I: pbuilder: network access will be disabled during build I: Current time: Thu Jul 16 06:42:14 -12 2020 I: pbuilder-time-stamp: 1594924934 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [augustus_3.3.2+dfsg-2.dsc] I: copying [./augustus_3.3.2+dfsg.orig.tar.xz] I: copying [./augustus_3.3.2+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon Mar 18 04:04:09 2019 -12 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./augustus_3.3.2+dfsg-2.dsc dpkg-source: info: extracting augustus in augustus-3.3.2+dfsg dpkg-source: info: unpacking augustus_3.3.2+dfsg.orig.tar.xz dpkg-source: info: unpacking augustus_3.3.2+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying search_config_path dpkg-source: info: applying set_installdir dpkg-source: info: applying keep_cflags dpkg-source: info: applying buildflags.patch dpkg-source: info: applying spelling.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/21460/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='5bd6fce88bdb4f31893a6f79731ed461' 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='21460' PS1='# ' PS2='> ' 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.0pbloe2LoX/pbuilderrc_ppbe --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.0pbloe2LoX/b1 --logfile b1/build.log augustus_3.3.2+dfsg-2.dsc' SUDO_GID='114' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux jtx1b 4.19.0-9-arm64 #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) aarch64 GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 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 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 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 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 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 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 124508 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 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 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 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 15 20:25 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 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/21460/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbam-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, libcurl4-nss-dev, libssl-dev, asciidoctor dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on liblpsolve55-dev; however: Package liblpsolve55-dev is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on lzma-dev; however: Package lzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libncurses5-dev; however: Package libncurses5-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-nss-dev; however: Package libcurl4-nss-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libamd2{a} libarchive-zip-perl{a} libbam-dev{a} libbamtools-dev{a} libbamtools2.5.1{a} libblas-dev{a} libblas3{a} libboost-iostreams-dev{a} libboost-iostreams1.67-dev{a} libboost-regex1.67-dev{a} libboost-regex1.67.0{a} libboost1.67-dev{a} libbsd0{a} libbtf1{a} libbz2-dev{a} libcamd2{a} libccolamd2{a} libcholmod3{a} libcolamd2{a} libcroco3{a} libcurl3-gnutls{a} libcurl3-nss{a} libcurl4-nss-dev{a} libcxsparse3{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgraphblas2{a} libgsl-dev{a} libgsl23{a} libgslcblas0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu-dev{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libklu1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.4-2{a} libldap-common{a} libldl2{a} liblpsolve55-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmetis5{a} libmongoose2{a} libncurses-dev{a} libncurses5-dev{a} libncurses6{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libpipeline1{a} libpsl5{a} librbio2{a} libreadline7{a} librtmp1{a} libruby2.5{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libspqr2{a} libsqlite3-dev{a} libssh2-1{a} libssl-dev{a} libssl1.1{a} libsuitesparse-dev{a} libsuitesparseconfig5{a} libtool{a} libuchardet0{a} libumfpack5{a} libxml2{a} libyaml-0-2{a} lzma-dev{a} m4{a} man-db{a} openssl{a} po-debconf{a} rake{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-did-you-mean{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-test-unit{a} ruby-xmlrpc{a} ruby2.5{a} rubygems-integration{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl fonts-lato krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs zip 0 packages upgraded, 117 newly installed, 0 to remove and 0 not upgraded. Need to get 65.5 MB of archives. After unpacking 371 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf readline-common all 7.0-5 [70.6 kB] Get: 8 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 10 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 11 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 12 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 13 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 14 http://deb.debian.org/debian buster/main armhf openssl armhf 1.1.1d-0+deb10u3 [818 kB] Get: 15 http://deb.debian.org/debian buster/main armhf ca-certificates all 20190110 [157 kB] Get: 16 http://deb.debian.org/debian buster/main armhf rubygems-integration all 1.11+deb10u1 [5212 B] Get: 17 http://deb.debian.org/debian buster/main armhf rake all 12.3.1-3+deb10u1 [67.1 kB] Get: 18 http://deb.debian.org/debian buster/main armhf ruby-did-you-mean all 1.2.1-1 [14.4 kB] Get: 19 http://deb.debian.org/debian buster/main armhf ruby-minitest all 5.11.3-1 [54.8 kB] Get: 20 http://deb.debian.org/debian buster/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 21 http://deb.debian.org/debian buster/main armhf ruby-power-assert all 1.1.1-1 [10.9 kB] Get: 22 http://deb.debian.org/debian buster/main armhf ruby-test-unit all 3.2.8-1 [72.4 kB] Get: 23 http://deb.debian.org/debian buster/main armhf ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 24 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libreadline7 armhf 7.0-5 [131 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libyaml-0-2 armhf 0.2.1-1 [40.6 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libruby2.5 armhf 2.5.5-3+deb10u1 [3198 kB] Get: 28 http://deb.debian.org/debian buster/main armhf ruby2.5 armhf 2.5.5-3+deb10u1 [400 kB] Get: 29 http://deb.debian.org/debian buster/main armhf ruby armhf 1:2.5.1 [11.3 kB] Get: 30 http://deb.debian.org/debian buster/main armhf ruby-asciidoctor all 1.5.8-1 [188 kB] Get: 31 http://deb.debian.org/debian buster/main armhf asciidoctor all 1.5.8-1 [75.8 kB] Get: 32 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 33 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 34 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 35 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 36 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 37 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 38 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 39 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 40 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 41 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 42 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 44 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 46 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 47 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 48 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 49 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 50 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 51 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 52 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 53 http://deb.debian.org/debian buster/main armhf icu-devtools armhf 63.1-6+deb10u1 [168 kB] Get: 54 http://deb.debian.org/debian buster/main armhf libsuitesparseconfig5 armhf 1:5.4.0+dfsg-1 [20.5 kB] Get: 55 http://deb.debian.org/debian buster/main armhf libamd2 armhf 1:5.4.0+dfsg-1 [26.9 kB] Get: 56 http://deb.debian.org/debian buster/main armhf libbam-dev armhf 0.1.19-4 [112 kB] Get: 57 http://deb.debian.org/debian buster/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-3 [135 kB] Get: 58 http://deb.debian.org/debian buster/main armhf libbamtools-dev armhf 2.5.1+dfsg-3 [21.8 kB] Get: 59 http://deb.debian.org/debian buster/main armhf libgfortran5 armhf 8.3.0-6 [213 kB] Get: 60 http://deb.debian.org/debian buster/main armhf libblas3 armhf 3.8.0-2 [109 kB] Get: 61 http://deb.debian.org/debian buster/main armhf libblas-dev armhf 3.8.0-2 [117 kB] Get: 62 http://deb.debian.org/debian buster/main armhf libboost1.67-dev armhf 1.67.0-13+deb10u1 [8388 kB] Get: 63 http://deb.debian.org/debian buster/main armhf libboost-regex1.67.0 armhf 1.67.0-13+deb10u1 [438 kB] Get: 64 http://deb.debian.org/debian buster/main armhf libicu-dev armhf 63.1-6+deb10u1 [8940 kB] Get: 65 http://deb.debian.org/debian buster/main armhf libboost-regex1.67-dev armhf 1.67.0-13+deb10u1 [538 kB] Get: 66 http://deb.debian.org/debian buster/main armhf libboost-iostreams1.67-dev armhf 1.67.0-13+deb10u1 [254 kB] Get: 67 http://deb.debian.org/debian buster/main armhf libboost-iostreams-dev armhf 1.67.0.1 [3632 B] Get: 68 http://deb.debian.org/debian buster/main armhf libbtf1 armhf 1:5.4.0+dfsg-1 [20.9 kB] Get: 69 http://deb.debian.org/debian buster/main armhf libbz2-dev armhf 1.0.6-9.2~deb10u1 [28.8 kB] Get: 70 http://deb.debian.org/debian buster/main armhf libcamd2 armhf 1:5.4.0+dfsg-1 [27.7 kB] Get: 71 http://deb.debian.org/debian buster/main armhf libccolamd2 armhf 1:5.4.0+dfsg-1 [28.2 kB] Get: 72 http://deb.debian.org/debian buster/main armhf libcolamd2 armhf 1:5.4.0+dfsg-1 [25.2 kB] Get: 73 http://deb.debian.org/debian buster/main armhf liblapack3 armhf 3.8.0-2 [1631 kB] Get: 74 http://deb.debian.org/debian buster/main armhf libmetis5 armhf 5.1.0.dfsg-5+b2 [136 kB] Get: 75 http://deb.debian.org/debian buster/main armhf libcholmod3 armhf 1:5.4.0+dfsg-1 [227 kB] Get: 76 http://deb.debian.org/debian buster/main armhf libkeyutils1 armhf 1.6-6 [13.9 kB] Get: 77 http://deb.debian.org/debian buster/main armhf libkrb5support0 armhf 1.17-3 [62.3 kB] Get: 78 http://deb.debian.org/debian buster/main armhf libk5crypto3 armhf 1.17-3 [119 kB] Get: 79 http://deb.debian.org/debian buster/main armhf libkrb5-3 armhf 1.17-3 [323 kB] Get: 80 http://deb.debian.org/debian buster/main armhf libgssapi-krb5-2 armhf 1.17-3 [137 kB] Get: 81 http://deb.debian.org/debian buster/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-1+deb10u1 [67.4 kB] Get: 82 http://deb.debian.org/debian buster/main armhf libsasl2-2 armhf 2.1.27+dfsg-1+deb10u1 [98.9 kB] Get: 83 http://deb.debian.org/debian buster/main armhf libldap-common all 2.4.47+dfsg-3+deb10u2 [89.7 kB] Get: 84 http://deb.debian.org/debian buster/main armhf libldap-2.4-2 armhf 2.4.47+dfsg-3+deb10u2 [202 kB] Get: 85 http://deb.debian.org/debian buster/main armhf libnghttp2-14 armhf 1.36.0-2+deb10u1 [74.4 kB] Get: 86 http://deb.debian.org/debian buster/main armhf libpsl5 armhf 0.20.2-2 [52.4 kB] Get: 87 http://deb.debian.org/debian buster/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.9 kB] Get: 88 http://deb.debian.org/debian buster/main armhf libssh2-1 armhf 1.8.0-2.1 [129 kB] Get: 89 http://deb.debian.org/debian buster/main armhf libcurl3-gnutls armhf 7.64.0-4+deb10u1 [295 kB] Get: 90 http://deb.debian.org/debian buster/main armhf libnspr4 armhf 2:4.20-1 [90.0 kB] Get: 91 http://deb.debian.org/debian buster/main armhf libnss3 armhf 2:3.42.1-1+deb10u2 [969 kB] Get: 92 http://deb.debian.org/debian buster/main armhf libcurl3-nss armhf 7.64.0-4+deb10u1 [301 kB] Get: 93 http://deb.debian.org/debian buster/main armhf libcurl4-nss-dev armhf 7.64.0-4+deb10u1 [396 kB] Get: 94 http://deb.debian.org/debian buster/main armhf libcxsparse3 armhf 1:5.4.0+dfsg-1 [50.0 kB] Get: 95 http://deb.debian.org/debian buster/main armhf libdeflate0 armhf 1.2-1 [46.4 kB] Get: 96 http://deb.debian.org/debian buster/main armhf libgraphblas2 armhf 1:5.4.0+dfsg-1 [1657 kB] Get: 97 http://deb.debian.org/debian buster/main armhf libgslcblas0 armhf 2.5+dfsg-6 [79.1 kB] Get: 98 http://deb.debian.org/debian buster/main armhf libgsl23 armhf 2.5+dfsg-6 [718 kB] Get: 99 http://deb.debian.org/debian buster/main armhf libgsl-dev armhf 2.5+dfsg-6 [903 kB] Get: 100 http://deb.debian.org/debian buster/main armhf libhts2 armhf 1.9-11 [261 kB] Get: 101 http://deb.debian.org/debian buster/main armhf liblzma-dev armhf 5.2.4-1 [204 kB] Get: 102 http://deb.debian.org/debian buster/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [207 kB] Get: 103 http://deb.debian.org/debian buster/main armhf libhts-dev armhf 1.9-11 [4289 kB] Get: 104 http://deb.debian.org/debian buster/main armhf libklu1 armhf 1:5.4.0+dfsg-1 [49.7 kB] Get: 105 http://deb.debian.org/debian buster/main armhf liblapack-dev armhf 3.8.0-2 [1680 kB] Get: 106 http://deb.debian.org/debian buster/main armhf libldl2 armhf 1:5.4.0+dfsg-1 [20.7 kB] Get: 107 http://deb.debian.org/debian buster/main armhf libmongoose2 armhf 1:5.4.0+dfsg-1 [40.8 kB] Get: 108 http://deb.debian.org/debian buster/main armhf libumfpack5 armhf 1:5.4.0+dfsg-1 [131 kB] Get: 109 http://deb.debian.org/debian buster/main armhf librbio2 armhf 1:5.4.0+dfsg-1 [29.5 kB] Get: 110 http://deb.debian.org/debian buster/main armhf libspqr2 armhf 1:5.4.0+dfsg-1 [66.1 kB] Get: 111 http://deb.debian.org/debian buster/main armhf libsuitesparse-dev armhf 1:5.4.0+dfsg-1 [2171 kB] Get: 112 http://deb.debian.org/debian buster/main armhf liblpsolve55-dev armhf 5.5.0.15-4+b1 [334 kB] Get: 113 http://deb.debian.org/debian buster/main armhf libncurses-dev armhf 6.1+20181013-2+deb10u2 [295 kB] Get: 114 http://deb.debian.org/debian buster/main armhf libncurses5-dev armhf 6.1+20181013-2+deb10u2 [948 B] Get: 115 http://deb.debian.org/debian buster/main armhf libsqlite3-dev armhf 3.27.2-3 [722 kB] Get: 116 http://deb.debian.org/debian buster/main armhf libssl-dev armhf 1.1.1d-0+deb10u3 [1597 kB] Get: 117 http://deb.debian.org/debian buster/main armhf lzma-dev all 9.22-2.1 [44.7 kB] Fetched 65.5 MB in 13s (5129 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (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 ... 18932 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../002-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../004-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.8.5-2_armhf.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../006-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../007-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../008-libmagic-mgc_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../009-libmagic1_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../010-file_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../011-gettext-base_0.19.8.1-9_armhf.