,
from /usr/include/c++/8/bits/locale_classes.h:40,
from /usr/include/c++/8/bits/ios_base.h:41,
from /usr/include/c++/8/ios:42,
from /usr/include/c++/8/istream:38,
from /usr/include/c++/8/sstream:38,
from ../include/lldouble.hh:29,
from ../include/types.hh:27,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from ../include/namgene.hh:15,
from namgene.cc:21:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 9
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/extrinsicinfo.hh:24,
from ../include/evaluation.hh:23,
from evaluation.cc:15:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/evaluation.hh:23,
from evaluation.cc:15:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
In file included from ../include/motif.hh:21,
from motif.cc:14:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from motif.cc:17:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
motif.cc: In static member function 'static void BaseCount::init()':
motif.cc:57:14: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError) {
^~~~~~~~~~~~
motif.cc:70:11: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError) {
^~~~~~~~~~~~
motif.cc: In member function 'void Motif::addSequence(const char*, int, bool)':
motif.cc:302:37: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {}
^
motif.cc: In member function 'Double Motif::seqProb(const char*, bool, bool)':
motif.cc:330:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
motif.cc: In constructor 'ContentStairs::ContentStairs()':
motif.cc:519:12: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError) {
^~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../include/matrix.hh:26,
from ../include/motif.hh:20,
from motif.cc:14:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' {aka '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' {aka '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from ../include/matrix.hh:26,
from ../include/motif.hh:20,
from ../include/gene.hh:14,
from gene.cc:21:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../include/matrix.hh:26,
from ../include/motif.hh:20,
from motif.cc:14:
/usr/include/c++/8/bits/stl_vector.h: In member function 'Double Motif::getProbThreshold(double, int)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o geneticcode.o geneticcode.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o hints.o hints.cc -I../include
In file included from geneticcode.cc:15:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
geneticcode.cc: In static member function 'static char GeneticCode::translate(const char*)':
geneticcode.cc:182:14: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError) {
^~~~~~~~~~~~~~~~~~~~~~
geneticcode.cc: In static member function 'static char GeneticCode::revtranslate(const char*)':
geneticcode.cc:189:14: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError) {
^~~~~~~~~~~~~~~~~~~~~~
In file included from hints.cc:14:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
hints.cc: In function 'std::istream& operator>>(std::istream&, Feature&)':
hints.cc:229:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o extrinsicinfo.o extrinsicinfo.cc -I../include
In file included from /usr/include/c++/8/list:64,
from ../include/vitmatrix.hh:19,
from ../include/pp_scoring.hh:21,
from ../include/gene.hh:15,
from gene.cc:21:
/usr/include/c++/8/bits/list.tcc: In member 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++/8/bits/list.tcc:308:7: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
list<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/list.tcc:308:7: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
In file included from ../include/extrinsicinfo.hh:24,
from extrinsicinfo.cc:31:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/extrinsicinfo.hh:25,
from extrinsicinfo.cc:31:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/pp_scoring.hh:21,
from ../include/gene.hh:15,
from ../include/extrinsicinfo.hh:25,
from extrinsicinfo.cc:31:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o projectio.o projectio.cc -I../include
In file included from extrinsicinfo.cc:31:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o intronmodel.o intronmodel.cc -I../include
/usr/include/c++/8/bits/list.tcc: In static member function 'static StatePath* StatePath::condenseStatePath(StatePath*)':
/usr/include/c++/8/bits/list.tcc:286:4: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
^~~~~~~~~~~~~~~~~~
extrinsicinfo.cc: In member function 'void FeatureCollection::readExtrinsicCFGFile()':
extrinsicinfo.cc:2076:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
extrinsicinfo.cc: In member function 'void FeatureCollection::readTypeInfo(std::istream&)':
extrinsicinfo.cc:2134:25: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
extrinsicinfo.cc: In member function 'void FeatureCollection::readGFFFile(const char*)':
extrinsicinfo.cc:2287:28: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e){}
^
extrinsicinfo.cc:2304:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
/usr/include/c++/8/bits/list.tcc: In copy constructor 'Gene::Gene(const Gene&)':
/usr/include/c++/8/bits/list.tcc:286:4: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
^~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o exonmodel.o exonmodel.cc -I../include
In file included from /usr/include/c++/8/algorithm:62,
from ../include/types.hh:37,
from ../include/geneticcode.hh:17,
from ../include/motif.hh:21,
from ../include/gene.hh:14,
from gene.cc:21:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from ../include/types.hh:37,
from ../include/geneticcode.hh:17,
from ../include/motif.hh:21,
from ../include/gene.hh:14,
from gene.cc:21:
/usr/include/c++/8/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++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../include/types.hh:37,
from ../include/geneticcode.hh:17,
from ../include/motif.hh:21,
from ../include/gene.hh:14,
from gene.cc:21:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../include/matrix.hh:26,
from ../include/motif.hh:20,
from ../include/gene.hh:14,
from gene.cc:21:
/usr/include/c++/8/bits/vector.tcc: In function 'void examineBaseCountOfGeneSeq(AnnoSequence*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../include/types.hh:37,
from ../include/geneticcode.hh:17,
from ../include/motif.hh:21,
from ../include/gene.hh:14,
from gene.cc:21:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/statemodel.hh:16,
from ../include/intronmodel.hh:17,
from intronmodel.cc:26:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/extrinsicinfo.hh:24,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/intronmodel.hh:17,
from intronmodel.cc:26:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/extrinsicinfo.hh:25,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/intronmodel.hh:17,
from intronmodel.cc:26:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/statemodel.hh:16,
from ../include/exonmodel.hh:22,
from exonmodel.cc:25:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/extrinsicinfo.hh:24,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/exonmodel.hh:22,
from exonmodel.cc:25:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/intronmodel.hh:17,
from intronmodel.cc:26:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/extrinsicinfo.hh:25,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/exonmodel.hh:22,
from exonmodel.cc:25:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
intronmodel.cc: In static member function 'static void IntronModel::init()':
intronmodel.cc:129:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
}catch( ProjectError e) {
^
intronmodel.cc:134:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
}catch( ProjectError e) {
^
intronmodel.cc:139:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
}catch( ProjectError e) {
^
intronmodel.cc:144:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
}catch( ProjectError e) {
^
intronmodel.cc:149:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
}catch( ProjectError e) {
^
intronmodel.cc:154:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
