Diff of the two buildlogs: -- --- b1/build.log 2021-06-16 21:16:06.697102659 +0000 +++ b2/build.log 2021-06-16 21:20:54.698143533 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jul 19 15:38:35 -12 2022 -I: pbuilder-time-stamp: 1658288315 +I: Current time: Thu Jun 17 11:16:09 +14 2021 +I: pbuilder-time-stamp: 1623878169 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./proftmb_1.1.12-9.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.H4W2rGVH/trustedkeys.kbx': General error -gpgv: Signature made Wed Nov 25 19:13:30 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.yM4PPEVL/trustedkeys.kbx': General error +gpgv: Signature made Thu Nov 26 21:13:30 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -31,137 +31,171 @@ dpkg-source: info: applying gcc-6.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/851/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/837/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/837/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/837/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='11d2962b3b38489eb8bbcc61d54eb7cb' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='851' - PS1='# ' - PS2='> ' + INVOCATION_ID=a806ee83c1fc48adafea647a8cc523a5 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=837 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.TjyAPcvSNP/pbuilderrc_gp7d --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.TjyAPcvSNP/b1 --logfile b1/build.log proftmb_1.1.12-9.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.TjyAPcvSNP/pbuilderrc_8htX --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.TjyAPcvSNP/b2 --logfile b2/build.log --extrapackages usrmerge proftmb_1.1.12-9.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos6-i386 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-16-686-pae #1 SMP Debian 4.19.181-1 (2021-03-19) i686 GNU/Linux I: ls -l /bin - total 5776 - -rwxr-xr-x 1 root root 1367848 Feb 24 2021 bash - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat - -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown - -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp - -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash - -rwxr-xr-x 1 root root 124904 Sep 22 2020 date - -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd - -rwxr-xr-x 1 root root 100752 Sep 22 2020 df - -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir - -rwxr-xr-x 1 root root 83644 Feb 7 2021 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 34664 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 71928 Feb 7 2021 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 100952 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln - -rwxr-xr-x 1 root root 55572 Feb 7 2020 login - -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls - -rwxr-xr-x 1 root root 153124 Feb 7 2021 lsblk - -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 58920 Feb 7 2021 more - -rwsr-xr-x 1 root root 50720 Feb 7 2021 mount - -rwxr-xr-x 1 root root 13856 Feb 7 2021 mountpoint - -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Feb 24 2021 rbash -> bash - -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm - -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 18 03:47 sh -> dash - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty - -rwsr-xr-x 1 root root 79396 Feb 7 2021 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar - -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch - -rwxr-xr-x 1 root root 34664 Sep 22 2020 true - -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Feb 7 2021 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Feb 7 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/851/tmp/hooks/D02_print_environment finished + total 5784 + -rwxr-xr-x 1 root root 1367848 Feb 25 10:57 bash + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 38824 Sep 23 2020 cat + -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown + -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp + -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash + -rwxr-xr-x 1 root root 124904 Sep 23 2020 date + -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd + -rwxr-xr-x 1 root root 100752 Sep 23 2020 df + -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir + -rwxr-xr-x 1 root root 83644 Feb 8 04:38 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 34664 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 34664 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 71928 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 100952 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln + -rwxr-xr-x 1 root root 55572 Feb 8 2020 login + -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls + -rwxr-xr-x 1 root root 153124 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 58920 Feb 8 04:38 more + -rwsr-xr-x 1 root root 50720 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 