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libssl1.1:armhf. Preparing to unpack .../012-libssl1.1_1.1.1d-0+deb10u3_armhf.deb ... Unpacking libssl1.1:armhf (1.1.1d-0+deb10u3) ... Selecting previously unselected package openssl. Preparing to unpack .../013-openssl_1.1.1d-0+deb10u3_armhf.deb ... Unpacking openssl (1.1.1d-0+deb10u3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../014-ca-certificates_20190110_all.deb ... Unpacking ca-certificates (20190110) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../015-rubygems-integration_1.11+deb10u1_all.deb ... Unpacking rubygems-integration (1.11+deb10u1) ... Selecting previously unselected package rake. Preparing to unpack .../016-rake_12.3.1-3+deb10u1_all.deb ... Unpacking rake (12.3.1-3+deb10u1) ... Selecting previously unselected package ruby-did-you-mean. Preparing to unpack .../017-ruby-did-you-mean_1.2.1-1_all.deb ... Unpacking ruby-did-you-mean (1.2.1-1) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../018-ruby-minitest_5.11.3-1_all.deb ... Unpacking ruby-minitest (5.11.3-1) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../019-ruby-net-telnet_0.1.1-2_all.deb ... Unpacking ruby-net-telnet (0.1.1-2) ... Selecting previously unselected package ruby-power-assert. Preparing to unpack .../020-ruby-power-assert_1.1.1-1_all.deb ... Unpacking ruby-power-assert (1.1.1-1) ... Selecting previously unselected package ruby-test-unit. Preparing to unpack .../021-ruby-test-unit_3.2.8-1_all.deb ... Unpacking ruby-test-unit (3.2.8-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../022-ruby-xmlrpc_0.3.0-2_all.deb ... Unpacking ruby-xmlrpc (0.3.0-2) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../023-libncurses6_6.1+20181013-2+deb10u2_armhf.deb ... Unpacking libncurses6:armhf (6.1+20181013-2+deb10u2) ... Selecting previously unselected package libreadline7:armhf. Preparing to unpack .../024-libreadline7_7.0-5_armhf.deb ... Unpacking libreadline7:armhf (7.0-5) ... Selecting previously unselected package libyaml-0-2:armhf. Preparing to unpack .../025-libyaml-0-2_0.2.1-1_armhf.deb ... Unpacking libyaml-0-2:armhf (0.2.1-1) ... Selecting previously unselected package libruby2.5:armhf. Preparing to unpack .../026-libruby2.5_2.5.5-3+deb10u1_armhf.deb ... Unpacking libruby2.5:armhf (2.5.5-3+deb10u1) ... Selecting previously unselected package ruby2.5. Preparing to unpack .../027-ruby2.5_2.5.5-3+deb10u1_armhf.deb ... Unpacking ruby2.5 (2.5.5-3+deb10u1) ... Selecting previously unselected package ruby. Preparing to unpack .../028-ruby_1%3a2.5.1_armhf.deb ... Unpacking ruby (1:2.5.1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../029-ruby-asciidoctor_1.5.8-1_all.deb ... Unpacking ruby-asciidoctor (1.5.8-1) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../030-asciidoctor_1.5.8-1_all.deb ... Unpacking asciidoctor (1.5.8-1) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../031-libsigsegv2_2.12-2_armhf.deb ... Unpacking libsigsegv2:armhf (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../032-m4_1.4.18-2_armhf.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../033-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../034-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../035-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../036-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../037-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../038-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../039-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../040-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../041-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../042-libelf1_0.176-1.1_armhf.deb ... Unpacking libelf1:armhf (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../043-dwz_0.12-3_armhf.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../044-libglib2.0-0_2.58.3-2+deb10u2_armhf.deb ... Unpacking libglib2.0-0:armhf (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:armhf. Preparing to unpack .../045-libicu63_63.1-6+deb10u1_armhf.deb ... Unpacking libicu63:armhf (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../046-libxml2_2.9.4+dfsg1-7+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:armhf. Preparing to unpack .../047-libcroco3_0.6.12-3_armhf.deb ... Unpacking libcroco3:armhf (0.6.12-3) ... Selecting previously unselected package gettext. Preparing to unpack .../048-gettext_0.19.8.1-9_armhf.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../049-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../050-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../051-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../052-icu-devtools_63.1-6+deb10u1_armhf.deb ... Unpacking icu-devtools (63.1-6+deb10u1) ... Selecting previously unselected package libsuitesparseconfig5:armhf. Preparing to unpack .../053-libsuitesparseconfig5_1%3a5.4.0+dfsg-1_armhf.deb ... Unpacking libsuitesparseconfig5:armhf (1:5.4.0+dfsg-1) ... Selecting previously unselected package libamd2:armhf. Preparing to unpack .../054-libamd2_1%3a5.4.0+dfsg-1_armhf.deb ... Unpacking libamd2:armhf (1:5.4.0+dfsg-1) ... Selecting previously unselected package libbam-dev. Preparing to unpack .../055-libbam-dev_0.1.19-4_armhf.deb ... Unpacking libbam-dev (0.1.19-4) ... Selecting previously unselected package libbamtools2.5.1:armhf. Preparing to unpack .../056-libbamtools2.5.1_2.5.1+dfsg-3_armhf.deb ... Unpacking libbamtools2.5.1:armhf (2.5.1+dfsg-3) ... Selecting previously unselected package libbamtools-dev:armhf. Preparing to unpack .../057-libbamtools-dev_2.5.1+dfsg-3_armhf.deb ... Unpacking libbamtools-dev:armhf (2.5.1+dfsg-3) ... Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../058-libgfortran5_8.3.0-6_armhf.deb ... Unpacking libgfortran5:armhf (8.3.0-6) ... Selecting previously unselected package libblas3:armhf. Preparing to unpack .../059-libblas3_3.8.0-2_armhf.deb ... Unpacking libblas3:armhf (3.8.0-2) ... Selecting previously unselected package libblas-dev:armhf. Preparing to unpack .../060-libblas-dev_3.8.0-2_armhf.deb ... Unpacking libblas-dev:armhf (3.8.0-2) ... Selecting previously unselected package libboost1.67-dev:armhf. Preparing to unpack .../061-libboost1.67-dev_1.67.0-13+deb10u1_armhf.deb ... Unpacking libboost1.67-dev:armhf (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-regex1.67.0:armhf. Preparing to unpack .../062-libboost-regex1.67.0_1.67.0-13+deb10u1_armhf.deb ... Unpacking libboost-regex1.67.0:armhf (1.67.0-13+deb10u1) ... Selecting previously unselected package libicu-dev:armhf. Preparing to unpack .../063-libicu-dev_63.1-6+deb10u1_armhf.deb ... Unpacking libicu-dev:armhf (63.1-6+deb10u1) ... Selecting previously unselected package libboost-regex1.67-dev:armhf. Preparing to unpack .../064-libboost-regex1.67-dev_1.67.0-13+deb10u1_armhf.deb ... Unpacking libboost-regex1.67-dev:armhf (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-iostreams1.67-dev:armhf. Preparing to unpack .../065-libboost-iostreams1.67-dev_1.67.0-13+deb10u1_armhf.deb ... Unpacking libboost-iostreams1.67-dev:armhf (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-iostreams-dev:armhf. Preparing to unpack .../066-libboost-iostreams-dev_1.67.0.1_armhf.deb ... Unpacking libboost-iostreams-dev:armhf (1.67.0.1) ... Selecting previously unselected package libbtf1:armhf. Preparing to unpack .../067-libbtf1_1%3a5.4.0+dfsg-1_armhf.deb ... Unpacking libbtf1:armhf (1:5.4.0+dfsg-1) ... Selecting previously unselected package libbz2-dev:armhf. Preparing to unpack .../068-libbz2-dev_1.0.6-9.2~deb10u1_armhf.deb ... Unpacking libbz2-dev:armhf (1.0.6-9.2~deb10u1) ... Selecting previously unselected package libcamd2:armhf. Preparing to unpack .../069-libcamd2_1%3a5.4.0+dfsg-1_armhf.deb ... Unpacking libcamd2:armhf (1:5.4.0+dfsg-1) ... Selecting previously unselected package libccolamd2:armhf. Preparing to unpack .../070-libccolamd2_1%3a5.4.0+dfsg-1_armhf.deb ... Unpacking libccolamd2:armhf (1:5.4.0+dfsg-1) ... Selecting previously unselected package libcolamd2:armhf. Preparing to unpack .../071-libcolamd2_1%3a5.4.0+dfsg-1_armhf.deb ... Unpacking libcolamd2:armhf (1:5.4.0+dfsg-1) ... Selecting previously unselected package liblapack3:armhf. Preparing to unpack .../072-liblapack3_3.8.0-2_armhf.deb ... Unpacking liblapack3:armhf (3.8.0-2) ... Selecting previously unselected package libmetis5:armhf. Preparing to unpack .../073-libmetis5_5.1.0.dfsg-5+b2_armhf.deb ... Unpacking libmetis5:armhf (5.1.0.dfsg-5+b2) ... Selecting previously unselected package libcholmod3:armhf. Preparing to unpack .../074-libcholmod3_1%3a5.4.0+dfsg-1_armhf.deb ... Unpacking libcholmod3:armhf (1:5.4.0+dfsg-1) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../075-libkeyutils1_1.6-6_armhf.deb ... Unpacking libkeyutils1:armhf (1.6-6) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../076-libkrb5support0_1.17-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.17-3) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../077-libk5crypto3_1.17-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.17-3) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../078-libkrb5-3_1.17-3_armhf.deb ... Unpacking libkrb5-3:armhf (1.17-3) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../079-libgssapi-krb5-2_1.17-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.17-3) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../080-libsasl2-modules-db_2.1.27+dfsg-1+deb10u1_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../081-libsasl2-2_2.1.27+dfsg-1+deb10u1_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libldap-common. Preparing to unpack .../082-libldap-common_2.4.47+dfsg-3+deb10u2_all.deb ... Unpacking libldap-common (2.4.47+dfsg-3+deb10u2) ... Selecting previously unselected package libldap-2.4-2:armhf. Preparing to unpack .../083-libldap-2.4-2_2.4.47+dfsg-3+deb10u2_armhf.deb ... Unpacking libldap-2.4-2:armhf (2.4.47+dfsg-3+deb10u2) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../084-libnghttp2-14_1.36.0-2+deb10u1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.36.0-2+deb10u1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../085-libpsl5_0.20.2-2_armhf.deb ... Unpacking libpsl5:armhf (0.20.2-2) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../086-librtmp1_2.4+20151223.gitfa8646d.1-2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../087-libssh2-1_1.8.0-2.1_armhf.deb ... Unpacking libssh2-1:armhf (1.8.0-2.1) ... Selecting previously unselected package libcurl3-gnutls:armhf. Preparing to unpack .../088-libcurl3-gnutls_7.64.0-4+deb10u1_armhf.deb ... Unpacking libcurl3-gnutls:armhf (7.64.0-4+deb10u1) ... Selecting previously unselected package libnspr4:armhf. Preparing to unpack .../089-libnspr4_2%3a4.20-1_armhf.deb ... Unpacking libnspr4:armhf (2:4.20-1) ... Selecting previously unselected package libnss3:armhf. Preparing to unpack .../090-libnss3_2%3a3.42.1-1+deb10u2_armhf.deb ... Unpacking libnss3:armhf (2:3.42.1-1+deb10u2) ... Selecting previously unselected package libcurl3-nss:armhf. Preparing to unpack .../091-libcurl3-nss_7.64.0-4+deb10u1_armhf.deb ... Unpacking libcurl3-nss:armhf (7.64.0-4+deb10u1) ... Selecting previously unselected package libcurl4-nss-dev:armhf. Preparing to unpack .../092-libcurl4-nss-dev_7.64.0-4+deb10u1_armhf.deb ... Unpacking libcurl4-nss-dev:armhf (7.64.0-4+deb10u1) ... Selecting previously unselected package libcxsparse3:armhf. Preparing to unpack .../093-libcxsparse3_1%3a5.4.0+dfsg-1_armhf.deb ... Unpacking libcxsparse3:armhf (1:5.4.0+dfsg-1) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../094-libdeflate0_1.2-1_armhf.deb ... Unpacking libdeflate0:armhf (1.2-1) ... Selecting previously unselected package libgraphblas2:armhf. Preparing to unpack .../095-libgraphblas2_1%3a5.4.0+dfsg-1_armhf.deb ... Unpacking libgraphblas2:armhf (1:5.4.0+dfsg-1) ... Selecting previously unselected package libgslcblas0:armhf. Preparing to unpack .../096-libgslcblas0_2.5+dfsg-6_armhf.deb ... Unpacking libgslcblas0:armhf (2.5+dfsg-6) ... Selecting previously unselected package libgsl23:armhf. Preparing to unpack .../097-libgsl23_2.5+dfsg-6_armhf.deb ... Unpacking libgsl23:armhf (2.5+dfsg-6) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../098-libgsl-dev_2.5+dfsg-6_armhf.deb ... Unpacking libgsl-dev (2.5+dfsg-6) ... Selecting previously unselected package libhts2:armhf. Preparing to unpack .../099-libhts2_1.9-11_armhf.deb ... Unpacking libhts2:armhf (1.9-11) ... Selecting previously unselected package liblzma-dev:armhf. Preparing to unpack .../100-liblzma-dev_5.2.4-1_armhf.deb ... Unpacking liblzma-dev:armhf (5.2.4-1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../101-zlib1g-dev_1%3a1.2.11.dfsg-1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-1) ... Selecting previously unselected package libhts-dev:armhf. Preparing to unpack .../102-libhts-dev_1.9-11_armhf.deb ... Unpacking libhts-dev:armhf (1.9-11) ... Selecting previously unselected package libklu1:armhf. Preparing to unpack .../103-libklu1_1%3a5.4.0+dfsg-1_armhf.deb ... Unpacking libklu1:armhf (1:5.4.0+dfsg-1) ... Selecting previously unselected package liblapack-dev:armhf. Preparing to unpack .../104-liblapack-dev_3.8.0-2_armhf.deb ... Unpacking liblapack-dev:armhf (3.8.0-2) ... Selecting previously unselected package libldl2:armhf. Preparing to unpack .../105-libldl2_1%3a5.4.0+dfsg-1_armhf.deb ... Unpacking libldl2:armhf (1:5.4.0+dfsg-1) ... Selecting previously unselected package libmongoose2:armhf. Preparing to unpack .../106-libmongoose2_1%3a5.4.0+dfsg-1_armhf.deb ... Unpacking libmongoose2:armhf (1:5.4.0+dfsg-1) ... Selecting previously unselected package libumfpack5:armhf. Preparing to unpack .../107-libumfpack5_1%3a5.4.0+dfsg-1_armhf.deb ... Unpacking libumfpack5:armhf (1:5.4.0+dfsg-1) ... Selecting previously unselected package librbio2:armhf. Preparing to unpack .../108-librbio2_1%3a5.4.0+dfsg-1_armhf.deb ... Unpacking librbio2:armhf (1:5.4.0+dfsg-1) ... Selecting previously unselected package libspqr2:armhf. Preparing to unpack .../109-libspqr2_1%3a5.4.0+dfsg-1_armhf.deb ... Unpacking libspqr2:armhf (1:5.4.0+dfsg-1) ... Selecting previously unselected package libsuitesparse-dev:armhf. Preparing to unpack .../110-libsuitesparse-dev_1%3a5.4.0+dfsg-1_armhf.deb ... Unpacking libsuitesparse-dev:armhf (1:5.4.0+dfsg-1) ... Selecting previously unselected package liblpsolve55-dev. Preparing to unpack .../111-liblpsolve55-dev_5.5.0.15-4+b1_armhf.deb ... Unpacking liblpsolve55-dev (5.5.0.15-4+b1) ... Selecting previously unselected package libncurses-dev:armhf. Preparing to unpack .../112-libncurses-dev_6.1+20181013-2+deb10u2_armhf.deb ... Unpacking