I: pbuilder: network access will be disabled during build I: Current time: Sat Jun 22 10:30:17 +14 2024 I: pbuilder-time-stamp: 1719001817 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. 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 [ghmm_0.9~rc3-4.dsc] I: copying [./ghmm_0.9~rc3.orig.tar.gz] I: copying [./ghmm_0.9~rc3-4.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Jan 25 09:31:00 2021 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./ghmm_0.9~rc3-4.dsc: no acceptable signature found dpkg-source: info: extracting ghmm in ghmm-0.9~rc3 dpkg-source: info: unpacking ghmm_0.9~rc3.orig.tar.gz dpkg-source: info: unpacking ghmm_0.9~rc3-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying buildError.patch dpkg-source: info: applying pythonpaths.patch dpkg-source: info: applying fix_libxml2_config.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying python3_build_system.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2724077/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 22 10:30 /bin/sh -> /bin/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/2724077/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2724077/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=baf59777f63647c48a25911e275aa777 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2724077 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.jCTWwd3r/pbuilderrc_BZEZ --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.jCTWwd3r/b2 --logfile b2/build.log --extrapackages usrmerge ghmm_0.9~rc3-4.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 24 2023 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 2023 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 2023 more -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed lrwxrwxrwx 1 root root 9 Jun 22 10:30 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 2023 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/2724077/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), d-shlibs, python3-dev, pkg-config, libxml2-dev, libgsl-dev, libatlas-base-dev, liblapack-dev, zlib1g-dev, swig dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 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-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libxml2-dev; however: Package libxml2-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on libatlas-base-dev; however: Package libatlas-base-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on swig; however: Package swig 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: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} d-shlibs{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} libarchive-zip-perl{a} libatlas-base-dev{a} libatlas3-base{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libicu-dev{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack-dev{a} liblapack3{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpkgconf3{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libxml2-dev{a} m4{a} man-db{a} media-types{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} swig{a} swig4.0{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 71 newly installed, 0 to remove and 0 not upgraded. Need to get 63.6 MB of archives. After unpacking 277 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 d-shlibs all 0.104 [18.6 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 icu-devtools amd64 72.1-3 [206 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libatlas3-base amd64 3.10.3-13 [3305 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libatlas-base-dev amd64 3.10.3-13 [3510 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libgslcblas0 amd64 2.7.1+dfsg-3+b1 [116 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libgsl27 amd64 2.7.1+dfsg-3+b1 [948 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libgsl-dev amd64 2.7.1+dfsg-3+b1 [1152 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libicu-dev amd64 72.1-3 [10.3 MB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 liblapack-dev amd64 3.11.0-2 [4631 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6 [1988 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6 [4738 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libxml2-dev amd64 2.9.14+dfsg-1.2 [781 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6 [615 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 swig4.0 amd64 4.1.0-0.2 [1388 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 swig all 4.1.0-0.2 [321 kB] Fetched 63.6 MB in 2s (41.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. 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Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (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 ... 20346 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... 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Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up libgsl27:amd64 (2.7.1+dfsg-3+b1) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:amd64 (1.8.1-1) ... Setting up libexpat1-dev:amd64 (2.5.0-1) ... Setting up autopoint (0.21-12) ... Setting up icu-devtools (72.1-3) ... Setting up d-shlibs (0.104) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up swig4.0 (4.1.0-0.2) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libicu-dev:amd64 (72.1-3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libgsl-dev (2.7.1+dfsg-3+b1) ... Setting up swig (4.1.0-0.2) ... Setting up libatlas3-base:amd64 (3.10.3-13) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libtool (2.4.7-5) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libatlas-base-dev:amd64 (3.10.3-13) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/atlas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/atlas/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up pkgconf:amd64 (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libxml2-dev:amd64 (2.9.14+dfsg-1.2) ... Setting up pkg-config:amd64 (1.8.1-1) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up liblapack3:amd64 (3.11.0-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up liblapack-dev:amd64 (3.11.0-2) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libpython3.11:amd64 (3.11.2-6) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libpython3.11-dev:amd64 (3.11.2-6) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-distutils (3.11.2-3) ... Setting up libpython3-dev:amd64 (3.11.2-1+b1) ... Setting up python3.11-dev (3.11.2-6) ... Setting up python3-dev (3.11.2-1+b1) ... Processing triggers for libc-bin (2.36-9) ... 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... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/2724077/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/2724077/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/ghmm-0.9~rc3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../ghmm_0.9~rc3-4_source.changes dpkg-buildpackage: info: source package ghmm dpkg-buildpackage: info: source version 0.9~rc3-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/ghmm-0.9~rc3' if [ -r Makefile ]; then /usr/bin/make clean; fi find . -name Makefile -delete find . \( -name "*.o" -o -name "*.lo" \) -delete rm -f ghmmwrapper/ghmmwrapper.py ghmmwrapper/ghmmwrapper_wrap.c rm -rf HMMEd/build/ ghmmwrapper/build/ rm -f config.h config.log config.status rm -f libtool stamp-h1 tests/chmm_test.2JNcXz rm -f tools/ghmm-config rm -rf ghmm/.deps/ tests/.deps/ tools/.deps/ make[1]: Leaving directory '/build/ghmm-0.9~rc3' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.in, libtoolize: and rerunning libtoolize and aclocal. libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am. aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:47: warning: 'AM_CONFIG_HEADER': this macro is obsolete. configure.in:47: You should use the 'AC_CONFIG_HEADERS' macro instead. ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:9833: AM_CONFIG_HEADER is expanded from... configure.in:47: the top level configure.in:63: warning: The macro `AM_PROG_LIBTOOL' is obsolete. configure.in:63: You should run autoupdate. aclocal.m4:123: AM_PROG_LIBTOOL is expanded from... configure.in:63: the top level configure.in:75: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:75: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.in:75: the top level configure.in:93: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:93: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.in:93: the top level configure.in:104: warning: The macro `AC_LANG_C' is obsolete. configure.in:104: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... configure.in:104: the top level configure.in:111: warning: The macro `AC_HEADER_STDC' is obsolete. configure.in:111: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.in:111: the top level configure.in:117: warning: The macro `AC_HEADER_TIME' is obsolete. configure.in:117: You should run autoupdate. ./lib/autoconf/headers.m4:743: AC_HEADER_TIME is expanded from... configure.in:117: the top level configure.in:136: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:136: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.in:136: the top level configure.in:135: warning: The macro `AC_TRY_RUN' is obsolete. configure.in:135: You should run autoupdate. ./lib/autoconf/general.m4:2997: AC_TRY_RUN is expanded from... acinclude.m4:10: AM_PATH_GSL is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.in:135: the top level configure.in:135: warning: The macro `AC_TRY_LINK' is obsolete. configure.in:135: You should run autoupdate. ./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from... acinclude.m4:10: AM_PATH_GSL is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.in:135: the top level configure.in:135: warning: The macro `AC_TRY_COMPILE' is obsolete. configure.in:135: You should run autoupdate. ./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.in:135: the top level configure.in:135: warning: The macro `AC_TRY_LINK' is obsolete. configure.in:135: You should run autoupdate. ./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.in:135: the top level configure.in:194: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:194: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.in:194: the top level configure.in:207: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:207: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.in:207: the top level configure.in:206: warning: The macro `AC_TRY_COMPILE' is obsolete. configure.in:206: You should run autoupdate. ./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.in:206: the top level configure.in:323: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:323: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1553: AC_ARG_WITH is expanded from... configure.in:323: the top level configure.in:354: warning: AC_OUTPUT should be used without arguments. configure.in:354: You should run autoupdate. autoheader: warning: autoconf input should be named 'configure.ac', not 'configure.in' automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:62: installing './compile' configure.in:49: installing './missing' ghmm/Makefile.am:77: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' ghmm/Makefile.am: installing './depcomp' tests/Makefile.am:51: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') parallel-tests: installing './test-driver' tools/Makefile.am:48: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') debian/rules override_dh_auto_configure make[1]: Entering directory '/build/ghmm-0.9~rc3' dh_auto_configure -- --enable-atlas ./configure --build=x86_64-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/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-atlas checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/time.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gawk... (cached) mawk checking for doxygen... no checking for rm... /usr/bin/rm checking for pkg-config... /usr/bin/pkg-config checking for expect... no checking for runtest... no configure: obsolete features disabled configure: unsupported features disabled checking for pthread_join in -lpthread... yes checking for egrep... (cached) /usr/bin/grep -E checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for sqrt in -lm... yes checking for exp in -lm... yes checking for pow in -lm... yes configure: "not using gsl" checking for cos in -lm... yes configure: "not using diagonal covariance matrix hack" checking for lapack with pkg-config... yes checking for clapack_dgetrf in -llapack... yes checking for clapack_dgetri in -llapack... yes checking for clapack_dpotrf in -llapack... yes configure: using internal Mersenne-Twister random number generator checking for python3... /usr/bin/python3 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating ghmm/Makefile config.status: creating ghmm/ghmmconfig.h config.status: creating tools/Makefile config.status: creating tests/Makefile config.status: creating tests/data/Makefile config.status: creating tools/ghmm-config config.status: creating ghmmwrapper/Makefile config.status: creating HMMEd/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands /usr/bin/rm: cannot remove 'libtoolT': No such file or directory make[1]: Leaving directory '/build/ghmm-0.9~rc3' dh_auto_build make -j16 make[1]: Entering directory '/build/ghmm-0.9~rc3' make all-recursive make[2]: Entering directory '/build/ghmm-0.9~rc3' Making all in ghmm make[3]: Entering directory '/build/ghmm-0.9~rc3/ghmm' Making all in . make[4]: Entering directory '/build/ghmm-0.9~rc3/ghmm' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o rng.lo rng.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o randvar.lo randvar.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o matrixop.lo matrixop.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o gauss_tail.lo gauss_tail.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o mes.lo mes.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o ghmm_internals.lo ghmm_internals.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o mprintf.lo mprintf.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o vector.lo vector.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o matrix.lo matrix.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o scanner.lo scanner.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o linkedlist.lo linkedlist.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sequence.lo sequence.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o psequence.lo psequence.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o xmlreader.lo xmlreader.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o xmlwriter.lo xmlwriter.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o model.lo model.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c randvar.c -fPIC -DPIC -o .libs/randvar.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c vector.c -fPIC -DPIC -o .libs/vector.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c mes.c -fPIC -DPIC -o .libs/mes.