I: pbuilder: network access will be disabled during build
I: Current time: Wed Feb 12 16:12:09 +14 2025
I: pbuilder-time-stamp: 1739326329
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [ghmm_0.9~rc3-11.dsc]
I: copying [./ghmm_0.9~rc3.orig.tar.gz]
I: copying [./ghmm_0.9~rc3-11.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./ghmm_0.9~rc3-11.dsc: unsupported subcommand
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~rc3-11.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
dpkg-source: info: applying python3.13-build-fix.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/140055/tmp/hooks/D01_modify_environment starting
debug: Running on ionos1-amd64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Feb 12 02:12 /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/140055/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/140055/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]="x86_64-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=amd64
  DEBIAN_FRONTEND=noninteractive
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
  DIRSTACK=()
  DISTRIBUTION=unstable
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=x86_64
  HOST_ARCH=amd64
  IFS=' 	
  '
  INVOCATION_ID=3f44bdd0358043f79cf3fb6524b2f324
  LANG=C
  LANGUAGE=et_EE:et
  LC_ALL=C
  MACHTYPE=x86_64-pc-linux-gnu
  MAIL=/var/mail/root
  OPTERR=1
  OPTIND=1
  OSTYPE=linux-gnu
  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
  PBCURRENTCOMMANDLINEOPERATION=build
  PBUILDER_OPERATION=build
  PBUILDER_PKGDATADIR=/usr/share/pbuilder
  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
  PBUILDER_SYSCONFDIR=/etc
  PIPESTATUS=([0]="0")
  POSIXLY_CORRECT=y
  PPID=140055
  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.Cd0qNjaq/pbuilderrc_Zm8w --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Cd0qNjaq/b2 --logfile b2/build.log ghmm_0.9~rc3-11.dsc'
  SUDO_GID=110
  SUDO_UID=105
  SUDO_USER=jenkins
  TERM=unknown
  TZ=/usr/share/zoneinfo/Etc/GMT-14
  UID=0
  USER=root
  _='I: set'
  http_proxy=http://46.16.76.132:3128
I: uname -a
  Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/140055/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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 ... 19806 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} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libicu-dev{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack-dev{a} liblapack3{a} liblapacke{a} liblapacke-dev{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpkgconf3{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtmglib-dev{a} libtmglib3{a} libtool{a} libuchardet0{a} libunistring5{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} python3.13{a} python3.13-dev{a} python3.13-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 libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 
0 packages upgraded, 86 newly installed, 0 to remove and 0 not upgraded.
Need to get 62.6 MB of archives. After unpacking 272 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 11.0.0 [27.6 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-1 [745 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B]
Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.1-2 [28.0 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.109 [11.1 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 36 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 37 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 40 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 41 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
Get: 42 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 43 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 44 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 45 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get: 46 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 47 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 48 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 49 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB]
Get: 50 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 51 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 52 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 53 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB]
Get: 54 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 55 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 56 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.6.0-1 [720 kB]
Get: 57 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250108 [113 kB]
Get: 58 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-6 [210 kB]
Get: 59 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-2 [160 kB]
Get: 60 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-2 [170 kB]
Get: 61 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB]
Get: 62 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-16 [836 kB]
Get: 63 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB]
Get: 64 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB]
Get: 65 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB]
Get: 66 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-6 [10.4 MB]
Get: 67 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 68 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 69 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB]
Get: 70 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB]
Get: 71 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.1-2 [4998 kB]
Get: 72 http://deb.debian.org/debian unstable/main amd64 libtmglib3 amd64 3.12.1-2 [125 kB]
Get: 73 http://deb.debian.org/debian unstable/main amd64 liblapacke amd64 3.12.1-2 [381 kB]
Get: 74 http://deb.debian.org/debian unstable/main amd64 libtmglib-dev amd64 3.12.1-2 [129 kB]
Get: 75 http://deb.debian.org/debian unstable/main amd64 liblapacke-dev amd64 3.12.1-2 [381 kB]
Get: 76 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB]
Get: 77 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.2-1 [2151 kB]
Get: 78 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get: 79 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.2-1 [5005 kB]
Get: 80 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.1-2 [10.2 kB]
Get: 81 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [795 kB]
Get: 82 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB]
Get: 83 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB]
Get: 84 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.2-1 [507 kB]
Get: 85 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.1-2 [26.1 kB]
Get: 86 http://deb.debian.org/debian unstable/main amd64 swig amd64 4.3.0-1 [1503 kB]
Fetched 62.6 MB in 4s (17.5 MB/s)
Preconfiguring packages ...
