augustus →
3.3.2+dfsg-2 →
armhf → 2019-03-29 05:47:56
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| augustus 3.3.2+dfsg-2 (armhf) Fri, 29 Mar 2019 05:10:20 +0000 |
+==============================================================================+
Package: augustus
Version: 3.3.2+dfsg-2
Source Version: 3.3.2+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-71996d1d-08ea-4fd0-9009-82abb2de5e9b' 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 [11.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.0 MB]
Fetched 24.4 MB in 27s (917 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 66.0 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main augustus 3.3.2+dfsg-2 (dsc) [2305 B]
Get:2 http://172.17.0.1/private buster-staging/main augustus 3.3.2+dfsg-2 (tar) [66.0 MB]
Get:3 http://172.17.0.1/private buster-staging/main augustus 3.3.2+dfsg-2 (diff) [16.1 kB]
Fetched 66.0 MB in 6s (10.3 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/augustus-1CMmDu/augustus-3.3.2+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/augustus-1CMmDu' 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-uKVGeJ/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-uKVGeJ/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-uKVGeJ/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-uKVGeJ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-uKVGeJ/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-uKVGeJ/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-uKVGeJ/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-uKVGeJ/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (3069 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 krb5-locales libexpat1
libgpg-error-l10n libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 libnss-systemd libpam-systemd 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 56 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-uKVGeJ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14158 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, libcurl4-nss-dev, libssl-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, libcurl4-nss-dev, libssl-dev, asciidoctor
dpkg-deb: building package 'sbuild-build-depends-augustus-dummy' in '/<<BUILDDIR>>/resolver-uKVGeJ/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-uKVGeJ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-uKVGeJ/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-uKVGeJ/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-uKVGeJ/apt_archive ./ Sources [574 B]
Get:5 copy:/<<BUILDDIR>>/resolver-uKVGeJ/apt_archive ./ Packages [655 B]
Fetched 2562 B in 1s (3701 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 krb5-locales libexpat1
libgpg-error-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 cpp-8
debhelper dh-autoreconf dh-strip-nondeterminism dwz file g++-8 gcc-8
gcc-8-base gettext gettext-base groff-base icu-devtools intltool-debian
libamd2 libarchive-zip-perl libasan5 libatomic1 libbam-dev libbamtools-dev
libbamtools2.5.1 libblas-dev libblas3 libboost-iostreams-dev
libboost-iostreams1.67-dev libboost-iostreams1.67.0 libboost-regex1.67-dev
libboost-regex1.67.0 libboost1.67-dev libbsd0 libbtf1 libbz2-dev libcamd2
libcc1-0 libccolamd2 libcholmod3 libcolamd2 libcroco3 libcurl3-gnutls
libcurl3-nss libcurl4-nss-dev libcxsparse3 libdeflate0 libelf1
libfile-stripnondeterminism-perl libgcc-8-dev libgcc1 libgfortran5
libglib2.0-0 libgomp1 libgraphblas2 libgsl-dev libgsl23 libgslcblas0
libhts-dev libhts2 libicu-dev libicu63 libklu1 liblapack-dev liblapack3
libldl2 liblpsolve55-dev liblzma-dev libmagic-mgc libmagic1 libmetis5
libmongoose2 libncurses-dev libncurses5-dev libnghttp2-14 libnspr4 libnss3
libpipeline1 libpsl5 librbio2 librtmp1 libruby2.5 libsigsegv2 libspqr2
libsqlite3-0 libsqlite3-dev libssh2-1 libssl-dev libssl1.1 libstdc++-8-dev
libstdc++6 libsuitesparse-dev libsuitesparseconfig5 libtool libubsan1
libuchardet0 libumfpack5 libxml2 libyaml-0-2 lzma-dev m4 man-db po-debconf
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 gcc-8-locales dh-make gcc-8-doc libstdc++6-8-dbg libgcc1-dbg
libgomp1-dbg libitm1-dbg libatomic1-dbg libasan5-dbg liblsan0-dbg
libtsan0-dbg libubsan1-dbg libmpx2-dbg libquadmath0-dbg gettext-doc
libasprintf-dev libgettextpo-dev groff libbamtools-doc liblapack-doc
libboost1.67-doc libboost-atomic1.67-dev libboost-chrono1.67-dev
libboost-container1.67-dev libboost-context1.67-dev
libboost-coroutine1.67-dev libboost-date-time1.67-dev
libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-filesystem1.67-dev libboost-graph1.67-dev
libboost-graph-parallel1.67-dev libboost-locale1.67-dev libboost-log1.67-dev
libboost-math1.67-dev libboost-mpi1.67-dev libboost-mpi-python1.67-dev
libboost-numpy1.67-dev libboost-program-options1.67-dev
libboost-python1.67-dev libboost-random1.67-dev
libboost-serialization1.67-dev libboost-signals1.67-dev
libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev
libcurl4-doc libidn11-dev libkrb5-dev libldap2-dev libnss3-dev librtmp-dev
libssh2-1-dev pkg-config gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info
| gsl-ref-html icu-doc liblzma-doc ncurses-doc sqlite3-doc libssl-doc
libstdc++-8-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc
apparmor less www-browser libmail-box-perl ri ruby-dev bundler
Recommended packages:
curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs 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 gettext gettext-base
groff-base icu-devtools intltool-debian libamd2 libarchive-zip-perl
libbam-dev libbamtools-dev libbamtools2.5.1 libblas-dev libblas3
libboost-iostreams-dev libboost-iostreams1.67-dev libboost-iostreams1.67.0
libboost-regex1.67-dev libboost-regex1.67.0 libboost1.67-dev libbsd0 libbtf1
libbz2-dev libcamd2 libccolamd2 libcholmod3 libcolamd2 libcroco3
libcurl3-gnutls libcurl3-nss libcurl4-nss-dev libcxsparse3 libdeflate0
libelf1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0
libgraphblas2 libgsl-dev libgsl23 libgslcblas0 libhts-dev libhts2 libicu-dev
libicu63 libklu1 liblapack-dev liblapack3 libldl2 liblpsolve55-dev
liblzma-dev libmagic-mgc libmagic1 libmetis5 libmongoose2 libncurses-dev
libncurses5-dev libnghttp2-14 libnspr4 libnss3 libpipeline1 libpsl5 librbio2
librtmp1 libruby2.5 libsigsegv2 libspqr2 libsqlite3-dev libssh2-1 libssl-dev
libsuitesparse-dev libsuitesparseconfig5 libtool libuchardet0 libumfpack5
libxml2 libyaml-0-2 lzma-dev m4 man-db po-debconf 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:
cpp-8 g++-8 gcc-8 gcc-8-base libasan5 libatomic1 libcc1-0 libgcc-8-dev
libgcc1 libgomp1 libsqlite3-0 libssl1.1 libstdc++-8-dev libstdc++6 libubsan1
15 upgraded, 103 newly installed, 0 to remove and 41 not upgraded.