13856 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Feb 25 10:57 rbash -> bash + -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm + -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jun 17 11:19 sh -> bash + lrwxrwxrwx 1 root root 4 Jun 16 23:27 sh.distrib -> dash + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty + -rwsr-xr-x 1 root root 79396 Feb 8 04:38 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch + -rwxr-xr-x 1 root root 34664 Sep 23 2020 true + -rwxr-xr-x 1 root root 17768 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 Feb 8 04:38 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/837/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -240,7 +274,7 @@ Get: 35 http://deb.debian.org/debian bullseye/main i386 libgsl25 i386 2.6+dfsg-2 [911 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 libgsl-dev i386 2.6+dfsg-2 [1146 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 opt i386 3.19-1.3+b1 [47.5 kB] -Fetched 21.0 MB in 0s (91.7 MB/s) +Fetched 21.0 MB in 7s (3122 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19675 files and directories currently installed.) @@ -403,8 +437,44 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (2194 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 21958 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/proftmb-1.1.12/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/proftmb-1.1.12/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package proftmb dpkg-buildpackage: info: source version 1.1.12-9 dpkg-buildpackage: info: source distribution unstable @@ -426,7 +496,7 @@ ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a thread-safe mkdir -p... /bin/mkdir -p +checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -455,8 +525,8 @@ checking for main in -lgslcblas... yes checking for main in -lgsl... yes checking how to run the C preprocessor... gcc -E -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes @@ -483,7 +553,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j18 + make -j10 make[1]: Entering directory '/build/proftmb-1.1.12' make all-recursive make[2]: Entering directory '/build/proftmb-1.1.12' @@ -503,15 +573,7 @@ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GradientDescent.o GradientDescent.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o HMMEval.o HMMEval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o HMMOutput.o HMMOutput.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o HTools.o HTools.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Krogh1Best.o Krogh1Best.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Load.o Load.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Output.o Output.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Par.o Par.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Params.o Params.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Posterior.o Posterior.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Regularization.o Regularization.cpp -In file included from BaumWelch.cpp:1: +In file included from GradientDescent.cpp:1: Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 34 | static void LoadL2L(char*) throw (string&); | ^~~~~ @@ -527,23 +589,20 @@ Par.h:40:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 40 | vector&) throw (string&); | ^~~~~ -In file included from Backward.cpp:1: -Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 34 | static void LoadL2L(char*) throw (string&); - | ^~~~~ -Par.h:35:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 35 | static void LoadL2A(char*) throw (string&); - | ^~~~~ -Par.h:36:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 36 | static void LoadA2E(char*) throw (string&); - | ^~~~~ -Par.h:37:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 37 | static void LoadConnect(char*) throw (string&); +In file included from Forward.cpp:1: +Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 85 | bool InitLabels(set >&) throw (string&); + | ^~~~~ +Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 194 | static map > > Read(char*) throw (string&); + | ^~~~~ +Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 120 | static void ReadZCurve(char *) throw (string &); | ^~~~~ -Par.h:40:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 40 | vector&) throw (string&); - | ^~~~~ -In file included from Params.cpp:1: +Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 121 | static void ReadNullFreq(char *) throw (string &); + | ^~~~~ +In file included from Forward.cpp:2: Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 34 | static void LoadL2L(char*) throw (string&); | ^~~~~ @@ -559,13 +618,7 @@ Par.h:40:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 40 | vector&) throw (string&); | ^~~~~ -Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 120 | static void ReadZCurve(char *) throw (string &); - | ^~~~~ -Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 