Selecting previously unselected package libpython3.13-minimal:amd64.
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Preparing to unpack .../libpython3.13-minimal_3.13.2-1_amd64.deb ...
Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ...
Unpacking libexpat1:amd64 (2.6.4-1) ...
Selecting previously unselected package python3.13-minimal.
Preparing to unpack .../python3.13-minimal_3.13.2-1_amd64.deb ...
Unpacking python3.13-minimal (3.13.2-1) ...
Setting up libpython3.13-minimal:amd64 (3.13.2-1) ...
Setting up libexpat1:amd64 (2.6.4-1) ...
Setting up python3.13-minimal (3.13.2-1) ...
Selecting previously unselected package python3-minimal.
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Preparing to unpack .../0-python3-minimal_3.13.1-2_amd64.deb ...
Unpacking python3-minimal (3.13.1-2) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_11.0.0_all.deb ...
Unpacking media-types (11.0.0) ...
Selecting previously unselected package netbase.
Preparing to unpack .../2-netbase_6.4_all.deb ...
Unpacking netbase (6.4) ...
Selecting previously unselected package tzdata.
Preparing to unpack .../3-tzdata_2025a-2_all.deb ...
Unpacking tzdata (2025a-2) ...
Selecting previously unselected package libffi8:amd64.
Preparing to unpack .../4-libffi8_3.4.6-1_amd64.deb ...
Unpacking libffi8:amd64 (3.4.6-1) ...
Selecting previously unselected package readline-common.
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Current default time zone: 'Etc/UTC'
Local time is now:      Wed Feb 12 02:15:51 UTC 2025.
Universal Time is now:  Wed Feb 12 02:15:51 UTC 2025.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

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Processing triggers for libc-bin (2.40-6) ...
Reading package lists...
Building dependency tree...
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Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/140055/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/140055/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~rc3-11_source.changes
dpkg-buildpackage: info: source package ghmm
dpkg-buildpackage: info: source version 0.9~rc3-11
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/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.
aclocal.m4:9913: 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=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-lapacke
checking for a BSD-compatible install... /usr/bin/install -c
checking whether sleep supports fractional seconds... yes
checking filesystem timestamp resolution... 0.01
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 xargs -n works... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... none
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for file... file
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ranlib... ranlib
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for sys/time.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gawk... (cached) mawk
checking for doxygen... no
checking for rm... /usr/bin/rm
checking for pkg-config... /usr/bin/pkg-config
checking for expect... no
checking for runtest... no
configure: obsolete features disabled
configure: unsupported features disabled
checking for pthread_join in -lpthread... yes
checking for egrep... (cached) /usr/bin/grep -E
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for sqrt in -lm... yes
checking for exp in -lm... yes
checking for pow in -lm... yes
configure: "not using gsl"
checking for cos in -lm... yes
configure: "not using diagonal covariance matrix hack"
checking for 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 3.13 --dir HMMEd
I: pybuild base:311: python3.13 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 -j20
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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o rng.lo rng.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o randvar.lo randvar.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o matrixop.lo matrixop.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o gauss_tail.lo gauss_tail.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o mes.lo mes.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o ghmm_internals.lo ghmm_internals.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o mprintf.lo mprintf.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o vector.lo vector.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o matrix.lo matrix.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o scanner.lo scanner.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o linkedlist.lo linkedlist.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o sequence.lo sequence.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o psequence.lo psequence.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o xmlreader.lo xmlreader.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o xmlwriter.lo xmlwriter.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o gradescent.lo gradescent.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c randvar.c  -fPIC -DPIC -o .libs/randvar.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c matrixop.c  -fPIC -DPIC -o .libs/matrixop.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c rng.c  -fPIC -DPIC -o .libs/rng.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c mprintf.c  -fPIC -DPIC -o .libs/mprintf.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sequence.c  -fPIC -DPIC -o .libs/sequence.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c matrix.c  -fPIC -DPIC -o .libs/matrix.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c gauss_tail.c  -fPIC -DPIC -o .libs/gauss_tail.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c vector.c  -fPIC -DPIC -o .libs/vector.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c ghmm_internals.c  -fPIC -DPIC -o .libs/ghmm_internals.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c mes.c  -fPIC -DPIC -o .libs/mes.