I: pbuilder: network access will be disabled during build I: Current time: Mon Jan 2 04:21:48 +14 2023 I: pbuilder-time-stamp: 1672582908 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [augustus_3.3.2+dfsg-2.dsc] I: copying [./augustus_3.3.2+dfsg.orig.tar.xz] I: copying [./augustus_3.3.2+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Tue Mar 19 06:04:09 2019 +14 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 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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1628508/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1628508/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1628508/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=b25f6f58b3964434a08a46c51637df81 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1628508 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.Zqvl7vIRP5/pbuilderrc_m5Sx --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Zqvl7vIRP5/b2 --logfile b2/build.log augustus_3.3.2+dfsg-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash -rwxr-xr-x 1 root root 109408 Mar 1 2019 date -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd -rwxr-xr-x 1 root root 93744 Mar 1 2019 df -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 35424 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln -rwxr-xr-x 1 root root 56760 Jul 27 2018 login -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 10 2019 more -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jan 2 04:22 sh -> bash lrwxrwxrwx 1 root root 4 Dec 11 18:21 sh.distrib -> dash -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty -rwsr-xr-x 1 root root 63568 Jan 10 2019 su -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch -rwxr-xr-x 1 root root 35424 Mar 1 2019 true -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/1628508/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. 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 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on liblpsolve55-dev; however: Package liblpsolve55-dev is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on lzma-dev; however: Package lzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libncurses5-dev; however: Package libncurses5-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-nss-dev; however: Package libcurl4-nss-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libamd2{a} libarchive-zip-perl{a} libbam-dev{a} libbamtools-dev{a} libbamtools2.5.1{a} libblas-dev{a} libblas3{a} libboost-iostreams-dev{a} libboost-iostreams1.67-dev{a} libboost-regex1.67-dev{a} libboost-regex1.67.0{a} libboost1.67-dev{a} libbsd0{a} libbtf1{a} libbz2-dev{a} libcamd2{a} libccolamd2{a} libcholmod3{a} libcolamd2{a} libcroco3{a} libcurl3-gnutls{a} libcurl3-nss{a} libcurl4-nss-dev{a} libcxsparse3{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgraphblas2{a} libgsl-dev{a} libgsl23{a} libgslcblas0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu-dev{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libklu1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.4-2{a} libldap-common{a} libldl2{a} liblpsolve55-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmetis5{a} libmongoose2{a} libncurses-dev{a} libncurses5-dev{a} libncurses6{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libpipeline1{a} libpsl5{a} librbio2{a} libreadline7{a} librtmp1{a} libruby2.5{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libspqr2{a} libsqlite3-dev{a} libssh2-1{a} libssl-dev{a} libssl1.1{a} libsuitesparse-dev{a} libsuitesparseconfig5{a} libtool{a} libuchardet0{a} libumfpack5{a} libxml2{a} libyaml-0-2{a} lzma-dev{a} m4{a} man-db{a} openssl{a} po-debconf{a} rake{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-did-you-mean{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-test-unit{a} ruby-xmlrpc{a} ruby2.5{a} rubygems-integration{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl fonts-lato krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs zip 0 packages upgraded, 117 newly installed, 0 to remove and 0 not upgraded. Need to get 70.6 MB of archives. After unpacking 415 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u7 [1539 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1d-0+deb10u7 [845 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 rubygems-integration all 1.11+deb10u1 [5212 B] Get: 17 http://deb.debian.org/debian buster/main amd64 rake all 12.3.1-3+deb10u1 [67.1 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 ruby-did-you-mean all 1.2.1-1 [14.4 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 ruby-minitest all 5.11.3-1 [54.8 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 ruby-power-assert all 1.1.1-1 [10.9 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 ruby-test-unit all 3.2.8-1 [72.4 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libruby2.5 amd64 2.5.5-3+deb10u3 [3438 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 ruby2.5 amd64 2.5.5-3+deb10u3 [400 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 ruby amd64 1:2.5.1 [11.3 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 ruby-asciidoctor all 1.5.8-1 [188 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 asciidoctor all 1.5.8-1 [75.8 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 icu-devtools amd64 63.1-6+deb10u1 [189 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libsuitesparseconfig5 amd64 1:5.4.0+dfsg-1 [20.9 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libamd2 amd64 1:5.4.0+dfsg-1 [33.4 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 libbam-dev amd64 0.1.19-4 [125 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-3 [154 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libbamtools-dev amd64 2.5.1+dfsg-3 [21.8 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 libblas-dev amd64 3.8.0-2 [154 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libboost1.67-dev amd64 1.67.0-13+deb10u1 [8388 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 libboost-regex1.67.0 amd64 1.67.0-13+deb10u1 [485 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libicu-dev amd64 63.1-6+deb10u1 [9186 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libboost-regex1.67-dev amd64 1.67.0-13+deb10u1 [539 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libboost-iostreams1.67-dev amd64 1.67.0-13+deb10u1 [255 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libboost-iostreams-dev amd64 1.67.0.1 [3632 B] Get: 68 http://deb.debian.org/debian buster/main amd64 libbtf1 amd64 1:5.4.0+dfsg-1 [22.7 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libbz2-dev amd64 1.0.6-9.2~deb10u1 [30.2 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libcamd2 amd64 1:5.4.0+dfsg-1 [35.0 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libccolamd2 amd64 1:5.4.0+dfsg-1 [36.4 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libcolamd2 amd64 1:5.4.0+dfsg-1 [30.3 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libmetis5 