I: pbuilder: network access will be disabled during build I: Current time: Tue Jan 13 06:16:07 +14 2026 I: pbuilder-time-stamp: 1768234567 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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: using eatmydata during job I: Copying source file I: copying [ghmm_0.9~rc3-10.dsc] I: copying [./ghmm_0.9~rc3.orig.tar.gz] I: copying [./ghmm_0.9~rc3-10.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Dec 7 11:05:14 2024 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~rc3-10.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~rc3-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_imp_func_issue.patch 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 dpkg-source: info: applying lapacke.patch dpkg-source: info: applying python3_syntax.patch dpkg-source: info: applying fix-test-mcmc.patch dpkg-source: info: applying python3.12.patch dpkg-source: info: applying gcc-14.patch dpkg-source: info: applying python3.12-syntax.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/47509/tmp/hooks/D01_modify_environment starting debug: Running on ionos6-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 12 16:16 /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/47509/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/47509/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]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=29d84a2f50ef49b89370db0da75fb6a0 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=47509 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.89hivhCX/pbuilderrc_EHKK --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.89hivhCX/b2 --logfile b2/build.log ghmm_0.9~rc3-10.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/47509/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: i386 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: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), dh-sequence-python3, d-shlibs (>= 0.106~), python3-dev, python3-setuptools, pkgconf, libxml2-dev, libgsl-dev, liblapacke-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 ... 19952 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 dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs (>= 0.106~); 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 python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf 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 liblapacke-dev; however: Package liblapacke-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-python{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} libblas-dev{a} libblas3{a} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libgssapi-krb5-2{a} libicu-dev{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} liblapacke{a} liblapacke-dev{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libpipeline1{a} libpkgconf3{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} libtirpc-common{a} libtirpc3t64{a} libtmglib-dev{a} libtmglib3{a} libtool{a} libuchardet0{a} libxml2{a} libxml2-dev{a} m4{a} man-db{a} media-types{a} netbase{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} swig{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 93 newly installed, 0 to remove and 0 not upgraded. Need to get 62.6 MB of archives. After unpacking 261 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libpython3.12-minimal i386 3.12.8-1 [815 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 python3.12-minimal i386 3.12.8-1 [2240 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 tzdata all 2024b-4 [256 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.2~rc1-2 [24.0 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 12 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libnsl2 i386 1.3.0-3+b3 [42.7 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-5 [173 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libpython3.12-stdlib i386 3.12.8-1 [1968 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 python3.12 i386 3.12.8-1 [677 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main i386 python3 i386 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-6 [1198 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-12 [95.9 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 d-shlibs all 0.108 [11.0 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 45 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 python3-inflect all 7.3.1-2 [32.4 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 59 http://deb.debian.org/debian trixie/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 python3-zipp all 3.21.0-1 [10.6 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 python3-setuptools all 75.2.0-1 [731 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 dh-python all 6.20241024 [109 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 icu-devtools i386 72.1-5+b1 [218 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-4 [143 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 libblas-dev i386 3.12.0-4 [155 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 libexpat1-dev i386 2.6.4-1 [165 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14.2.0-8 [735 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 libgslcblas0 i386 2.8+dfsg-5 [106 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 libgsl28 i386 2.8+dfsg-5 [978 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 libgsl-dev i386 2.8+dfsg-5 [1240 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 libicu-dev i386 72.1-5+b1 [10.6 MB] Get: 74 http://deb.debian.org/debian trixie/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-4 [2194 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 liblapack-dev i386 3.12.0-4 [4452 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 libtmglib3 i386 3.12.0-4 [122 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 liblapacke i386 3.12.0-4 [376 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 libtmglib-dev i386 3.12.0-4 [127 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 liblapacke-dev i386 3.12.0-4 [350 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 libpython3.12t64 i386 3.12.8-1 [2172 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 libpython3.12-dev i386 3.12.8-1 [5295 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 libpython3-dev i386 3.12.6-1 [9956 B] Get: 88 http://deb.debian.org/debian trixie/main i386 libxml2-dev i386 2.12.7+dfsg+really2.9.14-0.2+b1 [857 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-4 [26.2 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 python3.12-dev i386 3.12.8-1 [505 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 python3-dev i386 3.12.6-1 [26.1 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 swig i386 4.2.1-1 [1499 kB] Fetched 62.6 MB in 1s (54.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:i386. (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 ... 19952 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.8-1_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.8-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-1_i386.deb ... Unpacking python3.12-minimal (3.12.8-1) ... Setting up libpython3.12-minimal:i386 (3.12.8-1) ... Setting up libexpat1:i386 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-1) ... Selecting previously unselected package python3-minimal. (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 ... 20272 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_i386.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) ... Selecting previously unselected package libkrb5support0:i386. Preparing to unpack .../04-libkrb5support0_1.21.3-3_i386.deb ... Unpacking libkrb5support0:i386 (1.21.3-3) ... Selecting previously unselected package libcom-err2:i386. Preparing to unpack .../05-libcom-err2_1.47.2~rc1-2_i386.deb ... Unpacking libcom-err2:i386 (1.47.2~rc1-2) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../06-libk5crypto3_1.21.3-3_i386.deb ... Unpacking libk5crypto3:i386 (1.21.3-3) ... 