Need to get 87.5 MB of archives.
After this operation, 397 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-uKVGeJ/apt_archive ./ sbuild-build-depends-augustus-dummy 0.invalid.0 [940 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-2 [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 libcc1-0 armhf 8.3.0-2+rpi1 [37.9 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf gcc-8-base armhf 8.3.0-2+rpi1 [190 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libgcc1 armhf 1:8.3.0-2+rpi1 [36.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libgomp1 armhf 8.3.0-2+rpi1 [64.3 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libatomic1 armhf 8.3.0-2+rpi1 [8108 B]
Get:9 http://172.17.0.1/private buster-staging/main armhf libasan5 armhf 8.3.0-2+rpi1 [317 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libubsan1 armhf 8.3.0-2+rpi1 [103 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf g++-8 armhf 8.3.0-2+rpi1 [7480 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libstdc++-8-dev armhf 8.3.0-2+rpi1 [1545 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libgcc-8-dev armhf 8.3.0-2+rpi1 [595 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf gcc-8 armhf 8.3.0-2+rpi1 [7234 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf cpp-8 armhf 8.3.0-2+rpi1 [6805 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libstdc++6 armhf 8.3.0-2+rpi1 [325 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.4-3 [782 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.5-2 [1230 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libsqlite3-0 armhf 3.27.2-1 [550 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.35-4 [242 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.35-4 [110 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.35-4 [65.3 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf rubygems-integration all 1.11 [4994 B]
Get:27 http://172.17.0.1/private buster-staging/main armhf rake all 12.3.1-3 [66.9 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf ruby-did-you-mean all 1.2.1-1 [14.4 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf ruby-minitest all 5.11.3-1 [54.8 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf ruby-power-assert all 1.1.1-1 [10.9 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf ruby-test-unit all 3.2.8-1 [72.4 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf ruby-xmlrpc all 0.3.0-2 [23.7 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libssl1.1 armhf 1.1.1b-1 [1258 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libyaml-0-2 armhf 0.2.1-1 [38.8 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libruby2.5 armhf 2.5.3-4 [3140 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf ruby2.5 armhf 2.5.3-4 [393 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf ruby armhf 1:2.5.1+b1 [11.6 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf ruby-asciidoctor all 1.5.8-1 [188 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf asciidoctor all 1.5.8-1 [75.8 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.176-1 [158 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.3-1 [1077 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-6 [7973 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf debhelper all 12.1.1 [1016 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 63.1-6 [163 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libsuitesparseconfig5 armhf 1:5.4.0+dfsg-1 [20.5 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libamd2 armhf 1:5.4.0+dfsg-1 [27.1 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libbam-dev armhf 0.1.19-4 [111 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-3 [128 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libbamtools-dev armhf 2.5.1+dfsg-3 [21.8 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.3.0-2+rpi1 [206 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-2 [103 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.8.0-2 [113 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libboost1.67-dev armhf 1.67.0-13 [8386 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.67.0 armhf 1.67.0-13 [430 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 63.1-6 [8841 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.67-dev armhf 1.67.0-13 [527 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.67.0 armhf 1.67.0-13 [245 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.67-dev armhf 1.67.0-13 [252 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams-dev armhf 1.67.0.1+b1 [3908 B]
Get:78 http://172.17.0.1/private buster-staging/main armhf libbtf1 armhf 1:5.4.0+dfsg-1 [21.1 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-9 [27.7 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libcamd2 armhf 1:5.4.0+dfsg-1 [27.7 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libccolamd2 armhf 1:5.4.0+dfsg-1 [28.4 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libcolamd2 armhf 1:5.4.0+dfsg-1 [25.3 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-2 [1493 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libmetis5 armhf 5.1.0.dfsg-5 [131 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libcholmod3 armhf 1:5.4.0+dfsg-1 [215 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.36.0-2 [73.6 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.64.0-1 [291 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf libnspr4 armhf 2:4.20-1 [89.6 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf libnss3 armhf 2:3.42.1-1 [943 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf libcurl3-nss armhf 7.64.0-1 [297 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf libcurl4-nss-dev armhf 7.64.0-1 [371 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf libcxsparse3 armhf 1:5.4.0+dfsg-1 [48.8 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf libdeflate0 armhf 1.2-1 [48.4 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf libgraphblas2 armhf 1:5.4.0+dfsg-1 [1524 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf libgslcblas0 armhf 2.5+dfsg-6 [79.0 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf libgsl23 armhf 2.5+dfsg-6 [704 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf libgsl-dev armhf 2.5+dfsg-6 [893 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.9-10 [254 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.9-10 [4284 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf libklu1 armhf 1:5.4.0+dfsg-1 [48.6 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.8.0-2 [1551 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf libldl2 armhf 1:5.4.0+dfsg-1 [20.9 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf libmongoose2 armhf 1:5.4.0+dfsg-1 [40.9 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf libumfpack5 armhf 1:5.4.0+dfsg-1 [126 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf librbio2 armhf 1:5.4.0+dfsg-1 [29.7 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf libspqr2 armhf 1:5.4.0+dfsg-1 [66.7 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf libsuitesparse-dev armhf 1:5.4.0+dfsg-1 [1970 kB]
Get:113 http://172.17.0.1/private buster-staging/main armhf liblpsolve55-dev armhf 5.5.0.15-4 [350 kB]
Get:114 http://172.17.0.1/private buster-staging/main armhf libncurses-dev armhf 6.1+20181013-2 [278 kB]
Get:115 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1+20181013-2 [940 B]
Get:116 http://172.17.0.1/private buster-staging/main armhf libsqlite3-dev armhf 3.27.2-1 [687 kB]
Get:117 http://172.17.0.1/private buster-staging/main armhf libssl-dev armhf 1.1.1b-1 [1560 kB]
Get:118 http://172.17.0.1/private buster-staging/main armhf lzma-dev all 9.22-2.1 [44.7 kB]
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Setting up libpipeline1:armhf (1.5.1-2) ...