amd64 5.1.0.dfsg-5+b2 [175 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libcholmod3 amd64 1:5.4.0+dfsg-1 [324 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u3 [65.8 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u3 [122 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u3 [370 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u3 [158 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 libnspr4 amd64 2:4.20-1 [112 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libnss3 amd64 2:3.42.1-1+deb10u3 [1159 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 libcurl3-nss amd64 7.64.0-4+deb10u2 [336 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 libcurl4-nss-dev amd64 7.64.0-4+deb10u2 [425 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 libcxsparse3 amd64 1:5.4.0+dfsg-1 [75.7 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 libgraphblas2 amd64 1:5.4.0+dfsg-1 [1664 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 libgslcblas0 amd64 2.5+dfsg-6 [101 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 libgsl23 amd64 2.5+dfsg-6 [880 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 libgsl-dev amd64 2.5+dfsg-6 [1063 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 liblzma-dev amd64 5.2.4-1 [210 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 libhts-dev amd64 1.9-12~deb10u1 [4347 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 libklu1 amd64 1:5.4.0+dfsg-1 [85.3 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 liblapack-dev amd64 3.8.0-2 [2140 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 libldl2 amd64 1:5.4.0+dfsg-1 [22.1 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 libmongoose2 amd64 1:5.4.0+dfsg-1 [44.7 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 libumfpack5 amd64 1:5.4.0+dfsg-1 [243 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 librbio2 amd64 1:5.4.0+dfsg-1 [37.8 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 libspqr2 amd64 1:5.4.0+dfsg-1 [78.6 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 libsuitesparse-dev amd64 1:5.4.0+dfsg-1 [2448 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 liblpsolve55-dev amd64 5.5.0.15-4+b1 [399 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 libncurses-dev amd64 6.1+20181013-2+deb10u2 [333 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 libncurses5-dev amd64 6.1+20181013-2+deb10u2 [948 B] Get: 115 http://deb.debian.org/debian buster/main amd64 libsqlite3-dev amd64 3.27.2-3+deb10u1 [787 kB] Get: 116 http://deb.debian.org/debian buster/main amd64 libssl-dev amd64 1.1.1d-0+deb10u7 [1795 kB] Get: 117 http://deb.debian.org/debian buster/main amd64 lzma-dev all 9.22-2.1 [44.7 kB] Fetched 70.6 MB in 2s (45.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../002-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-3+deb10u1_amd64.deb ... Unpacking groff-base (1.22.4-3+deb10u1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../004-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../006-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../007-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../008-libmagic-mgc_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../009-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../010-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../011-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../012-libssl1.1_1.1.1d-0+deb10u7_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-0+deb10u7) ... Selecting previously unselected package openssl. Preparing to unpack .../013-openssl_1.1.1d-0+deb10u7_amd64.deb ... Unpacking openssl (1.1.1d-0+deb10u7) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../014-ca-certificates_20200601~deb10u2_all.deb ... Unpacking ca-certificates (20200601~deb10u2) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../015-rubygems-integration_1.11+deb10u1_all.deb ... Unpacking rubygems-integration (1.11+deb10u1) ... Selecting previously unselected package rake. Preparing to unpack .../016-rake_12.3.1-3+deb10u1_all.deb ... Unpacking rake (12.3.1-3+deb10u1) ... Selecting previously unselected package ruby-did-you-mean. Preparing to unpack .../017-ruby-did-you-mean_1.2.1-1_all.deb ... Unpacking ruby-did-you-mean (1.2.1-1) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../018-ruby-minitest_5.11.3-1_all.deb ... Unpacking ruby-minitest (5.11.3-1) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../019-ruby-net-telnet_0.1.1-2_all.deb ... Unpacking ruby-net-telnet (0.1.1-2) ... Selecting previously unselected package ruby-power-assert. Preparing to unpack .../020-ruby-power-assert_1.1.1-1_all.deb ... Unpacking ruby-power-assert (1.1.1-1) ... Selecting previously unselected package ruby-test-unit. Preparing to unpack .../021-ruby-test-unit_3.2.8-1_all.deb ... Unpacking ruby-test-unit (3.2.8-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../022-ruby-xmlrpc_0.3.0-2_all.deb ... Unpacking ruby-xmlrpc (0.3.0-2) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../023-libncurses6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../024-libreadline7_7.0-5_amd64.deb ... Unpacking libreadline7:amd64 (7.0-5) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../025-libyaml-0-2_0.2.1-1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.1-1) ... Selecting previously unselected package libruby2.5:amd64. Preparing to unpack .../026-libruby2.5_2.5.5-3+deb10u3_amd64.deb ... Unpacking libruby2.5:amd64 (2.5.5-3+deb10u3) ... Selecting previously unselected package ruby2.5. Preparing to unpack .../027-ruby2.5_2.5.5-3+deb10u3_amd64.deb ... Unpacking ruby2.5 (2.5.5-3+deb10u3) ... Selecting previously unselected package ruby. Preparing to unpack .../028-ruby_1%3a2.5.1_amd64.deb ... Unpacking ruby (1:2.5.1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../029-ruby-asciidoctor_1.5.8-1_all.deb ... Unpacking ruby-asciidoctor (1.5.8-1) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../030-asciidoctor_1.5.8-1_all.deb ... Unpacking asciidoctor (1.5.8-1) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../031-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../032-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../033-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../034-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../035-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../036-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../037-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../038-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../039-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../040-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../041-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../042-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../043-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../044-libglib2.0-0_2.58.3-2+deb10u3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../045-libicu63_63.1-6+deb10u1_amd64.deb ... Unpacking libicu63:amd64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../046-libxml2_2.9.4+dfsg1-7+deb10u2_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../047-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package gettext. Preparing to unpack .../048-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../049-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../050-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../051-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../052-icu-devtools_63.1-6+deb10u1_amd64.deb ... Unpacking icu-devtools (63.1-6+deb10u1) ... Selecting previously unselected package libsuitesparseconfig5:amd64. Preparing to unpack .../053-libsuitesparseconfig5_1%3a5.4.0+dfsg-1_amd64.deb ... Unpacking libsuitesparseconfig5:amd64 (1:5.4.0+dfsg-1) ... Selecting previously unselected package libamd2:amd64. Preparing to unpack .../054-libamd2_1%3a5.4.0+dfsg-1_amd64.deb ... Unpacking libamd2:amd64 (1:5.4.0+dfsg-1) ... Selecting previously unselected package libbam-dev. Preparing to unpack .../055-libbam-dev_0.1.19-4_amd64.deb ... Unpacking libbam-dev (0.1.19-4) ... Selecting previously unselected package libbamtools2.5.1:amd64. Preparing to unpack .../056-libbamtools2.5.1_2.5.1+dfsg-3_amd64.deb ... Unpacking libbamtools2.5.1:amd64 (2.5.1+dfsg-3) ... Selecting previously unselected package libbamtools-dev:amd64. Preparing to unpack .../057-libbamtools-dev_2.5.1+dfsg-3_amd64.deb ... Unpacking libbamtools-dev:amd64 (2.5.1+dfsg-3) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../058-libgfortran5_8.3.0-6_amd64.deb ... Unpacking libgfortran5:amd64 (8.3.0-6) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../059-libblas3_3.8.0-2_amd64.deb ... Unpacking libblas3:amd64 (3.8.0-2) ... Selecting previously unselected package libblas-dev:amd64. Preparing to unpack .../060-libblas-dev_3.8.0-2_amd64.deb ... Unpacking libblas-dev:amd64 (3.8.0-2) ... Selecting previously unselected package libboost1.67-dev:amd64. Preparing to unpack .../061-libboost1.67-dev_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost1.67-dev:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-regex1.67.0:amd64. Preparing to unpack .../062-libboost-regex1.67.0_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-regex1.67.0:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libicu-dev:amd64. Preparing to unpack .../063-libicu-dev_63.1-6+deb10u1_amd64.deb ... Unpacking libicu-dev:amd64 (63.1-6+deb10u1) ... Selecting previously unselected package libboost-regex1.67-dev:amd64. Preparing to unpack .../064-libboost-regex1.67-dev_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-regex1.67-dev:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-iostreams1.67-dev:amd64. Preparing to unpack .../065-libboost-iostreams1.67-dev_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-iostreams1.67-dev:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-iostreams-dev:amd64. Preparing to unpack .../066-libboost-iostreams-dev_1.67.0.1_amd64.deb ... Unpacking libboost-iostreams-dev:amd64 (1.67.0.1) ... Selecting previously unselected package libbtf1:amd64. Preparing to unpack .../067-libbtf1_1%3a5.4.0+dfsg-1_amd64.deb ... Unpacking libbtf1:amd64 (1:5.4.0+dfsg-1) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../068-libbz2-dev_1.0.6-9.2~deb10u1_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.6-9.2~deb10u1) ... Selecting previously unselected package libcamd2:amd64. Preparing to unpack .../069-libcamd2_1%3a5.4.0+dfsg-1_amd64.deb ... Unpacking libcamd2:amd64 (1:5.4.0+dfsg-1) ... Selecting previously unselected package libccolamd2:amd64. Preparing to unpack .../070-libccolamd2_1%3a5.4.0+dfsg-1_amd64.deb ... Unpacking libccolamd2:amd64 (1:5.4.0+dfsg-1) ... Selecting previously unselected package libcolamd2:amd64. Preparing to unpack .../071-libcolamd2_1%3a5.4.0+dfsg-1_amd64.deb ... Unpacking libcolamd2:amd64 (1:5.4.0+dfsg-1) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../072-liblapack3_3.8.0-2_amd64.deb ... 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Unpacking libldl2:amd64 (1:5.4.0+dfsg-1) ... Selecting previously unselected package libmongoose2:amd64. Preparing to unpack .../106-libmongoose2_1%3a5.4.0+dfsg-1_amd64.deb ... Unpacking libmongoose2:amd64 (1:5.4.0+dfsg-1) ... Selecting previously unselected package libumfpack5:amd64. Preparing to unpack .../107-libumfpack5_1%3a5.4.0+dfsg-1_amd64.deb ... Unpacking libumfpack5:amd64 (1:5.4.0+dfsg-1) ... Selecting previously unselected package librbio2:amd64. Preparing to unpack .../108-librbio2_1%3a5.4.0+dfsg-1_amd64.deb ... Unpacking librbio2:amd64 (1:5.4.0+dfsg-1) ... Selecting previously unselected package libspqr2:amd64. Preparing to unpack .../109-libspqr2_1%3a5.4.0+dfsg-1_amd64.deb ... Unpacking libspqr2:amd64 (1:5.4.0+dfsg-1) ... Selecting previously unselected package libsuitesparse-dev:amd64. Preparing to unpack .../110-libsuitesparse-dev_1%3a5.4.0+dfsg-1_amd64.deb ... Unpacking libsuitesparse-dev:amd64 (1:5.4.0+dfsg-1) ... 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Selecting previously unselected package lzma-dev. Preparing to unpack .../116-lzma-dev_9.22-2.1_all.deb ... Unpacking lzma-dev (9.22-2.1) ... Setting up libboost1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up libgslcblas0:amd64 (2.5+dfsg-6) ... Setting up ruby-power-assert (1.1.1-1) ... Setting up libmagic-mgc (1:5.35-4+deb10u2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libyaml-0-2:amd64 (0.2.1-1) ... Setting up libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... No schema files found: doing nothing. Setting up libssl1.1:amd64 (1.1.1d-0+deb10u7) ... Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libmetis5:amd64 (5.1.0.dfsg-5+b2) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u6) ... Setting up libicu63:amd64 (63.1-6+deb10u1) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up ruby-minitest (5.11.3-1) ... Setting up autotools-dev (20180224.1) ... Setting up libsqlite3-dev:amd64 (3.27.2-3+deb10u1) ... Setting up ruby-test-unit (3.2.8-1) ... Setting up libnspr4:amd64 (2:4.20-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libgsl23:amd64 (2.5+dfsg-6) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libbamtools2.5.1:amd64 (2.5.1+dfsg-3) ... Setting up libssl-dev:amd64 (1.1.1d-0+deb10u7) ... Setting up autopoint (0.19.8.1-9) ... Setting up icu-devtools (63.1-6+deb10u1) ... Setting up libbam-dev (0.1.19-4) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up libgfortran5:amd64 (8.3.0-6) ... Setting up liblzma-dev:amd64 (5.2.4-1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u3) ... Setting up ruby-did-you-mean (1.2.1-1) ... Setting up openssl (1.1.1d-0+deb10u7) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libicu-dev:amd64 (63.1-6+deb10u1) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Setting up libsuitesparseconfig5:amd64 (1:5.4.0+dfsg-1) ... Setting up librbio2:amd64 (1:5.4.0+dfsg-1) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libbz2-dev:amd64 (1.0.6-9.2~deb10u1) ... Setting up libgraphblas2:amd64 (1:5.4.0+dfsg-1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libamd2:amd64 (1:5.4.0+dfsg-1) ... Setting up libncurses-dev:amd64 (6.1+20181013-2+deb10u2) ... Setting up libgsl-dev (2.5+dfsg-6) ... Setting up libboost-regex1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libcolamd2:amd64 (1:5.4.0+dfsg-1) ... Setting up libtool (2.4.6-9) ... Setting up libboost-regex1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up libldl2:amd64 (1:5.4.0+dfsg-1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up m4 (1.4.18-2) ... Setting up libnss3:amd64 (2:3.42.1-1+deb10u3) ... Setting up libbtf1:amd64 (1:5.4.0+dfsg-1) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 137 added, 0 removed; done. Setting up libcamd2:amd64 (1:5.4.0+dfsg-1) ... Setting up libmongoose2:amd64 (1:5.4.0+dfsg-1) ... Setting up libblas3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libbamtools-dev:amd64 (2.5.1+dfsg-3) ... Setting up bsdmainutils (11.1.2+b1) ... 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 libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up lzma-dev (9.22-2.1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up libcurl3-nss:amd64 (7.64.0-4+deb10u2) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libklu1:amd64 (1:5.4.0+dfsg-1) ... Setting up libccolamd2:amd64 (1:5.4.0+dfsg-1) ... Setting up libncurses5-dev:amd64 (6.1+20181013-2+deb10u2) ... Setting up libcxsparse3:amd64 (1:5.4.0+dfsg-1) ... Setting up libcurl4-nss-dev:amd64 (7.64.0-4+deb10u2) ... Setting up libboost-iostreams1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up libblas-dev:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode 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 liblapack3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up rubygems-integration (1.11+deb10u1) ... Setting up libboost-iostreams-dev:amd64 (1.67.0.1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up liblapack-dev:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libcholmod3:amd64 (1:5.4.0+dfsg-1) ... Setting up libspqr2:amd64 (1:5.4.0+dfsg-1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up po-debconf (1.0.21) ... Setting up libhts-dev:amd64 (1.9-12~deb10u1) ... Setting up libumfpack5:amd64 (1:5.4.0+dfsg-1) ... Setting up libsuitesparse-dev:amd64 (1:5.4.0+dfsg-1) ... Setting up liblpsolve55-dev (5.5.0.15-4+b1) ... Setting up dh-autoreconf (19) ... Setting up rake (12.3.1-3+deb10u1) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up libruby2.5:amd64 (2.5.5-3+deb10u3) ... Setting up debhelper (12.1.1) ... Setting up ruby2.5 (2.5.5-3+deb10u3) ... Setting up ruby (1:2.5.1) ... Setting up ruby-asciidoctor (1.5.8-1) ... Setting up asciidoctor (1.5.8-1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package hostname: Name or service not known I: Running cd /build/augustus-3.3.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../augustus_3.3.2+dfsg-2_source.changes dpkg-buildpackage: info: source package augustus dpkg-buildpackage: info: source version 3.3.2+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/augustus-3.3.2+dfsg' /usr/bin/make -C auxprogs/bam2hints clean make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/bam2hints' rm -f bam2hints.o bam2hints ../../bin/bam2hints make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/bam2hints' /usr/bin/make -C auxprogs/homGeneMapping clean make[2]: Entering directory '/build/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 '/build/augustus-3.3.2+dfsg/auxprogs/homGeneMapping/src' rm -f homGeneMapping gene.o genome.o make[3]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/homGeneMapping/src' /bin/sh: line 0: cd: ../bin: No such file or directory /bin/sh: line 0: cd: ../../../bin: No such file or directory make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/homGeneMapping' /usr/bin/make -C auxprogs/joingenes clean make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/joingenes' rm -rf *o joingenes; rm -rf ../../bin/joingenes make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/joingenes' /usr/bin/make -C auxprogs/aln2wig clean make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/aln2wig' rm -f aln2wig aln2wig.o; rm -f ../../bin/aln2wig make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/aln2wig' /usr/bin/make -C auxprogs/bam2wig clean make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/bam2wig' rm -f bam2wig bam2wig.o rm -f ../../bin/bam2wig make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/bam2wig' /usr/bin/make -C auxprogs/checkTargetSortedness clean make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/checkTargetSortedness' rm -f *.o checkTargetSortedness make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/checkTargetSortedness' /usr/bin/make -C auxprogs/compileSpliceCands clean make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/compileSpliceCands' rm -f compileSpliceCands compileSpliceCands.o ../../bin/compileSpliceCands list.o make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/compileSpliceCands' /usr/bin/make -C auxprogs/filterBam clean make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/filterBam' (cd src; make clean;) make[3]: Entering directory '/build/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 '/build/augustus-3.3.2+dfsg/auxprogs/filterBam/src' make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/filterBam' rm -rf bin make[1]: Leaving directory '/build/augustus-3.3.2+dfsg' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/augustus-3.3.2+dfsg' mkdir -p bin /usr/bin/make -C auxprogs/aln2wig make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/aln2wig' gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -O2 -ggdb -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 '/build/augustus-3.3.2+dfsg/auxprogs/aln2wig' /usr/bin/make -C auxprogs/bam2hints make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/bam2hints' g++ -Wall -O2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 '/build/augustus-3.3.2+dfsg/auxprogs/bam2hints' /usr/bin/make -C auxprogs/bam2wig make[2]: Entering directory '/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 '/build/augustus-3.3.2+dfsg/auxprogs/bam2wig' /usr/bin/make -C auxprogs/checkTargetSortedness make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/checkTargetSortedness' cc -g -Wall -O2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 '/build/augustus-3.3.2+dfsg/auxprogs/checkTargetSortedness' /usr/bin/make -C auxprogs/compileSpliceCands make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/compileSpliceCands' cc -Wall -pedantic -ansi -g -O2 -ffile-prefix-map=/build/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 'parseList': compileSpliceCands.c:350:36: warning: 'left' may be used uninitialized in this function [-Wmaybe-uninitialized] findPossibleSpliceSites(left->name,actualChromosome,left->startPos,left->endPos,right->startPos,right->endPos,left->strand,right->strand); ~~~~^~~~~~ compileSpliceCands.c: In function 'main': compileSpliceCands.c:563:3: warning: 'chromosomeLength' may be used uninitialized in this function [-Wmaybe-uninitialized] parseList(&L,actualChromosome,chromosomeLength,oldname,maxSpliceSiteDiff,threshold,maxIntronLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now; make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/compileSpliceCands' /usr/bin/make -C auxprogs/filterBam make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/filterBam' (cd src;make) make[3]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/filterBam/src' g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 '/build/augustus-3.3.2+dfsg/auxprogs/filterBam/src' make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/filterBam' /usr/bin/make -C auxprogs/homGeneMapping/src make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/homGeneMapping/src' g++ -c -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 '/build/augustus-3.3.2+dfsg/auxprogs/homGeneMapping/src' /usr/bin/make -C auxprogs/joingenes make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/joingenes' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 '/build/augustus-3.3.2+dfsg/auxprogs/joingenes' dh_auto_build make -j16 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/augustus-3.3.2+dfsg' mkdir -p bin cd src && make make[3]: Entering directory '/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_hitseq.o pp_hitseq.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_scoring.o pp_scoring.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o statemodel.o statemodel.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o namgene.o namgene.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o types.o types.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o gene.o gene.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o motif.o motif.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o hints.o hints.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o projectio.o projectio.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o intronmodel.o intronmodel.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o exonmodel.o exonmodel.cc -I../include 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) { ^ 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) {} ^ types.cc:245:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError 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) {} ^ types.cc:250:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError 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) {} ^ types.cc:253:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError 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) {} ^ types.cc:259:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError 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) {} ^ 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) { ^ ../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: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/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 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) {} ^ 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 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){} ^~~~~~~~~~~~~~~~~~~~~~ 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/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) {} ^ 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/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/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){} ^~~~~~~~~~~~~~~~~~~~~~ ../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/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/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/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 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) {} ^ 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/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) {} ^ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/statemodel.hh:16, from statemodel.cc:16: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/extrinsicinfo.hh:25, from extrinsicinfo.cc:31: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/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) {} ^~~~~~~~~~~~~~~~~~ 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) { ^ 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_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) { ^~~~~~~~~~~~~~~~~~ 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) { ^~~~~~~~~~~~~~~~~~~~~~ ../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 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/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) {} ^~~~~~~~~~~~~~~~~~ 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) { ^~~~~~~~~~~~ In file included from ../include/pp_profile.hh:21, from ../include/pp_hitseq.hh:18, from ../include/pp_scoring.hh:22, from pp_scoring.cc:14: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../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/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) { ^~~~~~~~~~~~~~~~~~ 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) {} ^~~~~~~~~~~~~~~~~~ ../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/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) {} ^ 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) { ^ 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){} ^~~~~~~~~~~~~~~~~~~~~~ motif.cc: In constructor 'ContentStairs::ContentStairs()': motif.cc:519:12: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError) { ^~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/pp_scoring.hh:21, from ../include/gene.hh:15, from ../include/extrinsicinfo.hh:25, from extrinsicinfo.cc:31: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ 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 ../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 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) {} ^ 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_profile.cc: In member function 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map*)': 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) { ^ 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) { ^~~~~~~~~~~~ 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/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 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) { ^ 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 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) {} ^~~~~~~~~~~~~~~~ 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) { ^ In file included from ../include/evaluation.hh:23, from evaluation.cc:15: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ In file included from ../include/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) {} ^~~~~~~~~~~~~~~~ 