121 | static void ReadNullFreq(char *) throw (string &); - | ^~~~~ -In file included from Par.cpp:1: +In file included from Backward.cpp:1: Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 34 | static void LoadL2L(char*) throw (string&); | ^~~~~ @@ -593,45 +646,24 @@ Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 121 | static void ReadNullFreq(char *) throw (string &); | ^~~~~ -Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 120 | static void ReadZCurve(char *) throw (string &); - | ^~~~~ -Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 121 | static void ReadNullFreq(char *) throw (string &); - | ^~~~~ -In file included from Krogh1Best.cpp:1: -Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 34 | static void LoadL2L(char*) throw (string&); - | ^~~~~ -Par.h:35:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 35 | static void LoadL2A(char*) throw (string&); - | ^~~~~ -Par.h:36:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 36 | static void LoadA2E(char*) throw (string&); - | ^~~~~ -Par.h:37:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 37 | static void LoadConnect(char*) throw (string&); - | ^~~~~ -Par.h:40:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 40 | vector&) throw (string&); - | ^~~~~ In file included from TrainSeq.h:5, - from HMMEval.h:5, - from HMMEval.cpp:1: + from GradientDescent.cpp:2: Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 85 | bool InitLabels(set >&) throw (string&); | ^~~~~ Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 194 | static map > > Read(char*) throw (string&); | ^~~~~ -In file included from TrainSeq.h:5, - from ExpectC.cpp:1: +In file included from HMMOutput.h:4, + from HMMOutput.cpp:1: Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 85 | bool InitLabels(set >&) throw (string&); | ^~~~~ -In file included from TrainSeq.h:6, - from HMMEval.h:5, - from HMMEval.cpp:1: +Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 194 | static map > > Read(char*) throw (string&); + | ^~~~~ +In file included from HMMOutput.h:5, + from HMMOutput.cpp:1: Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 34 | static void LoadL2L(char*) throw (string&); | ^~~~~ @@ -647,10 +679,16 @@ Par.h:40:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 40 | vector&) throw (string&); | ^~~~~ +In file included from HTools.h:4, + from Backward.cpp:2: +Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 85 | bool InitLabels(set >&) throw (string&); + | ^~~~~ Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 194 | static map > > Read(char*) throw (string&); | ^~~~~ -In file included from Posterior.cpp:1: +In file included from TrainSeq.h:5, + from ExpectA.cpp:1: Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 85 | bool InitLabels(set >&) throw (string&); | ^~~~~ @@ -658,7 +696,7 @@ 194 | static map > > Read(char*) throw (string&); | ^~~~~ In file included from TrainSeq.h:6, - from ExpectC.cpp:1: + from ExpectA.cpp:1: Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 34 | static void LoadL2L(char*) throw (string&); | ^~~~~ @@ -674,7 +712,41 @@ Par.h:40:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 40 | vector&) throw (string&); | ^~~~~ -In file included from Regularization.cpp:7: +Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 120 | static void ReadZCurve(char *) throw (string &); + | ^~~~~ +Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 121 | static void ReadNullFreq(char *) throw (string &); + | ^~~~~ +In file included from HMMOutput.cpp:1: +HMMOutput.h:21:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 21 | void DisplayArch(ostream&,Par&,uint,char* =""); + | ^ +HMMOutput.h:24:44: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 24 | void PrintEmit(ostream&,Par&,uint,char* =""); + | ^ +In file included from HMMOutput.cpp:2: +Eval.h:48:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 48 | float RelativeEntropy(vector& A, vector& B) throw (char *); + | ^~~~~ +Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 120 | static void ReadZCurve(char *) throw (string &); + | ^~~~~ +Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 121 | static void ReadNullFreq(char *) throw (string &); + | ^~~~~ +In file included from TrainSeq.h:5, + from HMMEval.h:5, + from HMMEval.cpp:1: +Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 85 | bool InitLabels(set >&) throw (string&); + | ^~~~~ +Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 194 | static map > > Read(char*) throw (string&); + | ^~~~~ +In file included from TrainSeq.h:6, + from HMMEval.h:5, + from HMMEval.cpp:1: Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 34 | static void LoadL2L(char*) throw (string&); | ^~~~~ @@ -690,7 +762,7 @@ Par.h:40:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 40 | vector&) throw (string&); | ^~~~~ -In file included from Posterior.cpp:2: +In file included from