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Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3 to /lib/i386-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3.0.0 to /lib/i386-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:i386. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_i386.deb ... Unpacking libnsl2:i386 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../14-libreadline8t64_8.2-5_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../15-libpython3.12-stdlib_3.12.8-1_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.8-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.8-1_i386.deb ... Unpacking python3.12 (3.12.8-1) ... Selecting previously unselected package libpython3-stdlib:i386. 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Setting up libgslcblas0:i386 (2.8+dfsg-5) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:i386 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:i386 (1.47.2~rc1-2) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up libkrb5support0:i386 (1.21.3-3) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jan 12 16:16:49 UTC 2026. Universal Time is now: Mon Jan 12 16:16:49 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.12.0-4) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libpkgconf3:i386 (1.8.1-4) ... Setting up libexpat1-dev:i386 (2.6.4-1) ... Setting up autopoint (0.22.5-2) ... Setting up icu-devtools (72.1-5+b1) ... Setting up d-shlibs (0.108) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:i386 (1.21.3-3) ... Setting up libgfortran5:i386 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:i386 (0.0.8-1+b2) ... Setting up netbase (6.4) ... Setting up libkrb5-3:i386 (1.21.3-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libgsl28:i386 (2.8+dfsg-5) ... Setting up readline-common (8.2-5) ... Setting up libicu-dev:i386 (72.1-5+b1) ... Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libblas-dev:i386 (3.12.0-4) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode 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 (1.14.0-1) ... Setting up liblapack3:i386 (3.12.0-4) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libtool (2.4.7-8) ... Setting up pkgconf:i386 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libxml2-dev:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libtmglib3:i386 (3.12.0-4) ... Setting up liblapack-dev:i386 (3.12.0-4) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so to provide /usr/lib/i386-linux-gnu/liblapack.so (liblapack.so-i386-linux-gnu) in auto mode Setting up libgssapi-krb5-2:i386 (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up libreadline8t64:i386 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-6) ... Setting up liblapacke:i386 (3.12.0-4) ... Setting up libtmglib-dev:i386 (3.12.0-4) ... Setting up libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up liblapacke-dev:i386 (3.12.0-4) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:i386 (1.3.0-3+b3) ... Setting up libpython3.12-stdlib:i386 (3.12.8-1) ... Setting up python3.12 (3.12.8-1) ... Setting up debhelper (13.20) ... Setting up libpython3.12t64:i386 (3.12.8-1) ... Setting up libpython3-stdlib:i386 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up libpython3.12-dev:i386 (3.12.8-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3.12-dev (3.12.8-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up libpython3-dev:i386 (3.12.6-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.12.6-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up dh-python (6.20241024) ... Processing triggers for libc-bin (2.40-4) ... 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 I: Building the package I: user script /srv/workspace/pbuilder/47509/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/47509/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/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~rc3-10_source.changes dpkg-buildpackage: info: source package ghmm dpkg-buildpackage: info: source version 0.9~rc3-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/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/ HMMEd/HMMEd.egg-info HMMEd/dist rm -rf ghmmwrapper/ghmmwrapper.egg-info ghmmwrapper/dist 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/ rm -rf ghmm/ghmmconfig.h make[1]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/ghmm.substvars debian/libghmm-dev.substvars debian/libghmm1t64.substvars debian/files rm -fr -- debian/ghmm/ debian/tmp/ debian/libghmm-dev/ debian/libghmm1t64/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config cp -an --reflink=auto config.guess debian/.debhelper/bucket/files/9be3de218833c076786b919dc34aab691611f4cd73316e7705f2673e2c41921b.tmp mv debian/.debhelper/bucket/files/9be3de218833c076786b919dc34aab691611f4cd73316e7705f2673e2c41921b.tmp debian/.debhelper/bucket/files/9be3de218833c076786b919dc34aab691611f4cd73316e7705f2673e2c41921b cp -f /usr/share/misc/config.guess ./config.guess cp -an --reflink=auto config.sub debian/.debhelper/bucket/files/3cd488ca40af79af9b139188c440d64d3cf52eee56f4908907b61e12850646cf.tmp mv debian/.debhelper/bucket/files/3cd488ca40af79af9b139188c440d64d3cf52eee56f4908907b61e12850646cf.tmp debian/.debhelper/bucket/files/3cd488ca40af79af9b139188c440d64d3cf52eee56f4908907b61e12850646cf cp -f /usr/share/misc/config.sub ./config.sub dh_autoreconf find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.in autoreconf -f -i 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:40: warning: file 'version.m4' included several times 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.m4:663: 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.m4:702: 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.m4:2995: AC_TRY_RUN is expanded from... acinclude.m4:10: AM_PATH_GSL is expanded from... lib/m4sugar/m4sh.m4:697: 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.m4:2918: AC_TRY_LINK is expanded from... acinclude.m4:10: AM_PATH_GSL is expanded from... lib/m4sugar/m4sh.m4:697: 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.m4:2845: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:697: 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.m4:2918: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:697: 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:284: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:284: 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:284: the top level configure.in:315: warning: AC_OUTPUT should be used without arguments. configure.in:315: 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') find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3' dh_auto_configure --sourcedirectory=/build/reproducible-path/ghmm-0.9~rc3 -- --enable-lapacke ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-lapacke 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... i686-pc-linux-gnu checking host system type... i686-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 i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop checking how to convert i686-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) 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 lapacke with pkg-config... 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 dh_auto_configure --buildsystem=pybuild --sourcedirectory=HMMEd pybuild --configure -i python{version} -p 3.12 --dir HMMEd I: pybuild base:311: python3.12 setup.py config make[1]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3' rm -f debian/ghmm.debhelper.log debian/libghmm-dev.debhelper.log debian/libghmm1t64.debhelper.log debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3' dh_auto_build make -j21 make[2]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3' make all-recursive make[3]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3' Making all in ghmm make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/ghmm' Making all in . make[5]: Entering directory '/build/reproducible-path/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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o model.lo model.