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Setting up libpsl5:armhf (0.20.2-2) ...
Setting up libgslcblas0:armhf (2.5+dfsg-6) ...
Setting up ruby-power-assert (1.1.1-1) ...
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Setting up libarchive-zip-perl (1.64-1) ...
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No schema files found: removed existing output file.
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Setting up libmagic1:armhf (1:5.35-4) ...
Setting up libdeflate0:armhf (1.2-1) ...
Setting up gettext-base (0.19.8.1-9) ...
Setting up rubygems-integration (1.11) ...
Setting up libmetis5:armhf (5.1.0.dfsg-5) ...
Setting up file (1:5.35-4) ...
Setting up libgomp1:armhf (8.3.0-2+rpi1) ...
Setting up libicu63:armhf (63.1-6) ...
Setting up ruby-minitest (5.11.3-1) ...
Setting up libasan5:armhf (8.3.0-2+rpi1) ...
Setting up autotools-dev (20180224.1) ...
Setting up libsqlite3-dev:armhf (3.27.2-1) ...
Setting up ruby-test-unit (3.2.8-1) ...
Setting up libnspr4:armhf (2:4.20-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ...
Setting up libgsl23:armhf (2.5+dfsg-6) ...
Setting up ruby-net-telnet (0.1.1-2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libbamtools2.5.1:armhf (2.5.1+dfsg-3) ...
Setting up libssl-dev:armhf (1.1.1b-1) ...
Setting up libatomic1:armhf (8.3.0-2+rpi1) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up icu-devtools (63.1-6) ...
Setting up libboost-iostreams1.67.0:armhf (1.67.0-13) ...
Setting up libbam-dev (0.1.19-4) ...
Setting up libgfortran5:armhf (8.3.0-2+rpi1) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up libubsan1:armhf (8.3.0-2+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libncurses5-dev:armhf (6.1+20181013-2) ...
Setting up libssh2-1:armhf (1.8.0-2) ...
Setting up ruby-did-you-mean (1.2.1-1) ...
Setting up cpp-8 (8.3.0-2+rpi1) ...
Setting up libbsd0:armhf (0.9.1-2) ...
Setting up libelf1:armhf (0.176-1) ...
Setting up libicu-dev:armhf (63.1-6) ...
Setting up ruby-xmlrpc (0.3.0-2) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+b1) ...
Setting up libsuitesparseconfig5:armhf (1:5.4.0+dfsg-1) ...
Setting up libcc1-0:armhf (8.3.0-2+rpi1) ...
Setting up librbio2:armhf (1:5.4.0+dfsg-1) ...
Setting up libbz2-dev:armhf (1.0.6-9) ...
Setting up libgraphblas2:armhf (1:5.4.0+dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (1.1.2-1) ...
Setting up libamd2:armhf (1:5.4.0+dfsg-1) ...
Setting up libgsl-dev (2.5+dfsg-6) ...
Setting up libboost-regex1.67.0:armhf (1.67.0-13) ...
Setting up libcolamd2:armhf (1:5.4.0+dfsg-1) ...
Setting up libtool (2.4.6-9) ...
Setting up libldl2:armhf (1:5.4.0+dfsg-1) ...
Setting up m4 (1.4.18-2) ...
Setting up libcurl3-gnutls:armhf (7.64.0-1) ...
Setting up libnss3:armhf (2:3.42.1-1) ...
Setting up libbtf1:armhf (1:5.4.0+dfsg-1) ...
Setting up libcamd2:armhf (1:5.4.0+dfsg-1) ...
Setting up libmongoose2:armhf (1:5.4.0+dfsg-1) ...
Setting up libblas3:armhf (3.8.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libbamtools-dev:armhf (2.5.1+dfsg-3) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libcroco3:armhf (0.6.12-3) ...
Setting up libgcc-8-dev:armhf (8.3.0-2+rpi1) ...
Setting up lzma-dev (9.22-2.1) ...
Setting up autoconf (2.69-11) ...
Setting up dwz (0.12-3) ...
Setting up libcurl3-nss:armhf (7.64.0-1) ...
Setting up groff-base (1.22.4-3) ...