BaumWelch.cpp:1: Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 34 | static void LoadL2L(char*) throw (string&); | ^~~~~ @@ -712,12 +784,24 @@ Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 121 | static void ReadNullFreq(char *) throw (string &); | ^~~~~ -In file included from HMMOutput.h:4, - from HMMOutput.cpp:1: +Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 120 | static void ReadZCurve(char *) throw (string &); + | ^~~~~ +Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 121 | static void ReadNullFreq(char *) throw (string &); + | ^~~~~ +In file included from TrainSeq.h:5, + from Eval.h:11, + from Eval.cpp:6: Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 85 | bool InitLabels(set >&) throw (string&); | ^~~~~ -In file included from GradientDescent.cpp:1: +Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 194 | static map > > Read(char*) throw (string&); + | ^~~~~ +In file included from TrainSeq.h:6, + from Eval.h:11, + from Eval.cpp:6: Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 34 | static void LoadL2L(char*) throw (string&); | ^~~~~ @@ -733,20 +817,34 @@ Par.h:40:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 40 | vector&) throw (string&); | ^~~~~ +In file included from TrainSeq.h:5, + from BaumWelch.cpp:2: +Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 85 | bool InitLabels(set >&) throw (string&); + | ^~~~~ Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 194 | static map > > Read(char*) throw (string&); | ^~~~~ +Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 120 | static void ReadZCurve(char *) throw (string &); + | ^~~~~ +Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 121 | static void ReadNullFreq(char *) throw (string &); + | ^~~~~ +In file included from Eval.cpp:6: +Eval.h:48:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 48 | float RelativeEntropy(vector& A, vector& B) throw (char *); + | ^~~~~ In file included from TrainSeq.h:5, - from Load.h:4, - from Load.cpp:1: + from ExpectC.cpp:1: Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 85 | bool InitLabels(set >&) throw (string&); | ^~~~~ Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 194 | static map > > Read(char*) throw (string&); | ^~~~~ -In file included from HMMOutput.h:5, - from HMMOutput.cpp:1: +In file included from TrainSeq.h:6, + from ExpectC.cpp:1: Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 34 | static void LoadL2L(char*) throw (string&); | ^~~~~ @@ -768,9 +866,10 @@ Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 121 | static void ReadNullFreq(char *) throw (string &); | ^~~~~ -In file included from TrainSeq.h:6, - from Load.h:4, - from Load.cpp:1: +Eval.cpp:654:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 654 | float RelativeEntropy(vector& A, vector& B) throw (char *){ + | ^~~~~ +In file included from proftmb.cpp:14: Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 34 | static void LoadL2L(char*) throw (string&); | ^~~~~ @@ -793,78 +892,39 @@ 121 | static void ReadNullFreq(char *) throw (string &); | ^~~~~ In file included from TrainSeq.h:5, - from BaumWelch.cpp:2: -Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 85 | bool InitLabels(set >&) throw (string&); - | ^~~~~ -Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 194 | static map > > Read(char*) throw (string&); - | ^~~~~ -Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 120 | static void ReadZCurve(char *) throw (string &); - | ^~~~~ -Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 121 | static void ReadNullFreq(char *) throw (string &); - | ^~~~~ -Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 120 | static void ReadZCurve(char *) throw (string &); - | ^~~~~ -Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 121 | static void ReadNullFreq(char *) throw (string &); - | ^~~~~ -Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 120 | static void ReadZCurve(char *) throw (string &); - | ^~~~~ -Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 121 | static void ReadNullFreq(char *) throw (string &); - | ^~~~~ -In file included from HTools.h:4, - from Backward.cpp:2: + from proftmb.cpp:15: Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 85 | bool InitLabels(set >&) throw (string&); | ^~~~~ Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 194 | static map > > Read(char*) throw (string&); | ^~~~~ -In file included from proftmb.cpp:14: -Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 34 | static void LoadL2L(char*) throw (string&); - | ^~~~~ -Par.h:35:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 35 | static void LoadL2A(char*) throw (string&); - | ^~~~~ -Par.h:36:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 36 | static void LoadA2E(char*) throw (string&); - | ^~~~~ -Par.h:37:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 37 | static void LoadConnect(char*) throw (string&); - | ^~~~~ -Par.h:40:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 