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 ../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) {} ^~~~~~~~~~~~~~~~ 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*, 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) { ^~~~~~~~~~~~~~~~~~~~~~ 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) { ^ 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) { ^~~~~~~~~~~~~~~~~~~~ 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) { ^~~~~~~~~~~~~~~~~~ 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) { ^ ../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) {} ^~~~~~~~~~~~~~~~~~ intronmodel.cc: In member function 'virtual void IntronModel::viterbiForwardAndSampling(ViterbiMatrixType&, ViterbiMatrixType&, int, int, AlgorithmVariant, OptionListItem&)': intronmodel.cc:799:12: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ intronmodel.cc:866:28: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ intronmodel.cc: In member function 'virtual Double IntronModel::emiProbUnderModel(int, int) const': intronmodel.cc:926:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ intronmodel.cc: In member function 'Double IntronModel::seqProb(int, int) const': intronmodel.cc:1082:35: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ intronmodel.cc:1108:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ intronmodel.cc: In static member function 'static Double IntronModel::aSSProb(int, bool)': intronmodel.cc:1187:37: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ intronmodel.cc: In static member function 'static Double IntronModel::dSSProb(int, bool)': intronmodel.cc:1254:37: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ In file included from ../include/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/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){} ^~~~~~~~~~~~~~~~~~~~~~ extrinsicinfo.cc: In member function 'void FeatureCollection::readExtrinsicCFGFile()': extrinsicinfo.cc:2076:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ extrinsicinfo.cc: In member function 'void FeatureCollection::readTypeInfo(std::istream&)': extrinsicinfo.cc:2134:25: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ extrinsicinfo.cc: In member function 'void FeatureCollection::readGFFFile(const char*)': extrinsicinfo.cc:2287:28: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e){} ^ extrinsicinfo.cc:2304:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o igenicmodel.o igenicmodel.cc -I../include In file included from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from exonmodel.cc:25: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ exonmodel.cc: In static member function 'static void ExonModel::init()': exonmodel.cc:318:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] }catch( ProjectError e) { ^ exonmodel.cc:323:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] }catch( ProjectError e) { ^ exonmodel.cc:328:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] }catch( ProjectError e) { ^ exonmodel.cc:333:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] }catch( ProjectError e) { ^ exonmodel.cc:338:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] }catch( ProjectError e) { ^ exonmodel.cc:343:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] }catch( ProjectError e) { ^ exonmodel.cc:348:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch( ProjectError e) { ^ exonmodel.cc:353:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch( ProjectError e) { ^ exonmodel.cc:358:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch( ProjectError e) { ^ exonmodel.cc:363:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch( ProjectError e) { ^ exonmodel.cc:368:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch( ProjectError e) { ^ exonmodel.cc:373:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch( ProjectError e) { ^ exonmodel.cc:382:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch( ProjectError e) {} ^ exonmodel.cc:385:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch( ProjectError e) {} ^ exonmodel.cc: In member function 'virtual void ExonModel::viterbiForwardAndSampling(ViterbiMatrixType&, ViterbiMatrixType&, int, int, AlgorithmVariant, OptionListItem&)': exonmodel.cc:1129:31: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch(NoSubmapFoundError e) {} ^ exonmodel.cc:1156:28: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ exonmodel.cc: In member function 'Double ExonModel::notEndPartEmiProb(int, int, int, Feature*) const': exonmodel.cc:1588:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ exonmodel.cc:1618:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ exonmodel.cc: In member function 'Double ExonModel::seqProb(int, int, int) const': exonmodel.cc:1964:45: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ exonmodel.cc:1981:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ exonmodel.cc: In member function 'Double ExonModel::eTermSeqProb(int, int, int) const': exonmodel.cc:2019:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ exonmodel.cc: In member function 'Double ExonModel::initialSeqProb(int, int, int) const': exonmodel.cc:2046:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o utrmodel.o utrmodel.cc -I../include In file included from ../include/statemodel.hh:16, from ../include/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) {} ^~~~~~~~~~~~~~~~ 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) {} ^~~~~~~~~~~~~~~~~~ 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) { ^ 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) {} ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o merkmal.o merkmal.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/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) {} ^~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o vitmatrix.o vitmatrix.cc -I../include utrmodel.cc: In static member function 'static void UtrModel::init()': utrmodel.cc:167:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { ^ utrmodel.cc:172:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:175:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:178:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:181:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:184:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:187:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:190:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:193:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:196:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:199:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:202:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:205:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:208:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:211:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:214:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:217:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:220:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:223:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ utrmodel.cc:228:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:231:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:234:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) {} ^ utrmodel.cc:237:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) {} ^ utrmodel.cc:240:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) {} ^ utrmodel.cc:243:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) {} ^ utrmodel.cc:246:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) {} ^ utrmodel.cc:249:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) {} ^ utrmodel.cc:252:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) {} ^ utrmodel.cc: In member function 'virtual void UtrModel::viterbiForwardAndSampling(ViterbiMatrixType&, ViterbiMatrixType&, int, int, AlgorithmVariant, OptionListItem&)': utrmodel.cc:1062:28: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ utrmodel.cc: In member function 'Double UtrModel::notEndPartEmiProb(int, int, int, Feature*) const': utrmodel.cc:1275:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ utrmodel.cc:1409:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ utrmodel.cc: In member function 'Double UtrModel::seqProb(int, int, bool, int) const': utrmodel.cc:1700:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ utrmodel.cc:1735:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ utrmodel.cc: In member function 'Double UtrModel::tssupSeqProb(int, int, bool) const': utrmodel.cc:1760:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ utrmodel.cc: In static member function 'static void UtrModel::computeTtsProbs(int, int)': utrmodel.cc:1889:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ utrmodel.cc:1916:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ In file included from ../include/extrinsicinfo.hh:24, from ../include/merkmal.hh:17, from merkmal.cc:13: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/extrinsicinfo.hh:25, from ../include/merkmal.hh:17, from merkmal.cc:13: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/pp_scoring.hh:21, from ../include/gene.hh:15, from ../include/extrinsicinfo.hh:25, from ../include/merkmal.hh:17, from merkmal.cc:13: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ 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/x86_64-linux-gnu/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 vitmatrix.cc:10: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/merkmal.hh:17, from merkmal.cc:13: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o lldouble.o lldouble.cc -I../include namgene.cc: In member function 'std::__cxx11::list* 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/x86_64-linux-gnu/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 ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o graph.o graph.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o meaPath.o meaPath.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o exoncand.o exoncand.cc -I../include In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/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 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/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){} ^~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o randseqaccess.o randseqaccess.cc -I../include In file included from ../include/pp_scoring.hh:21, from ../include/gene.hh:15, from ../include/graph.hh:9, from meaPath.cc:3: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/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/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/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/statemodel.hh:16, from ../include/exonmodel.hh:22, from ../include/exoncand.hh:27, from exoncand.cc:16: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/extrinsicinfo.hh:24, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from ../include/exoncand.hh:27, from exoncand.cc:16: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/graph.hh:10, from meaPath.cc:3: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/extrinsicinfo.hh:25, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from ../include/exoncand.hh:27, from exoncand.cc:16: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/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 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) {} ^~~~~~~~~~~~~~~~ In file included from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from ../include/exoncand.hh:27, from ../include/graph.hh:11, from graph.cc:9: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ In file included from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from ../include/exoncand.hh:27, from exoncand.cc:16: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/randseqaccess.hh:14, from randseqaccess.cc:15: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o fasta.o fasta.cc -I../include 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) {} ^~~~~~~~~~~~~~~~ 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/x86_64-linux-gnu/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 ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ randseqaccess.cc: In member function 'void SpeciesCollection::readExtrinsicCFGFile(std::vector >&)': randseqaccess.cc:98:29: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] }catch(ProjectError e){ ^ randseqaccess.cc:137:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ randseqaccess.cc: In member function 'void SpeciesCollection::readGFFFile(const char*)': randseqaccess.cc:166:35: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e){} ^ randseqaccess.cc:196:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o ncmodel.o ncmodel.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o commontrain.o commontrain.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o igenictrain.o igenictrain.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o introntrain.o introntrain.