Setting up libklu1:armhf (1:5.4.0+dfsg-1) ...
Setting up libccolamd2:armhf (1:5.4.0+dfsg-1) ...
Setting up libcxsparse3:armhf (1:5.4.0+dfsg-1) ...
Setting up libcurl4-nss-dev:armhf (7.64.0-1) ...
Setting up libblas-dev:armhf (3.8.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up libstdc++-8-dev:armhf (8.3.0-2+rpi1) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libboost1.67-dev:armhf (1.67.0-13) ...
Setting up liblapack3:armhf (3.8.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up gettext (0.19.8.1-9) ...
Setting up gcc-8 (8.3.0-2+rpi1) ...
Setting up libhts2:armhf (1.9-10) ...
Setting up libboost-regex1.67-dev:armhf (1.67.0-13) ...
Setting up libhts-dev:armhf (1.9-10) ...
Setting up man-db (2.8.5-2) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer -> /lib/systemd/system/man-db.timer.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up liblapack-dev:armhf (3.8.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up g++-8 (8.3.0-2+rpi1) ...
Setting up libcholmod3:armhf (1:5.4.0+dfsg-1) ...
Setting up libboost-iostreams1.67-dev:armhf (1.67.0-13) ...
Setting up libspqr2:armhf (1:5.4.0+dfsg-1) ...
Setting up po-debconf (1.0.21) ...
Setting up libboost-iostreams-dev:armhf (1.67.0.1+b1) ...
Setting up libumfpack5:armhf (1:5.4.0+dfsg-1) ...
Setting up libsuitesparse-dev:armhf (1:5.4.0+dfsg-1) ...
Setting up liblpsolve55-dev (5.5.0.15-4) ...
Setting up dh-autoreconf (19) ...
Setting up rake (12.3.1-3) ...
Setting up dh-strip-nondeterminism (1.1.2-1) ...
Setting up libruby2.5:armhf (2.5.3-4) ...
Setting up debhelper (12.1.1) ...
Setting up ruby2.5 (2.5.3-4) ...
Setting up ruby (1:2.5.1+b1) ...
Setting up ruby-asciidoctor (1.5.8-1) ...
Setting up asciidoctor (1.5.8-1) ...
Setting up sbuild-build-depends-augustus-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-7+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_2.31.1-11+rpi1 dpkg-dev_1.19.5 g++-8_8.3.0-2+rpi1 gcc-8_8.3.0-2+rpi1 libc6-dev_2.28-7+rpi1 libstdc++-8-dev_8.3.0-2+rpi1 libstdc++6_8.3.0-2+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~rc3 asciidoctor_1.5.8-1 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.46 bash_5.0-2 binutils_2.31.1-11+rpi1 binutils-arm-linux-gnueabihf_2.31.1-11+rpi1 binutils-common_2.31.1-11+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20190110 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.3.0-2+rpi1 dash_0.5.10.2-5 dbus_1.12.12-1 dbus-user-session_1.12.12-1 debconf_1.5.70 debhelper_12.1.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.2-1 diffutils_1:3.7-2 dirmngr_2.2.12-1+rpi1 dmsetup_2:1.02.155-2 dpkg_1.19.5 dpkg-dev_1.19.5 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 e2fsprogs-l10n_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-4 findutils_4.6.0+git+20190209-2 g++_4:8.2.0-2+rpi1 g++-8_8.3.0-2+rpi1 gcc_4:8.2.0-2+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_6.5.0-1+rpi1 gcc-8_8.3.0-2+rpi1 gcc-8-base_8.3.0-2+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.21 icu-devtools_63.1-6 inetutils-ping_2:1.9.4-7 init-system-helpers_1.56+nmu1 initramfs-tools_0.133 initramfs-tools-core_0.133 intltool-debian_0.35.0+20060710.5 klibc-utils_2.0.6-1+rpi1 kmod_26-1 krb5-locales_1.17-1 libacl1_2.2.52-5 libamd2_1:5.4.0+dfsg-1 libapparmor1_2.13.2-7 libapt-pkg5.0_1.8.0~rc3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.2 libasan5_8.3.0-2+rpi1 libassuan0_2.5.2-1 libatomic1_8.3.0-2+rpi1 libattr1_1:2.4.47-4 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2+b1 libbam-dev_0.1.19-4 libbamtools-dev_2.5.1+dfsg-3 libbamtools2.5.1_2.5.1+dfsg-3 libbinutils_2.31.1-11+rpi1 libblas-dev_3.8.0-2 libblas3_3.8.0-2 libblkid1_2.33.1-0.1 libboost-iostreams-dev_1.67.0.1+b1 libboost-iostreams1.67-dev_1.67.0-13 libboost-iostreams1.67.0_1.67.0-13 libboost-regex1.67-dev_1.67.0-13 libboost-regex1.67.0_1.67.0-13 libboost1.67-dev_1.67.0-13 libbsd0_0.9.1-2 libbtf1_1:5.4.0+dfsg-1 libbz2-1.0_1.0.6-9 libbz2-dev_1.0.6-9 libc-bin_2.28-7+rpi1 libc-dev-bin_2.28-7+rpi1 libc6_2.28-7+rpi1 libc6-dev_2.28-7+rpi1 libcamd2_1:5.4.0+dfsg-1 libcap-ng0_0.7.9-2 libcap2_1:2.25-2 libcc1-0_8.3.0-2+rpi1 libccolamd2_1:5.4.0+dfsg-1 libcholmod3_1:5.4.0+dfsg-1 libcolamd2_1:5.4.0+dfsg-1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.1.0-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.64.0-1 libcurl3-nss_7.64.0-1 libcurl4-nss-dev_7.64.0-1 libcxsparse3_1:5.4.0+dfsg-1 libdb5.3_5.3.28+dfsg1-0.3 libdbus-1-3_1.12.12-1 libdebconfclient0_0.247 libdeflate0_1.2-1 libdevmapper1.02.1_2:1.02.155-2 libdpkg-perl_1.19.5 libdrm-common_2.4.97-1+rpi1 libdrm2_2.4.97-1+rpi1 libelf1_0.176-1 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.2-1 libgcc-8-dev_8.3.0-2+rpi1 libgcc1_1:8.3.0-2+rpi1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-3 libgdbm3_1.8.3-14 libgdbm6_1.18.1-3 libgfortran5_8.3.0-2+rpi1 libglib2.0-0_2.58.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.6-2 libgomp1_8.3.0-2+rpi1 libgpg-error-l10n_1.35-1 libgpg-error0_1.35-1 libgraphblas2_1:5.4.0+dfsg-1 libgsl-dev_2.5+dfsg-6 libgsl23_2.5+dfsg-6 libgslcblas0_2.5+dfsg-6 libgssapi-krb5-2_1.17-1 libhogweed4_3.4.1-1 libhts-dev_1.9-10 libhts2_1.9-10 libicu-dev_63.1-6 libicu63_63.1-6 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3 libisl19_0.20-2 libjson-c3_0.12.1+ds-2 libk5crypto3_1.17-1 libkeyutils1_1.6-2 libklibc_2.0.6-1+rpi1 libklu1_1:5.4.0+dfsg-1 libkmod2_26-1 libkrb5-3_1.17-1 libkrb5support0_1.17-1 libksba8_1.3.5-2 liblapack-dev_3.8.0-2 liblapack3_3.8.0-2 libldap-2.4-2_2.4.47+dfsg-3+rpi1 libldap-common_2.4.47+dfsg-3+rpi1 libldl2_1:5.4.0+dfsg-1 liblpsolve55-dev_5.5.0.15-4 liblz4-1_1.8.3-1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-4 libmagic1_1:5.35-4 libmetis5_5.1.0.dfsg-5 libmongoose2_1:5.4.0+dfsg-1 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses-dev_6.1+20181013-2 libncurses5_6.1+20181013-2 libncurses5-dev_6.1+20181013-2 libncurses6_6.1+20181013-2 libncursesw5_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libnghttp2-14_1.36.0-2 libnpth0_1.6-1 libnspr4_2:4.20-1 libnss-systemd_241-1+rpi1 libnss3_2:3.42.1-1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam-systemd_241-1+rpi1 libpam0g_1.3.1-5 libpcre3_2:8.39-11+rpi1 libperl5.28_5.28.1-4 libpipeline1_1.5.1-2 libplymouth4_0.9.4-1 libpng16-16_1.6.36-5 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 librbio2_1:5.4.0+dfsg-1 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libruby2.5_2.5.3-4 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libspqr2_1:5.4.0+dfsg-1 libsqlite3-0_3.27.2-1 libsqlite3-dev_3.27.2-1 libss2_1.44.5-1 libssh2-1_1.8.0-2 libssl-dev_1.1.1b-1 libssl1.1_1.1.1b-1 libstdc++-8-dev_8.3.0-2+rpi1 libstdc++6_8.3.0-2+rpi1 libsuitesparse-dev_1:5.4.0+dfsg-1 libsuitesparseconfig5_1:5.4.0+dfsg-1 libsystemd0_241-1+rpi1 libtasn1-6_4.13-3 libtinfo5_6.1+20181013-2 libtinfo6_6.1+20181013-2 libtool_2.4.6-9 libubsan1_8.3.0-2+rpi1 libuchardet0_0.0.6-3 libudev1_241-1+rpi1 libumfpack5_1:5.4.0+dfsg-1 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libxml2_2.9.4+dfsg1-7+b1 libyaml-0-2_0.2.1-1 libzstd1_1.3.8+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 lzma-dev_9.22-2.1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.5-2 mawk_1.3.3-17 mount_2.33.1-0.1 multiarch-support_2.28-7+rpi1 nano_3.2-2 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 netbase_5.6 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-4 perl-base_5.28.1-4 perl-modules-5.28_5.28.1-4 pinentry-curses_1.1.0-1 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 rake_12.3.1-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 ruby_1:2.5.1+b1 ruby-asciidoctor_1.5.8-1 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_2.5.3-4 rubygems-integration_1.11 sbuild-build-depends-augustus-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_241-1+rpi1 systemd-sysv_241-1+rpi1 sysvinit-utils_2.93-8 tar_1.30+dfsg-5 tzdata_2018i-1 udev_241-1+rpi1 util-linux_2.33.1-0.1 xz-utils_5.2.4-1 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 Mon Mar 18 16:04:09 2019 UTC
gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./augustus_3.3.2+dfsg-2.dsc
dpkg-source: info: extracting augustus in /<<BUILDDIR>>/augustus-3.3.2+dfsg
dpkg-source: info: unpacking augustus_3.3.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking augustus_3.3.2+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying search_config_path
dpkg-source: info: applying set_installdir
