Diff of the two buildlogs: -- --- b1/build.log 2021-11-29 07:58:43.488382734 +0000 +++ b2/build.log 2021-11-29 08:02:01.861574929 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Nov 28 19:47:10 -12 2021 -I: pbuilder-time-stamp: 1638172030 +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 @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Mon Mar 18 04:04:09 2019 -12 +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 @@ -32,136 +32,170 @@ dpkg-source: info: applying spelling.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/802268/tmp/hooks/D02_print_environment starting +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 - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + 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='3274bb6adcb742c8984583ca2e160d6d' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='802268' - PS1='# ' - PS2='> ' + 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' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.Zqvl7vIRP5/pbuilderrc_hgNQ --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Zqvl7vIRP5/b1 --logfile b1/build.log augustus_3.3.2+dfsg-2.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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 ionos11-amd64 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux + 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 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Nov 7 09:58 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/802268/tmp/hooks/D02_print_environment finished + -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 @@ -342,7 +376,7 @@ 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 4s (19.3 MB/s) +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.) @@ -844,7 +878,8 @@ 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 -I: Running cd /build/augustus-3.3.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../augustus_3.3.2+dfsg-2_source.changes +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 @@ -865,8 +900,8 @@ 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: 1: cd: can't cd to ../bin -/bin/sh: 1: cd: can't cd to ../../../bin +/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' @@ -979,7 +1014,7 @@ cp joingenes ../../bin/ make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/joingenes' dh_auto_build - make -j15 "INSTALL=install --strip-program=true" + make -j16 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/augustus-3.3.2+dfsg' mkdir -p bin cd src && make @@ -999,6 +1034,8 @@ 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=] @@ -1044,24 +1081,53 @@ 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) { ^ @@ -1104,19 +1170,6 @@ types.cc:341:27: 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 intronmodel.o intronmodel.cc -I../include -In file included from ../include/motif.hh:21, - from ../include/gene.hh:14, - from ../include/genbank.hh:19, - from genbank.cc:15: -../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': -../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError){} - ^~~~~~~~~~~~~~~~~~~~~~ -../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': -../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError){} - ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/pp_profile.hh:21, from ../include/pp_hitseq.hh:18, from pp_hitseq.cc:14: @@ -1128,19 +1181,7 @@ ../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 ../include/namgene.hh:15, - from namgene.cc:21: +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) {} @@ -1169,6 +1210,35 @@ ../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&)': @@ -1179,10 +1249,21 @@ ../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) {} @@ -1199,43 +1280,10 @@ ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ -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:22, - from ../include/pp_hitseq.hh:18, - from pp_hitseq.cc:14: -../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': -../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] - } catch (NoSubmapFoundError) { - ^~~~~~~~~~~~~~~~~~ -../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': -../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] - } catch (NoSubmapFoundError) {} - ^~~~~~~~~~~~~~~~~~ -In file included from ../include/pp_scoring.hh:21, - from ../include/gene.hh:15, - from ../include/genbank.hh:19, - from genbank.cc:15: -../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': -../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] - } catch (NoSubmapFoundError) { - ^~~~~~~~~~~~~~~~~~ -../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': -../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] - } catch (NoSubmapFoundError) {} - ^~~~~~~~~~~~~~~~~~ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, - from ../include/extrinsicinfo.hh:25, - from ../include/namgene.hh:15, - from namgene.cc:21: + 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){} @@ -1244,16 +1292,10 @@ ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ -In file included from ../include/pp_profile.hh:22, - from pp_profile.cc:14: -../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': -../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] - } catch (NoSubmapFoundError) { - ^~~~~~~~~~~~~~~~~~ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, - from ../include/extrinsicinfo.hh:25, - from extrinsicinfo.cc:31: + 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){} @@ -1262,19 +1304,9 @@ ../include/geneticcode.hh:344:11: 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) {} - ^~~~~~~~~~~~~~~~~~ -geneticcode.cc: In static member function 'static char GeneticCode::translate(const char*)': -geneticcode.cc:182:14: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError) { - ^~~~~~~~~~~~~~~~~~~~~~ -geneticcode.cc: In static member function 'static char GeneticCode::revtranslate(const char*)': -geneticcode.cc:189:14: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError) { - ^~~~~~~~~~~~~~~~~~~~~~ -In file included from properties.cc:17: +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) {} @@ -1303,7 +1335,7 @@ ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ -In file included from hints.cc:14: +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) {} @@ -1312,6 +1344,12 @@ ../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) {} @@ -1332,11 +1370,12 @@ ../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/extrinsicinfo.hh:25, - from ../include/namgene.hh:15, - from namgene.cc:21: +../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) { @@ -1347,7 +1386,8 @@ ^~~~~~~~~~~~~~~~~~ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, - from gene.cc:21: + 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){} @@ -1356,8 +1396,26 @@ ../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 motif.cc:14: + 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){} @@ -1366,19 +1424,29 @@ ../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: +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 motif.cc:17: +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) {} @@ -1407,8 +1475,8 @@ ../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 statemodel.cc:16: +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) { @@ -1417,12 +1485,28 @@ ../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/pp_scoring.hh:21, +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) { @@ -1433,7 +1517,16 @@ ^~~~~~~~~~~~~~~~~~ In file included from ../include/pp_scoring.hh:21, from ../include/gene.hh:15, - from gene.cc:21: + 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) { @@ -1442,46 +1535,22 @@ ../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) { - ^~~~~~~~~~~~ +../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 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 pp_profile.cc: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) {} @@ -1510,25 +1579,6 @@ ../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/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){} - ^~~~~~~~~~~~~~~~~~~~~~ -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){ - ^ 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) {} @@ -1537,28 +1587,6 @@ motif.cc:330:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ -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){} - ^~~~~~~~~~~~~~~~~~~~~~ -motif.cc: In constructor 'ContentStairs::ContentStairs()': -motif.cc:519:12: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] - } catch (ProjectError) { - ^~~~~~~~~~~~ -In file included from ../include/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/motif.hh:21, from ../include/gene.hh:14, from ../include/extrinsicinfo.hh:25, @@ -1569,28 +1597,18 @@ ../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){} ^~~~~~~~~~~~~~~~~~~~~~ -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) { - ^ In file included from ../include/pp_scoring.hh:21, from ../include/gene.hh:15, - from ../include/evaluation.hh:22, - from evaluation.cc: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) { @@ -1599,7 +1617,35 @@ ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ -In file included from genbank.cc:19: +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) {} @@ -1628,70 +1674,7 @@ ../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) { - ^ -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 member function 'AnnoSequence* GBProcessor::getAnnoSequenceList()': -genbank.cc:312:19: warning: catching polymorphic type 'class GBError' by value [-Wcatch-value=] - } catch (GBError e) { - ^ -genbank.cc: In constructor 'GBFeature::GBFeature(const char*)': -genbank.cc:490:25: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] - } catch (ProjectError e) { - ^ -namgene.cc: In constructor 'NAMGene::NAMGene()': -namgene.cc:116:41: warning: catching polymorphic type 'struct PP::ProfileNotFoundError' by value [-Wcatch-value=] - } catch (PP::ProfileNotFoundError e) { - ^ -namgene.cc:119:17: warning: catching polymorphic type 'struct PP::ProfileNotFoundError' by value [-Wcatch-value=] - } catch (PP::ProfileNotFoundError) { - ^~~~~~~~~~~~~~~~~~~~ -namgene.cc:128:12: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] - } catch (KeyNotFoundError) { - ^~~~~~~~~~~~~~~~ -namgene.cc:130:34: warning: catching polymorphic type 'struct PP::ProfileInsigError' by value [-Wcatch-value=] - } catch (PP::ProfileInsigError e) { - ^ -In file included from ../include/statemodel.hh:16, - from ../include/intronmodel.hh:17, - from intronmodel.cc:26: -../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': -../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] - } catch (NoSubmapFoundError) { - ^~~~~~~~~~~~~~~~~~ -../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': -../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] - } catch (NoSubmapFoundError) {} - ^~~~~~~~~~~~~~~~~~ -extrinsicinfo.cc: In member function 'void FeatureCollection::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) { - ^ -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: +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) {} @@ -1720,6 +1703,28 @@ ../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: @@ -1751,7 +1756,9 @@ ../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: +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) {} @@ -1780,30 +1787,147 @@ ../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) { - ^~~~~~~~~~~~ -In file included from ../include/motif.hh:21, - from ../include/gene.hh:14, - from ../include/extrinsicinfo.hh:25, - from ../include/merkmal.hh:17, +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/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){} +../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) { ^~~~~~~~~~~~~~~~~~~~~~ -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) { - ^~~~~~~~~~~~ -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 +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: @@ -1811,10 +1935,42 @@ ../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, @@ -1863,6 +2019,22 @@ ../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, @@ -1943,166 +2115,6 @@ exonmodel.cc:2046:34: 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/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/extrinsicinfo.hh:24, - from ../include/evaluation.hh:23, - from evaluation.cc:15: -../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': -../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] - } catch (KeyNotFoundError e) {} - ^ -../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': -../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] - } catch (KeyNotFoundError e) {} - ^ -../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': -../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] - } catch (KeyNotFoundError e) {} - ^ -../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': -../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] - } catch (KeyNotFoundError e) {} - ^ -../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': -../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] - } catch (KeyNotFoundError e) {} - ^ -../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': -../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] - } catch (KeyNotFoundError e) {} - ^ -../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': -../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] - } catch (KeyNotFoundError e) {} - ^ -In file included from ../include/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 ../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/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) {} - ^~~~~~~~~~~~~~~~ -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) { - ^ -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) { - ^ -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::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 ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 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, @@ -2163,7 +2175,14 @@ ../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 merkmal.o merkmal.cc -I../include +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: @@ -2175,6 +2194,21 @@ ../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, @@ -2208,6 +2242,7 @@ ../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, @@ -2223,77 +2258,6 @@ ../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 merkmal.cc:13: -../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': -../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] - } catch (KeyNotFoundError e) {} - ^ -../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': -../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] - } catch (KeyNotFoundError e) {} - ^ -../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': -../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] - } catch (KeyNotFoundError e) {} - ^ -../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': -../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] - } catch (KeyNotFoundError e) {} - ^ -../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': -../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] - } catch (KeyNotFoundError e) {} - ^ -../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': -../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] - } catch (KeyNotFoundError e) {} - ^ -../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': -../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] - } catch (KeyNotFoundError e) {} - ^ -In file included from ../include/motif.hh:21, - from ../include/gene.hh:14, - from ../include/extrinsicinfo.hh:25, - from ../include/merkmal.hh:17, - from merkmal.cc:13: -../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': -../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError){} - ^~~~~~~~~~~~~~~~~~~~~~ -../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': -../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError){} - ^~~~~~~~~~~~~~~~~~~~~~ -In file included from ../include/pp_scoring.hh:21, - from ../include/gene.hh:15, - from ../include/extrinsicinfo.hh:25, - from ../include/merkmal.hh:17, - from merkmal.cc:13: -../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': -../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] - } catch (NoSubmapFoundError) { - ^~~~~~~~~~~~~~~~~~ -../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': -../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] - } catch (NoSubmapFoundError) {} - ^~~~~~~~~~~~~~~~~~ -In file included from ../include/merkmal.hh:17, - from merkmal.cc:13: -../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': -../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] - } catch (KeyNotFoundError) {} - ^~~~~~~~~~~~~~~~ -In file included from ../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/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/utrmodel.hh:17, @@ -2302,21 +2266,7 @@ ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ -igenicmodel.cc: In static member function 'static void IGenicModel::init()': -igenicmodel.cc:52:14: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] - } catch( ProjectError ) { } - ^~~~~~~~~~~~ -igenicmodel.cc: In member function 'virtual void IGenicModel::viterbiForwardAndSampling(ViterbiMatrixType&, ViterbiMatrixType&, int, int, AlgorithmVariant, OptionListItem&)': -igenicmodel.cc:279:24: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] - } catch (ProjectError e) { - ^ -igenicmodel.cc: In member function 'virtual Double IGenicModel::emiProbUnderModel(int, int) const': -igenicmodel.cc:343:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError e) { - ^ -igenicmodel.cc:355:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError e) { - ^ +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) { @@ -2402,7 +2352,6 @@ utrmodel.cc:252:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) {} ^ -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -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 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) { @@ -2432,6 +2381,86 @@ 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=] @@ -2441,12 +2470,13 @@ ../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 -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 -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 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)); @@ -2473,6 +2503,10 @@ ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __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, @@ -2509,6 +2543,19 @@ ../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, @@ -2521,7 +2568,6 @@ ../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 fasta.o fasta.cc -I../include In file included from ../include/graph.hh:10, from ../include/mea.hh:5, from mea.cc:1: @@ -2553,30 +2599,6 @@ ../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/graph.hh:9, - from graph.cc:9: -../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': -../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError){} - ^~~~~~~~~~~~~~~~~~~~~~ -../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': -../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError){} - ^~~~~~~~~~~~~~~~~~~~~~ -In file included from ../include/motif.hh:21, - from ../include/gene.hh:14, - from ../include/randseqaccess.hh:14, - from