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c mprintf.c -fPIC -DPIC -o .libs/mprintf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c psequence.c -fPIC -DPIC -o .libs/psequence.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c matrixop.c -fPIC -DPIC -o .libs/matrixop.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c scanner.c -fPIC -DPIC -o .libs/scanner.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c linkedlist.c -fPIC -DPIC -o .libs/linkedlist.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c xmlreader.c -fPIC -DPIC -o .libs/xmlreader.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c gauss_tail.c -fPIC -DPIC -o .libs/gauss_tail.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c rng.c -fPIC -DPIC -o .libs/rng.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c ghmm_internals.c -fPIC -DPIC -o .libs/ghmm_internals.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c matrix.c -fPIC -DPIC -o .libs/matrix.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c model.c -fPIC -DPIC -o .libs/model.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sequence.c -fPIC -DPIC -o .libs/sequence.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c xmlwriter.c -fPIC -DPIC -o .libs/xmlwriter.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c scanner.c -o scanner.o >/dev/null 2>&1 psequence.c: In function 'ghmm_dpseq_free': psequence.c:78:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 78 | mes_check_ptr(seq, return(-1)); | ^ ghmm_internals.c: In function 'ighmm_log_out': ghmm_internals.c:69:17: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] 69 | message = strncat(message, error_str, slen); | ^ In function 'process_external_log', inlined from 'ighmm_log_out' at ghmm_internals.c:83:5: ghmm_internals.c:64:14: note: length computed here 64 | int slen = strlen(error_str); | ^~~~~~~~~~~~~~~~~ rng.c: In function 'ghmm_rng_init': rng.c:67:3: warning: argument 2 null where non-null expected [-Wnonnull] 67 | initstate(1, ighmm_rng_state, sizeof(ghmm_rng_state_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from rng.c:40: /usr/include/stdlib.h:411:14: note: in a call to function 'initstate' declared 'nonnull' 411 | extern char *initstate (unsigned int __seed, char *__statebuf, | ^~~~~~~~~ /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o foba.lo foba.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c rng.c -o rng.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c ghmm_internals.c -o ghmm_internals.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c matrixop.c -o matrixop.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c vector.c -o vector.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c linkedlist.c -o linkedlist.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c gauss_tail.c -o gauss_tail.o >/dev/null 2>&1 sequence.c: In function 'ghmm_dseq_subseq_free': sequence.c:685:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 685 | mes_check_ptr (sq, return (-1)); | ^ sequence.c: In function 'ghmm_cseq_subseq_free': sequence.c:715:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 715 | mes_check_ptr (sqd, return (-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c psequence.c -o psequence.o >/dev/null 2>&1 matrix.c: In function 'ighmm_cmatrix_stat_free': matrix.c:176:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 176 | mes_check_ptr (matrix, return (-1)); | ^ matrix.c: In function 'ighmm_dmatrix_stat_free': matrix.c:214:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 214 | mes_check_ptr (matrix, return (-1)); | ^ matrix.c: In function 'ighmm_cmatrix_3d_free': matrix.c:270:35: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 270 | mes_check_ptr(matrix, return(-1)); | ^ matrix.c: In function 'ighmm_cmatrix_free': matrix.c:285:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 285 | mes_check_ptr(matrix, return (-1)); | ^ matrix.c: In function 'ighmm_dmatrix_free': matrix.c:343:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 343 | mes_check_ptr (matrix, return (-1)); | ^ model.c: In function 'ghmm_dmodel_free': sequence.c: In function 'ghmm_dseq_free': matrix.c: In function 'ighmm_dmatrix_3d_free': sequence.c:1189:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1189 | mes_check_ptr(sq, return -1); | ^ matrix.c:378:35: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 378 | mes_check_ptr(matrix, return(-1)); | ^ model.c:632:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 632 | mes_check_ptr (mo, return (-1)); | ^ model.c:634:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 634 | mes_check_ptr (m, return (-1)); | ^ sequence.c: In function 'ghmm_cseq_free': sequence.c:1226:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1226 | mes_check_ptr(sqd, return -1); | ^ model.c: In function 'ghmm_dstate_clean': model.c:1758:35: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1758 | mes_check_ptr (my_state, return;); | ^ /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o viterbi.lo viterbi.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c foba.c -fPIC -DPIC -o .libs/foba.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c mes.c -o mes.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o reestimate.lo reestimate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c randvar.c -o randvar.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o gradescent.lo gradescent.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o kbest.lo kbest.c foba.c: In function 'ghmm_dmodel_backward': foba.c:286:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 286 | mes_check_0 (scale[t], goto STOP); | ^ foba.c: In function 'ghmm_dmodel_label_backward': foba.c:848:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 848 | mes_check_0 (scale[t], goto STOP); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c matrix.c -o matrix.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o discrime.lo discrime.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o modelutil.lo modelutil.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c viterbi.c -fPIC -DPIC -o .libs/viterbi.o /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o cluster.lo cluster.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c gradescent.c -fPIC -DPIC -o .libs/gradescent.o viterbi.c: In function 'viterbi_free': viterbi.c:71:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 71 | mes_check_ptr(v, return -1); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c kbest.c -fPIC -DPIC -o .libs/kbest.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c reestimate.c -fPIC -DPIC -o .libs/reestimate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c discrime.c -fPIC -DPIC -o .libs/discrime.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c mprintf.c -o mprintf.o >/dev/null 2>&1 reestimate.c: In function 'reestimate_free': reestimate.c:79:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 79 | mes_check_ptr (r, return (-1)); | ^ reestimate.c: In function 'reestimate_setlambda': reestimate.c:306:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 306 | mes_check_0 (r->pi_denom, goto STOP); | ^ /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o root_finder.lo root_finder.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o smodel.lo smodel.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c modelutil.c -fPIC -DPIC -o .libs/modelutil.o /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sfoba.lo sfoba.