dpkg-source: info: applying 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-71996d1d-08ea-4fd0-9009-82abb2de5e9b
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package augustus
dpkg-buildpackage: info: source version 3.3.2+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg'
/usr/bin/make -C auxprogs/bam2hints clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/bam2hints'
rm -f bam2hints.o bam2hints ../../bin/bam2hints
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/homGeneMapping clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/homGeneMapping'
(cd src; make clean; cd ../bin; rm -f homGeneMapping; cd ../../../bin; rm -f homGeneMapping)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/homGeneMapping/src'
rm -f homGeneMapping gene.o genome.o
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/homGeneMapping/src'
/bin/sh: 1: cd: can't cd to ../bin
/bin/sh: 1: cd: can't cd to ../../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/homGeneMapping'
/usr/bin/make -C auxprogs/joingenes clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/joingenes'
rm -rf *o joingenes; rm -rf ../../bin/joingenes
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/joingenes'
/usr/bin/make -C auxprogs/aln2wig clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/aln2wig'
rm -f aln2wig aln2wig.o; rm -f ../../bin/aln2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2wig clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/bam2wig'
rm -f bam2wig bam2wig.o
rm -f ../../bin/bam2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/checkTargetSortedness clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/checkTargetSortedness'
rm -f *.o checkTargetSortedness
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/checkTargetSortedness'
/usr/bin/make -C auxprogs/compileSpliceCands clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/compileSpliceCands'
rm -f compileSpliceCands compileSpliceCands.o ../../bin/compileSpliceCands list.o
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/filterBam'
(cd src; make clean;)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+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-3.3.2+dfsg/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/filterBam'
rm -rf bin
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+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-3.3.2+dfsg'
mkdir -p bin
/usr/bin/make -C auxprogs/aln2wig
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/aln2wig'
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -O2 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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-3.3.2+dfsg/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2hints
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/bam2hints'
g++ -Wall -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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-3.3.2+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-3.3.2+dfsg/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/bam2wig
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+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-3.3.2+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-3.3.2+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 -lcurl -lssl -lcrypto -lbz2 -llzma
cp bam2wig ../../bin/bam2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/checkTargetSortedness
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/checkTargetSortedness'
cc -g -Wall -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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-3.3.2+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-3.3.2+dfsg/auxprogs/checkTargetSortedness'
/usr/bin/make -C auxprogs/compileSpliceCands
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/compileSpliceCands'
cc -Wall -pedantic -ansi -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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-3.3.2+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-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now;
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/filterBam/src'
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+dfsg/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/filterBam'
/usr/bin/make -C auxprogs/homGeneMapping/src
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/homGeneMapping/src'
g++ -c -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+dfsg/auxprogs/homGeneMapping/src'
/usr/bin/make -C auxprogs/joingenes
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/joingenes'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+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-3.3.2+dfsg/auxprogs/joingenes'
dh_auto_build
make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg'
mkdir -p bin
cd src && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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 -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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 -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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 -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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 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: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: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) {}
^~~~~~~~~~~~~~~~~~
properties.cc: In static member function 'static void Properties::init(int, char**)':
properties.cc:444:27: warning: catching polymorphic type 'struct PropertiesError' by value [-Wcatch-value=]
} catch (PropertiesError e){
^
properties.cc:469:30: warning: catching polymorphic type 'struct PropertiesError' by value [-Wcatch-value=]
} catch (PropertiesError e){
^
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) {}
^~~~~~~~~~~~~~~~~~
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 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 -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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 /usr/include/c++/8/vector:69,
from ../include/types.hh:36,
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>::
^~~~~~~~~~~~~~~~~~~
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){}
^~~~~~~~~~~~~~~~~~~~~~
/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>::
^~~~~~~~~~~~~~~~~~~
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) {}
^
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_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:36,
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:36,
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>::
^~~~~~~~~~~~~~~~~~~
/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)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../include/types.hh:36,
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:39,
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:64,
from ../include/types.hh:36,
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);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:60,
from ../include/types.hh:39,
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>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o statemodel.o statemodel.cc -I../include
In file included from /usr/include/c++/8/vector:64,
from ../include/types.hh:36,
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:39,
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 /usr/include/c++/8/map:60,
from ../include/types.hh:39,
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>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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 = {std::pair<SubstateId, ViterbiSubmapEntry>&}; _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/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
/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);
^~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from ../include/types.hh:39,
from ../include/vitmatrix.hh:14,
from ../include/pp_scoring.hh:21,
from pp_scoring.cc:14:
/usr/include/c++/8/bits/stl_map.h:876:35: note: parameter passing for argument of type 'std::map<SubstateId, ViterbiSubmapEntry>::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
std::forward<_Pair>(__x));
^