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o foba.lo foba.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o viterbi.lo viterbi.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o reestimate.lo reestimate.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o kbest.lo kbest.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c viterbi.c -fPIC -DPIC -o .libs/viterbi.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c scanner.c -o scanner.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c gradescent.c -fPIC -DPIC -o .libs/gradescent.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c foba.c -fPIC -DPIC -o .libs/foba.o 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)); | ^ /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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o discrime.lo discrime.c 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); | ^ 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); | ^~~~~~~~~~~~~~~~~ sequence.c: In function 'ghmm_dseq_subseq_free': model.c: In function 'ghmm_dmodel_free': sequence.c:685:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 685 | mes_check_ptr (sq, 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_subseq_free': sequence.c:715:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 715 | mes_check_ptr (sqd, return (-1)); | ^ sequence.c: In function 'ghmm_dseq_free': sequence.c:1189:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1189 | mes_check_ptr(sq, 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;); | ^ 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)); | ^ matrix.c: In function 'ighmm_dmatrix_3d_free': matrix.c:378:35: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 378 | mes_check_ptr(matrix, return(-1)); | ^ 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:530:14: note: in a call to function 'initstate' declared 'nonnull' 530 | extern char *initstate (unsigned int __seed, char *__statebuf, | ^~~~~~~~~ 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); | ^ 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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c psequence.c -o psequence.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c gauss_tail.c -o gauss_tail.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c vector.c -o vector.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o modelutil.lo modelutil.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c viterbi.c -o viterbi.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c randvar.c -o randvar.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c discrime.c -fPIC -DPIC -o .libs/discrime.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c gradescent.c -o gradescent.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c mprintf.c -o mprintf.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c cluster.c -fPIC -DPIC -o .libs/cluster.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c modelutil.c -fPIC -DPIC -o .libs/modelutil.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c root_finder.c -fPIC -DPIC -o .libs/root_finder.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o sreestimate.lo sreestimate.c 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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c kbest.c -o kbest.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o scluster.lo scluster.c 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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c root_finder.c -o root_finder.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c sviterbi.c -fPIC -DPIC -o .libs/sviterbi.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c modelutil.c -o modelutil.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o smixturehmm.lo smixturehmm.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c reestimate.c -o reestimate.o >/dev/null 2>&1 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)); | ^ /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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o smap_classify.lo smap_classify.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o sdmodel.lo sdmodel.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o sdfoba.lo sdfoba.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c sreestimate.c -fPIC -DPIC -o .libs/sreestimate.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o sdviterbi.lo sdviterbi.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c sviterbi.c -o sviterbi.o >/dev/null 2>&1 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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c smap_classify.c -fPIC -DPIC -o .libs/smap_classify.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c sfoba.c -o sfoba.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c smap_classify.c -o smap_classify.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o pviterbi_propagate.lo pviterbi_propagate.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o fbgibbs.lo fbgibbs.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o cfbgibbs.lo cfbgibbs.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c sdfoba.c -fPIC -DPIC -o .libs/sdfoba.o 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)); | ^ 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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c pmodel.c -fPIC -DPIC -o .libs/pmodel.o 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)); | ^ 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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c pviterbi.c -fPIC -DPIC -o .libs/pviterbi.o 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)); | ^ 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); | ^ 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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c xmlreader.c -o xmlreader.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c sgenerate.c -o sgenerate.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c cfbgibbs.c -fPIC -DPIC -o .libs/cfbgibbs.o 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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c sdviterbi.c -o sdviterbi.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c model.c -o model.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c cfbgibbs.c -o cfbgibbs.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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c discrime.c -o discrime.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=link gcc -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -version-info 1:0:0 -Wl,-z,relro -Wl,-z,now -o libghmm.la -rpath /usr/lib/i386-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 -llapacke -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 -llapacke -lxml2 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -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[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/ghmm' make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/ghmm' Making all in tools make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tools' make all-recursive make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tools' Making all in . make[6]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tools' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o smix_hmm.o smix_hmm.c /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -o scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -o smix_hmm smix_hmm.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -o cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -o probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o smix_hmm smix_hmm.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 make[6]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tools' make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tools' make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tools' Making all in tests make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests' Making all in data make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' Making all in . make[6]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[6]: Nothing to be done for 'all-am'. make[6]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -c -o mcmc.o mcmc.c /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -o root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -o test_gsl_ran_gaussian_tail test_gsl_ran_gaussian_tail.