}catch( ProjectError e) {
^
intronmodel.cc:159:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
}catch( ProjectError e) {
^
intronmodel.cc:164:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
}catch( ProjectError e) {
^
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o igenicmodel.o igenicmodel.cc -I../include
intronmodel.cc: In member function 'virtual void IntronModel::viterbiForwardAndSampling(ViterbiMatrixType&, ViterbiMatrixType&, int, int, AlgorithmVariant, OptionListItem&)':
intronmodel.cc:799:12: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
intronmodel.cc:866:28: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
intronmodel.cc: In member function 'virtual Double IntronModel::emiProbUnderModel(int, int) const':
intronmodel.cc:926:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
intronmodel.cc: In member function 'Double IntronModel::seqProb(int, int) const':
intronmodel.cc:1082:35: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
intronmodel.cc:1108:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
intronmodel.cc: In static member function 'static Double IntronModel::aSSProb(int, bool)':
intronmodel.cc:1187:37: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
intronmodel.cc: In static member function 'static Double IntronModel::dSSProb(int, bool)':
intronmodel.cc:1254:37: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
In file included from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/exonmodel.hh:22,
from exonmodel.cc:25:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
exonmodel.cc: In static member function 'static void ExonModel::init()':
exonmodel.cc:318:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
}catch( ProjectError e) {
^
exonmodel.cc:323:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
}catch( ProjectError e) {
^
exonmodel.cc:328:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
}catch( ProjectError e) {
^
exonmodel.cc:333:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
}catch( ProjectError e) {
^
exonmodel.cc:338:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
}catch( ProjectError e) {
^
exonmodel.cc:343:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
}catch( ProjectError e) {
^
exonmodel.cc:348:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch( ProjectError e) {
^
exonmodel.cc:353:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch( ProjectError e) {
^
exonmodel.cc:358:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch( ProjectError e) {
^
exonmodel.cc:363:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch( ProjectError e) {
^
exonmodel.cc:368:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch( ProjectError e) {
^
exonmodel.cc:373:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch( ProjectError e) {
^
exonmodel.cc:382:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch( ProjectError e) {}
^
exonmodel.cc:385:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch( ProjectError e) {}
^
exonmodel.cc: In member function 'virtual void ExonModel::viterbiForwardAndSampling(ViterbiMatrixType&, ViterbiMatrixType&, int, int, AlgorithmVariant, OptionListItem&)':
exonmodel.cc:1129:31: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch(NoSubmapFoundError e) {}
^
exonmodel.cc:1156:28: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
exonmodel.cc: In member function 'Double ExonModel::notEndPartEmiProb(int, int, int, Feature*) const':
exonmodel.cc:1588:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
exonmodel.cc:1618:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
exonmodel.cc: In member function 'Double ExonModel::seqProb(int, int, int) const':
exonmodel.cc:1964:45: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
exonmodel.cc:1981:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
exonmodel.cc: In member function 'Double ExonModel::eTermSeqProb(int, int, int) const':
exonmodel.cc:2019:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
exonmodel.cc: In member function 'Double ExonModel::initialSeqProb(int, int, int) const':
exonmodel.cc:2046:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
In file included from ../include/statemodel.hh:16,
from ../include/igenicmodel.hh:20,
from igenicmodel.cc:14:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/extrinsicinfo.hh:24,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/igenicmodel.hh:20,
from igenicmodel.cc:14:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/extrinsicinfo.hh:25,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/igenicmodel.hh:20,
from igenicmodel.cc:14:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/igenicmodel.hh:20,
from igenicmodel.cc:14:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
igenicmodel.cc: In static member function 'static void IGenicModel::init()':
igenicmodel.cc:52:14: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch( ProjectError ) { }
^~~~~~~~~~~~
igenicmodel.cc: In member function 'virtual void IGenicModel::viterbiForwardAndSampling(ViterbiMatrixType&, ViterbiMatrixType&, int, int, AlgorithmVariant, OptionListItem&)':
igenicmodel.cc:279:24: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
igenicmodel.cc: In member function 'virtual Double IGenicModel::emiProbUnderModel(int, int) const':
igenicmodel.cc:343:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
igenicmodel.cc:355:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
intronmodel.cc: In static member function 'static void IntronModel::readAllParameters()':
intronmodel.cc:398:23: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=]
sprintf(zusString, "[%d]", idx+1);
^~~~~~
intronmodel.cc:398:23: note: directive argument in the range [1, 2147483647]
In file included from /usr/include/stdio.h:862,
from /usr/include/c++/8/cstdio:42,
from /usr/include/c++/8/ext/string_conversions.h:43,
from /usr/include/c++/8/bits/basic_string.h:6391,
from /usr/include/c++/8/string:52,
from /usr/include/c++/8/bits/locale_classes.h:40,
from /usr/include/c++/8/bits/ios_base.h:41,
from /usr/include/c++/8/ios:42,
from /usr/include/c++/8/ostream:38,
from ../include/matrix.hh:27,
from ../include/statemodel.hh:15,
from ../include/intronmodel.hh:17,
from intronmodel.cc:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 6
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:60,
from ../include/types.hh:38,
from ../include/vitmatrix.hh:14,
from ../include/statemodel.hh:16,
from ../include/intronmodel.hh:17,
from intronmodel.cc:26:
/usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, LLDouble>; _KeyOfValue = std::_Select1st<std::pair<const int, LLDouble> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, LLDouble> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, LLDouble>, std::_Select1st<std::pair<const int, LLDouble> >, std::less<int>, std::allocator<std::pair<const int, LLDouble> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, LLDouble> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from ../include/types.hh:38,
from ../include/vitmatrix.hh:14,
from ../include/statemodel.hh:16,
from ../include/intronmodel.hh:17,
from intronmodel.cc:26:
/usr/include/c++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = LLDouble; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, LLDouble> >]':
/usr/include/c++/8/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, LLDouble> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o utrmodel.o utrmodel.cc -I../include
In file included from ../include/statemodel.hh:16,
from ../include/utrmodel.hh:17,
from utrmodel.cc:23:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/extrinsicinfo.hh:24,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/utrmodel.hh:17,
from utrmodel.cc:23:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/extrinsicinfo.hh:25,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/utrmodel.hh:17,
from utrmodel.cc:23:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o merkmal.o merkmal.cc -I../include
In file included from /usr/include/c++/8/map:60,