/usr/include/c++/8/bits/stl_map.h:876:35: note: parameter passing for argument of type 'std::map<SubstateId, ViterbiSubmapEntry>::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
std::forward<_Pair>(__x));
^
In file included from /usr/include/c++/8/map:60,
from ../include/types.hh:39,
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 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>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from ../include/types.hh:39,
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 ViterbiSubmapType::eraseAndDecCounts(ViterbiSubmapType::iterator) const':
/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/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) {}
^~~~~~~~~~~~~~~~~~
/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,
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) {}
^
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){}
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_map.h: In member function 'void PP::BonusProbType::mergeIntoSubmap(int, ViterbiSubmapType&, SubstateIdMap*)':
/usr/include/c++/8/bits/stl_map.h:876:35: note: parameter passing for argument of type 'std::map<SubstateId, ViterbiSubmapEntry>::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >'} changed in GCC 7.1
std::forward<_Pair>(__x));
^
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o namgene.o namgene.cc -I../include
In file included from /usr/include/c++/8/map:60,
from ../include/types.hh:39,
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::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);
^~~~~~~~~~~~
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) {}
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from ../include/types.hh:39,
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,
/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,
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o types.o types.cc -I../include
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) {
^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:60,
from ../include/types.hh:39,
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:39,
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: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:250:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {}
^
types.cc:253:27: 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:289:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=]
} catch (ProjectError e) {
^
types.cc:295:27: 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) {
^
types.cc:341:27: 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/types.hh:36,
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 /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 -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o gene.o gene.cc -I../include
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:38,
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,
^~~~~~~~~~~~~~~~~~~~~~~~~
/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:38,
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:38,
from types.cc:18:
/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: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: 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 -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o evaluation.o evaluation.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o motif.o motif.cc -I../include
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:873,
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:6400,
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:28,
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:36:34: 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/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) {}
^~~~~~~~~~~~~~~~~~
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 ../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 /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: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);
^~~~~~~~~~~~~~~~~
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>::
^~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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 -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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 -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o extrinsicinfo.o extrinsicinfo.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o projectio.o projectio.cc -I../include
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){}
^~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o intronmodel.o intronmodel.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
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o exonmodel.o exonmodel.cc -I../include
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) {}
^~~~~~~~~~~~~~~~~~
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) {}
^~~~~~~~~~~~~~~~
/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) {
^
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) {}
^~~~~~~~~~~~~~~~~~
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) {
^
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) {}
^~~~~~~~~~~~~~~~~~
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) {
^
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/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/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/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){}
^~~~~~~~~~~~~~~~~~~~~~
/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());
^~~~~~~~~~~~~~~~~~
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/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) {}
^~~~~~~~~~~~~~~~
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) {
^
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) {}
^
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) {
^
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 /usr/include/c++/8/algorithm:62,
from ../include/types.hh:38,
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:38,
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:38,
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:38,
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);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o igenicmodel.o igenicmodel.cc -I../include
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:873,
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:6400,
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:36:34: 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:39,
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:39,
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 -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o utrmodel.o utrmodel.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o merkmal.o merkmal.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){}
^~~~~~~~~~~~~~~~~~~~~~
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 ../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) {}
^
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) {}
^
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){}
^~~~~~~~~~~~~~~~~~~~~~
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) {
^
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) {
^~~~~~~~~~~~~~~~~~
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) {
^
../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) {}
^~~~~~~~~~~~~~~~~~
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) {
^
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/map:60,
from ../include/types.hh:39,
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 -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o vitmatrix.o vitmatrix.cc -I../include
In file included from /usr/include/c++/8/map:60,
from ../include/types.hh:39,
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:38,
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:39,
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);
^
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) {}
^~~~~~~~~~~~~~~~~~
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:38,
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:38,
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:38,
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:38,
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 /usr/include/c++/8/vector:69,