libncurses-dev:armhf (6.1+20181013-2+deb10u2) ... Selecting previously unselected package libncurses5-dev:armhf. Preparing to unpack .../113-libncurses5-dev_6.1+20181013-2+deb10u2_armhf.deb ... Unpacking libncurses5-dev:armhf (6.1+20181013-2+deb10u2) ... Selecting previously unselected package libsqlite3-dev:armhf. Preparing to unpack .../114-libsqlite3-dev_3.27.2-3_armhf.deb ... Unpacking libsqlite3-dev:armhf (3.27.2-3) ... Selecting previously unselected package libssl-dev:armhf. Preparing to unpack .../115-libssl-dev_1.1.1d-0+deb10u3_armhf.deb ... Unpacking libssl-dev:armhf (1.1.1d-0+deb10u3) ... Selecting previously unselected package lzma-dev. Preparing to unpack .../116-lzma-dev_9.22-2.1_all.deb ... Unpacking lzma-dev (9.22-2.1) ... Setting up libboost1.67-dev:armhf (1.67.0-13+deb10u1) ... Setting up libpipeline1:armhf (1.5.1-2) ... Setting up libkeyutils1:armhf (1.6-6) ... Setting up libpsl5:armhf (0.20.2-2) ... Setting up libgslcblas0:armhf (2.5+dfsg-6) ... Setting up ruby-power-assert (1.1.1-1) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libyaml-0-2:armhf (0.2.1-1) ... Setting up libglib2.0-0:armhf (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libssl1.1:armhf (1.1.1d-0+deb10u3) ... Setting up libnghttp2-14:armhf (1.36.0-2+deb10u1) ... Setting up libmagic1:armhf (1:5.35-4+deb10u1) ... Setting up libdeflate0:armhf (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libmetis5:armhf (5.1.0.dfsg-5+b2) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u2) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up libkrb5support0:armhf (1.17-3) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-1+deb10u1) ... Setting up ruby-minitest (5.11.3-1) ... Setting up autotools-dev (20180224.1) ... Setting up libsqlite3-dev:armhf (3.27.2-3) ... Setting up ruby-test-unit (3.2.8-1) ... Setting up libnspr4:armhf (2:4.20-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ... Setting up libgsl23:armhf (2.5+dfsg-6) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up libbamtools2.5.1:armhf (2.5.1+dfsg-3) ... Setting up libssl-dev:armhf (1.1.1d-0+deb10u3) ... Setting up autopoint (0.19.8.1-9) ... Setting up icu-devtools (63.1-6+deb10u1) ... Setting up libbam-dev (0.1.19-4) ... Setting up libk5crypto3:armhf (1.17-3) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-1+deb10u1) ... Setting up libgfortran5:armhf (8.3.0-6) ... Setting up liblzma-dev:armhf (5.2.4-1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libssh2-1:armhf (1.8.0-2.1) ... Setting up libkrb5-3:armhf (1.17-3) ... Setting up ruby-did-you-mean (1.2.1-1) ... Setting up openssl (1.1.1d-0+deb10u3) ... Setting up libbsd0:armhf (0.9.1-2) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libicu-dev:armhf (63.1-6+deb10u1) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up libsuitesparseconfig5:armhf (1:5.4.0+dfsg-1) ... Setting up librbio2:armhf (1:5.4.0+dfsg-1) ... Setting up libreadline7:armhf (7.0-5) ... Setting up libbz2-dev:armhf (1.0.6-9.2~deb10u1) ... Setting up libgraphblas2:armhf (1:5.4.0+dfsg-1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libamd2:armhf (1:5.4.0+dfsg-1) ... Setting up libncurses-dev:armhf (6.1+20181013-2+deb10u2) ... Setting up libgsl-dev (2.5+dfsg-6) ... Setting up libboost-regex1.67.0:armhf (1.67.0-13+deb10u1) ... Setting up libcolamd2:armhf (1:5.4.0+dfsg-1) ... Setting up libtool (2.4.6-9) ... Setting up libboost-regex1.67-dev:armhf (1.67.0-13+deb10u1) ... Setting up libldl2:armhf (1:5.4.0+dfsg-1) ... Setting up libldap-2.4-2:armhf (2.4.47+dfsg-3+deb10u2) ... Setting up m4 (1.4.18-2) ... Setting up libnss3:armhf (2:3.42.1-1+deb10u2) ... Setting up libbtf1:armhf (1:5.4.0+dfsg-1) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up libcamd2:armhf (1:5.4.0+dfsg-1) ... Setting up libmongoose2:armhf (1:5.4.0+dfsg-1) ... Setting up libblas3:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libbamtools-dev:armhf (2.5.1+dfsg-3) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:armhf (1.17-3) ... Setting up libcroco3:armhf (0.6.12-3) ... Setting up lzma-dev (9.22-2.1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up libcurl3-nss:armhf (7.64.0-4+deb10u1) ... Setting up groff-base (1.22.4-3) ... Setting up libklu1:armhf (1:5.4.0+dfsg-1) ... Setting up libccolamd2:armhf (1:5.4.0+dfsg-1) ... Setting up libncurses5-dev:armhf (6.1+20181013-2+deb10u2) ... Setting up libcxsparse3:armhf (1:5.4.0+dfsg-1) ... Setting up libcurl4-nss-dev:armhf (7.64.0-4+deb10u1) ... Setting up libboost-iostreams1.67-dev:armhf (1.67.0-13+deb10u1) ... Setting up libblas-dev:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up liblapack3:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libcurl3-gnutls:armhf (7.64.0-4+deb10u1) ... Setting up rubygems-integration (1.11+deb10u1) ... Setting up libboost-iostreams-dev:armhf (1.67.0.1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up liblapack-dev:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode Setting up libcholmod3:armhf (1:5.4.0+dfsg-1) ... Setting up libspqr2:armhf (1:5.4.0+dfsg-1) ... Setting up libhts2:armhf (1.9-11) ... Setting up po-debconf (1.0.21) ... Setting up libhts-dev:armhf (1.9-11) ... Setting up libumfpack5:armhf (1:5.4.0+dfsg-1) ... Setting up libsuitesparse-dev:armhf (1:5.4.0+dfsg-1) ... Setting up liblpsolve55-dev (5.5.0.15-4+b1) ... Setting up dh-autoreconf (19) ... Setting up rake (12.3.1-3+deb10u1) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up libruby2.5:armhf (2.5.5-3+deb10u1) ... Setting up debhelper (12.1.1) ... Setting up ruby2.5 (2.5.5-3+deb10u1) ... Setting up ruby (1:2.5.1) ... Setting up ruby-asciidoctor (1.5.8-1) ... Setting up asciidoctor (1.5.8-1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package 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 dpkg-buildpackage: info: source package augustus dpkg-buildpackage: info: source version 3.3.2+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/augustus-3.3.2+dfsg' /usr/bin/make -C auxprogs/bam2hints clean make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/bam2hints' rm -f bam2hints.o bam2hints ../../bin/bam2hints make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/bam2hints' /usr/bin/make -C auxprogs/homGeneMapping clean make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/homGeneMapping' (cd src; make clean; cd ../bin; rm -f homGeneMapping; cd ../../../bin; rm -f homGeneMapping) make[3]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/homGeneMapping/src' rm -f homGeneMapping gene.o genome.o make[3]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/homGeneMapping/src' /bin/sh: 1: cd: can't cd to ../bin /bin/sh: 1: cd: can't cd to ../../../bin make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/homGeneMapping' /usr/bin/make -C auxprogs/joingenes clean make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/joingenes' rm -rf *o joingenes; rm -rf ../../bin/joingenes make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/joingenes' /usr/bin/make -C auxprogs/aln2wig clean make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/aln2wig' rm -f aln2wig aln2wig.o; rm -f ../../bin/aln2wig make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/aln2wig' /usr/bin/make -C auxprogs/bam2wig clean make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/bam2wig' rm -f bam2wig bam2wig.o rm -f ../../bin/bam2wig make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/bam2wig' /usr/bin/make -C auxprogs/checkTargetSortedness clean make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/checkTargetSortedness' rm -f *.o checkTargetSortedness make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/checkTargetSortedness' /usr/bin/make -C auxprogs/compileSpliceCands clean make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/compileSpliceCands' rm -f compileSpliceCands compileSpliceCands.o ../../bin/compileSpliceCands list.o make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/compileSpliceCands' /usr/bin/make -C auxprogs/filterBam clean make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/filterBam' (cd src; make clean;) make[3]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/filterBam/src' rm -f *~ filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o rm -f ../../../bin/filterBam make[3]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/filterBam/src' make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/filterBam' rm -rf bin make[1]: Leaving directory '/build/augustus-3.3.2+dfsg' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/augustus-3.3.2+dfsg' mkdir -p bin /usr/bin/make -C auxprogs/aln2wig make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/aln2wig' gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -O2 -ggdb -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -c aln2wig.c gcc -Wall -Wno-sign-compare -ansi -pedantic -O2 -ggdb -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o aln2wig aln2wig.o; cp aln2wig ../../bin make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/aln2wig' /usr/bin/make -C auxprogs/bam2hints make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/bam2hints' g++ -Wall -O2 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c bam2hints.cc -o bam2hints.o -I/usr/include/bamtools g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o bam2hints bam2hints.o -lbamtools -lz cp bam2hints ../../bin make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/bam2hints' /usr/bin/make -C auxprogs/bam2wig make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/bam2wig' cc -Wall -O2 -I/usr/include/samtools/ -I. -I/usr/include/htslib/ -I/usr/include/bcftools/ -I/usr/include/tabix/ -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c bam2wig.c -o bam2wig.o cc -Wall -O2 -I/usr/include/samtools/ -I. -I/usr/include/htslib/ -I/usr/include/bcftools/ -I/usr/include/tabix/ -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now bam2wig.o -o bam2wig /usr/lib/libbam.a -lhts -lcurses -lm -lz -lpthread -lcurl -lssl -lcrypto -lbz2 -llzma cp bam2wig ../../bin/bam2wig make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/bam2wig' /usr/bin/make -C auxprogs/checkTargetSortedness make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/checkTargetSortedness' cc -g -Wall -O2 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c checkTargetSortedness.c -o checkTargetSortedness.o -I/usr/include/samtools -I. cc -g -Wall -O2 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now checkTargetSortedness.o -o checkTargetSortedness -lbam -lcurses -lm -lz -lpthread make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/checkTargetSortedness' /usr/bin/make -C auxprogs/compileSpliceCands make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/compileSpliceCands' cc -Wall -pedantic -ansi -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compileSpliceCands.c compileSpliceCands.c: In function 'getChromosome': compileSpliceCands.c:226:2: warning: this decimal constant is unsigned only in ISO C90 s = malloc(3500000000); ^ compileSpliceCands.c:226:6: warning: argument 1 value '3500000000' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] s = malloc(3500000000); ^~~~~~~~~~~~~~~~~~ In file included from compileSpliceCands.c:14: /usr/include/stdlib.h:539:14: note: in a call to allocation function 'malloc' declared here extern void *malloc (size_t __size) __THROW __attribute_malloc__ __wur; ^~~~~~ compileSpliceCands.c: In function 'parseList': compileSpliceCands.c:344:35: warning: 'left' may be used uninitialized in this function [-Wmaybe-uninitialized] findPossibleSpliceSites(left->name,actualChromosome,left->startPos-maxSpliceSiteDiff,left->endPos+maxSpliceSiteDiff,right->startPos-maxSpliceSiteDiff,right->startPos+maxSpliceSiteDiff,left->strand,right->strand); ~~~~^~~~~~ compileSpliceCands.c: In function 'main': compileSpliceCands.c:563:3: warning: 'chromosomeLength' may be used uninitialized in this function [-Wmaybe-uninitialized] parseList(&L,actualChromosome,chromosomeLength,oldname,maxSpliceSiteDiff,threshold,maxIntronLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o list.o list.c cc -o compileSpliceCands compileSpliceCands.o list.o -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now; make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/compileSpliceCands' /usr/bin/make -C auxprogs/filterBam make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/filterBam' (cd src;make) make[3]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/filterBam/src' g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c filterBam.cc -o filterBam.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/MatePairs.cc -o MatePairs.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/getReferenceName.cc -o getReferenceName.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/initOptions.cc -o initOptions.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/SingleAlignment.cc -o SingleAlignment.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/printElapsedTime.cc -o printElapsedTime.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumMandIOperations.cc -o sumMandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumDandIOperations.cc -o sumDandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/PairednessCoverage.cc -o PairednessCoverage.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz filterBam compiled with BAMTOOLS=/usr/include/bamtools mv filterBam ../../../bin/filterBam make[3]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/filterBam/src' make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/filterBam' /usr/bin/make -C auxprogs/homGeneMapping/src make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/homGeneMapping/src' g++ -c -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -o gene.o gene.cc -I../include g++ -c -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -o genome.o genome.cc -I../include g++ -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -o homGeneMapping main.cc gene.o genome.o -I../include -Wl,-z,relro -Wl,-z,now cp homGeneMapping ../../../bin/homGeneMapping make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/homGeneMapping/src' /usr/bin/make -C auxprogs/joingenes make[2]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/joingenes' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x joingenes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x jg_transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x jg_ios.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x joingenes.o jg_transcript.o jg_ios.o -o joingenes -Wl,-z,relro -Wl,-z,now cp joingenes ../../bin/ make[2]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/joingenes' dh_auto_build make -j3 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/augustus-3.3.2+dfsg' mkdir -p bin cd src && make make[3]: Entering directory '/build/augustus-3.3.2+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o genbank.o genbank.