from ../include/types.hh:38,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/8/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++/8/bits/stl_tree.h:2146:5: note: parameter passing for argument of type 'std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::const_iterator' {aka 'std::_Rb_tree_const_iterator<Feature>'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/set:61,
from ../include/extrinsicinfo.hh:28,
from extrinsicinfo.cc:31:
/usr/include/c++/8/bits/stl_set.h: In constructor 'std::set<_Key, _Compare, _Alloc>::set(_InputIterator, _InputIterator) [with _InputIterator = std::_List_iterator<Feature>; _Key = Feature; _Compare = std::less<Feature>; _Alloc = std::allocator<Feature>]':
/usr/include/c++/8/bits/stl_set.h:191:2: note: parameter passing for argument of type 'std::_List_iterator<Feature>' changed in GCC 7.1
set(_InputIterator __first, _InputIterator __last)
^~~
/usr/include/c++/8/bits/stl_set.h:191:2: note: parameter passing for argument of type 'std::_List_iterator<Feature>' changed in GCC 7.1
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o vitmatrix.o vitmatrix.cc -I../include
In file included from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/utrmodel.hh:17,
from utrmodel.cc:23:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:60,
from ../include/types.hh:38,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Arg&&, _NodeGen&) [with _Arg = const Feature&; _NodeGen = std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::_Alloc_node; _Key = Feature; _Val = Feature; _KeyOfValue = std::_Identity<Feature>; _Compare = std::less<Feature>; _Alloc = std::allocator<Feature>]':
/usr/include/c++/8/bits/stl_tree.h:2207:7: note: parameter passing for argument of type 'std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::const_iterator' {aka 'std::_Rb_tree_const_iterator<Feature>'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../include/types.hh:37,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/8/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++/8/bits/stl_algo.h:5332:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
__set_difference(_InputIterator1 __first1, _InputIterator1 __last1,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:5332:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5332:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5332:5: 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++/8/map:60,
from ../include/types.hh:38,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/8/bits/stl_tree.h:1042:65: note: parameter passing for argument of type 'std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::const_iterator' {aka 'std::_Rb_tree_const_iterator<Feature>'} changed in GCC 7.1
return _M_insert_unique_(__pos, std::forward<_Arg>(__x), __an);
^
/usr/include/c++/8/bits/stl_tree.h:1042:65: note: parameter passing for argument of type 'std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::const_iterator' {aka 'std::_Rb_tree_const_iterator<Feature>'} changed in GCC 7.1
return _M_insert_unique_(__pos, std::forward<_Arg>(__x), __an);
^
utrmodel.cc: In static member function 'static void UtrModel::init()':
utrmodel.cc:167:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) {
^
utrmodel.cc:172:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:175:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:178:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:181:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:184:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:187:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:190:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:193:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:196:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:199:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:202:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:205:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:208:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:211:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:214:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:217:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:220:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:223:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
utrmodel.cc:228:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:231:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) { cerr << e.getMessage(); }
^
utrmodel.cc:234:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) {}
^
utrmodel.cc:237:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) {}
^
utrmodel.cc:240:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) {}
^
utrmodel.cc:243:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) {}
^
utrmodel.cc:246:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) {}
^
utrmodel.cc:249:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) {}
^
utrmodel.cc:252:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) {}
^
utrmodel.cc: In member function 'virtual void UtrModel::viterbiForwardAndSampling(ViterbiMatrixType&, ViterbiMatrixType&, int, int, AlgorithmVariant, OptionListItem&)':
utrmodel.cc:1062:28: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
utrmodel.cc: In member function 'Double UtrModel::notEndPartEmiProb(int, int, int, Feature*) const':
utrmodel.cc:1275:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
utrmodel.cc:1409:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
utrmodel.cc: In member function 'Double UtrModel::seqProb(int, int, bool, int) const':
utrmodel.cc:1700:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
utrmodel.cc:1735:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
utrmodel.cc: In member function 'Double UtrModel::tssupSeqProb(int, int, bool) const':
utrmodel.cc:1760:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
utrmodel.cc: In static member function 'static void UtrModel::computeTtsProbs(int, int)':
utrmodel.cc:1889:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
utrmodel.cc:1916:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
extrinsicinfo.cc: In member function 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)':
extrinsicinfo.cc:2532:54: note: parameter passing for argument of type 'std::_List_iterator<Feature>' changed in GCC 7.1
set <Feature> startHS(flist.begin(), flist.end());
^
In file included from /usr/include/c++/8/algorithm:62,
from ../include/types.hh:37,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
^
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
^
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
^
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
extrinsicinfo.cc:2573:53: note: parameter passing for argument of type 'std::_List_iterator<Feature>' changed in GCC 7.1
set <Feature> stopHS(flist.begin(), flist.end());
^
In file included from /usr/include/c++/8/algorithm:62,
from ../include/types.hh:37,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
^
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
^
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
^
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
extrinsicinfo.cc:2611:52: note: parameter passing for argument of type 'std::_List_iterator<Feature>' changed in GCC 7.1
set <Feature> dssHS(flist.begin(), flist.end());
^
In file included from /usr/include/c++/8/algorithm:62,
from ../include/types.hh:37,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
^
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
^
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
^
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
extrinsicinfo.cc:2657:52: note: parameter passing for argument of type 'std::_List_iterator<Feature>' changed in GCC 7.1
set <Feature> assHS(flist.begin(), flist.end());
^
In file included from /usr/include/c++/8/algorithm:62,
from ../include/types.hh:37,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
^
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
^
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
^
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In file included from ../include/extrinsicinfo.hh:24,
from ../include/merkmal.hh:17,