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c cluster.c -fPIC -DPIC -o .libs/cluster.o modelutil.c: In function 'topo_free': modelutil.c:89:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 89 | mes_check_ptr (v, return (-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c cluster.c -o cluster.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c viterbi.c -o viterbi.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sviterbi.lo sviterbi.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c modelutil.c -o modelutil.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c smodel.c -fPIC -DPIC -o .libs/smodel.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sfoba.c -fPIC -DPIC -o .libs/sfoba.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c xmlwriter.c -o xmlwriter.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c root_finder.c -fPIC -DPIC -o .libs/root_finder.o smodel.c: In function 'ghmm_cmodel_free': smodel.c:765:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 765 | mes_check_ptr (smo, return (-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sequence.c -o sequence.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c gradescent.c -o gradescent.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sreestimate.lo sreestimate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sviterbi.c -fPIC -DPIC -o .libs/sviterbi.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c root_finder.c -o root_finder.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o scluster.lo scluster.c sviterbi.c: In function 'sviterbi_free': sviterbi.c:89:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 89 | mes_check_ptr (v, return (-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c xmlreader.c -o xmlreader.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sgenerate.lo sgenerate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c kbest.c -o kbest.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sreestimate.c -fPIC -DPIC -o .libs/sreestimate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c foba.c -o foba.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o smixturehmm.lo smixturehmm.c sreestimate.c: In function 'sreestimate_free': sreestimate.c:174:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 174 | mes_check_ptr (r, return (-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sviterbi.c -o sviterbi.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c scluster.c -fPIC -DPIC -o .libs/scluster.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c scluster.c -o scluster.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sgenerate.c -fPIC -DPIC -o .libs/sgenerate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c model.c -o model.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o smap_classify.lo smap_classify.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c smixturehmm.c -fPIC -DPIC -o .libs/smixturehmm.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sfoba.c -o sfoba.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sdmodel.lo sdmodel.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c reestimate.c -o reestimate.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c smixturehmm.c -o smixturehmm.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sdfoba.lo sdfoba.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sdviterbi.lo sdviterbi.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o pmodel.lo pmodel.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c smap_classify.c -fPIC -DPIC -o .libs/smap_classify.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c smap_classify.c -o smap_classify.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sdviterbi.c -fPIC -DPIC -o .libs/sdviterbi.o /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o pviterbi.lo pviterbi.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sdmodel.c -fPIC -DPIC -o .libs/sdmodel.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sdfoba.c -fPIC -DPIC -o .libs/sdfoba.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c pmodel.c -fPIC -DPIC -o .libs/pmodel.o /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o pviterbi_propagate.lo pviterbi_propagate.c sdviterbi.c: In function 'sdviterbi_free': sdviterbi.c:111:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 111 | mes_check_ptr (v, return (-1)); | ^ /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o fbgibbs.lo fbgibbs.c pmodel.c: In function 'ghmm_dpmodel_free': pmodel.c:127:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 127 | mes_check_ptr(mo, return(-1)); | ^ sdmodel.c: In function 'ghmm_dsmodel_free': sdmodel.c:211:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 211 | mes_check_ptr (mo, return (-1)); | ^ sdfoba.c: In function 'ghmm_dsmodel_backward': sdfoba.c:336:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 336 | mes_check_0 (scale[t], goto STOP); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c smodel.c -o smodel.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c pviterbi.c -fPIC -DPIC -o .libs/pviterbi.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c pmodel.c -o pmodel.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sgenerate.c -o sgenerate.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o cfbgibbs.lo cfbgibbs.c pviterbi.c: In function 'pviterbi_free': pviterbi.c:151:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 151 | mes_check_ptr(v, return(-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c fbgibbs.c -fPIC -DPIC -o .libs/fbgibbs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c pviterbi_propagate.c -fPIC -DPIC -o .libs/pviterbi_propagate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sdfoba.c -o sdfoba.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sreestimate.c -o sreestimate.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sdviterbi.c -o sdviterbi.o >/dev/null 2>&1 pviterbi_propagate.c: In function 'pviterbi_propagate_free': pviterbi_propagate.c:255:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 255 | mes_check_ptr(v, return(-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c cfbgibbs.c -fPIC -DPIC -o .libs/cfbgibbs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c discrime.c -o discrime.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c pviterbi.c -o pviterbi.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sdmodel.c -o sdmodel.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c fbgibbs.c -o fbgibbs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c pviterbi_propagate.c -o pviterbi_propagate.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c cfbgibbs.c -o cfbgibbs.