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o properties.o properties.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_profile.o pp_profile.cc -I../include 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_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 properties.cc:17: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/pp_profile.hh:21, from pp_profile.cc:14: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ properties.cc: In static member function 'static void Properties::init(int, char**)': properties.cc:444:27: warning: catching polymorphic type 'struct PropertiesError' by value [-Wcatch-value=] } catch (PropertiesError e){ ^ properties.cc:469:30: warning: catching polymorphic type 'struct PropertiesError' by value [-Wcatch-value=] } catch (PropertiesError e){ ^ In file included from ../include/pp_profile.hh:22, from pp_profile.cc:14: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from genbank.cc:19: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ genbank.cc: In member function 'AnnoSequence* GBProcessor::getAnnoSequence(GBPositions*)': genbank.cc:51:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ genbank.cc:58:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ genbank.cc: In member function 'AnnoSequence* GBProcessor::getAnnoSequenceList()': genbank.cc:312:19: warning: catching polymorphic type 'class GBError' by value [-Wcatch-value=] } catch (GBError e) { ^ genbank.cc: In constructor 'GBFeature::GBFeature(const char*)': genbank.cc:490:25: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ In file included from pp_profile.cc:17: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ pp_profile.cc: In member function 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map*)': 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 /usr/include/c++/8/vector:69, from ../include/types.hh:36, from ../include/geneticcode.hh:17, from ../include/pp_profile.hh:21, from pp_profile.cc:14: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PP::Column&}; _Tp = PP::Column; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'bool PP::Block::initThresholds()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../include/types.hh:36, from ../include/geneticcode.hh:17, from ../include/pp_profile.hh:21, from pp_profile.cc:14: /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'PP::Block::Block(PP::DistanceType, const std::vector >&, std::__cxx11::string)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../include/types.hh:36, from ../include/geneticcode.hh:17, from ../include/pp_profile.hh:21, from pp_profile.cc:14: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {PP::Block}; _Tp = PP::Block; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void PP::Profile::parse_stream(std::istream&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_hitseq.o pp_hitseq.cc -I../include In file included from /usr/include/c++/8/map:60, from ../include/types.hh:39, from ../include/geneticcode.hh:17, from ../include/pp_profile.hh:21, from pp_profile.cc:14: /usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../include/types.hh:36, from ../include/geneticcode.hh:17, from ../include/pp_profile.hh:21, from pp_profile.cc:14: /usr/include/c++/8/bits/stl_vector.h: In member function 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map*)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from ../include/types.hh:39, from ../include/geneticcode.hh:17, from ../include/pp_profile.hh:21, from pp_profile.cc:14: /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from ../include/pp_profile.hh:21, from ../include/pp_hitseq.hh:18, from pp_hitseq.cc:14: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/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) {} ^~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_scoring.o pp_scoring.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o statemodel.o statemodel.cc -I../include In file included from ../include/pp_scoring.hh:21, from pp_scoring.cc:14: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/pp_profile.hh:21, from ../include/pp_hitseq.hh:18, from ../include/pp_scoring.hh:22, from pp_scoring.cc:14: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o namgene.o namgene.cc -I../include In file included from ../include/statemodel.hh:16, from statemodel.cc:16: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/extrinsicinfo.hh:24, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from statemodel.cc:16: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/extrinsicinfo.hh:25, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from statemodel.cc:16: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from pp_scoring.cc:17: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ pp_scoring.cc: In member function 'void PP::SubstateModel::scoreAssOrRDss(ViterbiSubmapType&, bool, int, const Double&)': pp_scoring.cc:119:15: warning: catching polymorphic type 'class std::out_of_range' by value [-Wcatch-value=] } catch (out_of_range) { ^~~~~~~~~~~~ pp_scoring.cc: In member function 'void PP::MultiTargetExonScorer::initBonusProbs(PP::BonusProbType&, int, int)': pp_scoring.cc:271:11: warning: catching polymorphic type 'class std::out_of_range' by value [-Wcatch-value=] } catch (out_of_range) { ^~~~~~~~~~~~ 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) {} ^~~~~~~~~~~~~~~~ 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) { ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/extrinsicinfo.hh:24, from ../include/namgene.hh:15, from namgene.cc:21: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/extrinsicinfo.hh:25, from ../include/namgene.hh:15, from namgene.cc:21: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/pp_scoring.hh:21, from ../include/gene.hh:15, from ../include/extrinsicinfo.hh:25, from ../include/namgene.hh:15, from namgene.cc:21: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/namgene.hh:15, from namgene.cc:21: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ namgene.cc: In constructor 'NAMGene::NAMGene()': namgene.cc:116:41: warning: catching polymorphic type 'struct PP::ProfileNotFoundError' by value [-Wcatch-value=] } catch (PP::ProfileNotFoundError e) { ^ namgene.cc:119:17: warning: catching polymorphic type 'struct PP::ProfileNotFoundError' by value [-Wcatch-value=] } catch (PP::ProfileNotFoundError) { ^~~~~~~~~~~~~~~~~~~~ namgene.cc:128:12: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) { ^~~~~~~~~~~~~~~~ namgene.cc:130:34: warning: catching polymorphic type 'struct PP::ProfileInsigError' by value [-Wcatch-value=] } catch (PP::ProfileInsigError e) { ^ In file included from /usr/include/c++/8/vector:69, from ../include/types.hh:36, from ../include/vitmatrix.hh:14, from ../include/pp_scoring.hh:21, from pp_scoring.cc:14: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PP::BonusProbEntry&}; _Tp = PP::BonusProbEntry; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:60, from ../include/types.hh:39, from ../include/vitmatrix.hh:14, from ../include/pp_scoring.hh:21, from pp_scoring.cc:14: /usr/include/c++/8/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2500:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tree.h:2500:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::size_type std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const _Key&) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2518:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _M_erase_aux(__p.first, __p.second); ^~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../include/matrix.hh:26, from ../include/statemodel.hh:15, from statemodel.cc:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Ancestor}; _Tp = Ancestor; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void StateModel::initPredecessors(Matrix&, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../include/types.hh:36, from ../include/vitmatrix.hh:14, from ../include/pp_scoring.hh:21, from pp_scoring.cc:14: /usr/include/c++/8/bits/stl_vector.h: In member function 'void PP::MultiTargetExonScorer::initBonusProbs(PP::BonusProbType&, int, int)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:60, from ../include/types.hh:39, from ../include/vitmatrix.hh:14, from ../include/pp_scoring.hh:21, from pp_scoring.cc:14: /usr/include/c++/8/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2146:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {std::pair&}; _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/stl_tree.h: In member function 'void PP::SubstateModel::scoreAssOrRDss(ViterbiSubmapType&, bool, int, const Double&)': /usr/include/c++/8/bits/stl_tree.h:1169:2: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _M_erase_aux(__first, __last); ^~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from ../include/types.hh:39, from ../include/vitmatrix.hh:14, from ../include/pp_scoring.hh:21, from pp_scoring.cc:14: /usr/include/c++/8/bits/stl_map.h:876:35: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 std::forward<_Pair>(__x)); ^ /usr/include/c++/8/bits/stl_map.h:876:35: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 std::forward<_Pair>(__x)); ^ In file included from /usr/include/c++/8/map:60, from ../include/types.hh:39, from ../include/vitmatrix.hh:14, from ../include/pp_scoring.hh:21, from pp_scoring.cc:14: /usr/include/c++/8/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from ../include/types.hh:39, from ../include/vitmatrix.hh:14, from ../include/pp_scoring.hh:21, from pp_scoring.cc:14: /usr/include/c++/8/bits/stl_map.h: In member function 'void ViterbiSubmapType::eraseAndDecCounts(ViterbiSubmapType::iterator) const': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h: In member function 'void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h: In member function 'void PP::BonusProbType::mergeIntoSubmap(int, ViterbiSubmapType&, SubstateIdMap*)': /usr/include/c++/8/bits/stl_map.h:876:35: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 std::forward<_Pair>(__x)); ^ In file included from /usr/include/c++/8/map:60, from ../include/types.hh:39, from ../include/vitmatrix.hh:14, from ../include/pp_scoring.hh:21, from pp_scoring.cc:14: /usr/include/c++/8/bits/stl_tree.h: In member function 'virtual void PP::MultiTargetExonScorer::postProcessing(const Double&)': /usr/include/c++/8/bits/stl_tree.h:1169:2: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _M_erase_aux(__first, __last); ^~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from ../include/types.hh:39, from ../include/vitmatrix.hh:14, from ../include/pp_scoring.hh:21, from pp_scoring.cc:14: /usr/include/c++/8/bits/stl_map.h: In member function 'virtual void PP::SingleTargetExonScorer::exportSubstates(ViterbiSubmapType&)': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h: In member function 'void PP::MultiTargetExonScorer::updateBonusProbs(PP::Position, const Double&)': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/8/map:60, from ../include/types.hh:39, from ../include/vitmatrix.hh:14, from ../include/pp_scoring.hh:21, from pp_scoring.cc:14: /usr/include/c++/8/bits/stl_tree.h: In member function 'virtual void PP::MultiTargetExonScorer::scoreInternal(ViterbiColumnType&, int, const Double&)': /usr/include/c++/8/bits/stl_tree.h:1169:2: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _M_erase_aux(__first, __last); ^~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from ../include/types.hh:39, from ../include/vitmatrix.hh:14, from ../include/pp_scoring.hh:21, from pp_scoring.cc:14: /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o types.o types.cc -I../include namgene.cc: In member function 'std::__cxx11::list* NAMGene::findGenes(const char*, Strand, bool)': namgene.cc:864:19: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] sprintf(gr, "s%d-", (i+1)); ^~~~~~ namgene.cc:864:19: note: directive argument in the range [1, 2147483646] In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from /usr/include/c++/8/ext/string_conversions.h:43, from /usr/include/c++/8/bits/basic_string.h:6400, from /usr/include/c++/8/string:52, from /usr/include/c++/8/bits/locale_classes.h:40, from /usr/include/c++/8/bits/ios_base.h:41, from /usr/include/c++/8/ios:42, from /usr/include/c++/8/istream:38, from /usr/include/c++/8/sstream:38, from ../include/lldouble.hh:29, from ../include/types.hh:28, from ../include/hints.hh:18, from ../include/extrinsicinfo.hh:23, from ../include/namgene.hh:15, from namgene.cc:21: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 9 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from types.cc:21: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ types.cc: In static member function 'static void Constant::init()': types.cc:220:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:225:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:230:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:235:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:240:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:245:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:250:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) {} ^ types.cc:253:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:259:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:264:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:269:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:274:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:279:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:284:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:289:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:295:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:301:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:306:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:311:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:316:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:321:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:326:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:331:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:336:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ types.cc:341:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ In file included from /usr/include/c++/8/vector:69, from ../include/types.hh:36, from types.cc:18: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o gene.o gene.cc -I../include In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from