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -o libxml-test libxml-test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -o shmm_viterbi_test shmm_viterbi_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -o sequences_test sequences_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -o sequences_old_format sequences_old_format.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -o two_states_three_symbols two_states_three_symbols.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -o chmm chmm.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -o randvar_test randvar_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -o chmm_test chmm_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -o coin_toss_test coin_toss_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -o read_fa read_fa.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -o mcmc mcmc.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -o label_higher_order_test label_higher_order_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o libxml-test libxml-test.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o test_gsl_ran_gaussian_tail test_gsl_ran_gaussian_tail.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o sequences_old_format sequences_old_format.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o shmm_viterbi_test shmm_viterbi_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o two_states_three_symbols two_states_three_symbols.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o randvar_test randvar_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o chmm_test chmm_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o sequences_test sequences_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o chmm chmm.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o coin_toss_test coin_toss_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o read_fa read_fa.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o mcmc mcmc.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/i386-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o label_higher_order_test label_higher_order_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests' make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests' Making all in ghmmwrapper make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/ghmmwrapper' Making all in . make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/ghmmwrapper' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/ghmmwrapper' /usr/bin/python3 setup.py build file ghmmwrapper.py (for module ghmmwrapper) not found file ghmmwrapper.py (for module ghmmwrapper) not found ghmmwrapper_wrap.c: In function 'PythonCallBack': ghmmwrapper_wrap.c:3528:9: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] 3528 | PyEval_CallObject(func, arglist); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/python3.12/Python.h:95, from ghmmwrapper_wrap.c:198: /usr/include/python3.12/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:3733:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 3733 | for(i=0; isize; ++i) | ^ ghmmwrapper_wrap.c: In function 'ghmm_cmodel_getStateName': ghmmwrapper_wrap.c:3986:16: warning: the comparison will always evaluate as 'true' for the pointer operand in 'self->s + (sizetype)(index * 60)' must not be NULL [-Waddress] 3986 | if((self->s + index) && index < self->N) return (self->s + index)->desc; | ^ ghmmwrapper_wrap.c:3986:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 3986 | if((self->s + index) && index < self->N) return (self->s + index)->desc; | ^ ghmmwrapper_wrap.c: In function 'ghmm_dbackground_setName': ghmmwrapper_wrap.c:4019:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 4019 | if(index < self->n){ | ^ ghmmwrapper_wrap.c: In function 'ghmm_dmodel_getStateName': ghmmwrapper_wrap.c:4067:16: warning: the comparison will always evaluate as 'true' for the pointer operand in 'self->s + (sizetype)(index * 52)' must not be NULL [-Waddress] 4067 | if((self->s + index) && index < self->N) return (self->s + index)->desc; | ^ ghmmwrapper_wrap.c:4067:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 4067 | if((self->s + index) && index < self->N) return (self->s + index)->desc; | ^ ghmmwrapper_wrap.c: In function 'int_matrix_alloc': ghmmwrapper_wrap.c:4178:28: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] 4178 | for (i=0; iseq_index = seq_index; | ^~ pclasschange.c:96:10: note: object of size 4 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[4]' [-Warray-bounds=] 98 | td->threshold = threshold; | ^~ pclasschange.c:96:10: note: object of size 4 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[4]' [-Warray-bounds=] 99 | td->offset_x = offset_x; | ^~ pclasschange.c:96:10: note: object of size 4 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[4]' [-Warray-bounds=] 100 | td->offset_y = offset_y; | ^~ pclasschange.c:96:10: note: object of size 4 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[4]' [-Warray-bounds=] 112 | td->seq_index = seq_index; | ^~ pclasschange.c:111:10: note: object of size 4 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[4]' [-Warray-bounds=] 113 | td->threshold = threshold; | ^~ pclasschange.c:111:10: note: object of size 4 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[4]' [-Warray-bounds=] 114 | td->offset_x = offset_x; | ^~ pclasschange.c:111:10: note: object of size 4 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[4]' [-Warray-bounds=] 115 | td->offset_y = offset_y; | ^~ pclasschange.c:111:10: note: object of size 4 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[4]' [-Warray-bounds=] 127 | td->seq_index = seq_index; | ^~ pclasschange.c:126:10: note: object of size 4 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[4]' [-Warray-bounds=] 128 | td->offset_x = offset_x; | ^~ pclasschange.c:126:10: note: object of size 4 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[4]' [-Warray-bounds=] 129 | td->offset_y = offset_y; | ^~ pclasschange.c:126:10: note: object of size 4 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[4]' [-Warray-bounds=] 141 | td->seq_index = seq_index; | ^~ pclasschange.c:140:10: note: object of size 4 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[4]' [-Warray-bounds=] 142 | td->offset_x = offset_x; | ^~ pclasschange.c:140:10: note: object of size 4 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[4]' [-Warray-bounds=] 143 | td->offset_y = offset_y; | ^~ pclasschange.c:140:10: note: object of size 4 allocated by 'calloc' 140 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/ghmmwrapper' Making all in HMMEd make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/HMMEd' Making all in . make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/HMMEd' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/HMMEd' /usr/bin/python3 setup.py build make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/HMMEd' make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3' make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3' make[3]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3' make[2]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3' dh_auto_build --buildsystem=pybuild --sourcedirectory=HMMEd pybuild --build -i python{version} -p 3.12 --dir HMMEd I: pybuild base:311: /usr/bin/python3 setup.py build make[1]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3' rm -f debian/ghmm.debhelper.log debian/libghmm-dev.debhelper.log debian/libghmm1t64.