40 | vector&) throw (string&); - | ^~~~~ -Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 120 | static void ReadZCurve(char *) throw (string &); - | ^~~~~ -Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 121 | static void ReadNullFreq(char *) throw (string &); - | ^~~~~ -In file included from HMMOutput.cpp:1: +In file included from proftmb.cpp:18: HMMOutput.h:21:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 21 | void DisplayArch(ostream&,Par&,uint,char* =""); | ^ HMMOutput.h:24:44: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 24 | void PrintEmit(ostream&,Par&,uint,char* =""); | ^ -In file included from HMMOutput.cpp:2: +In file included from proftmb.cpp:20: +Zscore.h:9:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 9 | Z_Calibrate(set >&,int,double) throw (string&); + | ^~~~~ +In file included from proftmb.cpp:22: Eval.h:48:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 48 | float RelativeEntropy(vector& A, vector& B) throw (char *); | ^~~~~ -Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 120 | static void ReadZCurve(char *) throw (string &); - | ^~~~~ -Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 121 | static void ReadNullFreq(char *) throw (string &); - | ^~~~~ +proftmb.cpp:68:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 68 | const char *, double, Par&, const char*, bool) throw (string &); + | ^~~~~ +proftmb.cpp:273:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 273 | const char *datfile, double cut, Par& m, const char *name, bool multiQ) throw (string &) { + | ^~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o HTools.o HTools.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Krogh1Best.o Krogh1Best.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Load.o Load.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Output.o Output.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Par.o Par.cpp In file included from HTools.h:4, from HTools.cpp:1: Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -873,12 +933,6 @@ Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 194 | static map > > Read(char*) throw (string&); | ^~~~~ -Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 120 | static void ReadZCurve(char *) throw (string &); - | ^~~~~ -Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 121 | static void ReadNullFreq(char *) throw (string &); - | ^~~~~ In file included from HTools.h:5, from HTools.cpp:1: Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -896,16 +950,14 @@ Par.h:40:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 40 | vector&) throw (string&); | ^~~~~ -In file included from TrainSeq.h:5, - from ExpectA.cpp:1: -Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 85 | bool InitLabels(set >&) throw (string&); - | ^~~~~ -Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 194 | static map > > Read(char*) throw (string&); - | ^~~~~ -In file included from TrainSeq.h:6, - from ExpectA.cpp:1: +Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 120 | static void ReadZCurve(char *) throw (string &); + | ^~~~~ +Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 121 | static void ReadNullFreq(char *) throw (string &); + | ^~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Params.o Params.cpp +In file included from Krogh1Best.cpp:1: Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 34 | static void LoadL2L(char*) throw (string&); | ^~~~~ @@ -921,15 +973,6 @@ Par.h:40:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 40 | vector&) throw (string&); | ^~~~~ -In file included from TrainSeq.h:5, - from Load.h:4, - from Par.cpp:4: -Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 85 | bool InitLabels(set >&) throw (string&); - | ^~~~~ -Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 194 | static map > > Read(char*) throw (string&); - | ^~~~~ Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 120 | static void ReadZCurve(char *) throw (string &); | ^~~~~ @@ -943,23 +986,9 @@ Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 194 | static map > > Read(char*) throw (string&); | ^~~~~ -Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 120 | static void ReadZCurve(char *) throw (string &); - | ^~~~~ -Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 121 | static void ReadNullFreq(char *) throw (string &); - | ^~~~~ In file included from TrainSeq.h:5, - from GradientDescent.cpp:2: -Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 85 | bool InitLabels(set >&) throw (string&); - | ^~~~~ -Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 194 | static map > > Read(char*) throw (string&); - | ^~~~~ -In file included from TrainSeq.h:5, - from Eval.h:11, - from Eval.cpp:6: + from Load.h:4, + from Load.cpp:1: Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 85 | bool InitLabels(set >&) throw (string&); | ^~~~~ @@ -967,8 +996,8 @@ 194 | static map > > Read(char*) throw (string&); | ^~~~~ In file included from TrainSeq.h:6, - from Eval.h:11, - from Eval.cpp:6: + from Load.h:4, + from Load.cpp:1: Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 34 | static void LoadL2L(char*) throw (string&); | ^~~~~ @@ -981,40 +1010,16 @@ Par.h:37:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 37 | static void LoadConnect(char*) throw (string&); | ^~~~~ -In file included from TrainSeq.h:5, - from proftmb.cpp:15: -Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 85 | bool InitLabels(set >&) throw (string&); - | ^~~~~ Par.h:40:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 40 | vector&) throw (string&); | ^~~~~ -Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 194 | static map > > Read(char*) throw (string&); - | ^~~~~ -In file included from proftmb.cpp:18: -HMMOutput.h:21:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 21 | void DisplayArch(ostream&,Par&,uint,char* =""); - | ^ -HMMOutput.h:24:44: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 24 | void PrintEmit(ostream&,Par&,uint,char* =""); - | ^ -In file included from proftmb.cpp:20: -Zscore.h:9:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 9 | Z_Calibrate(set >&,int,double) throw (string&); - | ^~~~~ -In file included from Forward.cpp:1: -Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 85 | bool InitLabels(set >&) throw (string&); - | ^~~~~ -Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 194 | static map > > Read(char*) throw (string&); - | ^~~~~ -In file included from proftmb.cpp:22: -Eval.h:48:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 48 | float RelativeEntropy(vector& A, vector& B) throw (char *); - | ^~~~~ -In file included from Forward.cpp:2: +Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 120 | static void ReadZCurve(char *) throw (string &); + | ^~~~~ +Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 121 | static void ReadNullFreq(char *) throw (string &); + | ^~~~~ +In file included from Par.cpp:1: Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 34 | static void LoadL2L(char*) throw (string&); | ^~~~~ @@ -1030,59 +1035,122 @@ Par.h:40:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 40 | vector&) throw (string&); | ^~~~~ -proftmb.cpp:68:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 68 | const char *, double, Par&, const char*, bool) throw (string &); - | ^~~~~ Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 120 | static void ReadZCurve(char *) throw (string &); | ^~~~~ Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 121 | static void ReadNullFreq(char *) throw (string &); | ^~~~~ -In file included from Eval.cpp:6: -Eval.h:48:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 48 | float RelativeEntropy(vector& A, vector& B) throw (char *); - | ^~~~~ +In file included from Params.cpp:1: +Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 34 | static void LoadL2L(char*) throw (string&); + | ^~~~~ +Par.h:35:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 35 | static void LoadL2A(char*) throw (string&); + | ^~~~~ +Par.h:36:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 36 | static void LoadA2E(char*) throw (string&); + | ^~~~~ +Par.h:37:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 37 | static void LoadConnect(char*) throw (string&); + | ^~~~~ +Par.h:40:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 40 | vector&) throw (string&); + | ^~~~~ Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 120 | static void ReadZCurve(char *) throw (string &); | ^~~~~ Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 121 | static void ReadNullFreq(char *) throw (string &); | ^~~~~ -proftmb.cpp:273:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 273 | const char *datfile, double cut, Par& m, const char *name, bool multiQ) throw (string &) { - | ^~~~~ -Eval.cpp:654:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 654 | float RelativeEntropy(vector& A, vector& B) throw (char *){ - | ^~~~~ +In file included from TrainSeq.h:5, + from Load.h:4, + from Par.cpp:4: +Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 85 | bool InitLabels(set >&) throw (string&); + | ^~~~~ +Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 194 | static map > > Read(char*) throw (string&); + | ^~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Posterior.o Posterior.cpp Par.cpp:263:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 263 | void Par::LoadConnect(char* cf) throw (string&){ | ^~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Seq.o Seq.cpp Par.cpp:348:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 348 | void Par::LoadL2L(char* l2lfile) throw (string&){ | ^~~~~ Par.cpp:415:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 415 | void Par::LoadL2A(char* l2afile) throw (string&){ | ^~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Sov.o Sov.cpp