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c xmlwriter.c  -fPIC -DPIC -o .libs/xmlwriter.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c psequence.c  -fPIC -DPIC -o .libs/psequence.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c scanner.c  -fPIC -DPIC -o .libs/scanner.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c model.c  -fPIC -DPIC -o .libs/model.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c foba.c  -fPIC -DPIC -o .libs/foba.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c linkedlist.c  -fPIC -DPIC -o .libs/linkedlist.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c reestimate.c  -fPIC -DPIC -o .libs/reestimate.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c xmlreader.c  -fPIC -DPIC -o .libs/xmlreader.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c viterbi.c  -fPIC -DPIC -o .libs/viterbi.o
sequence.c: In function 'ghmm_dseq_subseq_free':
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));
      |                                ^
sequence.c:685:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
  685 |   mes_check_ptr (sq, return (-1));
      |                                 ^
sequence.c: In function 'ghmm_cseq_subseq_free':
sequence.c:715:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
  715 |   mes_check_ptr (sqd, return (-1));
      |                                  ^
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);
      |                               ^
/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o kbest.lo kbest.c
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':
ghmm_internals.c: In function 'ighmm_log_out':
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':
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);
      |              ^~~~~~~~~~~~~~~~~
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,
      |              ^~~~~~~~~
model.c: In function 'ghmm_dmodel_free':
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));
      |                                ^
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':
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;);
      |                                   ^
foba.c:848:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
  848 |     mes_check_0 (scale[t], goto STOP);
      |                                     ^
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);
      |                                      ^
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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c rng.c -o rng.o >/dev/null 2>&1
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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c ghmm_internals.c -o ghmm_internals.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c linkedlist.c -o linkedlist.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c kbest.c  -fPIC -DPIC -o .libs/kbest.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o discrime.lo discrime.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o cluster.lo cluster.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c randvar.c -o randvar.o >/dev/null 2>&1
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o root_finder.lo root_finder.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c discrime.c  -fPIC -DPIC -o .libs/discrime.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c matrixop.c -o matrixop.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o smodel.lo smodel.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c matrix.c -o matrix.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c cluster.c  -fPIC -DPIC -o .libs/cluster.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o sfoba.lo sfoba.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c cluster.c -o cluster.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o sviterbi.lo sviterbi.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c root_finder.c  -fPIC -DPIC -o .libs/root_finder.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c smodel.c  -fPIC -DPIC -o .libs/smodel.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c mes.c -o mes.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sfoba.c  -fPIC -DPIC -o .libs/sfoba.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sviterbi.c  -fPIC -DPIC -o .libs/sviterbi.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c modelutil.c -o modelutil.o >/dev/null 2>&1
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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c mprintf.c -o mprintf.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o sreestimate.lo sreestimate.c
sviterbi.c: In function 'sviterbi_free':
sviterbi.c:89:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
   89 |   mes_check_ptr (v, return (-1));
      |                                ^
/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o scluster.lo scluster.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o sgenerate.lo sgenerate.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o smixturehmm.lo smixturehmm.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o sdmodel.lo sdmodel.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sreestimate.c  -fPIC -DPIC -o .libs/sreestimate.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c scluster.c  -fPIC -DPIC -o .libs/scluster.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c kbest.c -o kbest.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c scluster.c -o scluster.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sgenerate.c  -fPIC -DPIC -o .libs/sgenerate.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sviterbi.c -o sviterbi.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c smixturehmm.c  -fPIC -DPIC -o .libs/smixturehmm.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c smap_classify.c  -fPIC -DPIC -o .libs/smap_classify.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sdmodel.c  -fPIC -DPIC -o .libs/sdmodel.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c smap_classify.c -o smap_classify.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c smixturehmm.c -o smixturehmm.o >/dev/null 2>&1