from merkmal.cc:13:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/extrinsicinfo.hh:25,
from ../include/merkmal.hh:17,
from merkmal.cc:13:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/pp_scoring.hh:21,
from ../include/gene.hh:15,
from ../include/extrinsicinfo.hh:25,
from ../include/merkmal.hh:17,
from merkmal.cc:13:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from vitmatrix.cc:10:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/merkmal.hh:17,
from merkmal.cc:13:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../include/types.hh:35,
from ../include/vitmatrix.hh:14,
from vitmatrix.cc:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<ViterbiSubmapType>::iterator' {aka '__gnu_cxx::__normal_iterator<ViterbiSubmapType*, std::vector<ViterbiSubmapType> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:60,
from ../include/types.hh:38,
from ../include/vitmatrix.hh:14,
from vitmatrix.cc:10:
/usr/include/c++/8/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++/8/bits/stl_tree.h:2500:5: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h:2500:5: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
/usr/include/c++/8/bits/stl_tree.h: In member function 'void ViterbiSubmapType::useMaximum(Double&)':
/usr/include/c++/8/bits/stl_tree.h:1169:2: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
_M_erase_aux(__first, __last);
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h:1169:2: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
_M_erase_aux(__first, __last);
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h: In member function 'int ViterbiSubmapType::eraseUnneededSubstate(SubstateId)':
/usr/include/c++/8/bits/stl_tree.h:2518:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
_M_erase_aux(__p.first, __p.second);
^~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../include/types.hh:35,
from ../include/vitmatrix.hh:14,
from vitmatrix.cc:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<ViterbiEntryType>::iterator' {aka '__gnu_cxx::__normal_iterator<ViterbiEntryType*, std::vector<ViterbiEntryType> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void ViterbiColumnType::addState(int, signed char)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ViterbiEntryType*, std::vector<ViterbiEntryType> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../include/types.hh:35,
from ../include/vitmatrix.hh:14,
from vitmatrix.cc:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'ViterbiSubmapType& ViterbiColumnType::addSubstates(const ViterbiSubmapType&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ViterbiSubmapType*, std::vector<ViterbiSubmapType> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:60,
from ../include/types.hh:38,
from ../include/vitmatrix.hh:14,
from vitmatrix.cc:10:
/usr/include/c++/8/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++/8/bits/stl_tree.h:2146:5: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_tree.h:2411:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h:2411:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
In file included from /usr/include/c++/8/map:61,
from ../include/types.hh:38,
from ../include/vitmatrix.hh:14,
from vitmatrix.cc:10:
/usr/include/c++/8/bits/stl_map.h: In member function 'void ViterbiSubmapType::registerPredecessors()':
/usr/include/c++/8/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o lldouble.o lldouble.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o mea.o mea.cc -I../include
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/mea.hh:4,
from mea.cc:1:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/pp_scoring.hh:21,
from ../include/gene.hh:15,
from ../include/mea.hh:4,
from mea.cc:1:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o graph.o graph.cc -I../include
utrmodel.cc: In static member function 'static void UtrModel::readAllParameters()':
utrmodel.cc:624:26: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=]
sprintf(zusString, "[%d]", idx+1);
^~~~~~
utrmodel.cc:624:26: note: directive argument in the range [1, 2147483647]
In file included from /usr/include/stdio.h:862,
from /usr/include/c++/8/cstdio:42,
from /usr/include/c++/8/ext/string_conversions.h:43,
from /usr/include/c++/8/bits/basic_string.h:6391,
from /usr/include/c++/8/string:52,
from /usr/include/c++/8/bits/locale_classes.h:40,
from /usr/include/c++/8/bits/ios_base.h:41,
from /usr/include/c++/8/ios:42,
from /usr/include/c++/8/ostream:38,
from ../include/matrix.hh:27,
from ../include/statemodel.hh:15,
from ../include/utrmodel.hh:17,
from utrmodel.cc:23:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 6
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/graph.hh:10,
from ../include/mea.hh:5,
from mea.cc:1:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/exonmodel.hh:22,
from ../include/exoncand.hh:27,
from ../include/graph.hh:11,
from ../include/mea.hh:5,
from mea.cc:1:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../include/types.hh:35,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/8/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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' {aka '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/graph.hh:9,
from graph.cc:9:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/pp_scoring.hh:21,
from ../include/gene.hh:15,
from ../include/graph.hh:9,
from graph.cc:9:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/graph.hh:10,
from graph.cc:9:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/exonmodel.hh:22,
from ../include/exoncand.hh:27,
from ../include/graph.hh:11,
from graph.cc:9:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../include/types.hh:37,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/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++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from ../include/types.hh:37,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/8/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++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../include/types.hh:37,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
__heap_select(_RandomAccessIterator __first,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1933:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
std::__heap_select(__first, __middle, __last, __comp);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'void BinnedMMGroup::trainBins(int)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from ../include/types.hh:37,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/8/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++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../include/types.hh:37,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In static member function 'static std::vector<double> CRF::capOutliers(std::vector<double>)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../include/matrix.hh:26,
from ../include/motif.hh:20,
from ../include/gene.hh:14,
from ../include/mea.hh:4,
from mea.cc:1:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'AugustusGraph::AugustusGraph(std::__cxx11::list<Status>*, const char*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../include/types.hh:35,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/8/bits/stl_vector.h: In static member function 'static void CRF::onlineLargeMarginTraining(Parameters*, std::vector<AnnoSequence*>, FeatureCollection&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o meaPath.o meaPath.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o exoncand.o exoncand.cc -I../include
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/graph.hh:9,
from meaPath.cc:3:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/pp_scoring.hh:21,
from ../include/gene.hh:15,
from ../include/graph.hh:9,
from meaPath.cc:3:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/statemodel.hh:16,
from ../include/exonmodel.hh:22,
from ../include/exoncand.hh:27,
from exoncand.cc:16:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/extrinsicinfo.hh:24,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/exonmodel.hh:22,