Par.cpp:554:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 554 | void Par::LoadA2E(char* a2efile) throw (string&){ | ^~~~~ Par.cpp:652:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 652 | vector& redux) throw (string&){ | ^~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o structs.o structs.cpp Par.cpp:742:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 742 | void Par::ReadZCurve(char *ifile) throw (string&){ | ^~~~~ Par.cpp:763:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 763 | void Par::ReadNullFreq(char *ifile) throw (string&){ | ^~~~~ +In file included from Posterior.cpp:1: +Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 85 | bool InitLabels(set >&) throw (string&); + | ^~~~~ +Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 194 | static map > > Read(char*) throw (string&); + | ^~~~~ +In file included from Posterior.cpp:2: +Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 34 | static void LoadL2L(char*) throw (string&); + | ^~~~~ +Par.h:35:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 35 | static void LoadL2A(char*) throw (string&); + | ^~~~~ +Par.h:36:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 36 | static void LoadA2E(char*) throw (string&); + | ^~~~~ +Par.h:37:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 37 | static void LoadConnect(char*) throw (string&); + | ^~~~~ +Par.h:40:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 40 | vector&) throw (string&); + | ^~~~~ +Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 120 | static void ReadZCurve(char *) throw (string &); + | ^~~~~ +Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 121 | static void ReadNullFreq(char *) throw (string &); + | ^~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Regularization.o Regularization.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Seq.o Seq.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Sov.o Sov.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o structs.o structs.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Tally.o Tally.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Tools.o Tools.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o TrainSeq.o TrainSeq.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Viterbi.o Viterbi.cpp +In file included from Regularization.cpp:7: +Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 34 | static void LoadL2L(char*) throw (string&); + | ^~~~~ +Par.h:35:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 35 | static void LoadL2A(char*) throw (string&); + | ^~~~~ +Par.h:36:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 36 | static void LoadA2E(char*) throw (string&); + | ^~~~~ +Par.h:37:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 37 | static void LoadConnect(char*) throw (string&); + | ^~~~~ +Par.h:40:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 40 | vector&) throw (string&); + | ^~~~~ +Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 120 | static void ReadZCurve(char *) throw (string &); + | ^~~~~ +Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 121 | static void ReadNullFreq(char *) throw (string &); + | ^~~~~ In file included from structs.cpp:2: Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 34 | static void LoadL2L(char*) throw (string&); @@ -1134,7 +1202,6 @@ Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 121 | static void ReadNullFreq(char *) throw (string &); | ^~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Zscore.o Zscore.cpp In file included from TrainSeq.h:5, from Tally.cpp:1: Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -1172,15 +1239,20 @@ Seq.cpp:313:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 313 | map Seq::Read(char* file) throw (string&){ | ^~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o TrainSeq.o TrainSeq.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Viterbi.o Viterbi.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proftmb-1.1.12=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Zscore.o Zscore.cpp sed -e 's|__pkgdatadir__|/usr/share/proftmb|g;s|__datadir__|/usr/share|g;s|__PACKAGE__|proftmb|g;' < proftmb_example.txt.raw > proftmb_example.txt -In file included from Viterbi.cpp:1: +In file included from TrainSeq.h:5, + from TrainSeq.cpp:1: Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 85 | bool InitLabels(set >&) throw (string&); | ^~~~~ Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 194 | static map > > Read(char*) throw (string&); | ^~~~~ -In file included from Viterbi.cpp:2: +In file included from TrainSeq.h:6, + from TrainSeq.cpp:1: Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 34 | static void LoadL2L(char*) throw (string&); | ^~~~~ @@ -1196,26 +1268,27 @@ Par.h:40:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 40 | vector&) throw (string&); | ^~~~~ +In file included from Zscore.cpp:24: +Zscore.h:9:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 