gene.cc:21: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/pp_scoring.hh:21, from ../include/gene.hh:15, from gene.cc:21: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/graph.hh:10, from ../include/mea.hh:5, from gene.cc:22: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from ../include/exoncand.hh:27, from ../include/graph.hh:11, from ../include/mea.hh:5, from gene.cc:22: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../include/types.hh:38, from types.cc:18: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../include/types.hh:38, from types.cc:18: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = LLDouble; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../include/types.hh:38, from types.cc:18: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o evaluation.o evaluation.cc -I../include /usr/include/c++/8/bits/stl_algo.h: In function 'Double quantile(const std::vector&, float)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/evaluation.hh:22, from evaluation.cc:15: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/pp_scoring.hh:21, from ../include/gene.hh:15, from ../include/evaluation.hh:22, from evaluation.cc:15: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o motif.o motif.cc -I../include In file included from ../include/extrinsicinfo.hh:24, from ../include/evaluation.hh:23, from evaluation.cc:15: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/evaluation.hh:23, from evaluation.cc:15: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ In file included from ../include/motif.hh:21, from motif.cc:14: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from motif.cc:17: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ motif.cc: In static member function 'static void BaseCount::init()': motif.cc:57:14: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError) { ^~~~~~~~~~~~ motif.cc:70:11: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError) { ^~~~~~~~~~~~ motif.cc: In member function 'void Motif::addSequence(const char*, int, bool)': motif.cc:302:37: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) {} ^ motif.cc: In member function 'Double Motif::seqProb(const char*, bool, bool)': motif.cc:330:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ motif.cc: In constructor 'ContentStairs::ContentStairs()': motif.cc:519:12: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError) { ^~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../include/matrix.hh:26, from ../include/motif.hh:20, from motif.cc:14: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from ../include/matrix.hh:26, from ../include/motif.hh:20, from ../include/gene.hh:14, from gene.cc:21: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../include/matrix.hh:26, from ../include/motif.hh:20, from motif.cc:14: /usr/include/c++/8/bits/stl_vector.h: In member function 'Double Motif::getProbThreshold(double, int)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o geneticcode.o geneticcode.cc -I../include In file included from geneticcode.cc:15: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ geneticcode.cc: In static member function 'static char GeneticCode::translate(const char*)': geneticcode.cc:182:14: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError) { ^~~~~~~~~~~~~~~~~~~~~~ geneticcode.cc: In static member function 'static char GeneticCode::revtranslate(const char*)': geneticcode.cc:189:14: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError) { ^~~~~~~~~~~~~~~~~~~~~~ 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 In file included from hints.cc:14: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ hints.cc: In function 'std::istream& operator>>(std::istream&, Feature&)': hints.cc:229:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ In file included from /usr/include/c++/8/list:64, from ../include/vitmatrix.hh:19, from ../include/pp_scoring.hh:21, from ../include/gene.hh:15, from gene.cc:21: /usr/include/c++/8/bits/list.tcc: In member function 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator; _Tp = PP::Match; _Alloc = std::allocator]': /usr/include/c++/8/bits/list.tcc:308:7: note: parameter passing for argument of type 'std::_List_const_iterator' changed in GCC 7.1 list<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/list.tcc:308:7: note: parameter passing for argument of type 'std::_List_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/list.tcc: In static member function 'static StatePath* StatePath::condenseStatePath(StatePath*)': /usr/include/c++/8/bits/list.tcc:286:4: note: parameter passing for argument of type 'std::_List_const_iterator' changed in GCC 7.1 _M_assign_dispatch(__x.begin(), __x.end(), __false_type()); ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/list.tcc: In copy constructor 'Gene::Gene(const Gene&)': /usr/include/c++/8/bits/list.tcc:286:4: note: parameter passing for argument of type 'std::_List_const_iterator' changed in GCC 7.1 _M_assign_dispatch(__x.begin(), __x.end(), __false_type()); ^~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -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 In file included from /usr/include/c++/8/algorithm:62, from ../include/types.hh:38, from ../include/geneticcode.hh:17, from ../include/motif.hh:21, from ../include/gene.hh:14, from gene.cc:21: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../include/types.hh:38, from ../include/geneticcode.hh:17, from ../include/motif.hh:21, from ../include/gene.hh:14, from gene.cc:21: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../include/types.hh:38, from ../include/geneticcode.hh:17, from ../include/motif.hh:21, from ../include/gene.hh:14, from gene.cc:21: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../include/matrix.hh:26, from ../include/motif.hh:20, from ../include/gene.hh:14, from gene.cc:21: /usr/include/c++/8/bits/vector.tcc: In function 'void examineBaseCountOfGeneSeq(AnnoSequence*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../include/types.hh:38, from ../include/geneticcode.hh:17, from ../include/motif.hh:21, from ../include/gene.hh:14, from gene.cc:21: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/extrinsicinfo.hh:24, from extrinsicinfo.cc:31: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/extrinsicinfo.hh:25, from extrinsicinfo.cc:31: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -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/pp_scoring.hh:21, from ../include/gene.hh:15, from ../include/extrinsicinfo.hh:25, from extrinsicinfo.cc:31: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from extrinsicinfo.cc:31: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ 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: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/extrinsicinfo.hh:25, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/intronmodel.hh:17, from intronmodel.cc:26: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ 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 ../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) { ^ In file included from ../include/statemodel.hh:16, from ../include/exonmodel.hh:22, from exonmodel.cc:25: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/extrinsicinfo.hh:24, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from exonmodel.cc:25: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/extrinsicinfo.hh:25, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from exonmodel.cc:25: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from exonmodel.cc:25: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ exonmodel.cc: In static member function 'static void ExonModel::init()': exonmodel.cc:318:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] }catch( ProjectError e) { ^ exonmodel.cc:323:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] }catch( ProjectError e) { ^ exonmodel.cc:328:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] }catch( ProjectError e) { ^ exonmodel.cc:333:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] }catch( ProjectError e) { ^ exonmodel.cc:338:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] }catch( ProjectError e) { ^ exonmodel.cc:343:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] }catch( ProjectError e) { ^ exonmodel.cc:348:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch( ProjectError e) { ^ exonmodel.cc:353:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch( ProjectError e) { ^ exonmodel.cc:358:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch( ProjectError e) { ^ exonmodel.cc:363:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch( ProjectError e) { ^ exonmodel.cc:368:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch( ProjectError e) { ^ exonmodel.cc:373:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch( ProjectError e) { ^ exonmodel.cc:382:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch( ProjectError e) {} ^ exonmodel.cc:385:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch( ProjectError e) {} ^ exonmodel.cc: In member function 'virtual void ExonModel::viterbiForwardAndSampling(ViterbiMatrixType&, ViterbiMatrixType&, int, int, AlgorithmVariant, OptionListItem&)': exonmodel.cc:1129:31: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch(NoSubmapFoundError e) {} ^ exonmodel.cc:1156:28: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ exonmodel.cc: In member function 'Double ExonModel::notEndPartEmiProb(int, int, int, Feature*) const': exonmodel.cc:1588:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ exonmodel.cc:1618:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ exonmodel.cc: In member function 'Double ExonModel::seqProb(int, int, int) const': exonmodel.cc:1964:45: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ exonmodel.cc:1981:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ exonmodel.cc: In member function 'Double ExonModel::eTermSeqProb(int, int, int) const': exonmodel.cc:2019:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ exonmodel.cc: In member function 'Double ExonModel::initialSeqProb(int, int, int) const': exonmodel.cc:2046:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ intronmodel.cc: In static member function 'static void IntronModel::readAllParameters()': intronmodel.cc:398:23: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] sprintf(zusString, "[%d]", idx+1); ^~~~~~ intronmodel.cc:398:23: note: directive argument in the range [1, 2147483647] In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from /usr/include/c++/8/ext/string_conversions.h:43, from /usr/include/c++/8/bits/basic_string.h:6400, from /usr/include/c++/8/string:52, from /usr/include/c++/8/bits/locale_classes.h:40, from /usr/include/c++/8/bits/ios_base.h:41, from /usr/include/c++/8/ios:42, from /usr/include/c++/8/ostream:38, from ../include/matrix.hh:27, from ../include/statemodel.hh:15, from ../include/intronmodel.hh:17, from intronmodel.cc:26: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 6 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:60, from ../include/types.hh:39, from ../include/vitmatrix.hh:14, from ../include/statemodel.hh:16, from ../include/intronmodel.hh:17, from intronmodel.cc:26: /usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from ../include/types.hh:39, from ../include/vitmatrix.hh:14, from ../include/statemodel.hh:16, from ../include/intronmodel.hh:17, from intronmodel.cc:26: /usr/include/c++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = LLDouble; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -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/statemodel.hh:16, from ../include/igenicmodel.hh:20, from igenicmodel.cc:14: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/extrinsicinfo.hh:24, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/igenicmodel.hh:20, from igenicmodel.cc:14: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/extrinsicinfo.hh:25, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/igenicmodel.hh:20, from igenicmodel.cc:14: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/igenicmodel.hh:20, from igenicmodel.cc:14: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ igenicmodel.cc: In static member function 'static void IGenicModel::init()': igenicmodel.cc:52:14: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch( ProjectError ) { } ^~~~~~~~~~~~ igenicmodel.cc: In member function 'virtual void IGenicModel::viterbiForwardAndSampling(ViterbiMatrixType&, ViterbiMatrixType&, int, int, AlgorithmVariant, OptionListItem&)': igenicmodel.cc:279:24: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ igenicmodel.cc: In member function 'virtual Double IGenicModel::emiProbUnderModel(int, int) const': igenicmodel.cc:343:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ igenicmodel.cc:355:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ In file included from /usr/include/c++/8/map:60, from ../include/types.hh:39, from ../include/hints.hh:18, from ../include/extrinsicinfo.hh:23, from extrinsicinfo.cc:31: /usr/include/c++/8/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = Feature; _Val = Feature; _KeyOfValue = std::_Identity; _Compare = std::less; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_tree.h:2146:5: note: parameter passing for argument of type 'std::_Rb_tree, std::less, std::allocator >::const_iterator' {aka 'std::_Rb_tree_const_iterator'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/set:61, from ../include/extrinsicinfo.hh:28, from extrinsicinfo.cc:31: /usr/include/c++/8/bits/stl_set.h: In constructor 'std::set<_Key, _Compare, _Alloc>::set(_InputIterator, _InputIterator) [with _InputIterator = std::_List_iterator; _Key = Feature; _Compare = std::less; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_set.h:191:2: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 set(_InputIterator __first, _InputIterator __last) ^~~ /usr/include/c++/8/bits/stl_set.h:191:2: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/map:60, from ../include/types.hh:39, from ../include/hints.hh:18, from ../include/extrinsicinfo.hh:23, from extrinsicinfo.cc:31: /usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Arg&&, _NodeGen&) [with _Arg = const Feature&; _NodeGen = std::_Rb_tree, std::less, std::allocator >::_Alloc_node; _Key = Feature; _Val = Feature; _KeyOfValue = std::_Identity; _Compare = std::less; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_tree.h:2207:7: note: parameter passing for argument of type 'std::_Rb_tree, std::less, std::allocator >::const_iterator' {aka 'std::_Rb_tree_const_iterator'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../include/types.hh:38, from ../include/hints.hh:18, from ../include/extrinsicinfo.hh:23, from extrinsicinfo.cc:31: /usr/include/c++/8/bits/stl_algo.h: In function '_OutputIterator std::__set_difference(_InputIterator1, _InputIterator1, _InputIterator2, _InputIterator2, _OutputIterator, _Compare) [with _InputIterator1 = std::_Rb_tree_const_iterator; _InputIterator2 = std::_Rb_tree_const_iterator; _OutputIterator = std::insert_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:5332:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 __set_difference(_InputIterator1 __first1, _InputIterator1 __last1, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5332:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5332:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5332:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/map:60, from ../include/types.hh:39, from ../include/hints.hh:18, from ../include/extrinsicinfo.hh:23, from extrinsicinfo.cc:31: /usr/include/c++/8/bits/stl_tree.h:1042:65: note: parameter passing for argument of type 'std::_Rb_tree, std::less, std::allocator >::const_iterator' {aka 'std::_Rb_tree_const_iterator'} changed in GCC 7.1 return _M_insert_unique_(__pos, std::forward<_Arg>(__x), __an); ^ /usr/include/c++/8/bits/stl_tree.h:1042:65: note: parameter passing for argument of type 'std::_Rb_tree, std::less, std::allocator >::const_iterator' {aka 'std::_Rb_tree_const_iterator'} changed in GCC 7.1 return _M_insert_unique_(__pos, std::forward<_Arg>(__x), __an); ^ 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 extrinsicinfo.cc: In member function 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)': extrinsicinfo.cc:2532:54: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 set startHS(flist.begin(), flist.end()); ^ In file included from /usr/include/c++/8/algorithm:62, from ../include/types.hh:38, from ../include/hints.hh:18, from ../include/extrinsicinfo.hh:23, from extrinsicinfo.cc:31: /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 return _GLIBCXX_STD_A::__set_difference(__first1, __last1, ^ /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 return _GLIBCXX_STD_A::__set_difference(__first1, __last1, ^ /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 return _GLIBCXX_STD_A::__set_difference(__first1, __last1, ^ /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 extrinsicinfo.cc:2573:53: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 set stopHS(flist.begin(), flist.end()); ^ In file included from /usr/include/c++/8/algorithm:62, from ../include/types.hh:38, from ../include/hints.hh:18, from ../include/extrinsicinfo.hh:23, from extrinsicinfo.cc:31: /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 return _GLIBCXX_STD_A::__set_difference(__first1, __last1, ^ /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 return _GLIBCXX_STD_A::__set_difference(__first1, __last1, ^ /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 return _GLIBCXX_STD_A::__set_difference(__first1, __last1, ^ /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 extrinsicinfo.cc:2611:52: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 set dssHS(flist.begin(), flist.end()); ^ In file included from /usr/include/c++/8/algorithm:62, from ../include/types.hh:38, from ../include/hints.hh:18, from ../include/extrinsicinfo.hh:23, from extrinsicinfo.cc:31: /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 return _GLIBCXX_STD_A::__set_difference(__first1, __last1, ^ /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 return _GLIBCXX_STD_A::__set_difference(__first1, __last1, ^ /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 return _GLIBCXX_STD_A::__set_difference(__first1, __last1, ^ /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 extrinsicinfo.cc:2657:52: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 set assHS(flist.begin(), flist.end()); ^ In file included from /usr/include/c++/8/algorithm:62, from ../include/types.hh:38, from ../include/hints.hh:18, from ../include/extrinsicinfo.hh:23, from extrinsicinfo.cc:31: /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 return _GLIBCXX_STD_A::__set_difference(__first1, __last1, ^ /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 return _GLIBCXX_STD_A::__set_difference(__first1, __last1, ^ /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 return _GLIBCXX_STD_A::__set_difference(__first1, __last1, ^ /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5396:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 In file included from ../include/statemodel.hh:16, from ../include/utrmodel.hh:17, from utrmodel.cc:23: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/extrinsicinfo.hh:24, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/utrmodel.hh:17, from utrmodel.cc:23: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/extrinsicinfo.hh:25, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/utrmodel.hh:17, from utrmodel.cc:23: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/utrmodel.hh:17, from utrmodel.cc:23: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ utrmodel.cc: In static member function 'static void UtrModel::init()': utrmodel.cc:167:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { ^ utrmodel.cc:172:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:175:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:178:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:181:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:184:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:187:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:190:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:193:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:196:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:199:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:202:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:205:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:208:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:211:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:214:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:217:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:220:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:223:27: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ utrmodel.cc:228:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:231:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { cerr << e.getMessage(); } ^ utrmodel.cc:234:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) {} ^ utrmodel.cc:237:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) {} ^ utrmodel.cc:240:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) {} ^ utrmodel.cc:243:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) {} ^ utrmodel.cc:246:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) {} ^ utrmodel.cc:249:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) {} ^ utrmodel.cc:252:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) {} ^ utrmodel.cc: In member function 'virtual void UtrModel::viterbiForwardAndSampling(ViterbiMatrixType&, ViterbiMatrixType&, int, int, AlgorithmVariant, OptionListItem&)': utrmodel.cc:1062:28: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ utrmodel.cc: In member function 'Double UtrModel::notEndPartEmiProb(int, int, int, Feature*) const': utrmodel.cc:1275:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ utrmodel.cc:1409:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ utrmodel.cc: In member function 'Double UtrModel::seqProb(int, int, bool, int) const': utrmodel.cc:1700:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ utrmodel.cc:1735:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ utrmodel.cc: In member function 'Double UtrModel::tssupSeqProb(int, int, bool) const': utrmodel.cc:1760:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ utrmodel.cc: In static member function 'static void UtrModel::computeTtsProbs(int, int)': utrmodel.cc:1889:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ utrmodel.cc:1916:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ 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/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) {} ^~~~~~~~~~~~~~~~ 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::readAllParameters()': utrmodel.cc:624:26: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] sprintf(zusString, "[%d]", idx+1); ^~~~~~ utrmodel.cc:624:26: note: directive argument in the range [1, 2147483647] In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from /usr/include/c++/8/ext/string_conversions.h:43, from /usr/include/c++/8/bits/basic_string.h:6400, from /usr/include/c++/8/string:52, from /usr/include/c++/8/bits/locale_classes.h:40, from /usr/include/c++/8/bits/ios_base.h:41, from /usr/include/c++/8/ios:42, from /usr/include/c++/8/ostream:38, from ../include/matrix.hh:27, from ../include/statemodel.hh:15, from ../include/utrmodel.hh:17, from utrmodel.cc:23: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 6 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from vitmatrix.cc:10: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../include/types.hh:36, from ../include/vitmatrix.hh:14, from vitmatrix.cc:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ViterbiSubmapType&}; _Tp = ViterbiSubmapType; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:60, from ../include/types.hh:39, from ../include/vitmatrix.hh:14, from vitmatrix.cc:10: /usr/include/c++/8/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2500:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tree.h:2500:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/stl_tree.h: In member function 'void ViterbiSubmapType::useMaximum(Double&)': /usr/include/c++/8/bits/stl_tree.h:1169:2: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _M_erase_aux(__first, __last); ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tree.h:1169:2: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _M_erase_aux(__first, __last); ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tree.h: In member function 'int ViterbiSubmapType::eraseUnneededSubstate(SubstateId)': /usr/include/c++/8/bits/stl_tree.h:2518:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _M_erase_aux(__p.first, __p.second); ^~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../include/types.hh:36, from ../include/vitmatrix.hh:14, from vitmatrix.cc:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {ViterbiEntryType}; _Tp = ViterbiEntryType; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void ViterbiColumnType::addState(int, signed char)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../include/types.hh:36, from ../include/vitmatrix.hh:14, from vitmatrix.cc:10: /usr/include/c++/8/bits/stl_vector.h: In member function 'ViterbiSubmapType& ViterbiColumnType::addSubstates(const ViterbiSubmapType&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:60, from ../include/types.hh:39, from ../include/vitmatrix.hh:14, from vitmatrix.cc:10: /usr/include/c++/8/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2146:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from ../include/types.hh:39, from ../include/vitmatrix.hh:14, from vitmatrix.cc:10: /usr/include/c++/8/bits/stl_map.h: In member function 'void ViterbiSubmapType::registerPredecessors()': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o lldouble.o lldouble.cc -I../include In file included from /usr/include/c++/8/vector:69, from ../include/types.hh:36, from ../include/merkmal.hh:16, from merkmal.cc:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../include/types.hh:38, from ../include/merkmal.hh:16, from merkmal.cc:13: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../include/types.hh:38, from ../include/merkmal.hh:16, from merkmal.cc:13: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = LLDouble; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../include/types.hh:38, from ../include/merkmal.hh:16, from merkmal.cc:13: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In member function 'void BinnedMMGroup::trainBins(int)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../include/types.hh:38, from ../include/merkmal.hh:16, from merkmal.cc:13: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../include/types.hh:38, from ../include/merkmal.hh:16, from merkmal.cc:13: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 /usr/include/c++/8/bits/stl_algo.h: In static member function 'static std::vector CRF::capOutliers(std::vector)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o graph.o graph.cc -I../include In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/mea.hh:4, from mea.cc:1: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../include/types.hh:36, from ../include/merkmal.hh:16, from merkmal.cc:13: /usr/include/c++/8/bits/stl_vector.h: In static member function 'static void CRF::onlineLargeMarginTraining(Parameters*, std::vector, FeatureCollection&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from ../include/pp_scoring.hh:21, from ../include/gene.hh:15, from ../include/mea.hh:4, from mea.cc:1: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/graph.hh:10, from ../include/mea.hh:5, from mea.cc:1: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/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/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from ../include/exoncand.hh:27, from ../include/graph.hh:11, from ../include/mea.hh:5, from mea.cc:1: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ In file included from ../include/pp_scoring.hh:21, from ../include/gene.hh:15, from ../include/graph.hh:9, from graph.cc:9: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/graph.hh:10, from graph.cc:9: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from ../include/exoncand.hh:27, from ../include/graph.hh:11, from graph.cc:9: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../include/matrix.hh:26, from ../include/motif.hh:20, from ../include/gene.hh:14, from ../include/mea.hh:4, from mea.cc:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'AugustusGraph::AugustusGraph(std::__cxx11::list*, const char*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -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/graph.hh:9, from meaPath.cc:3: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/pp_scoring.hh:21, from ../include/gene.hh:15, from ../include/graph.hh:9, from meaPath.cc:3: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/graph.hh:10, from meaPath.cc:3: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/statemodel.hh:16, from ../include/exonmodel.hh:22, from ../include/exoncand.hh:27, from exoncand.cc:16: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from ../include/exoncand.hh:27, from ../include/graph.hh:11, from meaPath.cc:3: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ In file included from ../include/extrinsicinfo.hh:24, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from ../include/exoncand.hh:27, from exoncand.cc:16: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/extrinsicinfo.hh:25, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from ../include/exoncand.hh:27, from exoncand.cc:16: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from ../include/exoncand.hh:27, from exoncand.cc:16: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -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/motif.hh:21, from ../include/gene.hh:14, from ../include/randseqaccess.hh:14, from randseqaccess.cc:15: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/pp_scoring.hh:21, from ../include/gene.hh:15, from ../include/randseqaccess.hh:14, from randseqaccess.cc:15: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/extrinsicinfo.hh:24, from ../include/randseqaccess.hh:16, from randseqaccess.cc:15: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/randseqaccess.hh:16, from randseqaccess.cc:15: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ randseqaccess.cc: In member function 'void SpeciesCollection::readExtrinsicCFGFile(std::vector >&)': 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 fasta.o fasta.