from ../include/types.hh:36,
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:39,
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:36,
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:36,
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:39,
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>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from ../include/types.hh:39,
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,
In file included from /usr/include/c++/8/vector:69,
from ../include/types.hh:36,
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>::
^~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o lldouble.o lldouble.cc -I../include
/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)...);
^~~~~~~~~~~~~~~~~
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:873,
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:6400,
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:36:34: 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/algorithm:62,
from ../include/types.hh:38,
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:38,
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:38,
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<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: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: 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:38,
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:38,
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:64,
from ../include/types.hh:36,
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 -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o mea.o mea.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o graph.o graph.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) {}
^~~~~~~~~~~~~~~~~~
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 ../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 ../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) {}
^~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o meaPath.o meaPath.cc -I../include
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>::
^~~~~~~~~~~~~~~~~~~
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) {}
^~~~~~~~~~~~~~~~~~
/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 ../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/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 -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o exoncand.o exoncand.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o randseqaccess.o randseqaccess.cc -I../include
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/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 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) {}
^~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o fasta.o fasta.cc -I../include
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) {}
^~~~~~~~~~~~~~~~
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) {
^
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o ncmodel.o ncmodel.cc -I../include
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) {
^
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) {
^
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 -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o commontrain.o commontrain.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/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);
^~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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) {}
^
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o introntrain.o introntrain.cc -I../include
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 ../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) {}
^~~~~~~~~~~~~~~~
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 -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o exontrain.o exontrain.cc -I../include
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 /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>::
^~~~~~~~~~~~~~~~~~~
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 /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);
^~~~~~~~~~~~~~~~~
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 -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o utrtrain.o utrtrain.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o dummy.o dummy.cc -I../include
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 /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>::
^~~~~~~~~~~~~~~~~~~
/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/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) {}
^~~~~~~~~~~~~~~~
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){}
^~~~~~~~~~~~~~~~~~~~~~
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 ) {
^~~~~~~~~~~~
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);
^~~~~~~~~~~~~~~~~
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 -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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 -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security" > cxxflags
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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) {}
^~~~~~~~~~~~~~~~~~
cp prepareAlign ../bin/
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 ../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 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) {}
^
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 ../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/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) {}
^~~~~~~~~~~~~~~~~~
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) {
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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
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-3.3.2+dfsg/src'
cd auxprogs && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs'
cd bam2hints; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+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-3.3.2+dfsg/auxprogs/bam2hints'
cd compileSpliceCands; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+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-3.3.2+dfsg/auxprogs/compileSpliceCands'
cd filterBam; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/filterBam'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src;make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/filterBam/src'
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.2+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-3.3.2+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-3.3.2+dfsg/auxprogs/filterBam/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/filterBam'
cd homGeneMapping; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/homGeneMapping'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src; make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/homGeneMapping/src'
make[5]: Nothing to be done for 'all'.
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/homGeneMapping/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/homGeneMapping'
cd joingenes; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+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-3.3.2+dfsg/auxprogs/joingenes'
cd bam2wig; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+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-3.3.2+dfsg/auxprogs/bam2wig'
cd utrrnaseq/Debug; make all;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+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:387:64: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
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:1238:5: 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
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs/utrrnaseq/Debug'
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg/auxprogs'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg'
asciidoctor -a docdate='' -b manpage debian/mansrc/*adoc
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg'
dh_auto_test -a
make -j4 test
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg'
./bin/augustus --species=human --UTR=on examples/example.fa
# This output was generated with AUGUSTUS (version 3.3.2).
# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters using config directory /<<BUILDDIR>>/augustus-3.3.2+dfsg/config/ ...