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=link gcc -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -version-info 1:0:0 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o libghmm.la -rpath /usr/lib/x86_64-linux-gnu rng.lo randvar.lo matrixop.lo gauss_tail.lo mes.lo ghmm_internals.lo mprintf.lo vector.lo matrix.lo scanner.lo linkedlist.lo sequence.lo psequence.lo xmlreader.lo xmlwriter.lo model.lo foba.lo viterbi.lo reestimate.lo gradescent.lo kbest.lo discrime.lo modelutil.lo cluster.lo root_finder.lo smodel.lo sfoba.lo sviterbi.lo sreestimate.lo scluster.lo sgenerate.lo smixturehmm.lo smap_classify.lo sdmodel.lo sdfoba.lo sdviterbi.lo pmodel.lo pviterbi.lo pviterbi_propagate.lo fbgibbs.lo cfbgibbs.lo -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -shared -fPIC -DPIC .libs/rng.o .libs/randvar.o .libs/matrixop.o .libs/gauss_tail.o .libs/mes.o .libs/ghmm_internals.o .libs/mprintf.o .libs/vector.o .libs/matrix.o .libs/scanner.o .libs/linkedlist.o .libs/sequence.o .libs/psequence.o .libs/xmlreader.o .libs/xmlwriter.o .libs/model.o .libs/foba.o .libs/viterbi.o .libs/reestimate.o .libs/gradescent.o .libs/kbest.o .libs/discrime.o .libs/modelutil.o .libs/cluster.o .libs/root_finder.o .libs/smodel.o .libs/sfoba.o .libs/sviterbi.o .libs/sreestimate.o .libs/scluster.o .libs/sgenerate.o .libs/smixturehmm.o .libs/smap_classify.o .libs/sdmodel.o .libs/sdfoba.o .libs/sdviterbi.o .libs/pmodel.o .libs/pviterbi.o .libs/pviterbi_propagate.o .libs/fbgibbs.o .libs/cfbgibbs.o -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -Wl,-soname -Wl,libghmm.so.1 -o .libs/libghmm.so.1.0.0 libtool: link: (cd ".libs" && rm -f "libghmm.so.1" && ln -s "libghmm.so.1.0.0" "libghmm.so.1") libtool: link: (cd ".libs" && rm -f "libghmm.so" && ln -s "libghmm.so.1.0.0" "libghmm.so") libtool: link: ar cr .libs/libghmm.a rng.o randvar.o matrixop.o gauss_tail.o mes.o ghmm_internals.o mprintf.o vector.o matrix.o scanner.o linkedlist.o sequence.o psequence.o xmlreader.o xmlwriter.o model.o foba.o viterbi.o reestimate.o gradescent.o kbest.o discrime.o modelutil.o cluster.o root_finder.o smodel.o sfoba.o sviterbi.o sreestimate.o scluster.o sgenerate.o smixturehmm.o smap_classify.o sdmodel.o sdfoba.o sdviterbi.o pmodel.o pviterbi.o pviterbi_propagate.o fbgibbs.o cfbgibbs.o libtool: link: ranlib .libs/libghmm.a libtool: link: ( cd ".libs" && rm -f "libghmm.la" && ln -s "../libghmm.la" "libghmm.la" ) make[4]: Leaving directory '/build/ghmm-0.9~rc3/ghmm' make[3]: Leaving directory '/build/ghmm-0.9~rc3/ghmm' Making all in tools make[3]: Entering directory '/build/ghmm-0.9~rc3/tools' make all-recursive make[4]: Entering directory '/build/ghmm-0.9~rc3/tools' Making all in . make[5]: Entering directory '/build/ghmm-0.9~rc3/tools' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o probdist.o probdist.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o cluster.o cluster.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o scluster.o scluster.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o smix_hmm.o smix_hmm.c /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o smix_hmm smix_hmm.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o smix_hmm smix_hmm.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 make[5]: Leaving directory '/build/ghmm-0.9~rc3/tools' make[4]: Leaving directory '/build/ghmm-0.9~rc3/tools' make[3]: Leaving directory '/build/ghmm-0.9~rc3/tools' Making all in tests make[3]: Entering directory '/build/ghmm-0.9~rc3/tests' Making all in data make[4]: Entering directory '/build/ghmm-0.9~rc3/tests/data' Making all in . make[5]: Entering directory '/build/ghmm-0.9~rc3/tests/data' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/build/ghmm-0.9~rc3/tests/data' make[4]: Leaving directory '/build/ghmm-0.9~rc3/tests/data' make[4]: Entering directory '/build/ghmm-0.9~rc3/tests' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o randvar_test.o randvar_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o root_finder_test.o root_finder_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o coin_toss_test.o coin_toss_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o two_states_three_symbols.o two_states_three_symbols.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o libxml-test.o libxml-test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o chmm.o chmm.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o chmm_test.o chmm_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o shmm_viterbi_test.o shmm_viterbi_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o test_gsl_ran_gaussian_tail.o test_gsl_ran_gaussian_tail.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sequences_test.o sequences_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sequences_old_format.o sequences_old_format.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o label_higher_order_test.o label_higher_order_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o read_fa.o read_fa.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o mcmc.o mcmc.c /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o test_gsl_ran_gaussian_tail test_gsl_ran_gaussian_tail.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sequences_old_format sequences_old_format.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 mcmc.c: In function 'main': mcmc.c:144:3: warning: implicit declaration of function 'init_priors' [-Wimplicit-function-declaration] 144 | init_priors(mo, &pA, &pB, &pPi); | ^~~~~~~~~~~ mcmc.c:146:15: warning: implicit declaration of function 'ghmm_dmodel_cfbgibbs'; did you mean 'ghmm_dmodel_logp'? [-Wimplicit-function-declaration] 146 | int * Q = ghmm_dmodel_cfbgibbs(mo, my_output, | ^~~~~~~~~~~~~~~~~~~~ | ghmm_dmodel_logp mcmc.c:146:15: warning: initialization of 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] mcmc.c:148:108: warning: passing argument 4 of 'ghmm_dmodel_viterbi_logp' makes pointer from integer without a cast [-Wint-conversion] 148 | printf("viterbi prob mcmc%f \n", ghmm_dmodel_viterbi_logp(mo, my_output->seq[0], my_output->seq_len[0], Q[0])); | ~^~~ | | | int In file included from mcmc.c:13: ../ghmm/viterbi.h:75:76: note: expected 'int *' but argument is of type 'int' 75 | double ghmm_dmodel_viterbi_logp (ghmm_dmodel * mo, int *o, int len, int *state_seq); | ~~~~~^~~~~~~~~ /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o two_states_three_symbols two_states_three_symbols.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o shmm_viterbi_test shmm_viterbi_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o libxml-test libxml-test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sequences_test sequences_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o chmm_test chmm_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o chmm chmm.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o randvar_test randvar_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o coin_toss_test coin_toss_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o mcmc mcmc.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o read_fa read_fa.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o label_higher_order_test label_higher_order_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o sequences_old_format sequences_old_format.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o test_gsl_ran_gaussian_tail test_gsl_ran_gaussian_tail.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o shmm_viterbi_test shmm_viterbi_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o libxml-test libxml-test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o chmm_test chmm_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o sequences_test sequences_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o randvar_test randvar_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o two_states_three_symbols two_states_three_symbols.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o chmm chmm.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o mcmc mcmc.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o coin_toss_test coin_toss_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o label_higher_order_test label_higher_order_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o read_fa read_fa.