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 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 In file included from ../include/statemodel.hh:16, from ../include/ncmodel.hh:15, from ncmodel.cc:13: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/extrinsicinfo.hh:24, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/ncmodel.hh:15, from ncmodel.cc:13: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/extrinsicinfo.hh:25, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/ncmodel.hh:15, from ncmodel.cc:13: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/ncmodel.hh:15, from ncmodel.cc:13: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ ncmodel.cc: In static member function 'static void NcModel::init()': ncmodel.cc:68:26: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { ^ ncmodel.cc: In member function 'virtual void NcModel::viterbiForwardAndSampling(ViterbiMatrixType&, ViterbiMatrixType&, int, int, AlgorithmVariant, OptionListItem&)': ncmodel.cc:264:28: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ ncmodel.cc:346:28: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ ncmodel.cc: In member function 'Double NcModel::notEndPartEmiProb(int, int, int, Feature*) const': ncmodel.cc:544:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o igenictrain.o igenictrain.cc -I../include In file included from /usr/include/c++/8/vector:69, from ../include/matrix.hh:26, from ../include/statemodel.hh:15, from ../include/ncmodel.hh:15, from ncmodel.cc:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../include/matrix.hh:26, from ../include/statemodel.hh:15, from ../include/ncmodel.hh:15, from ncmodel.cc:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'void NcModel::computeLengthDistributions()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from ../include/statemodel.hh:16, from ../include/igenicmodel.hh:20, from igenictrain.cc:13: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/extrinsicinfo.hh:24, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/igenicmodel.hh:20, from igenictrain.cc:13: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/extrinsicinfo.hh:25, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/igenicmodel.hh:20, from igenictrain.cc:13: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/igenicmodel.hh:20, from igenictrain.cc:13: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ igenictrain.cc: In member function 'void IGenicModel::processSequence(const char*, const char*)': igenictrain.cc:175:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) {} ^ igenictrain.cc: In member function 'virtual void IGenicModel::printProbabilities(int, BaseCount*, const char*)': igenictrain.cc:252:12: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] catch( ProjectError ) { ^~~~~~~~~~~~ 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/intronmodel.hh:17, from introntrain.cc:14: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/extrinsicinfo.hh:24, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/intronmodel.hh:17, from introntrain.cc:14: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/extrinsicinfo.hh:25, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/intronmodel.hh:17, from introntrain.cc:14: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/intronmodel.hh:17, from introntrain.cc:14: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ 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 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 ) { ^~~~~~~~~~~~ In file included from ../include/statemodel.hh:16, from ../include/exonmodel.hh:22, from exontrain.cc:13: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/extrinsicinfo.hh:24, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from exontrain.cc:13: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/extrinsicinfo.hh:25, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from exontrain.cc:13: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/exonmodel.hh:22, from exontrain.cc:13: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ In file included from ../include/statemodel.hh:16, from ../include/utrmodel.hh:17, from utrtrain.cc:15: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/extrinsicinfo.hh:24, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/utrmodel.hh:17, from utrtrain.cc:15: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/extrinsicinfo.hh:25, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/utrmodel.hh:17, from utrtrain.cc:15: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ exontrain.cc: In member function 'virtual void ExonModel::printProbabilities(int, BaseCount*, const char*)': exontrain.cc:522:9: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] catch( ProjectError ) { ^~~~~~~~~~~~ exontrain.cc: In member function 'void ExonModel::processExons(const Gene*)': exontrain.cc:626:26: warning: catching polymorphic type 'class ExonModelError' by value [-Wcatch-value=] } catch (ExonModelError e) { ^ exontrain.cc:634:26: warning: catching polymorphic type 'class ExonModelError' by value [-Wcatch-value=] } catch( ExonModelError e ){ ^ exontrain.cc:643:30: warning: catching polymorphic type 'class ExonModelError' by value [-Wcatch-value=] } catch( ExonModelError e ){ ^ exontrain.cc:651:26: warning: catching polymorphic type 'class ExonModelError' by value [-Wcatch-value=] } catch( ExonModelError e ){ ^ exontrain.cc: In member function 'void ExonModel::processInternalExon(const State*)': exontrain.cc:811:29: warning: catching polymorphic type 'class ExonModelError' by value [-Wcatch-value=] } catch( ExonModelError e ){ ^ exontrain.cc: In member function 'void ExonModel::processInnerSequence(const char*, const char*, int)': exontrain.cc:896:34: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) {} ^ In file included from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/utrmodel.hh:17, from utrtrain.cc:15: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ utrtrain.cc: In member function 'void UtrModel::buildProbabilities(const AnnoSequence*)': utrtrain.cc:114:26: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=] } catch (UtrModelError e) { ^ utrtrain.cc: In member function 'void UtrModel::buildTSSModel(const AnnoSequence*)': utrtrain.cc:197:29: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=] } catch (UtrModelError e) { ^ utrtrain.cc: In member function 'void UtrModel::processStates(const Gene*)': utrtrain.cc:396:29: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=] } catch (UtrModelError e) { ^ utrtrain.cc:403:29: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=] } catch( UtrModelError e ){ ^ utrtrain.cc:413:26: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=] } catch( UtrModelError e ){ ^ utrtrain.cc:423:29: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=] } catch( UtrModelError e ){ ^ utrtrain.cc:438:29: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=] } catch (UtrModelError e) { ^ utrtrain.cc:445:29: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=] } catch( UtrModelError e ){ ^ utrtrain.cc:455:26: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=] } catch( UtrModelError e ){ ^ utrtrain.cc:465:29: warning: catching polymorphic type 'class UtrModelError' by value [-Wcatch-value=] } catch( UtrModelError e ){ ^ utrtrain.cc: In member function 'void UtrModel::process5InitSequence(const char*, const char*)': utrtrain.cc:796:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ utrtrain.cc: In member function 'void UtrModel::process5Sequence(const char*, const char*)': utrtrain.cc:810:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ utrtrain.cc: In member function 'void UtrModel::process3Sequence(const char*, const char*)': utrtrain.cc:824:39: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ utrtrain.cc: In member function 'void UtrModel::processTssupSequence(const char*, const char*)': utrtrain.cc:838:37: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ utrtrain.cc: In static member function 'static void UtrModel::storeGCPars(int)': utrtrain.cc:851:24: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch(ProjectError e) { ^ utrtrain.cc: In member function 'virtual void UtrModel::printProbabilities(int, BaseCount*, const char*)': utrtrain.cc:1018:14: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch( ProjectError ) { ^~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../include/matrix.hh:26, from ../include/statemodel.hh:15, from ../include/intronmodel.hh:17, from introntrain.cc:14: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../include/matrix.hh:26, from ../include/statemodel.hh:15, from ../include/intronmodel.hh:17, from introntrain.cc:14: /usr/include/c++/8/bits/stl_vector.h: In member function 'void IntronModel::makeDSSProbs()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../include/matrix.hh:26, from ../include/statemodel.hh:15, from ../include/exonmodel.hh:22, from exontrain.cc:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../include/matrix.hh:26, from ../include/statemodel.hh:15, from ../include/exonmodel.hh:22, from exontrain.cc:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'void ExonModel::buildProbabilities()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void IntronModel::buildProbabilities(const AnnoSequence*)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -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/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) {} ^~~~~~~~~~~~~~~~~~ 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/extrinsicinfo.hh:24, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/intronmodel.hh:17, from dummy.cc:13: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from ../include/extrinsicinfo.hh:25, from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/intronmodel.hh:17, from dummy.cc:13: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/merkmal.hh:17, from ../include/statemodel.hh:17, from ../include/intronmodel.hh:17, from dummy.cc:13: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ g++ -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 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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o dummy.o -I../include In file included from ../include/pp_profile.hh:21, from ../include/pp_fastBlockSearcher.hh:19, from pp_fastBlockSearcher.cc:1: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/pp_profile.hh:22, from ../include/pp_fastBlockSearcher.hh:19, from pp_fastBlockSearcher.cc:1: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from pp_fastBlockSearcher.cc:1: ../include/pp_fastBlockSearcher.hh: In member function 'void PP::CandidateCollection::pushSeeds(int)': ../include/pp_fastBlockSearcher.hh:371:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ In file included from ../include/motif.hh:21, from ../include/gene.hh:14, from augustus.cc:15: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/pp_scoring.hh:21, from ../include/gene.hh:15, from augustus.cc:15: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from ../include/extrinsicinfo.hh:24, from ../include/namgene.hh:15, from augustus.cc:17: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../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) {} ^~~~~~~~~~~~~~~~ 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) { ^ cp prepareAlign ../bin/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o -I../include g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include 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 fastBlockSearch.cc:14: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/pp_profile.hh:21, from fastBlockSearch.cc:15: ../include/geneticcode.hh: In static member function 'static bool GeneticCode::isStartcodon(const char*, bool)': ../include/geneticcode.hh:333:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ ../include/geneticcode.hh: In static member function 'static Double GeneticCode::startCodonProb(const char*, bool)': ../include/geneticcode.hh:344:11: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError){} ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/extrinsicinfo.hh:24, from etraining.cc:14: ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Integer&)': ../include/properties.hh:243:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, unsigned int&)': ../include/properties.hh:248:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Double&)': ../include/properties.hh:253:29: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, double&)': ../include/properties.hh:258:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, Boolean&)': ../include/properties.hh:263:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, std::__cxx11::string&)': ../include/properties.hh:268:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ ../include/properties.hh: In static member function 'static void Properties::assignProperty(std::__cxx11::string, const char*&)': ../include/properties.hh:273:28: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError e) {} ^ In file included from ../include/pp_profile.hh:22, from fastBlockSearch.cc:15: ../include/vitmatrix.hh: In member function 'Double