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c xmlwriter.c -o xmlwriter.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o pmodel.lo pmodel.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sdfoba.c  -fPIC -DPIC -o .libs/sdfoba.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c reestimate.c -o reestimate.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o pviterbi.lo pviterbi.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o pviterbi_propagate.lo pviterbi_propagate.c
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));
      |                                 ^
/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sdviterbi.c  -fPIC -DPIC -o .libs/sdviterbi.o
sdfoba.c: In function 'ghmm_dsmodel_backward':
sdfoba.c:336:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
  336 |     mes_check_0 (scale[t], goto STOP);
      |                                     ^
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c pmodel.c  -fPIC -DPIC -o .libs/pmodel.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c foba.c -o foba.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c pviterbi_propagate.c  -fPIC -DPIC -o .libs/pviterbi_propagate.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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));
      |                               ^
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));
      |                                ^
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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c fbgibbs.c  -fPIC -DPIC -o .libs/fbgibbs.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sequence.c -o sequence.o >/dev/null 2>&1
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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c cfbgibbs.c  -fPIC -DPIC -o .libs/cfbgibbs.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c pmodel.c -o pmodel.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sdfoba.c -o sdfoba.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sreestimate.c -o sreestimate.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sdmodel.c -o sdmodel.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c pviterbi.c -o pviterbi.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c fbgibbs.c -o fbgibbs.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c smodel.c -o smodel.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c discrime.c -o discrime.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c pviterbi_propagate.c -o pviterbi_propagate.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c cfbgibbs.c -o cfbgibbs.o >/dev/null 2>&1
/bin/sh ../libtool  --tag=CC   --mode=link gcc -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -version-info 1:0:0 -Wl,-z,relro -Wl,-z,now -o libghmm.la -rpath /usr/lib/x86_64-linux-gnu rng.lo randvar.lo matrixop.lo gauss_tail.lo mes.lo ghmm_internals.lo mprintf.lo vector.lo matrix.lo scanner.lo linkedlist.lo sequence.lo psequence.lo xmlreader.lo xmlwriter.lo model.lo foba.lo viterbi.lo reestimate.lo gradescent.lo kbest.lo discrime.lo modelutil.lo cluster.lo root_finder.lo smodel.lo sfoba.lo sviterbi.lo sreestimate.lo scluster.lo sgenerate.lo smixturehmm.lo smap_classify.lo sdmodel.lo sdfoba.lo sdviterbi.lo pmodel.lo pviterbi.lo pviterbi_propagate.lo fbgibbs.lo cfbgibbs.lo  -lm -lm -lm -lm -lpthread  -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 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -Werror=format-security -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" )
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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o probdist.o probdist.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o cluster.o cluster.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o scluster.o scluster.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o smix_hmm.o smix_hmm.c
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 
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libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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
libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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
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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o randvar_test.o randvar_test.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o root_finder_test.o root_finder_test.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o coin_toss_test.o coin_toss_test.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o two_states_three_symbols.o two_states_three_symbols.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o libxml-test.o libxml-test.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o chmm.o chmm.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o chmm_test.o chmm_test.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o shmm_viterbi_test.o shmm_viterbi_test.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o test_gsl_ran_gaussian_tail.o test_gsl_ran_gaussian_tail.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o sequences_test.o sequences_test.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o sequences_old_format.o sequences_old_format.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o label_higher_order_test.o label_higher_order_test.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o read_fa.o read_fa.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu  -I/usr/include/libxml2  -c -o mcmc.o mcmc.c
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/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 