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 make[4]: Leaving directory '/build/ghmm-0.9~rc3/tests' make[3]: Leaving directory '/build/ghmm-0.9~rc3/tests' Making all in ghmmwrapper make[3]: Entering directory '/build/ghmm-0.9~rc3/ghmmwrapper' Making all in . make[4]: Entering directory '/build/ghmm-0.9~rc3/ghmmwrapper' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/ghmm-0.9~rc3/ghmmwrapper' /usr/bin/python3 setup.py build /build/ghmm-0.9~rc3/ghmmwrapper/setup.py:38: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup,Extension running build running build_py file ghmmwrapper.py (for module ghmmwrapper) not found creating build creating build/lib.linux-x86_64-3.11 copying ghmm.py -> build/lib.linux-x86_64-3.11 copying ghmmhelper.py -> build/lib.linux-x86_64-3.11 copying modhmmer.py -> build/lib.linux-x86_64-3.11 copying class_change.py -> build/lib.linux-x86_64-3.11 file ghmmwrapper.py (for module ghmmwrapper) not found running build_ext building '_ghmmwrapper' extension swigging ghmmwrapper.i to ghmmwrapper_wrap.c swig -python -o ghmmwrapper_wrap.c ghmmwrapper.i creating build/temp.linux-x86_64-3.11 x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I.. -I/usr/include/python3.11 -c ghmmwrapper_wrap.c -o build/temp.linux-x86_64-3.11/ghmmwrapper_wrap.o -O2 -pipe -Wall ghmmwrapper_wrap.c: In function 'PythonCallBack': ghmmwrapper_wrap.c:3366:9: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] 3366 | PyEval_CallObject(func, arglist); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/python3.11/Python.h:95, from ghmmwrapper_wrap.c:168: /usr/include/python3.11/ceval.h:27:43: note: declared here 27 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ghmmwrapper_wrap.c: In function 'delete_ghmm_alphabet': ghmmwrapper_wrap.c:3567:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 3567 | for(i=0; isize; ++i) | ^ ghmmwrapper_wrap.c: In function 'ghmm_cmodel_getStateName': ghmmwrapper_wrap.c:3820:16: warning: the comparison will always evaluate as 'true' for the pointer operand in 'self->s + (sizetype)(index * 96)' must not be NULL [-Waddress] 3820 | if((self->s + index) && index < self->N) return (self->s + index)->desc; | ^ ghmmwrapper_wrap.c:3820:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3820 | if((self->s + index) && index < self->N) return (self->s + index)->desc; | ^ ghmmwrapper_wrap.c: In function 'ghmm_dbackground_setName': ghmmwrapper_wrap.c:3853:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3853 | if(index < self->n){ | ^ ghmmwrapper_wrap.c: In function 'ghmm_dmodel_getStateName': ghmmwrapper_wrap.c:3901:16: warning: the comparison will always evaluate as 'true' for the pointer operand in 'self->s + (sizetype)(index * 80)' must not be NULL [-Waddress] 3901 | if((self->s + index) && index < self->N) return (self->s + index)->desc; | ^ ghmmwrapper_wrap.c:3901:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3901 | if((self->s + index) && index < self->N) return (self->s + index)->desc; | ^ ghmmwrapper_wrap.c: In function 'int_matrix_alloc': ghmmwrapper_wrap.c:4012:28: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 4012 | for (i=0; iseq_index = seq_index; | ^~ pclasschange.c:96:10: note: object of size 8 allocated by 'calloc' 96 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:98:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 98 | td->threshold = threshold; | ^~ pclasschange.c:96:10: note: object of size 8 allocated by 'calloc' 96 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:99:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 99 | td->offset_x = offset_x; | ^~ pclasschange.c:96:10: note: object of size 8 allocated by 'calloc' 96 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:100:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 100 | td->offset_y = offset_y; | ^~ pclasschange.c:96:10: note: object of size 8 allocated by 'calloc' 96 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c: In function 'set_to_gt_sum': pclasschange.c:112:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 112 | td->seq_index = seq_index; | ^~ pclasschange.c:111:10: note: object of size 8 allocated by 'calloc' 111 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:113:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 113 | td->threshold = threshold; | ^~ pclasschange.c:111:10: note: object of size 8 allocated by 'calloc' 111 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:114:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 114 | td->offset_x = offset_x; | ^~ pclasschange.c:111:10: note: object of size 8 allocated by 'calloc' 111 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:115:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 115 | td->offset_y = offset_y; | ^~ pclasschange.c:111:10: note: object of size 8 allocated by 'calloc' 111 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c: In function 'set_to_boolean_and': pclasschange.c:127:7: warning: array subscript 'boolean_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 127 | td->seq_index = seq_index; | ^~ pclasschange.c:126:10: note: object of size 8 allocated by 'calloc' 126 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:128:7: warning: array subscript 'boolean_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 128 | td->offset_x = offset_x; | ^~ pclasschange.c:126:10: note: object of size 8 allocated by 'calloc' 126 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:129:7: warning: array subscript 'boolean_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 129 | td->offset_y = offset_y; | ^~ pclasschange.c:126:10: note: object of size 8 allocated by 'calloc' 126 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c: In function 'set_to_boolean_or': pclasschange.c:141:7: warning: array subscript 'boolean_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 141 | td->seq_index = seq_index; | ^~ pclasschange.c:140:10: note: object of size 8 allocated by 'calloc' 140 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:142:7: warning: array subscript 'boolean_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 142 | td->offset_x = offset_x; | ^~ pclasschange.c:140:10: note: object of size 8 allocated by 'calloc' 140 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:143:7: warning: array subscript 'boolean_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 143 | td->offset_y = offset_y; | ^~ pclasschange.c:140:10: note: object of size 8 allocated by 'calloc' 140 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I.. -I/usr/include/python3.11 -c sclass_change.c -o build/temp.linux-x86_64-3.11/sclass_change.o -O2 -pipe -Wall sclass_change.c: In function 'python_class_change': sclass_change.c:98:14: warning: implicit declaration of function 'PyString_FromString'; did you mean 'PyLong_FromString'? [-Wimplicit-function-declaration] 98 | pName = PyString_FromString(ModuleName); | ^~~~~~~~~~~~~~~~~~~ | PyLong_FromString sclass_change.c:98:12: warning: assignment to 'PyObject *' {aka 'struct _object *'} from 'int' makes pointer from integer without a cast [-Wint-conversion] 98 | pName = PyString_FromString(ModuleName); | ^ sclass_change.c:133:13: warning: implicit declaration of function 'PyInt_FromLong'; did you mean 'PyLong_FromLong'? [-Wimplicit-function-declaration] 133 | pValue = PyInt_FromLong((long)k); | ^~~~~~~~~~~~~~ | PyLong_FromLong sclass_change.c:133:11: warning: assignment to 'PyObject *' {aka 'struct _object *'} from 'int' makes pointer from integer without a cast [-Wint-conversion] 133 | pValue = PyInt_FromLong((long)k); | ^ sclass_change.c:136:11: warning: assignment to 'PyObject *' {aka 'struct _object *'} from 'int' makes pointer from integer without a cast [-Wint-conversion] 136 | pValue = PyInt_FromLong((long)t); | ^ sclass_change.c:142:12: warning: implicit declaration of function 'PyInt_AsLong'; did you mean 'PyLong_AsLong'? [-Wimplicit-function-declaration] 142 | class = PyInt_AsLong(pValue); | ^~~~~~~~~~~~ | PyLong_AsLong sclass_change.c: In function 'executePythonCallback': sclass_change.c:214:11: warning: assignment to 'PyObject *' {aka 'struct _object *'} from 'int' makes pointer from integer without a cast [-Wint-conversion] 214 | pValue = PyInt_FromLong((long)k); | ^ sclass_change.c:217:11: warning: assignment to 'PyObject *' {aka 'struct _object *'} from 'int' makes pointer from integer without a cast [-Wint-conversion] 217 | pValue = PyInt_FromLong((long)t); | ^ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.11/ghmmwrapper_wrap.o build/temp.linux-x86_64-3.11/gql.o build/temp.linux-x86_64-3.11/pclasschange.o build/temp.linux-x86_64-3.11/sclass_change.o -L../ghmm/.libs -lghmm -lm -lpthread -lxml2 -lz -o build/lib.linux-x86_64-3.11/_ghmmwrapper.cpython-311-x86_64-linux-gnu.so make[3]: Leaving directory '/build/ghmm-0.9~rc3/ghmmwrapper' Making all in HMMEd make[3]: Entering directory '/build/ghmm-0.9~rc3/HMMEd' Making all in . make[4]: Entering directory '/build/ghmm-0.9~rc3/HMMEd' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/ghmm-0.9~rc3/HMMEd' /usr/bin/python3 setup.py build /build/ghmm-0.9~rc3/HMMEd/setup.py:38: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup,Extension running build running build_py creating build creating build/lib copying HMMEditor.py -> build/lib copying ObjectHMM.py -> build/lib copying HMMEditingContext.py -> build/lib running build_scripts creating build/scripts-3.11 copying and adjusting HMMEd -> build/scripts-3.11 changing mode of build/scripts-3.11/HMMEd from 644 to 755 make[3]: Leaving directory '/build/ghmm-0.9~rc3/HMMEd' make[3]: Entering directory '/build/ghmm-0.9~rc3' make[3]: Leaving directory '/build/ghmm-0.9~rc3' make[2]: Leaving directory '/build/ghmm-0.9~rc3' make[1]: Leaving directory '/build/ghmm-0.9~rc3' debian/rules override_dh_auto_test make[1]: Entering directory '/build/ghmm-0.9~rc3' /usr/bin/make --directory=tests make[2]: Entering directory '/build/ghmm-0.9~rc3/tests' Making all in data make[3]: Entering directory '/build/ghmm-0.9~rc3/tests/data' Making all in . make[4]: Entering directory '/build/ghmm-0.9~rc3/tests/data' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/ghmm-0.9~rc3/tests/data' make[3]: Leaving directory '/build/ghmm-0.9~rc3/tests/data' make[3]: Entering directory '/build/ghmm-0.9~rc3/tests' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/ghmm-0.9~rc3/tests' make[2]: Leaving directory '/build/ghmm-0.9~rc3/tests' make[1]: Leaving directory '/build/ghmm-0.9~rc3' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j1 install DESTDIR=/build/ghmm-0.9\~rc3/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/ghmm-0.9~rc3' Making install in ghmm make[2]: Entering directory '/build/ghmm-0.9~rc3/ghmm' Making install in . make[3]: Entering directory '/build/ghmm-0.9~rc3/ghmm' make[4]: Entering directory '/build/ghmm-0.9~rc3/ghmm' /usr/bin/mkdir -p '/build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/sh ../libtool --mode=install /usr/bin/install -c libghmm.la '/build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libghmm.so.1.0.0 /build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.so.1.0.0 libtool: install: (cd /build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libghmm.so.1.0.0 libghmm.so.1 || { rm -f libghmm.so.1 && ln -s libghmm.so.1.0.0 libghmm.so.1; }; }) libtool: install: (cd /build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libghmm.so.1.0.0 libghmm.so || { rm -f libghmm.so && ln -s libghmm.so.1.0.0 libghmm.so; }; }) libtool: install: /usr/bin/install -c .libs/libghmm.lai /build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.la libtool: install: /usr/bin/install -c .libs/libghmm.a /build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.a libtool: install: chmod 644 /build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.a libtool: install: ranlib /build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /usr/bin/mkdir -p '/build/ghmm-0.9~rc3/debian/tmp/usr/include/ghmm' /usr/bin/install -c -m 644 ghmm.h ghmmconfig.h sequence.h psequence.h xmlreader.h xmlwriter.h model.h foba.h viterbi.h gradescent.h kbest.h discrime.h cluster.h scluster.h reestimate.h sfoba.h sviterbi.h smodel.h sdmodel.h sdfoba.h sreestimate.h sgenerate.h smixturehmm.h smap_classify.h pmodel.h pviterbi.h pviterbi_propagate.h rng.h scanner.h obsolete.h unsupported.h fbgibbs.h cfbgibbs.h '/build/ghmm-0.9~rc3/debian/tmp/usr/include/ghmm' make[4]: Leaving directory '/build/ghmm-0.9~rc3/ghmm' make[3]: Leaving directory '/build/ghmm-0.9~rc3/ghmm' make[2]: Leaving directory '/build/ghmm-0.9~rc3/ghmm' Making install in tools make[2]: Entering directory '/build/ghmm-0.9~rc3/tools' make install-recursive make[3]: Entering directory '/build/ghmm-0.9~rc3/tools' Making install in . make[4]: Entering directory '/build/ghmm-0.9~rc3/tools' make[5]: Entering directory '/build/ghmm-0.9~rc3/tools' /usr/bin/mkdir -p '/build/ghmm-0.9~rc3/debian/tmp/usr/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c probdist cluster scluster smix_hmm '/build/ghmm-0.9~rc3/debian/tmp/usr/bin' libtool: install: /usr/bin/install -c probdist /build/ghmm-0.9~rc3/debian/tmp/usr/bin/probdist libtool: install: /usr/bin/install -c cluster /build/ghmm-0.9~rc3/debian/tmp/usr/bin/cluster libtool: install: /usr/bin/install -c scluster /build/ghmm-0.9~rc3/debian/tmp/usr/bin/scluster libtool: install: /usr/bin/install -c smix_hmm /build/ghmm-0.9~rc3/debian/tmp/usr/bin/smix_hmm /usr/bin/mkdir -p '/build/ghmm-0.9~rc3/debian/tmp/usr/bin' /usr/bin/install -c ghmm-config '/build/ghmm-0.9~rc3/debian/tmp/usr/bin' make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/build/ghmm-0.9~rc3/tools' make[4]: Leaving directory '/build/ghmm-0.9~rc3/tools' make[3]: Leaving directory '/build/ghmm-0.9~rc3/tools' make[2]: Leaving directory '/build/ghmm-0.9~rc3/tools' Making install in tests make[2]: Entering directory '/build/ghmm-0.9~rc3/tests' Making install in data make[3]: Entering directory '/build/ghmm-0.9~rc3/tests/data' Making install in . make[4]: Entering directory '/build/ghmm-0.9~rc3/tests/data' make[5]: Entering directory '/build/ghmm-0.9~rc3/tests/data' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/build/ghmm-0.9~rc3/tests/data' make[4]: Leaving directory '/build/ghmm-0.9~rc3/tests/data' make[3]: Leaving directory '/build/ghmm-0.9~rc3/tests/data' make[3]: Entering directory '/build/ghmm-0.9~rc3/tests' make[4]: Entering directory '/build/ghmm-0.9~rc3/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/ghmm-0.9~rc3/tests' make[3]: Leaving directory '/build/ghmm-0.9~rc3/tests' make[2]: Leaving directory '/build/ghmm-0.9~rc3/tests' Making install in ghmmwrapper make[2]: Entering directory '/build/ghmm-0.9~rc3/ghmmwrapper' Making all in . make[3]: Entering directory '/build/ghmm-0.9~rc3/ghmmwrapper' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/ghmm-0.9~rc3/ghmmwrapper' /usr/bin/python3 setup.py build /build/ghmm-0.9~rc3/ghmmwrapper/setup.py:38: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup,Extension running build running build_py copying ghmmwrapper.py -> build/lib.linux-x86_64-3.11 running build_ext /usr/bin/python3 setup.py install --prefix=/build/ghmm-0.9~rc3/debian/tmp//usr /build/ghmm-0.9~rc3/ghmmwrapper/setup.py:38: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup,Extension running install running build running build_py running build_ext running install_lib creating /build/ghmm-0.9~rc3/debian/tmp/usr/lib/python3.11 creating /build/ghmm-0.9~rc3/debian/tmp/usr/lib/python3.11/site-packages copying build/lib.linux-x86_64-3.11/ghmmwrapper.