randseqaccess.cc:15: -../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': -../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError){} - ^~~~~~~~~~~~~~~~~~~~~~ -../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': -../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError){} - ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/pp_scoring.hh:21, from ../include/gene.hh:15, from ../include/graph.hh:9, @@ -2612,8 +2634,12 @@ ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ -In file included from ../include/graph.hh:10, - from graph.cc:9: +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) {} @@ -2642,12 +2668,8 @@ ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ -In file included from ../include/extrinsicinfo.hh:24, - from ../include/merkmal.hh:17, - from ../include/statemodel.hh:17, - from ../include/exonmodel.hh:22, - from ../include/exoncand.hh:27, - from exoncand.cc:16: +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) {} @@ -2676,8 +2698,24 @@ ../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 meaPath.cc:3: + 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) {} @@ -2711,32 +2749,34 @@ 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/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) {} - ^~~~~~~~~~~~~~~~~~ -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 -In file included from ../include/motif.hh:21, - from ../include/gene.hh:14, - from ../include/extrinsicinfo.hh:25, - from ../include/merkmal.hh:17, +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){} @@ -2745,22 +2785,11 @@ ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ -In file included from ../include/merkmal.hh:17, - from ../include/statemodel.hh:17, - from ../include/exonmodel.hh:22, - from ../include/exoncand.hh:27, - from ../include/graph.hh:11, - from meaPath.cc:3: -../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': -../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] - } catch (KeyNotFoundError) {} - ^~~~~~~~~~~~~~~~ -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -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 -In file included from ../include/statemodel.hh:16, - from ../include/ncmodel.hh:15, - from ncmodel.cc:13: +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) { @@ -2770,10 +2799,8 @@ } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/extrinsicinfo.hh:24, - from ../include/merkmal.hh:17, - from ../include/statemodel.hh:17, - from ../include/ncmodel.hh:15, - from ncmodel.cc:13: + 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) {} @@ -2802,9 +2829,72 @@ ../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/randseqaccess.hh:16, +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) {} @@ -2833,6 +2923,18 @@ ../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, @@ -2848,54 +2950,6 @@ ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ -In file included from ../include/merkmal.hh:17, - from ../include/statemodel.hh:17, - from ../include/exonmodel.hh:22, - from ../include/exoncand.hh:27, - from exoncand.cc:16: -../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': -../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] - } catch (KeyNotFoundError) {} - ^~~~~~~~~~~~~~~~ -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) {} - ^~~~~~~~~~~~~~~~ -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) {} - ^~~~~~~~~~~~~~~~ -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) { - ^ -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) { - ^ In file included from ../include/statemodel.hh:16, from ../include/intronmodel.hh:17, from introntrain.cc:14: @@ -2907,10 +2961,6 @@ ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ -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/extrinsicinfo.hh:24, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, @@ -2944,9 +2994,42 @@ ../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, +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) { @@ -2973,8 +3056,8 @@ 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: + 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) {} @@ -3018,78 +3101,56 @@ ../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/intronmodel.hh:17, - from introntrain.cc:14: + 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) {} ^~~~~~~~~~~~~~~~ -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 -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 ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, - from ../include/igenicmodel.hh:20, - from igenictrain.cc:13: + from ../include/intronmodel.hh:17, + from introntrain.cc:14: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ -introntrain.cc: In member function 'void IntronModel::processSequence(const char*, const char*)': -introntrain.cc:169:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError e) { - ^ -introntrain.cc: In member function 'void IntronModel::processASS(const char*, int, Boolean)': -introntrain.cc:252:37: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError e){ - ^ -introntrain.cc: In member function 'void IntronModel::processDSS(const char*, int)': -introntrain.cc:288:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError e) { - ^ -introntrain.cc: In member function 'void IntronModel::buildProbabilities(const AnnoSequence*)': -introntrain.cc:352:31: warning: catching polymorphic type 'class IntronModelError' by value [-Wcatch-value=] - } catch (IntronModelError e) { - ^ -introntrain.cc: In member function 'virtual void IntronModel::printProbabilities(int, BaseCount*, const char*)': -introntrain.cc:731:14: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] - } catch( ProjectError ) { - ^~~~~~~~~~~~ -igenictrain.cc: In member function 'void IGenicModel::processSequence(const char*, const char*)': -igenictrain.cc:175:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError e) {} - ^ -igenictrain.cc: In member function 'virtual void IGenicModel::printProbabilities(int, BaseCount*, const char*)': -igenictrain.cc:252:12: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] - catch( ProjectError ) { - ^~~~~~~~~~~~ -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 +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/exonmodel.hh:22, - from exontrain.cc:13: + 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) { @@ -3098,11 +3159,19 @@ ../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/exonmodel.hh:22, - from exontrain.cc:13: + 