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3' /usr/bin/make --directory=tests make[2]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests' Making all in data make[3]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' Making all in . make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[3]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[3]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests' make[2]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests' make[1]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/ghmm.substvars debian/libghmm-dev.substvars debian/libghmm1t64.substvars rm -fr -- debian/.debhelper/generated/ghmm/ debian/ghmm/ debian/tmp/ debian/.debhelper/generated/libghmm-dev/ debian/libghmm-dev/ debian/.debhelper/generated/libghmm1t64/ debian/libghmm1t64/ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3' dh_auto_install install -m0755 -d /build/reproducible-path/ghmm-0.9\~rc3/debian/tmp make -j1 install DESTDIR=/build/reproducible-path/ghmm-0.9\~rc3/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3' Making install in ghmm make[3]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/ghmm' Making install in . make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/ghmm' make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/ghmm' /usr/bin/mkdir -p '/build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/i386-linux-gnu' /bin/sh ../libtool --mode=install /usr/bin/install -c libghmm.la '/build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libghmm.so.1.0.0 /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/i386-linux-gnu/libghmm.so.1.0.0 libtool: install: (cd /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/i386-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/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/i386-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/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/i386-linux-gnu/libghmm.la libtool: install: /usr/bin/install -c .libs/libghmm.a /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/i386-linux-gnu/libghmm.a libtool: install: chmod 644 /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/i386-linux-gnu/libghmm.a libtool: install: ranlib /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/i386-linux-gnu/libghmm.a libtool: warning: remember to run 'libtool --finish /usr/lib/i386-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/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/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/include/ghmm' make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/ghmm' make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/ghmm' make[3]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/ghmm' Making install in tools make[3]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tools' make install-recursive make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tools' Making install in . make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tools' make[6]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tools' /usr/bin/mkdir -p '/build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c probdist cluster scluster smix_hmm '/build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/bin' libtool: install: /usr/bin/install -c probdist /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/bin/probdist libtool: install: /usr/bin/install -c cluster /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/bin/cluster libtool: install: /usr/bin/install -c scluster /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/bin/scluster libtool: install: /usr/bin/install -c smix_hmm /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/bin/smix_hmm /usr/bin/mkdir -p '/build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/bin' /usr/bin/install -c ghmm-config '/build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/bin' make[6]: Nothing to be done for 'install-data-am'. make[6]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tools' make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tools' make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tools' make[3]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tools' Making install in tests make[3]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests' Making install in data make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' Making install in . make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[6]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[6]: Nothing to be done for 'install-exec-am'. make[6]: Nothing to be done for 'install-data-am'. make[6]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests' make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests' 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/reproducible-path/ghmm-0.9~rc3/tests' make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests' make[3]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests' Making install in ghmmwrapper make[3]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/ghmmwrapper' Making all in . make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/ghmmwrapper' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/ghmmwrapper' /usr/bin/python3 setup.py build /usr/bin/python3 setup.py install --prefix=/build/reproducible-path/ghmm-0.9~rc3/debian/tmp//usr /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` and ``easy_install``. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://github.com/pypa/setuptools/issues/917 for details. ******************************************************************************** !! self.initialize_options() TEST FAILED: /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/local/lib/python3.12/dist-packages/ does NOT support .pth files bad install directory or PYTHONPATH You are attempting to install a package to a directory that is not on PYTHONPATH and which Python does not read ".pth" files from. The installation directory you specified (via --install-dir, --prefix, or the distutils default setting) was: /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/local/lib/python3.12/dist-packages/ and your PYTHONPATH environment variable currently contains: '' Here are some of your options for correcting the problem: * You can choose a different installation directory, i.e., one that is on PYTHONPATH or supports .pth files * You can add the installation directory to the PYTHONPATH environment variable. (It must then also be on PYTHONPATH whenever you run Python and want to use the package(s) you are installing.) * You can set up the installation directory to support ".pth" files by using one of the approaches described here: https://setuptools.pypa.io/en/latest/deprecated/easy_install.html#custom-installation-locations Please make the appropriate changes for your system and try again. build/bdist.linux-x86_64/egg/modhmmer.py:185: SyntaxWarning: invalid escape sequence '\s' self.acc = gotoLine(f,re.compile("^NAME\s+([\w+\s*]+)" ) ).group(1) # NAME as unique model identifier zip_safe flag not set; analyzing archive contents... __pycache__._ghmmwrapper.cpython-312: module references __file__ __pycache__.ghmm.cpython-312: module references __file__ /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/local/lib/python3.12/dist-packages/ghmmwrapper-0.8-py3.12-linux-x86_64.egg/modhmmer.py:185: SyntaxWarning: invalid escape sequence '\s' self.acc = gotoLine(f,re.compile("^NAME\s+([\w+\s*]+)" ) ).group(1) # NAME as unique model identifier make[3]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/ghmmwrapper' Making install in HMMEd make[3]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/HMMEd' /usr/bin/python3 setup.py install --prefix=/build/reproducible-path/ghmm-0.9~rc3/debian/tmp//usr /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` and ``easy_install``. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://github.com/pypa/setuptools/issues/917 for details. ******************************************************************************** !! self.initialize_options() TEST FAILED: /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/local/lib/python3.12/dist-packages/ does NOT support .pth files bad install directory or PYTHONPATH You are attempting to install a package to a directory that is not on PYTHONPATH and which Python does not read ".pth" files from. The installation directory you specified (via --install-dir, --prefix, or the distutils default setting) was: /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/local/lib/python3.12/dist-packages/ and your PYTHONPATH environment variable currently contains: '' Here are some of your options for correcting the problem: * You can choose a different installation directory, i.e., one that is on PYTHONPATH or supports .pth files * You can add the installation directory to the PYTHONPATH environment variable. (It must then also be on PYTHONPATH whenever you run Python and want to use the package(s) you are installing.) * You can set up the installation directory to support ".pth" files by using one of the approaches described here: https://setuptools.pypa.io/en/latest/deprecated/easy_install.html#custom-installation-locations Please make the appropriate changes for your system and try again. zip_safe flag not set; analyzing archive contents... make[3]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/HMMEd' make[3]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3' make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/share/ghmm' /usr/bin/install -c -m 644 doc/ghmm.dtd.1.0 '/build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/share/ghmm' make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3' make[3]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3' make[2]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3' dh_auto_install --buildsystem=pybuild --sourcedirectory=HMMEd install -m0755 -d /build/reproducible-path/ghmm-0.9\~rc3/debian/tmp pybuild --install -i python{version} -p 3.12 --dir HMMEd --dest-dir /build/reproducible-path/ghmm-0.9\~rc3/debian/tmp I: pybuild base:311: /usr/bin/python3 setup.py install --root '/build/reproducible-path/ghmm-0.9~rc3/debian/python3-HMMEd' /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() make[1]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3' rm -f debian/ghmm.debhelper.log debian/libghmm-dev.debhelper.log debian/libghmm1t64.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3' d-shlibmove --commit \ --t64 \ --multiarch \ --devunversioned \ --exclude-la \ --override s/libgsl23-dev/libgsl-dev/ \ --override s/liblapacke3-dev/liblapacke-dev/ \ --movedev debian/tmp/usr/include usr \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility --> liblapacke-dev package exists. --> libxml2-dev package exists. set -e install -d -m 755 debian/libghmm-dev/usr/lib/i386-linux-gnu install -d -m 755 debian/libghmm1t64/usr/lib/i386-linux-gnu mv debian/tmp/usr/lib/i386-linux-gnu/libghmm.a debian/libghmm-dev/usr/lib/i386-linux-gnu mv debian/tmp/usr/lib/i386-linux-gnu/libghmm.so debian/libghmm-dev/usr/lib/i386-linux-gnu mv /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/i386-linux-gnu/libghmm.so.1 debian/libghmm1t64/usr/lib/i386-linux-gnu mv /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/i386-linux-gnu/libghmm.so.1.0.0 debian/libghmm1t64/usr/lib/i386-linux-gnu PKGDEV=libghmm-dev PKGSHL=libghmm1t64 install -d -m 755 debian/libghmm-dev/usr mv debian/tmp/usr/include debian/libghmm-dev/usr dh_install install -m0755 -d debian/ghmm//usr cp --reflink=auto -a debian/tmp/usr/bin debian/ghmm//usr/ install -m0755 -d debian/ghmm//usr/share/ghmm cp --reflink=auto -a debian/tmp/usr/share/ghmm/ghmm.dtd.1.0 debian/ghmm//usr/share/ghmm/ install -m0755 -d debian/libghmm-dev/usr/include/ghmm cp --reflink=auto -a ./ghmm/ghmm_internals.h ./ghmm/matrix.h ./ghmm/matrixop.h ./ghmm/mes.h ./ghmm/randvar.h debian/libghmm-dev/usr/include/ghmm/ cd /build/reproducible-path/ghmm-0.9~rc3/debian/ghmm/usr/bin/ && mv cluster ghmm-cluster sed -i -e 's@ [^ ]*-f\(file\|debug\)-prefix-map=[^ ]*@@g' \ /build/reproducible-path/ghmm-0.9~rc3/debian/ghmm/usr/bin/ghmm-config find debian -name libghmm.la -delete # temporarily copy over ghmmwrapper to the pybuild created dir mkdir -p debian/python3-HMMEd/usr/lib/python3/dist-packages mv debian/tmp/usr/local/lib/python3.*/dist-packages/ghmmwrapper-0.8-py3*.egg debian/python3-HMMEd/usr/lib/python3/dist-packages/ghmm rm -rf debian/tmp/usr/local find debian -type d -name __pycache__ | xargs rm -rf make[1]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3' dh_installdocs install -m0755 -d debian/ghmm/usr/share/doc/ghmm install -m0755 -d debian/ghmm/usr/share/doc/ghmm cp --reflink=auto -a ./debian/tests/run-unit-test debian/ghmm/usr/share/doc/ghmm cp --reflink=auto -a ./debian/tests/ghmm_test.py debian/ghmm/usr/share/doc/ghmm chmod -R u\+rw,go=rX debian/ghmm/usr/share/doc install -p -m0644 debian/README.Debian debian/ghmm/usr/share/doc/ghmm/README.Debian install -p -m0644 debian/copyright debian/ghmm/usr/share/doc/ghmm/copyright install -m0755 -d debian/libghmm-dev/usr/share/doc/libghmm-dev install -p -m0644 debian/copyright debian/libghmm-dev/usr/share/doc/libghmm-dev/copyright install -m0755 -d debian/libghmm1t64/usr/share/doc/libghmm1t64 install -p -m0644 debian/copyright debian/libghmm1t64/usr/share/doc/libghmm1t64/copyright dh_installchangelogs install -m0755 -d debian/libghmm1t64/usr/share/doc/libghmm1t64 install -p -m0644 debian/.debhelper/generated/libghmm1t64/dh_installchangelogs.dch.trimmed debian/libghmm1t64/usr/share/doc/libghmm1t64/changelog.Debian install -m0755 -d debian/ghmm/usr/share/doc/ghmm install -p -m0644 debian/.debhelper/generated/ghmm/dh_installchangelogs.dch.trimmed debian/ghmm/usr/share/doc/ghmm/changelog.Debian install -m0755 -d debian/libghmm-dev/usr/share/doc/libghmm-dev install -p -m0644 debian/.debhelper/generated/libghmm-dev/dh_installchangelogs.dch.trimmed debian/libghmm-dev/usr/share/doc/libghmm-dev/changelog.Debian dh_installexamples install -m0755 -d debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./debian/tests/ghmm_test.py debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./debian/tests/autopkgtest.mk debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/chmm.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/chmm_test.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/coin_toss_test.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/label_higher_order_test.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/libxml-test.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/mcmc.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/randvar_test.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/read_fa.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/root_finder_test.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/sequences_old_format.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/sequences_test.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/shmm_viterbi_test.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/test_gsl_ran_gaussian_tail.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/two_states_three_symbols.c debian/ghmm/usr/share/doc/ghmm/examples rm -f debian/ghmm.debhelper.log debian/libghmm-dev.debhelper.log debian/libghmm1t64.debhelper.log debian/rules execute_after_dh_installexamples make[1]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3' # convert sequences_test.c from its national encoding iconv -f ISO-8859-1 -t UTF-8 tests/sequences_test.c \ -o debian/ghmm/usr/share/doc/ghmm/examples/sequences_test.c make[1]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3' debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3' # We do not provide a package python3-HMMEd thus copy the pybuild installed files over to ghmm mv debian/python3-HMMEd/usr/bin/* debian/ghmm/usr/bin mv debian/python3-HMMEd/usr/lib debian/ghmm/usr dh_python3 -p ghmm D: dh_python3 dh_python3:180: version: 6.20241024 D: dh_python3 dh_python3:181: argv: ['/usr/bin/dh_python3', '-p', 'ghmm'] D: dh_python3 dh_python3:182: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=['ghmm'], no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=None) D: dh_python3 dh_python3:183: supported Python versions: 3.12 (default=3.12) D: dh_python3 debhelper:174: source=ghmm, binary packages=['ghmm'] D: dh_python3 dh_python3:205: processing package ghmm... D: dh_python3 fs:50: moving files from debian/ghmm/usr/lib/python3.12/dist-packages to debian/ghmm/usr/lib/python3/dist-packages/ D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/scluster): cannot parse binary file D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/ghmm-cluster): cannot parse binary file D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/smix_hmm): cannot parse binary file D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/probdist): cannot parse binary file D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/ghmm-config): doesn't look like a shebang: #! /bin/sh D: dh_python3 fs:338: package ghmm details = {'requires.txt': set(), 'egg-info': {'debian/ghmm/usr/lib/python3/dist-packages/HMMEd-0.8.