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib.linux-x86_64-3.11/_ghmmwrapper.cpython-311-x86_64-linux-gnu.so -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib.linux-x86_64-3.11/class_change.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib.linux-x86_64-3.11/modhmmer.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib.linux-x86_64-3.11/ghmmhelper.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib.linux-x86_64-3.11/ghmm.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages byte-compiling /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ghmmwrapper.py to ghmmwrapper.cpython-311.pyc byte-compiling /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/class_change.py to class_change.cpython-311.pyc byte-compiling /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/modhmmer.py to modhmmer.cpython-311.pyc byte-compiling /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ghmmhelper.py to ghmmhelper.cpython-311.pyc byte-compiling /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ghmm.py to ghmm.cpython-311.pyc /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ghmm.py:1358: SyntaxWarning: "is" with a literal. Did you mean "=="? if emission_domain is 'd': /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ghmm.py:2868: SyntaxWarning: "is" with a literal. Did you mean "=="? if R is -1: running install_egg_info Writing /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ghmmwrapper-0.8-py3.11.egg-info make[2]: Leaving directory '/build/ghmm-0.9~rc3/ghmmwrapper' Making install in HMMEd make[2]: Entering directory '/build/ghmm-0.9~rc3/HMMEd' /usr/bin/python3 setup.py install --prefix=/build/ghmm-0.9~rc3/debian/tmp//usr /build/ghmm-0.9~rc3/HMMEd/setup.py:38: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup,Extension running install running build running build_py running build_scripts running install_lib copying build/lib/HMMEditingContext.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib/ObjectHMM.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib/HMMEditor.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages byte-compiling /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/HMMEditingContext.py to HMMEditingContext.cpython-311.pyc /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/HMMEditingContext.py:42: SyntaxWarning: "is" with a literal. Did you mean "=="? if parameter.CDataType is "int": /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/HMMEditingContext.py:45: SyntaxWarning: "is" with a literal. Did you mean "=="? elif parameter.CDataType is "double": byte-compiling /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ObjectHMM.py to ObjectHMM.cpython-311.pyc /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ObjectHMM.py:648: SyntaxWarning: "is" with a literal. Did you mean "=="? if name is "emission": /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ObjectHMM.py:650: SyntaxWarning: "is" with a literal. Did you mean "=="? elif name is "name": /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ObjectHMM.py:665: SyntaxWarning: "is" with a literal. Did you mean "=="? if name is "emission": /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ObjectHMM.py:667: SyntaxWarning: "is" with a literal. Did you mean "=="? elif name is "name": /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ObjectHMM.py:1053: SyntaxWarning: "is" with a literal. Did you mean "=="? if name is "p": /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ObjectHMM.py:1060: SyntaxWarning: "is" with a literal. Did you mean "=="? if name is "p": byte-compiling /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/HMMEditor.py to HMMEditor.cpython-311.pyc /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/HMMEditor.py:436: SyntaxWarning: "is" with a literal. Did you mean "=="? if file is "": /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/HMMEditor.py:471: SyntaxWarning: "is not" with a literal. Did you mean "!="? if file is not "": running install_scripts copying build/scripts-3.11/HMMEd -> /build/ghmm-0.9~rc3/debian/tmp//usr/bin changing mode of /build/ghmm-0.9~rc3/debian/tmp//usr/bin/HMMEd to 755 running install_egg_info Writing /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/HMMEd-0.8-py3.11.egg-info make[2]: Leaving directory '/build/ghmm-0.9~rc3/HMMEd' make[2]: Entering directory '/build/ghmm-0.9~rc3' make[3]: Entering directory '/build/ghmm-0.9~rc3' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/ghmm-0.9~rc3/debian/tmp/usr/share/ghmm' /usr/bin/install -c -m 644 doc/ghmm.dtd.1.0 '/build/ghmm-0.9~rc3/debian/tmp/usr/share/ghmm' make[3]: Leaving directory '/build/ghmm-0.9~rc3' make[2]: Leaving directory '/build/ghmm-0.9~rc3' make[1]: Leaving directory '/build/ghmm-0.9~rc3' debian/rules override_dh_install make[1]: Entering directory '/build/ghmm-0.9~rc3' dh_install find /build/ghmm-0.9~rc3/debian/tmp -name "*.pyc" -delete d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --override s/libgsl23-dev/libgsl-dev/ \ --movedev debian/tmp/usr/include usr \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility --> liblapack-dev package exists. --> libxml2-dev package exists. set -e install -d -m 755 debian/libghmm-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libghmm1/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.a debian/libghmm-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.so debian/libghmm-dev/usr/lib/x86_64-linux-gnu mv /build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.so.1 debian/libghmm1/usr/lib/x86_64-linux-gnu mv /build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.so.1.0.0 debian/libghmm1/usr/lib/x86_64-linux-gnu PKGDEV=libghmm-dev PKGSHL=libghmm1 install -d -m 755 debian/libghmm-dev/usr mv debian/tmp/usr/include debian/libghmm-dev/usr cd /build/ghmm-0.9~rc3/debian/ghmm/usr/bin/ && mv cluster ghmm-cluster sed -i -e 's@ [^ ]*-f\(file\|debug\)-prefix-map=[^ ]*@@g' \ /build/ghmm-0.9~rc3/debian/ghmm/usr/bin/ghmm-config find debian -name __pycache__ | xargs rm -rf find debian -name libghmm.la -delete make[1]: Leaving directory '/build/ghmm-0.9~rc3' dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libghmm-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package libghmm-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'ghmm' in '../ghmm_0.9~rc3-4_amd64.deb'. dpkg-deb: building package 'ghmm-dbgsym' in '../ghmm-dbgsym_0.9~rc3-4_amd64.deb'. dpkg-deb: building package 'libghmm-dev' in '../libghmm-dev_0.9~rc3-4_amd64.deb'. dpkg-deb: building package 'libghmm1' in '../libghmm1_0.9~rc3-4_amd64.deb'. dpkg-deb: building package 'libghmm1-dbgsym' in '../libghmm1-dbgsym_0.9~rc3-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../ghmm_0.9~rc3-4_amd64.buildinfo dpkg-genchanges --build=binary -O../ghmm_0.9~rc3-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2724077/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2724077/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/2724077 and its subdirectories I: Current time: Sat Jun 22 10:31:51 +14 2024 I: pbuilder-time-stamp: 1719001911