from ../include/exoncand.hh:27,
from exoncand.cc:16:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/graph.hh:10,
from meaPath.cc:3:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/extrinsicinfo.hh:25,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/exonmodel.hh:22,
from ../include/exoncand.hh:27,
from exoncand.cc:16:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/exonmodel.hh:22,
from ../include/exoncand.hh:27,
from ../include/graph.hh:11,
from meaPath.cc:3:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o randseqaccess.o randseqaccess.cc -I../include
In file included from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/exonmodel.hh:22,
from ../include/exoncand.hh:27,
from exoncand.cc:16:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/randseqaccess.hh:14,
from randseqaccess.cc:15:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/pp_scoring.hh:21,
from ../include/gene.hh:15,
from ../include/randseqaccess.hh:14,
from randseqaccess.cc:15:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/extrinsicinfo.hh:24,
from ../include/randseqaccess.hh:16,
from randseqaccess.cc:15:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/randseqaccess.hh:16,
from randseqaccess.cc:15:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o fasta.o fasta.cc -I../include
randseqaccess.cc: In member function 'void SpeciesCollection::readExtrinsicCFGFile(std::vector<std::__cxx11::basic_string<char> >&)':
randseqaccess.cc:98:29: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
}catch(ProjectError e){
^
randseqaccess.cc:137:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
randseqaccess.cc: In member function 'void SpeciesCollection::readGFFFile(const char*)':
randseqaccess.cc:166:35: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e){}
^
randseqaccess.cc:196:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o ncmodel.o ncmodel.cc -I../include
In file included from ../include/statemodel.hh:16,
from ../include/ncmodel.hh:15,
from ncmodel.cc:13:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/extrinsicinfo.hh:24,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/ncmodel.hh:15,
from ncmodel.cc:13:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/extrinsicinfo.hh:25,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/ncmodel.hh:15,
from ncmodel.cc:13:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/ncmodel.hh:15,
from ncmodel.cc:13:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
ncmodel.cc: In static member function 'static void NcModel::init()':
ncmodel.cc:68:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) {
^
ncmodel.cc: In member function 'virtual void NcModel::viterbiForwardAndSampling(ViterbiMatrixType&, ViterbiMatrixType&, int, int, AlgorithmVariant, OptionListItem&)':
ncmodel.cc:264:28: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
ncmodel.cc:346:28: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o commontrain.o commontrain.cc -I../include
ncmodel.cc: In member function 'Double NcModel::notEndPartEmiProb(int, int, int, Feature*) const':
ncmodel.cc:544:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o igenictrain.o igenictrain.cc -I../include
In file included from ../include/statemodel.hh:16,
from ../include/igenicmodel.hh:20,
from igenictrain.cc:13:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/extrinsicinfo.hh:24,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/igenicmodel.hh:20,
from igenictrain.cc:13:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/extrinsicinfo.hh:25,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/igenicmodel.hh:20,
from igenictrain.cc:13:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/ncmodel.hh:15,
from ncmodel.cc:13:
/usr/include/c++/8/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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' {aka '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/ncmodel.hh:15,
from ncmodel.cc:13:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void NcModel::computeLengthDistributions()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/igenicmodel.hh:20,
from igenictrain.cc:13:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o introntrain.o introntrain.cc -I../include
igenictrain.cc: In member function 'void IGenicModel::processSequence(const char*, const char*)':
igenictrain.cc:175:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {}
^
igenictrain.cc: In member function 'virtual void IGenicModel::printProbabilities(int, BaseCount*, const char*)':
igenictrain.cc:252:12: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
catch( ProjectError ) {
^~~~~~~~~~~~
In file included from ../include/statemodel.hh:16,
from ../include/intronmodel.hh:17,
from introntrain.cc:14:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/extrinsicinfo.hh:24,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/intronmodel.hh:17,
from introntrain.cc:14:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/extrinsicinfo.hh:25,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/intronmodel.hh:17,
from introntrain.cc:14:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/intronmodel.hh:17,
from introntrain.cc:14:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
introntrain.cc: In member function 'void IntronModel::processSequence(const char*, const char*)':
introntrain.cc:169:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
introntrain.cc: In member function 'void IntronModel::processASS(const char*, int, Boolean)':
introntrain.cc:252:37: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e){
^
introntrain.cc: In member function 'void IntronModel::processDSS(const char*, int)':
introntrain.cc:288:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
introntrain.cc: In member function 'void IntronModel::buildProbabilities(const AnnoSequence*)':
introntrain.cc:352:31: warning: catching polymorphic type 'class IntronModelError' by value [-Wcatch-value=]
} catch (IntronModelError e) {
^
introntrain.cc: In member function 'virtual void IntronModel::printProbabilities(int, BaseCount*, const char*)':
introntrain.cc:731:14: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch( ProjectError ) {
^~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o exontrain.o exontrain.cc -I../include
In file included from /usr/include/c++/8/vector:69,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/intronmodel.hh:17,
from introntrain.cc:14:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' {aka '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o utrtrain.o utrtrain.cc -I../include
In file included from /usr/include/c++/8/vector:64,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/intronmodel.hh:17,
from introntrain.cc:14:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void IntronModel::makeDSSProbs()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from ../include/statemodel.hh:16,
from ../include/exonmodel.hh:22,
from exontrain.cc:13:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/extrinsicinfo.hh:24,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/exonmodel.hh:22,
from exontrain.cc:13:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/extrinsicinfo.hh:25,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/exonmodel.hh:22,
from exontrain.cc:13:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/statemodel.hh:16,
from ../include/utrmodel.hh:17,
from utrtrain.cc:15:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/extrinsicinfo.hh:24,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/utrmodel.hh:17,
from utrtrain.cc:15:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/extrinsicinfo.hh:25,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/utrmodel.hh:17,
from utrtrain.cc:15:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/exonmodel.hh:22,
from exontrain.cc:13:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
In file included from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/utrmodel.hh:17,
from utrtrain.cc:15:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