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libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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
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libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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
libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/x86_64-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
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 'delete_ghmm_alphabet':
ghmmwrapper_wrap.c:3778:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
 3778 |             for(i=0; i<self->size; ++i)
      |                       ^
ghmmwrapper_wrap.c: In function 'ghmm_cmodel_getStateName':
ghmmwrapper_wrap.c:4031:16: warning: the comparison will always evaluate as 'true' for the pointer operand in 'self->s + (sizetype)(index * 96)' must not be NULL [-Waddress]
 4031 |             if((self->s + index) && index < self->N) return (self->s + index)->desc;
      |                ^
ghmmwrapper_wrap.c:4031:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
 4031 |             if((self->s + index) && index < self->N) return (self->s + index)->desc;
      |                                           ^
ghmmwrapper_wrap.c: In function 'ghmm_dbackground_setName':
ghmmwrapper_wrap.c:4064:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
 4064 |           if(index < self->n){
      |                    ^
ghmmwrapper_wrap.c: In function 'ghmm_dmodel_getStateName':
ghmmwrapper_wrap.c:4112:16: warning: the comparison will always evaluate as 'true' for the pointer operand in 'self->s + (sizetype)(index * 80)' must not be NULL [-Waddress]
 4112 |             if((self->s + index) && index < self->N) return (self->s + index)->desc;
      |                ^
ghmmwrapper_wrap.c:4112:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
 4112 |             if((self->s + index) && index < self->N) return (self->s + index)->desc;
      |                                           ^
ghmmwrapper_wrap.c: In function 'int_matrix_alloc':
ghmmwrapper_wrap.c:4223:28: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 4223 |                 for (i=0; i<rows; ++i) mat[i] = malloc(cols * sizeof(int));
      |                            ^
ghmmwrapper_wrap.c: In function 'int_matrix_free':
ghmmwrapper_wrap.c:4230:28: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 4230 |                 for (i=0; i<rows; ++i) free(mat[i]);
      |                            ^
ghmmwrapper_wrap.c: In function 'double_matrix_alloc':
ghmmwrapper_wrap.c:4243:28: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 4243 |                 for (i=0; i<rows; ++i) mat[i] = malloc(cols * sizeof(double));
      |                            ^
ghmmwrapper_wrap.c: In function 'double_matrix_free':
ghmmwrapper_wrap.c:4250:28: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 4250 |                 for (i=0; i<rows; ++i) free(mat[i]);
      |                            ^
ghmmwrapper_wrap.c: In function '_wrap_list2int_array':
ghmmwrapper_wrap.c:26182:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
26182 |       for (i = 0; i < arg2; i++) {
      |                     ^
ghmmwrapper_wrap.c: In function '_wrap_int_array2list':
ghmmwrapper_wrap.c:26242:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
26242 |       for (i=0; i<*arg3; i++) {
      |                  ^
ghmmwrapper_wrap.c: In function '_wrap_list2double_array':
ghmmwrapper_wrap.c:26276:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
26276 |       for (i = 0; i < arg2; i++) {
      |                     ^
ghmmwrapper_wrap.c: In function '_wrap_double_array2list':
ghmmwrapper_wrap.c:26343:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
26343 |       for (i=0; i<*arg3; i++) {
      |                  ^
pclasschange.c: In function 'set_to_lt_sum':
pclasschange.c:97:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
   97 |     td->seq_index = seq_index;
      |       ^~
pclasschange.c:96:10: note: object of size 8 allocated by 'calloc'
   96 |     td = calloc (1, sizeof (td));
      |          ^~~~~~~~~~~~~~~~~~~~~~~
pclasschange.c:98:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
   98 |     td->threshold = threshold;
      |       ^~
pclasschange.c:96:10: note: object of size 8 allocated by 'calloc'
   96 |     td = calloc (1, sizeof (td));
      |          ^~~~~~~~~~~~~~~~~~~~~~~
pclasschange.c:99:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
   99 |     td->offset_x = offset_x;
      |       ^~
pclasschange.c:96:10: note: object of size 8 allocated by 'calloc'
   96 |     td = calloc (1, sizeof (td));
      |          ^~~~~~~~~~~~~~~~~~~~~~~
pclasschange.c:100:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
  100 |     td->offset_y = offset_y;
      |       ^~
pclasschange.c:96:10: note: object of size 8 allocated by 'calloc'
   96 |     td = calloc (1, sizeof (td));
      |          ^~~~~~~~~~~~~~~~~~~~~~~
pclasschange.c: In function 'set_to_gt_sum':
pclasschange.c:112:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
  112 |     td->seq_index = seq_index;
      |       ^~
pclasschange.c:111:10: note: object of size 8 allocated by 'calloc'
  111 |     td = calloc (1, sizeof (td));
      |          ^~~~~~~~~~~~~~~~~~~~~~~
pclasschange.c:113:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
  113 |     td->threshold = threshold;
      |       ^~
pclasschange.c:111:10: note: object of size 8 allocated by 'calloc'
  111 |     td = calloc (1, sizeof (td));
      |          ^~~~~~~~~~~~~~~~~~~~~~~
pclasschange.c:114:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
  114 |     td->offset_x = offset_x;
      |       ^~
pclasschange.c:111:10: note: object of size 8 allocated by 'calloc'
  111 |     td = calloc (1, sizeof (td));
      |          ^~~~~~~~~~~~~~~~~~~~~~~