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': {/usr/bin/python3}, 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': {Version('3.12')}, 'ext_no_version': set()} D: dh_python3 depends:103: generating dependencies for package ghmm D: dh_python3 depends:253: D={'python3 (>= 3.12~)', 'python3:any', 'python3 (<< 3.13)'}; R=[]; S=[]; E=[], B=[]; RT=[] make[1]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3' dh_lintian install -m0755 -d debian/libghmm1t64/usr/share/lintian/overrides install -p -m0644 debian/libghmm1t64.lintian-overrides debian/libghmm1t64/usr/share/lintian/overrides/libghmm1t64 dh_perl dh_link install -m0755 -d debian/ghmm/usr/lib/ghmm/bin rm -f debian/ghmm/usr/lib/ghmm/bin/cluster ln -s ../../../bin/ghmm-cluster debian/ghmm/usr/lib/ghmm/bin/cluster rm -f debian/libghmm-dev/usr/lib/i386-linux-gnu/libghmm.so ln -s libghmm.so.1.0.0 debian/libghmm-dev/usr/lib/i386-linux-gnu/libghmm.so rm -f debian/libghmm1t64/usr/lib/i386-linux-gnu/libghmm.so.1 ln -s libghmm.so.1.0.0 debian/libghmm1t64/usr/lib/i386-linux-gnu/libghmm.so.1 dh_strip_nondeterminism dh_compress cd debian/ghmm cd debian/libghmm-dev cd debian/libghmm1t64 chmod a-x usr/share/doc/libghmm-dev/changelog.Debian gzip -9nf usr/share/doc/libghmm-dev/changelog.Debian chmod a-x usr/share/doc/ghmm/changelog.Debian chmod a-x usr/share/doc/libghmm1t64/changelog.Debian gzip -9nf usr/share/doc/ghmm/changelog.Debian cd '/build/reproducible-path/ghmm-0.9~rc3' gzip -9nf usr/share/doc/libghmm1t64/changelog.Debian cd '/build/reproducible-path/ghmm-0.9~rc3' cd '/build/reproducible-path/ghmm-0.9~rc3' rm -f debian/ghmm.debhelper.log debian/rules execute_before_dh_fixperms make[1]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3' chmod -v -x debian/ghmm/usr/share/doc/ghmm/examples/*.c mode of 'debian/ghmm/usr/share/doc/ghmm/examples/chmm.c' changed from 0775 (rwxrwxr-x) to 0664 (rw-rw-r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/chmm_test.c' retained as 0664 (rw-rw-r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/coin_toss_test.c' changed from 0775 (rwxrwxr-x) to 0664 (rw-rw-r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/label_higher_order_test.c' retained as 0664 (rw-rw-r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/libxml-test.c' retained as 0664 (rw-rw-r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/mcmc.c' retained as 0664 (rw-rw-r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/randvar_test.c' retained as 0664 (rw-rw-r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/read_fa.c' retained as 0664 (rw-rw-r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/root_finder_test.c' changed from 0775 (rwxrwxr-x) to 0664 (rw-rw-r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/sequences_old_format.c' retained as 0664 (rw-rw-r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/sequences_test.c' retained as 0664 (rw-rw-r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/shmm_viterbi_test.c' changed from 0775 (rwxrwxr-x) to 0664 (rw-rw-r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/test_gsl_ran_gaussian_tail.c' changed from 0775 (rwxrwxr-x) to 0664 (rw-rw-r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/two_states_three_symbols.c' changed from 0775 (rwxrwxr-x) to 0664 (rw-rw-r--) make[1]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3' dh_fixperms find debian/ghmm ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libghmm-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libghmm1t64 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/ghmm/usr/share/doc -type f -a -true -a ! -regex 'debian/ghmm/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libghmm1t64/usr/share/doc -type f -a -true -a ! -regex 'debian/libghmm1t64/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libghmm-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libghmm-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/ghmm/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libghmm-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libghmm1t64/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/ghmm -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libghmm-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libghmm1t64/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/ghmm/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/libghmm1t64 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libghmm-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/ghmm/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/libghmm1t64/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/libghmm-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing dh_dwz -a dwz -- debian/libghmm1t64/usr/lib/i386-linux-gnu/libghmm.so.1.0.0 install -m0755 -d debian/ghmm/usr/lib/debug/.dwz/i386-linux-gnu dwz -mdebian/ghmm/usr/lib/debug/.dwz/i386-linux-gnu/ghmm.debug -M/usr/lib/debug/.dwz/i386-linux-gnu/ghmm.debug -- debian/ghmm/usr/bin/ghmm-cluster debian/ghmm/usr/bin/probdist debian/ghmm/usr/bin/scluster debian/ghmm/usr/bin/smix_hmm debian/ghmm/usr/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-312-i386-linux-gnu.so objcopy --compress-debug-sections debian/ghmm/usr/lib/debug/.dwz/i386-linux-gnu/ghmm.debug chmod 0644 -- debian/ghmm/usr/lib/debug/.dwz/i386-linux-gnu/ghmm.debug dh_strip -a strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives -R .gnu.lto_\* -R .gnu.debuglto_\* -N __gnu_lto_slim -N __gnu_lto_v1 debian/libghmm-dev/usr/lib/i386-linux-gnu/libghmm.a install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/37 objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-312-i386-linux-gnu.so debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/37/8d98da42efdaebf0ce08395b54abdbd48cc999.debug install -m0755 -d debian/.debhelper/libghmm1t64/dbgsym-root/usr/lib/debug/.build-id/26 objcopy --only-keep-debug --compress-debug-sections debian/libghmm1t64/usr/lib/i386-linux-gnu/libghmm.so.1.0.0 debian/.debhelper/libghmm1t64/dbgsym-root/usr/lib/debug/.build-id/26/aa8f69f37400524564cc47d6cbdde5836923c9.debug chmod 0644 -- debian/.debhelper/libghmm1t64/dbgsym-root/usr/lib/debug/.build-id/26/aa8f69f37400524564cc47d6cbdde5836923c9.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libghmm1t64/usr/lib/i386-linux-gnu/libghmm.so.1.0.0 objcopy --add-gnu-debuglink debian/.debhelper/libghmm1t64/dbgsym-root/usr/lib/debug/.build-id/26/aa8f69f37400524564cc47d6cbdde5836923c9.debug debian/libghmm1t64/usr/lib/i386-linux-gnu/libghmm.so.1.0.0 install -m0755 -d debian/.debhelper/libghmm1t64/dbgsym-root/usr/share/doc ln -s libghmm1t64 debian/.debhelper/libghmm1t64/dbgsym-root/usr/share/doc/libghmm1t64-dbgsym install -m0755 -d debian/.debhelper/libghmm1t64 chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/37/8d98da42efdaebf0ce08395b54abdbd48cc999.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/ghmm/usr/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/37/8d98da42efdaebf0ce08395b54abdbd48cc999.debug debian/ghmm/usr/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/98 objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/scluster debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/98/a23399bee801970572965528f4664232edfedd.