exontrain.cc: In member function 'virtual void ExonModel::printProbabilities(int, BaseCount*, const char*)':
exontrain.cc:522:9: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
catch( ProjectError ) {
^~~~~~~~~~~~
exontrain.cc: In member function 'void ExonModel::processExons(const Gene*)':
exontrain.cc:626:26: warning: catching polymorphic type 'class ExonModelError' by value [-Wcatch-value=]
} catch (ExonModelError e) {
^
exontrain.cc:634:26: warning: catching polymorphic type 'class ExonModelError' by value [-Wcatch-value=]
} catch( ExonModelError e ){
^
exontrain.cc:643:30: warning: catching polymorphic type 'class ExonModelError' by value [-Wcatch-value=]
} catch( ExonModelError e ){
^
exontrain.cc:651:26: warning: catching polymorphic type 'class ExonModelError' by value [-Wcatch-value=]
} catch( ExonModelError e ){
^
exontrain.cc: In member function 'void ExonModel::processInternalExon(const State*)':
exontrain.cc:811:29: warning: catching polymorphic type 'class ExonModelError' by value [-Wcatch-value=]
} catch( ExonModelError e ){
^
exontrain.cc: In member function 'void ExonModel::processInnerSequence(const char*, const char*, int)':
exontrain.cc:896:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {}
^
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o dummy.o dummy.cc -I../include
utrtrain.cc: In member function 'void UtrModel::buildProbabilities(const AnnoSequence*)':
utrtrain.cc:114:26: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=]
} catch (UtrModelError e) {
^
utrtrain.cc: In member function 'void UtrModel::buildTSSModel(const AnnoSequence*)':
utrtrain.cc:197:29: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=]
} catch (UtrModelError e) {
^
utrtrain.cc: In member function 'void UtrModel::processStates(const Gene*)':
utrtrain.cc:396:29: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=]
} catch (UtrModelError e) {
^
utrtrain.cc:403:29: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=]
} catch( UtrModelError e ){
^
utrtrain.cc:413:26: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=]
} catch( UtrModelError e ){
^
utrtrain.cc:423:29: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=]
} catch( UtrModelError e ){
^
utrtrain.cc:438:29: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=]
} catch (UtrModelError e) {
^
utrtrain.cc:445:29: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=]
} catch( UtrModelError e ){
^
utrtrain.cc:455:26: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=]
} catch( UtrModelError e ){
^
utrtrain.cc:465:29: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=]
} catch( UtrModelError e ){
^
utrtrain.cc: In member function 'void UtrModel::process5InitSequence(const char*, const char*)':
utrtrain.cc:796:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
utrtrain.cc: In member function 'void UtrModel::process5Sequence(const char*, const char*)':
utrtrain.cc:810:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
utrtrain.cc: In member function 'void UtrModel::process3Sequence(const char*, const char*)':
utrtrain.cc:824:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
utrtrain.cc: In member function 'void UtrModel::processTssupSequence(const char*, const char*)':
utrtrain.cc:838:37: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
utrtrain.cc: In static member function 'static void UtrModel::storeGCPars(int)':
utrtrain.cc:851:24: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch(ProjectError e) {
^
utrtrain.cc: In member function 'virtual void UtrModel::printProbabilities(int, BaseCount*, const char*)':
utrtrain.cc:1018:14: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch( ProjectError ) {
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void IntronModel::buildProbabilities(const AnnoSequence*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from ../include/statemodel.hh:16,
from ../include/intronmodel.hh:17,
from dummy.cc:13:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/extrinsicinfo.hh:24,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/intronmodel.hh:17,
from dummy.cc:13:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/extrinsicinfo.hh:25,
from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/intronmodel.hh:17,
from dummy.cc:13:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/exonmodel.hh:22,
from exontrain.cc:13:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' {aka '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from ../include/merkmal.hh:17,
from ../include/statemodel.hh:17,
from ../include/intronmodel.hh:17,
from dummy.cc:13:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc
In file included from /usr/include/c++/8/vector:64,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/exonmodel.hh:22,
from exontrain.cc:13:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void ExonModel::buildProbabilities()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc -I../include
In file included from ../include/pp_profile.hh:21,
from ../include/pp_fastBlockSearcher.hh:19,
from pp_fastBlockSearcher.cc:1:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/pp_profile.hh:22,
from ../include/pp_fastBlockSearcher.hh:19,
from pp_fastBlockSearcher.cc:1:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from pp_fastBlockSearcher.cc:1:
../include/pp_fastBlockSearcher.hh: In member function 'void PP::CandidateCollection::pushSeeds(int)':
../include/pp_fastBlockSearcher.hh:371:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
echo "-Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security" > cxxflags
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -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 dummy.o -I../include
cp prepareAlign ../bin/
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -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
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from augustus.cc:15:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/pp_scoring.hh:21,
from ../include/gene.hh:15,
from augustus.cc:15:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/extrinsicinfo.hh:24,
from ../include/namgene.hh:15,
from augustus.cc:17:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from fastBlockSearch.cc:14:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from ../include/pp_profile.hh:21,
from fastBlockSearch.cc:15:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/namgene.hh:15,
from augustus.cc:17:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
In file included from ../include/pp_profile.hh:22,
from fastBlockSearch.cc:15:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -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 -I../include
augustus.cc: In function 'void predictOnInputSequences(AnnoSequence*, NAMGene&, FeatureCollection&, Strand)':
augustus.cc:427:29: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e){
^
augustus.cc: In function 'void setParameters()':
augustus.cc:462:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
In file included from fastBlockSearch.cc:16:
../include/pp_fastBlockSearcher.hh: In member function 'void PP::CandidateCollection::pushSeeds(int)':
../include/pp_fastBlockSearcher.hh:371:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError e) {
^
In file included from ../include/motif.hh:21,
from ../include/gene.hh:14,
from etraining.cc:13:
../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)':
../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)':
../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=]
} catch (InvalidNucleotideError){}
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/pp_scoring.hh:21,
from ../include/gene.hh:15,
from etraining.cc:13:
../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const':
../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {
^~~~~~~~~~~~~~~~~~
../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const':
../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=]
} catch (NoSubmapFoundError) {}
^~~~~~~~~~~~~~~~~~
In file included from ../include/extrinsicinfo.hh:24,
from etraining.cc:14:
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)':