9 | Z_Calibrate(set >&,int,double) throw (string&); + | ^~~~~ Par.h:120:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 120 | static void ReadZCurve(char *) throw (string &); | ^~~~~ Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 121 | static void ReadNullFreq(char *) throw (string &); | ^~~~~ -In file included from Zscore.cpp:24: -Zscore.h:9:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 9 | Z_Calibrate(set >&,int,double) throw (string&); - | ^~~~~ -In file included from TrainSeq.h:5, - from TrainSeq.cpp:1: +Zscore.cpp:36:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 36 | int windowsize,double zmax) throw (string&){ + | ^~~~~ +In file included from Viterbi.cpp:1: Seq.h:85:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 85 | bool InitLabels(set >&) throw (string&); | ^~~~~ Seq.h:194:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 194 | static map > > Read(char*) throw (string&); | ^~~~~ -In file included from TrainSeq.h:6, - from TrainSeq.cpp:1: +In file included from Viterbi.cpp:2: Par.h:34:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 34 | static void LoadL2L(char*) throw (string&); | ^~~~~ @@ -1237,9 +1310,6 @@ Par.h:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 121 | static void ReadNullFreq(char *) throw (string &); | ^~~~~ -Zscore.cpp:36:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 36 | int windowsize,double zmax) throw (string&){ - | ^~~~~ rm -f libhmm.a ar cru libhmm.a Backward.o BaumWelch.o Eval.o ExpectA.o ExpectC.o Forward.o GradientDescent.o HMMEval.o HMMOutput.o HTools.o Krogh1Best.o Load.o Output.o Par.o Params.o Posterior.o Regularization.o Seq.o Sov.o structs.o Tally.o Tools.o TrainSeq.o Viterbi.o Zscore.o ar: `u' modifier ignored since `D' is the default (see `U') @@ -1252,7 +1322,7 @@ make[2]: Leaving directory '/build/proftmb-1.1.12' make[1]: Leaving directory '/build/proftmb-1.1.12' dh_auto_test - make -j18 check VERBOSE=1 + make -j10 check VERBOSE=1 make[1]: Entering directory '/build/proftmb-1.1.12' Making check in examples make[2]: Entering directory '/build/proftmb-1.1.12/examples' @@ -1268,21 +1338,21 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j18 install DESTDIR=/build/proftmb-1.1.12/debian/proftmb AM_UPDATE_INFO_DIR=no + make -j10 install DESTDIR=/build/proftmb-1.1.12/debian/proftmb AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/proftmb-1.1.12' Making install in examples make[2]: Entering directory '/build/proftmb-1.1.12/examples' make[3]: Entering directory '/build/proftmb-1.1.12/examples' make[3]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/proftmb-1.1.12/debian/proftmb/usr/share/doc/proftmb/examples' + /usr/bin/mkdir -p '/build/proftmb-1.1.12/debian/proftmb/usr/share/doc/proftmb/examples' /usr/bin/install -c -m 644 16761001.Q 1a0s_P.f.1.Q 1af6_A.f.2.Q 1bt9_A.f.3.Q 1fep_A.f.4.Q 1prn.f.5.Q 1qd5_A.f.6.Q 1qj9_A.f.7.Q 1qjp_A.f.8.Q CADN_HUMAN.Q example.Q example_dat.txt example_proftmb_pretty.txt example_proftmb_tabular.txt YQIB_ECOLI.Q '/build/proftmb-1.1.12/debian/proftmb/usr/share/doc/proftmb/examples' make[3]: Leaving directory '/build/proftmb-1.1.12/examples' make[2]: Leaving directory '/build/proftmb-1.1.12/examples' Making install in src make[2]: Entering directory '/build/proftmb-1.1.12/src' make[3]: Entering directory '/build/proftmb-1.1.12/src' - /bin/mkdir -p '/build/proftmb-1.1.12/debian/proftmb/usr/bin' - /bin/mkdir -p '/build/proftmb-1.1.12/debian/proftmb/usr/share/man/man1' + /usr/bin/mkdir -p '/build/proftmb-1.1.12/debian/proftmb/usr/bin' + /usr/bin/mkdir -p '/build/proftmb-1.1.12/debian/proftmb/usr/share/man/man1' /usr/bin/install -c proftmb '/build/proftmb-1.1.12/debian/proftmb/usr/bin' /usr/bin/install -c -m 644 proftmb.1 '/build/proftmb-1.1.12/debian/proftmb/usr/share/man/man1' make[3]: Leaving directory '/build/proftmb-1.1.12/src' @@ -1291,7 +1361,7 @@ make[3]: Entering directory '/build/proftmb-1.1.12' make[3]: Nothing to be done for 'install-exec-am'. mkdir -p "/build/proftmb-1.1.12/debian/proftmb/usr/share/proftmb" - /bin/mkdir -p '/build/proftmb-1.1.12/debian/proftmb/usr/share/doc/proftmb' + /usr/bin/mkdir -p '/build/proftmb-1.1.12/debian/proftmb/usr/share/doc/proftmb' cp "."/input/* "/build/proftmb-1.1.12/debian/proftmb/usr/share/proftmb/" /usr/bin/install -c -m 644 README '/build/proftmb-1.1.12/debian/proftmb/usr/share/doc/proftmb' rm -rf `find "/build/proftmb-1.1.12/debian/proftmb/usr/share/proftmb" -name .svn` @@ -1332,12 +1402,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/837/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/837/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/851 and its subdirectories -I: Current time: Tue Jul 19 15:39:06 -12 2022 -I: pbuilder-time-stamp: 1658288346 +I: removing directory /srv/workspace/pbuilder/837 and its subdirectories +I: Current time: Thu Jun 17 11:20:54 +14 2021 +I: pbuilder-time-stamp: 1623878454