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/98/a23399bee801970572965528f4664232edfedd.debug strip --remove-section=.comment --remove-section=.note debian/ghmm/usr/bin/scluster objcopy --add-gnu-debuglink debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/98/a23399bee801970572965528f4664232edfedd.debug debian/ghmm/usr/bin/scluster install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/3f objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/ghmm-cluster debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/3f/b7247c501b86701bca9737477c129a76740170.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/3f/b7247c501b86701bca9737477c129a76740170.debug strip --remove-section=.comment --remove-section=.note debian/ghmm/usr/bin/ghmm-cluster objcopy --add-gnu-debuglink debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/3f/b7247c501b86701bca9737477c129a76740170.debug debian/ghmm/usr/bin/ghmm-cluster install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/20 objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/smix_hmm debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/20/3354c40f0e41199b1bd29f69af4718ab082299.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/20/3354c40f0e41199b1bd29f69af4718ab082299.debug strip --remove-section=.comment --remove-section=.note debian/ghmm/usr/bin/smix_hmm objcopy --add-gnu-debuglink debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/20/3354c40f0e41199b1bd29f69af4718ab082299.debug debian/ghmm/usr/bin/smix_hmm install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/9d objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/probdist debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/9d/50d827fa2cadb64947007cff57cf50e67d7004.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/9d/50d827fa2cadb64947007cff57cf50e67d7004.debug strip --remove-section=.comment --remove-section=.note debian/ghmm/usr/bin/probdist objcopy --add-gnu-debuglink debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/9d/50d827fa2cadb64947007cff57cf50e67d7004.debug debian/ghmm/usr/bin/probdist install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/ghmm/usr/lib/debug/.dwz/i386-linux-gnu debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/ghmm/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/ghmm/usr/lib/debug install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/share/doc ln -s ghmm debian/.debhelper/ghmm/dbgsym-root/usr/share/doc/ghmm-dbgsym install -m0755 -d debian/.debhelper/ghmm dh_makeshlibs -a rm -f debian/ghmm/DEBIAN/shlibs rm -f debian/libghmm-dev/DEBIAN/shlibs rm -f debian/libghmm1t64/DEBIAN/shlibs install -m0755 -d debian/libghmm1t64/DEBIAN echo "libghmm 1 libghmm1t64 (>= 0.9~rc3)" >> debian/libghmm1t64/DEBIAN/shlibs chmod 0644 -- debian/libghmm1t64/DEBIAN/shlibs mv debian/.debhelper/generated/libghmm1t64/triggers.new debian/.debhelper/generated/libghmm1t64/triggers mv debian/libghmm1t64.substvars.new debian/libghmm1t64.substvars dh_shlibdeps -a install -m0755 -d debian/libghmm1t64/DEBIAN dpkg-shlibdeps -Tdebian/libghmm1t64.substvars debian/libghmm1t64/usr/lib/i386-linux-gnu/libghmm.so.1.0.0 install -m0755 -d debian/ghmm/DEBIAN dpkg-shlibdeps -Tdebian/ghmm.substvars debian/ghmm/usr/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-312-i386-linux-gnu.so debian/ghmm/usr/bin/scluster debian/ghmm/usr/bin/ghmm-cluster debian/ghmm/usr/bin/smix_hmm debian/ghmm/usr/bin/probdist dh_installdeb install -m0755 -d debian/ghmm/DEBIAN printf '#!/bin/sh\nset -e\n' > debian/ghmm/DEBIAN/postinst cat debian/ghmm.postinst.debhelper >> debian/ghmm/DEBIAN/postinst chmod 0755 -- debian/ghmm/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/ghmm/DEBIAN/prerm cat debian/ghmm.prerm.debhelper >> debian/ghmm/DEBIAN/prerm chmod 0755 -- debian/ghmm/DEBIAN/prerm install -m0755 -d debian/libghmm-dev/DEBIAN install -m0755 -d debian/libghmm1t64/DEBIAN install -p -m0644 debian/.debhelper/generated/libghmm1t64/triggers debian/libghmm1t64/DEBIAN/triggers dh_gencontrol install -m0755 -d debian/libghmm-dev/DEBIAN echo misc:Depends= >> debian/libghmm-dev.substvars echo misc:Pre-Depends= >> debian/libghmm-dev.substvars dpkg-gencontrol -plibghmm-dev -ldebian/changelog -Tdebian/libghmm-dev.substvars -cdebian/control -Pdebian/libghmm-dev install -m0755 -d debian/libghmm1t64/DEBIAN echo misc:Depends= >> debian/libghmm1t64.substvars echo misc:Pre-Depends= >> debian/libghmm1t64.substvars install -m0755 -d debian/.debhelper/libghmm1t64/dbgsym-root/DEBIAN dpkg-gencontrol -plibghmm1t64 -ldebian/changelog -Tdebian/libghmm1t64.substvars -cdebian/control -Pdebian/.debhelper/libghmm1t64/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=libghmm1t64-dbgsym "-DDepends=libghmm1t64 (= \${binary:Version})" "-DDescription=debug symbols for libghmm1t64" -DBuild-Ids=26aa8f69f37400524564cc47d6cbdde5836923c9 -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/ghmm/DEBIAN echo misc:Depends= >> debian/ghmm.substvars echo misc:Pre-Depends= >> debian/ghmm.substvars install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/DEBIAN dpkg-gencontrol -pghmm -ldebian/changelog -Tdebian/ghmm.substvars -cdebian/control -Pdebian/.debhelper/ghmm/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=ghmm-dbgsym "-DDepends=ghmm (= \${binary:Version})" "-DDescription=debug symbols for ghmm" "-DBuild-Ids=203354c40f0e41199b1bd29f69af4718ab082299 378d98da42efdaebf0ce08395b54abdbd48cc999 3fb7247c501b86701bca9737477c129a76740170 98a23399bee801970572965528f4664232edfedd 9d50d827fa2cadb64947007cff57cf50e67d7004" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/libghmm1t64/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibghmm1t64 -ldebian/changelog -Tdebian/libghmm1t64.substvars -cdebian/control -Pdebian/libghmm1t64 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 chmod 0644 -- debian/libghmm-dev/DEBIAN/control chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/DEBIAN/control dpkg-gencontrol -pghmm -ldebian/changelog -Tdebian/ghmm.substvars -cdebian/control -Pdebian/ghmm chmod 0644 -- debian/libghmm1t64/DEBIAN/control chmod 0644 -- debian/ghmm/DEBIAN/control dh_md5sums install -m0755 -d debian/ghmm/DEBIAN install -m0755 -d debian/libghmm1t64/DEBIAN install -m0755 -d debian/libghmm-dev/DEBIAN cd debian/ghmm >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libghmm1t64 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libghmm-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libghmm1t64/DEBIAN/md5sums install -m0755 -d debian/.debhelper/libghmm1t64/dbgsym-root/DEBIAN chmod 0644 -- debian/libghmm-dev/DEBIAN/md5sums chmod 0644 -- debian/ghmm/DEBIAN/md5sums install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/DEBIAN cd debian/.debhelper/libghmm1t64/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/.debhelper/ghmm/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libghmm1t64/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/ghmm .. dpkg-deb --root-owner-group --build debian/.debhelper/ghmm/dbgsym-root .. dpkg-deb --root-owner-group --build debian/libghmm-dev .. dpkg-deb --root-owner-group --build debian/libghmm1t64 .. dpkg-deb --root-owner-group --build debian/.debhelper/libghmm1t64/dbgsym-root .. dpkg-deb: building package 'ghmm-dbgsym' in '../ghmm-dbgsym_0.9~rc3-10_i386.deb'. dpkg-deb: building package 'libghmm-dev' in '../libghmm-dev_0.9~rc3-10_i386.deb'. dpkg-deb: building package 'ghmm' in '../ghmm_0.9~rc3-10_i386.deb'. dpkg-deb: building package 'libghmm1t64' in '../libghmm1t64_0.9~rc3-10_i386.deb'. dpkg-deb: building package 'libghmm1t64-dbgsym' in '../libghmm1t64-dbgsym_0.9~rc3-10_i386.deb'. dpkg-genbuildinfo --build=binary -O../ghmm_0.9~rc3-10_i386.buildinfo dpkg-genchanges --build=binary -O../ghmm_0.9~rc3-10_i386.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/47509/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/47509/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/47509 and its subdirectories I: Current time: Tue Jan 13 06:18:00 +14 2026 I: pbuilder-time-stamp: 1768234681