../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)':
../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)':
../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)':
../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)':
../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)':
../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)':
../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError e) {}
^
In file included from etraining.cc:14:
../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()':
../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=]
} catch (KeyNotFoundError) {}
^~~~~~~~~~~~~~~~
etraining.cc: In function 'int main(int, char**)':
etraining.cc:72:24: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
cp augustus ../bin/
cp fastBlockSearch ../bin/
cp etraining ../bin/
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
cd auxprogs && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs'
cd bam2hints; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/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-3.3.1+dfsg/auxprogs/bam2hints'
cd compileSpliceCands; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/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-3.3.1+dfsg/auxprogs/compileSpliceCands'
cd filterBam; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src;make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam/src'
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
mv filterBam ../../../bin/filterBam
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam'
cd homGeneMapping; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src; make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping/src'
make[5]: Nothing to be done for 'all'.
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping'
cd joingenes; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/joingenes'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/joingenes'
cd bam2wig; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/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-3.3.1+dfsg/auxprogs/bam2wig'
cd utrrnaseq/Debug; make all;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/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:355:64: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
vector<double>::iterator jt = min_element(d.begin(), d.end());
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:71,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/string:40,
from ../src/Genomic_Data.hpp:8,
from ../src/UTRs.cpp:5:
/usr/include/c++/8/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++/8/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
operator()(_Iterator1 __it1, _Iterator2 __it2) const
^~~~~~~~
/usr/include/c++/8/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++/8/algorithm:62,
from /usr/include/boost/core/swap.hpp:25,
from /usr/include/boost/utility/swap.hpp:15,
from /usr/include/boost/tuple/detail/tuple_basic.hpp:40,
from /usr/include/boost/tuple/tuple.hpp:28,
from ../src/Compute_UTRs.hpp:16,
from ../src/UTRs.cpp:9:
/usr/include/c++/8/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++/8/bits/stl_algo.h:5588:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
__min_element(_ForwardIterator __first, _ForwardIterator __last,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:5588:5: 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++/8/bits/stl_algo.h:5595:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
if (__comp(__first, __result))
~~~~~~^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:5610:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
inline min_element(_ForwardIterator __first, _ForwardIterator __last)
^~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:5610:12: 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++/8/bits/stl_algo.h:5619:43: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
return _GLIBCXX_STD_A::__min_element(__first, __last,
^
In file included from /usr/include/c++/8/vector:64,
from ../src/Genomic_Data.hpp:9,
from ../src/UTRs.cpp:5:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/Genomic_Data.hpp:9,
from ../src/UTRs.cpp:5:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:63,
from ../src/Genomic_Data.hpp:9,
from ../src/UTRs.cpp:5:
/usr/include/c++/8/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++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
return std::__uninitialized_copy_a
~~~~~~~~~~~~~~~~~~~~~~~~~~~
(_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
{ return std::uninitialized_copy(__first, __last, __result); }
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*]':
/usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
uninitialized_copy(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
return std::__uninitialized_copy<__is_trivial(_ValueType1)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&& __is_trivial(_ValueType2)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&& __assignable>::
~~~~~~~~~~~~~~~~~~
__uninit_copy(__first, __last, __result);
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__uninit_copy(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
{ return std::copy(__first, __last, __result); }
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/string:40,
from ../src/Genomic_Data.hpp:8,
from ../src/UTRs.cpp:5:
/usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator<double*>; _OI = double*]':
/usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
copy(_II __first, _II __last, _OI __result)
^~~~
/usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algobase.h:67,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/string:40,
from ../src/Genomic_Data.hpp:8,
from ../src/UTRs.cpp:5:
/usr/include/c++/8/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++/8/bits/stl_iterator.h:1235:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__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
cp utrrnaseq ../../../bin/utrrnaseq
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
asciidoctor -a docdate='' -b manpage debian/mansrc/*adoc
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
mkdir -p debian/augustus/usr/bin
install bin/* debian/augustus/usr/bin
install auxprogs/checkTargetSortedness/checkTargetSortedness \
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/aln2wig
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 -r docs/tutorial \
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-3.3.1+dfsg'
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
dh_installchangelogs -k HISTORY.TXT
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
debian/rules override_dh_compress
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
dh_compress -Xtutorial
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
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/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/bam2hints contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/prepareAlign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/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/utrrnaseq 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/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: package could avoid a useless dependency if debian/augustus/usr/bin/bam2wig was not linked against libbz2.so.1.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/bam2wig was not linked against liblzma.so.5 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/checkTargetSortedness debian/augustus/usr/bin/bam2wig were not linked against libncurses.so.6 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/checkTargetSortedness debian/augustus/usr/bin/bam2wig were not linked against libtinfo.so.6 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/bam2wig was not linked against libhts.so.2 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: package augustus: unused substitution variable ${perl:Depends}
dpkg-gencontrol: warning: package augustus: unused substitution variable ${perl:Depends}
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.3.1+dfsg-2_armhf.deb'.