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/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/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) { ^~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o utrtrain.o utrtrain.cc -I../include ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o dummy.o dummy.cc -I../include 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) {} ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc 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/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/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/extrinsicinfo.hh:24, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/igenicmodel.hh:20, from igenictrain.cc:13: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/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/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/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/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/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){} ^~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/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/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) {} ^~~~~~~~~~~~~~~~ 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) {} ^~~~~~~~~~~~~~~~ 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) { ^ 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/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) {} ^~~~~~~~~~~~~~~~ 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/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from exontrain.cc:13: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ In file included from ../include/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) {} ^~~~~~~~~~~~~~~~~~ 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) { ^ 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){} ^~~~~~~~~~~~~~~~~~~~~~ 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) { ^ 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) {} ^ 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) {} ^ 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 ) { ^~~~~~~~~~~~ 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/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){} ^~~~~~~~~~~~~~~~~~~~~~ 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) {} ^ 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) {} ^~~~~~~~~~~~~~~~ echo "-Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security" > cxxflags 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) {} ^~~~~~~~~~~~~~~~ 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){} ^~~~~~~~~~~~~~~~~~~~~~ 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) { ^ 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) {} ^~~~~~~~~~~~~~~~~~ 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 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) { ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/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 cp prepareAlign ../bin/ In file included from fastBlockSearch.cc:14: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/pp_profile.hh:21, from fastBlockSearch.cc:15: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 augustus.cc:15: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/pp_scoring.hh:21, from ../include/gene.hh:15, from augustus.cc:15: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/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/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 ../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) {} ^~~~~~~~~~~~~~~~~~ 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/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 fastBlockSearch ../bin/ cp augustus ../bin/ cp etraining ../bin/ make[3]: Leaving directory '/build/augustus-3.3.2+dfsg/src' cd auxprogs && make make[3]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs' cd bam2hints; make; make[4]: Entering directory '/build/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 '/build/augustus-3.3.2+dfsg/auxprogs/bam2hints' cd compileSpliceCands; make; make[4]: Entering directory '/build/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 '/build/augustus-3.3.2+dfsg/auxprogs/compileSpliceCands' cd filterBam; make; make[4]: Entering directory '/build/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 '/build/augustus-3.3.2+dfsg/auxprogs/filterBam/src' g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 '/build/augustus-3.3.2+dfsg/auxprogs/filterBam/src' make[4]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/filterBam' cd homGeneMapping; make; make[4]: Entering directory '/build/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 '/build/augustus-3.3.2+dfsg/auxprogs/homGeneMapping/src' make[5]: Nothing to be done for 'all'. make[5]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/homGeneMapping/src' make[4]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/homGeneMapping' cd joingenes; make; make[4]: Entering directory '/build/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 '/build/augustus-3.3.2+dfsg/auxprogs/joingenes' cd bam2wig; make; make[4]: Entering directory '/build/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 '/build/augustus-3.3.2+dfsg/auxprogs/bam2wig' cd utrrnaseq/Debug; make all; make[4]: Entering directory '/build/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" 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 '/build/augustus-3.3.2+dfsg/auxprogs/utrrnaseq/Debug' make[3]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs' make[2]: Leaving directory '/build/augustus-3.3.2+dfsg' asciidoctor -a docdate='' -b manpage debian/mansrc/*adoc make[1]: Leaving directory '/build/augustus-3.3.2+dfsg' dh_auto_test make -j16 test make[1]: Entering directory '/build/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 /build/augustus-3.3.2+dfsg/config/ ... # human version. Using species specific transition matrix: /build/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 '/build/augustus-3.3.2+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/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 '/build/augustus-3.3.2+dfsg' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/augustus-3.3.2+dfsg' dh_installchangelogs -k HISTORY.TXT make[1]: Leaving directory '/build/augustus-3.3.2+dfsg' dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/augustus-3.3.2+dfsg' dh_compress -Xtutorial make[1]: Leaving directory '/build/augustus-3.3.2+dfsg' dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps 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) 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 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 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/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 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/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/bam2wig was not linked against liblzma.so.5 (it uses none of the library's symbols) dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/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 '/build/augustus-3.3.2+dfsg' dh_md5sums dh_builddeb dpkg-deb: building package 'augustus-data' in '../augustus-data_3.3.2+dfsg-2_all.deb'. dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.3.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'augustus' in '../augustus_3.3.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'augustus-doc' in '../augustus-doc_3.3.2+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../augustus_3.3.2+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1628508/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1628508/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1628508 and its subdirectories I: Current time: Mon Jan 2 04:25:03 +14 2023 I: pbuilder-time-stamp: 1672583103