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) {} @@ -3131,23 +3200,6 @@ ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ -In file included from ../include/motif.hh:21, - from ../include/gene.hh:14, - from ../include/extrinsicinfo.hh:25, - from ../include/merkmal.hh:17, - from ../include/statemodel.hh:17, - from ../include/exonmodel.hh:22, - from exontrain.cc:13: -../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': -../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError){} - ^~~~~~~~~~~~~~~~~~~~~~ -../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': -../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError){} - ^~~~~~~~~~~~~~~~~~~~~~ -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 -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/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, @@ -3157,8 +3209,8 @@ } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ In file included from ../include/statemodel.hh:16, - from ../include/utrmodel.hh:17, - from utrtrain.cc:15: + 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) { @@ -3167,11 +3219,42 @@ ../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, +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) {} @@ -3200,6 +3283,33 @@ ../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 ) { @@ -3225,22 +3335,6 @@ exontrain.cc:896:34: 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){} - ^~~~~~~~~~~~~~~~~~~~~~ -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/utrmodel.hh:17, @@ -3249,50 +3343,26 @@ ../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) {} - ^~~~~~~~~~~~~~~~~~ -In file included from ../include/extrinsicinfo.hh:24, - from ../include/merkmal.hh:17, +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/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) {} - ^ +../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) { @@ -3305,21 +3375,6 @@ utrtrain.cc:396:29: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=] } catch (UtrModelError e) { ^ -In file included from ../include/motif.hh:21, - from ../include/gene.hh:14, - from ../include/extrinsicinfo.hh:25, - from ../include/merkmal.hh:17, - from ../include/statemodel.hh:17, - from ../include/intronmodel.hh:17, - from dummy.cc:13: -../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': -../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError){} - ^~~~~~~~~~~~~~~~~~~~~~ -../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': -../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError){} - ^~~~~~~~~~~~~~~~~~~~~~ utrtrain.cc:403:29: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=] } catch( UtrModelError e ){ ^ @@ -3361,30 +3416,6 @@ utrtrain.cc:851:24: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { ^ -utrtrain.cc: In member function 'virtual void UtrModel::printProbabilities(int, BaseCount*, const char*)': -utrtrain.cc:1018:14: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] - } catch( ProjectError ) { - ^~~~~~~~~~~~ -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){} - ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/pp_profile.hh:22, from ../include/pp_fastBlockSearcher.hh:19, from pp_fastBlockSearcher.cc:1: @@ -3396,6 +3427,10 @@ ../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=] @@ -3470,28 +3505,6 @@ ../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 etraining.cc:13: -../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': -../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError){} - ^~~~~~~~~~~~~~~~~~~~~~ -../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': -../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] - } catch (InvalidNucleotideError){} - ^~~~~~~~~~~~~~~~~~~~~~ -In file included from ../include/pp_scoring.hh:21, - from ../include/gene.hh:15, - from etraining.cc:13: -../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': -../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] - } catch (NoSubmapFoundError) { - ^~~~~~~~~~~~~~~~~~ -../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': -../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] - } catch (NoSubmapFoundError) {} - ^~~~~~~~~~~~~~~~~~ In file included from ../include/pp_scoring.hh:21, from ../include/gene.hh:15, from augustus.cc:15: @@ -3503,8 +3516,20 @@ ../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 etraining.cc:14: + 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) {} @@ -3533,14 +3558,33 @@ ../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: +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 ../include/namgene.hh:15, - from augustus.cc:17: + 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) {} @@ -3569,27 +3613,18 @@ ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ -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) { - ^ -In file included from ../include/namgene.hh:15, - from augustus.cc:17: +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) {} ^~~~~~~~~~~~~~~~ -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) { - ^ +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 etraining ../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' @@ -3685,7 +3720,7 @@ asciidoctor -a docdate='' -b manpage debian/mansrc/*adoc make[1]: Leaving directory '/build/augustus-3.3.2+dfsg' dh_auto_test - make -j15 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). @@ -3819,14 +3854,14 @@ 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 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/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 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 liblzma.so.5 (it uses none of the library's symbols) -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/checkTargetSortedness debian/augustus/usr/bin/bam2wig were not linked against libncurses.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/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' @@ -3837,9 +3872,9 @@ make[1]: Leaving directory '/build/augustus-3.3.2+dfsg' dh_md5sums dh_builddeb -dpkg-deb: building package 'augustus' in '../augustus_3.3.2+dfsg-2_amd64.deb'. -dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.3.2+dfsg-2_amd64.deb'. 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 @@ -3848,12 +3883,14 @@ 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/802268 and its subdirectories -I: Current time: Sun Nov 28 19:58:42 -12 2021 -I: pbuilder-time-stamp: 1638172722 +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