dpkg-deb: building package 'augustus' in '../augustus_3.3.1+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../augustus_3.3.1+dfsg-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build augustus-3.3.1+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-09-16T05:15:57Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
augustus_3.3.1+dfsg-2_armhf.changes:
------------------------------------
Format: 1.8
Date: Thu, 13 Sep 2018 15:48:26 +0200
Source: augustus
Binary: augustus augustus-data augustus-doc
Architecture: armhf
Version: 3.3.1+dfsg-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
augustus - gene prediction in eukaryotic genomes
augustus-data - data files for AUGUSTUS
augustus-doc - documentation files for AUGUSTUS
Changes:
augustus (3.3.1+dfsg-2) unstable; urgency=medium
.
* Team upload.
* d/watch: Source download is now on Github
* Standards-Version: 4.2.1
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Files:
056ee834b9d299d4663400328faf91b1 22396212 debug optional augustus-dbgsym_3.3.1+dfsg-2_armhf.deb
f48d5a55d3274bb1cedb4a5c123db6c8 8270 science optional augustus_3.3.1+dfsg-2_armhf.buildinfo
591fe1def8f976d2bc8f0df15db03a9a 929336 science optional augustus_3.3.1+dfsg-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
augustus-dbgsym_3.3.1+dfsg-2_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 22396212 bytes: control archive=1184 bytes.
920 bytes, 13 lines control
1378 bytes, 13 lines md5sums
Package: augustus-dbgsym
Source: augustus
Version: 3.3.1+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 22805
Depends: augustus (= 3.3.1+dfsg-2)
Built-Using: samtools-legacy (= 0.1.19-2)
Section: debug
Priority: optional
Description: debug symbols for augustus
Build-Ids: 191620e74ee33415e31ce4a14ce74c2376eff592 1a04705fc52f7e1e040ce4f92162f3f930620f46 1cec23a3b37171fe05154b3be28d2fa0e2c0a7f6 2afe31681b9820471a63a7b4bf88ad50fb8c461a 335815c770746f14f975a8ac832d1f57e3a8e6ce 3c627be12e25b802d08b5840efc7a06f93226be4 4601631e055bcc1297a35562903e28042a99cde0 8b53bab17de66de908dfff4f758a235e04def1e8 bc734241f742a454dbab17e7633ebcca870ea0c3 de28c5d68f682abcfad16afc473263f1ffedda41 e4a303a0743117f5bc88603b1fd0ad6b0e34a798 e69e50dfb336c6dffe05aae3e716bcbed232f862 f8b801b877dc2ed7d750d409cac5ecd36105d998
drwxr-xr-x root/root 0 2018-09-13 13:48 ./
drwxr-xr-x root/root 0 2018-09-13 13:48 ./usr/
drwxr-xr-x root/root 0 2018-09-13 13:48 ./usr/lib/
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augustus_3.3.1+dfsg-2_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 929336 bytes: control archive=4612 bytes.
1334 bytes, 22 lines control
9589 bytes, 128 lines md5sums
Package: augustus
Version: 3.3.1+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4106
Depends: libbamtools2.5.1, libbz2-1.0, libc6 (>= 2.15), libgcc1 (>= 1:3.5), libhts2 (>= 1.0), liblzma5 (>= 5.1.1alpha+20110809), libncurses6 (>= 6), libstdc++6 (>= 6), libtinfo6 (>= 6), zlib1g (>= 1:1.2.3.3), augustus-data
Built-Using: samtools-legacy (= 0.1.19-2)
Section: science
Priority: optional
Homepage: http://bioinf.uni-greifswald.de/augustus/
Description: gene prediction in eukaryotic genomes
AUGUSTUS is a software for gene prediction in eukaryotic genomic sequences
that is based on a generalized hidden Markov model (HMM), a probabilistic
model of a sequence and its gene structure. After learning gene structures
from a reference annotation, AUGUSTUS uses the HMM to recognize genes in a new
sequence and annotates it with the regions of identified genes. External hints,
e.g. from RNA sequencing, EST or protein alignments etc. can be used to guide
and improve the gene finding process. The result is the set of most likely gene
structures that comply with all given user constraints, if such gene
structures exist.
AUGUSTUS already includes prebuilt HMMs for many species, as well as scripts
to train custom models using annotated genomes.
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drwxr-xr-x root/root 0 2018-09-13 13:48 ./usr/share/
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| Post Build |
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+------------------------------------------------------------------------------+
| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 934312
Build-Time: 1144
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 893
Job: augustus_3.3.1+dfsg-2
Machine Architecture: armhf
Package: augustus
Package-Time: 2139
Source-Version: 3.3.1+dfsg-2
Space: 934312
Status: successful
Version: 3.3.1+dfsg-2
--------------------------------------------------------------------------------
Finished at 2018-09-16T05:15:57Z
Build needed 00:35:39, 934312k disc space