ViterbiColumnType::get(int, SubstateId) const': ../include/vitmatrix.hh:488:11: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) { ^~~~~~~~~~~~~~~~~~ ../include/vitmatrix.hh: In member function 'void ViterbiColumnType::getMaxSubstate(int, SubstateId&, Double&) const': ../include/vitmatrix.hh:621:14: warning: catching polymorphic type 'struct NoSubmapFoundError' by value [-Wcatch-value=] } catch (NoSubmapFoundError) {} ^~~~~~~~~~~~~~~~~~ In file included from etraining.cc:14: ../include/extrinsicinfo.hh: In constructor 'FeatureCollection::FeatureCollection()': ../include/extrinsicinfo.hh:336:11: warning: catching polymorphic type 'struct KeyNotFoundError' by value [-Wcatch-value=] } catch (KeyNotFoundError) {} ^~~~~~~~~~~~~~~~ etraining.cc: In function 'int main(int, char**)': etraining.cc:72:24: warning: catching polymorphic type 'class ProjectError' by value [-Wcatch-value=] } catch (ProjectError e) { ^ In file included from fastBlockSearch.cc:16: ../include/pp_fastBlockSearcher.hh: In member function 'void PP::CandidateCollection::pushSeeds(int)': ../include/pp_fastBlockSearcher.hh:371:38: warning: catching polymorphic type 'class InvalidNucleotideError' by value [-Wcatch-value=] } catch (InvalidNucleotideError e) { ^ cp augustus ../bin/ cp etraining ../bin/ cp fastBlockSearch ../bin/ make[3]: Leaving directory '/build/augustus-3.3.2+dfsg/src' cd auxprogs && make make[3]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs' cd bam2hints; make; make[4]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/bam2hints' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: 'bam2hints' is up to date. make[4]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/bam2hints' cd compileSpliceCands; make; make[4]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/compileSpliceCands' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: 'compileSpliceCands' is up to date. make[4]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/compileSpliceCands' cd filterBam; make; make[4]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/filterBam' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src;make) make[5]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/filterBam/src' g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/build/augustus-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz filterBam compiled with BAMTOOLS=/usr/include/bamtools mv filterBam ../../../bin/filterBam make[5]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/filterBam/src' make[4]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/filterBam' cd homGeneMapping; make; make[4]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/homGeneMapping' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src; make) make[5]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/homGeneMapping/src' make[5]: Nothing to be done for 'all'. make[5]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/homGeneMapping/src' make[4]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/homGeneMapping' cd joingenes; make; make[4]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/joingenes' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/joingenes' cd bam2wig; make; make[4]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/bam2wig' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: 'bam2wig' is up to date. make[4]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/bam2wig' cd utrrnaseq/Debug; make all; make[4]: Entering directory '/build/augustus-3.3.2+dfsg/auxprogs/utrrnaseq/Debug' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. Building file: ../src/Compute_UTRs.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Compute_UTRs.d" -MT"src/Compute_UTRs.o" -o "src/Compute_UTRs.o" "../src/Compute_UTRs.cpp" Finished building: ../src/Compute_UTRs.cpp Building file: ../src/Coord_Transform.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Coord_Transform.d" -MT"src/Coord_Transform.o" -o "src/Coord_Transform.o" "../src/Coord_Transform.cpp" Finished building: ../src/Coord_Transform.cpp Building file: ../src/Genomic_Data.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Genomic_Data.d" -MT"src/Genomic_Data.o" -o "src/Genomic_Data.o" "../src/Genomic_Data.cpp" Finished building: ../src/Genomic_Data.cpp Building file: ../src/Splice_Sites.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Splice_Sites.d" -MT"src/Splice_Sites.o" -o "src/Splice_Sites.o" "../src/Splice_Sites.cpp" Finished building: ../src/Splice_Sites.cpp Building file: ../src/Supporting_Methods.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Supporting_Methods.d" -MT"src/Supporting_Methods.o" -o "src/Supporting_Methods.o" "../src/Supporting_Methods.cpp" Finished building: ../src/Supporting_Methods.cpp Building file: ../src/Test.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Test.d" -MT"src/Test.o" -o "src/Test.o" "../src/Test.cpp" Finished building: ../src/Test.cpp Building file: ../src/UTRs.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/UTRs.d" -MT"src/UTRs.o" -o "src/UTRs.o" "../src/UTRs.cpp" ../src/UTRs.cpp: In static member function 'static void UTRs::compute_UTRs(const Genomic_Data::Scaff_plus_Gen_Data&, const std::map&)': ../src/UTRs.cpp:387:64: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 vector::iterator jt = min_element(d.begin(), d.end()); ^ In file included from /usr/include/c++/8/bits/stl_algobase.h:71, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from ../src/Genomic_Data.hpp:8, from ../src/UTRs.cpp:5: /usr/include/c++/8/bits/predefined_ops.h: In member function 'constexpr bool __gnu_cxx::__ops::_Iter_less_iter::operator()(_Iterator1, _Iterator2) const [with _Iterator1 = __gnu_cxx::__normal_iterator > >; _Iterator2 = __gnu_cxx::__normal_iterator > >]': /usr/include/c++/8/bits/predefined_ops.h:42:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 operator()(_Iterator1 __it1, _Iterator2 __it2) const ^~~~~~~~ /usr/include/c++/8/bits/predefined_ops.h:42:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/core/swap.hpp:25, from /usr/include/boost/utility/swap.hpp:15, from /usr/include/boost/tuple/detail/tuple_basic.hpp:40, from /usr/include/boost/tuple/tuple.hpp:28, from ../src/Compute_UTRs.hpp:16, from ../src/UTRs.cpp:9: /usr/include/c++/8/bits/stl_algo.h: In function 'constexpr _ForwardIterator std::__min_element(_ForwardIterator, _ForwardIterator, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:5588:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 __min_element(_ForwardIterator __first, _ForwardIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5588:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5595:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 if (__comp(__first, __result)) ~~~~~~^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'constexpr _FIter std::min_element(_FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator > >]': /usr/include/c++/8/bits/stl_algo.h:5610:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 inline min_element(_ForwardIterator __first, _ForwardIterator __last) ^~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5610:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:5619:43: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 return _GLIBCXX_STD_A::__min_element(__first, __last, ^ In file included from /usr/include/c++/8/vector:64, from ../src/Genomic_Data.hpp:9, from ../src/UTRs.cpp:5: /usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../src/Genomic_Data.hpp:9, from ../src/UTRs.cpp:5: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from ../src/Genomic_Data.hpp:9, from ../src/UTRs.cpp:5: /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from ../src/Genomic_Data.hpp:8, from ../src/UTRs.cpp:5: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from ../src/Genomic_Data.hpp:8, from ../src/UTRs.cpp:5: /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __miter_base(move_iterator<_Iterator> __it) ^~~~~~~~~~~~ Finished building: ../src/UTRs.cpp Building file: ../src/main.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/main.d" -MT"src/main.o" -o "src/main.o" "../src/main.cpp" Finished building: ../src/main.cpp Building target: utrrnaseq Invoking: GCC C++ Linker g++ -o "utrrnaseq" ./src/Compute_UTRs.o ./src/Coord_Transform.o ./src/Genomic_Data.o ./src/Splice_Sites.o ./src/Supporting_Methods.o ./src/Test.o ./src/UTRs.o ./src/main.o Finished building target: utrrnaseq make[4]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs/utrrnaseq/Debug' make[3]: Leaving directory '/build/augustus-3.3.2+dfsg/auxprogs' make[2]: Leaving directory '/build/augustus-3.3.2+dfsg' asciidoctor -a docdate='' -b manpage debian/mansrc/*adoc make[1]: Leaving directory '/build/augustus-3.3.2+dfsg' dh_auto_test make -j3 test make[1]: Entering directory '/build/augustus-3.3.2+dfsg' ./bin/augustus --species=human --UTR=on examples/example.fa # This output was generated with AUGUSTUS (version 3.3.2). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), # O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. # Initialising the parameters using config directory /build/augustus-3.3.2+dfsg/config/ ... # human version. Using species specific transition matrix: /build/augustus-3.3.2+dfsg/config/species/human/human_trans_shadow_partial_utr.pbl # Looks like examples/example.fa is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- # # Predicted genes for sequence number 1 on both strands # start gene g1 HS04636 AUGUSTUS gene 836 8857 1 + . g1 HS04636 AUGUSTUS transcript 836 8857 . + . g1.t1 HS04636 AUGUSTUS tss 836 836 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 5072 5358 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 5860 6007 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 6494 8857 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS tts 8857 8857 . + . transcript_id "g1.t1"; gene_id "g1"; # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL] # end gene g1 ### # # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- # # Predicted genes for sequence number 2 on both strands # start gene g2 HS08198 AUGUSTUS gene 86 2344 1 + . g2 HS08198 AUGUSTUS transcript 86 2344 . + . g2.t1 HS08198 AUGUSTUS tss 86 86 . + . transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS exon 86 582 . + . transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS exon 812 894 . + . transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS exon 1053 1123 . + . transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS exon 1208 1315 . + . transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS exon 1587 1688 . + . transcript_id "g2.t1"; gene_id "g2"; # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY] # end gene g2 ### # command line: # ./bin/augustus --species=human --UTR=on examples/example.fa make[1]: Leaving directory '/build/augustus-3.3.2+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/augustus-3.3.2+dfsg' mkdir -p debian/augustus/usr/bin install bin/* debian/augustus/usr/bin install auxprogs/checkTargetSortedness/checkTargetSortedness \ debian/augustus/usr/bin install auxprogs/bam2wig/bam2wig \ debian/augustus/usr/bin install auxprogs/compileSpliceCands/compileSpliceCands \ debian/augustus/usr/bin install auxprogs/homGeneMapping/src/homGeneMapping \ debian/augustus/usr/bin install auxprogs/joingenes/joingenes \ debian/augustus/usr/bin mkdir -p debian/augustus/usr/share/augustus cp -r scripts debian/augustus/usr/share/augustus chmod -R -x debian/augustus/usr/share/augustus/scripts/* rm -rf debian/augustus/usr/share/augustus/scripts/*.patch \ debian/augustus/usr/share/augustus/scripts/aln2wig chmod +x debian/augustus/usr/share/augustus/scripts/checkUTR \ debian/augustus/usr/share/augustus/scripts/*.pl* mkdir -p debian/augustus-doc/usr/share/doc/augustus cp README* debian/augustus-doc/usr/share/doc/augustus cp docs/*.txt debian/augustus-doc/usr/share/doc/augustus cp -r docs/tutorial \ debian/augustus-doc/usr/share/doc/augustus mkdir -p debian/augustus-data/usr/share/augustus cp -r config debian/augustus-data/usr/share/augustus find debian/augustus-data/usr/share/augustus \ -type f -exec chmod -x {} \; make[1]: Leaving directory '/build/augustus-3.3.2+dfsg' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/augustus-3.3.2+dfsg' dh_installchangelogs -k HISTORY.TXT make[1]: Leaving directory '/build/augustus-3.3.2+dfsg' dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/augustus-3.3.2+dfsg' dh_compress -Xtutorial make[1]: Leaving directory '/build/augustus-3.3.2+dfsg' dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: debian/augustus/usr/bin/prepareAlign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/fastBlockSearch contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/bam2hints contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/etraining contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/joingenes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/homGeneMapping contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/filterBam contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/augustus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/bam2wig was not linked against libssl.so.1.1 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/bam2wig was not linked against libcurl-nss.so.4 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/bam2wig was not linked against libcrypto.so.1.1 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/checkTargetSortedness debian/augustus/usr/bin/bam2wig were not linked against libtinfo.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/bam2wig was not linked against libbz2.so.1.0 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/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) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/bam2wig was not linked against libhts.so.2 (it uses none of the library's symbols) dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/augustus-3.3.2+dfsg' dh_gencontrol -- \ -V'Built-Using:samtools=samtools-legacy (= 0.1.19-4)' dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined make[1]: Leaving directory '/build/augustus-3.3.2+dfsg' dh_md5sums dh_builddeb dpkg-deb: building package 'augustus-data' in '../augustus-data_3.3.2+dfsg-2_all.deb'. dpkg-deb: building package 'augustus' in '../augustus_3.3.2+dfsg-2_armhf.deb'. dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.3.2+dfsg-2_armhf.deb'. dpkg-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_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration 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/21460 and its subdirectories I: Current time: Thu Jul 16 07:02:04 -12 2020 I: pbuilder-time-stamp: 1594926124