# human version. Using species specific transition matrix: /<<BUILDDIR>>/augustus-3.3.2+dfsg/config/species/human/human_trans_shadow_partial_utr.pbl
# Looks like examples/example.fa is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
HS04636 AUGUSTUS gene 836 8857 1 + . g1
HS04636 AUGUSTUS transcript 836 8857 . + . g1.t1
HS04636 AUGUSTUS tss 836 836 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 5072 5358 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 5860 6007 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 6494 8857 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS tts 8857 8857 . + . transcript_id "g1.t1"; gene_id "g1";
# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
# end gene g1
###
#
# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
#
# Predicted genes for sequence number 2 on both strands
# start gene g2
HS08198 AUGUSTUS gene 86 2344 1 + . g2
HS08198 AUGUSTUS transcript 86 2344 . + . g2.t1
HS08198 AUGUSTUS tss 86 86 . + . transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS exon 86 582 . + . transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS exon 812 894 . + . transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS exon 1053 1123 . + . transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS exon 1208 1315 . + . transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS exon 1587 1688 . + . transcript_id "g2.t1"; gene_id "g2";
# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY]
# end gene g2
###
# command line:
# ./bin/augustus --species=human --UTR=on examples/example.fa
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg'
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-3.3.2+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-3.3.2+dfsg'
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg'
dh_installchangelogs -k HISTORY.TXT
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+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-3.3.2+dfsg'
dh_compress -Xtutorial
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg'
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
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/filterBam contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/joingenes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/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/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/bam2wig was not linked against libcrypto.so.1.1 (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)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/bam2wig was not linked against libssl.so.1.1 (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 libcurl-nss.so.4 (it uses none of the library's symbols)
dh_installdeb -a
debian/rules override_dh_gencontrol
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg'
dh_gencontrol -- \
-V'Built-Using:samtools=samtools-legacy (= 0.1.19-4)'
dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.2+dfsg'
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'augustus' in '../augustus_3.3.2+dfsg-2_armhf.deb'.
dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.3.2+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../augustus_3.3.2+dfsg-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-03-29T05:47:39Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
augustus_3.3.2+dfsg-2_armhf.changes:
------------------------------------
Format: 1.8
Date: Fri, 15 Mar 2019 17:11:10 +0100
Source: augustus
Binary: augustus augustus-dbgsym
Architecture: armhf
Version: 3.3.2+dfsg-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
augustus - gene prediction in eukaryotic genomes
Closes: 924359
Changes:
augustus (3.3.2+dfsg-2) unstable; urgency=medium
.
* Use dynamic Built-Using in d/control.
Thanks to Andreas Beckmann for useful hints.
Closes: #924359
Checksums-Sha1:
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5ac1af36e9821eb0a896805363694357242eab59 7244 augustus_3.3.2+dfsg-2_armhf.buildinfo
0f787d436810acab2877ac31645d49599d6ad606 894672 augustus_3.3.2+dfsg-2_armhf.deb
Checksums-Sha256:
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58df96f1796aa99ac52be1e8564fa1bf8cb972a2311d0fbea03e70484982cb4f 7244 augustus_3.3.2+dfsg-2_armhf.buildinfo
7a9c6b05e3296a9f8ed00aa362d8cc17b869f9cb517eb5048269377455abde18 894672 augustus_3.3.2+dfsg-2_armhf.deb
Files:
fc1eae86fd6f56edb61a356a23dadd5a 21722804 debug optional augustus-dbgsym_3.3.2+dfsg-2_armhf.deb
afe0893ab772bdc0683cf1bda732d8aa 7244 science optional augustus_3.3.2+dfsg-2_armhf.buildinfo
836a9d3c3a4c997a50bed26ee91c25f6 894672 science optional augustus_3.3.2+dfsg-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
augustus-dbgsym_3.3.2+dfsg-2_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 21722804 bytes: control archive=1124 bytes.
879 bytes, 13 lines control
1272 bytes, 12 lines md5sums
Package: augustus-dbgsym
Source: augustus
Version: 3.3.2+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 21902
Depends: augustus (= 3.3.2+dfsg-2)
Built-Using: samtools-legacy (= 0.1.19-4)
Section: debug
Priority: optional
Description: debug symbols for augustus
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drwxr-xr-x root/root 0 2019-03-15 16:11 ./
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augustus_3.3.2+dfsg-2_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 894672 bytes: control archive=4640 bytes.
1382 bytes, 22 lines control
9627 bytes, 128 lines md5sums
Package: augustus
Version: 3.3.2+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3903
Depends: libbamtools2.5.1, libbz2-1.0, libc6 (>= 2.15), libcurl3-nss (>= 7.23.1), libgcc1 (>= 1:3.5), libhts2 (>= 1.0), liblzma5 (>= 5.1.1alpha+20110809), libncurses6 (>= 6), libssl1.1 (>= 1.1.0), libstdc++6 (>= 6), libtinfo6 (>= 6), zlib1g (>= 1:1.2.3.3), augustus-data
Built-Using: samtools-legacy (= 0.1.19-4)
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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+------------------------------------------------------------------------------+
| Post Build |
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+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 983392
Build-Time: 1063
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 1067
Job: augustus_3.3.2+dfsg-2
Machine Architecture: armhf
Package: augustus
Package-Time: 2239
Source-Version: 3.3.2+dfsg-2
Space: 983392
Status: successful
Version: 3.3.2+dfsg-2
--------------------------------------------------------------------------------
Finished at 2019-03-29T05:47:39Z
Build needed 00:37:19, 983392k disc space