pclasschange.c:115:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
  115 |     td->offset_y = offset_y;
      |       ^~
pclasschange.c:111:10: note: object of size 8 allocated by 'calloc'
  111 |     td = calloc (1, sizeof (td));
      |          ^~~~~~~~~~~~~~~~~~~~~~~
pclasschange.c: In function 'set_to_boolean_and':
pclasschange.c:127:7: warning: array subscript 'boolean_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
  127 |     td->seq_index = seq_index;
      |       ^~
pclasschange.c:126:10: note: object of size 8 allocated by 'calloc'
  126 |     td = calloc (1, sizeof (td));
      |          ^~~~~~~~~~~~~~~~~~~~~~~
pclasschange.c:128:7: warning: array subscript 'boolean_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
  128 |     td->offset_x = offset_x;
      |       ^~
pclasschange.c:126:10: note: object of size 8 allocated by 'calloc'
  126 |     td = calloc (1, sizeof (td));
      |          ^~~~~~~~~~~~~~~~~~~~~~~
pclasschange.c:129:7: warning: array subscript 'boolean_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
  129 |     td->offset_y = offset_y;
      |       ^~
pclasschange.c:126:10: note: object of size 8 allocated by 'calloc'
  126 |     td = calloc (1, sizeof (td));
      |          ^~~~~~~~~~~~~~~~~~~~~~~
pclasschange.c: In function 'set_to_boolean_or':
pclasschange.c:141:7: warning: array subscript 'boolean_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
  141 |     td->seq_index = seq_index;
      |       ^~
pclasschange.c:140:10: note: object of size 8 allocated by 'calloc'
  140 |     td = calloc (1, sizeof (td));
      |          ^~~~~~~~~~~~~~~~~~~~~~~
pclasschange.c:142:7: warning: array subscript 'boolean_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
  142 |     td->offset_x = offset_x;
      |       ^~
pclasschange.c:140:10: note: object of size 8 allocated by 'calloc'
  140 |     td = calloc (1, sizeof (td));
      |          ^~~~~~~~~~~~~~~~~~~~~~~
pclasschange.c:143:7: warning: array subscript 'boolean_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
  143 |     td->offset_y = offset_y;
      |       ^~
pclasschange.c:140:10: note: object of size 8 allocated by 'calloc'
  140 |     td = calloc (1, sizeof (td));
      |          ^~~~~~~~~~~~~~~~~~~~~~~
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 3.13 --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/x86_64-linux-gnu'
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libghmm.la '/build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu'
libtool: install: /usr/bin/install -c .libs/libghmm.so.1.0.0 /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.so.1.0.0
libtool: install: (cd /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libghmm.so.1.0.0 libghmm.so.1 || { rm -f libghmm.so.1 && ln -s libghmm.so.1.0.0 libghmm.so.1; }; })
libtool: install: (cd /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libghmm.so.1.0.0 libghmm.so || { rm -f libghmm.so && ln -s libghmm.so.1.0.0 libghmm.so; }; })
libtool: install: /usr/bin/install -c .libs/libghmm.lai /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.la
libtool: install: /usr/bin/install -c .libs/libghmm.a /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.a
libtool: install: chmod 644 /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.a
libtool: install: ranlib /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.a
libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu'
 /usr/bin/mkdir -p '/build/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/python3.13/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/python3.13/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-313: module references __file__
__pycache__.ghmm.cpython-313: module references __file__
/build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/local/lib/python3.13/dist-packages/ghmmwrapper-0.8-py3.13-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/python3.13/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/python3.13/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 3.13 --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/x86_64-linux-gnu
install -d -m 755 debian/libghmm1t64/usr/lib/x86_64-linux-gnu
mv debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.a debian/libghmm-dev/usr/lib/x86_64-linux-gnu
mv debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.so debian/libghmm-dev/usr/lib/x86_64-linux-gnu
mv /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.so.1 debian/libghmm1t64/usr/lib/x86_64-linux-gnu
mv /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.so.1.0.0 debian/libghmm1t64/usr/lib/x86_64-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/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
	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/libghmm1t64/usr/share/doc/libghmm1t64
	install -p -m0644 debian/.debhelper/generated/libghmm1t64/dh_installchangelogs.dch.trimmed debian/libghmm1t64/usr/share/doc/libghmm1t64/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: 6.20250108
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: 3.12,3.13 (default=3.13)
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/python3.13/dist-packages to debian/ghmm/usr/lib/python3/dist-packages/
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/ghmm-config): doesn't look like a shebang: #! /bin/sh
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/probdist): cannot parse binary file
D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/smix_hmm): cannot parse binary file
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('3.13')}, 'ext_no_version': set()}
D: dh_python3 depends:103: generating dependencies for package ghmm
D: dh_python3 depends:253: D={'python3 (>= 3.13~)', 'python3:any', 'python3 (<< 3.14)'}; 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/x86_64-linux-gnu/libghmm.so
	ln -s libghmm.so.1.0.0 debian/libghmm-dev/usr/lib/x86_64-linux-gnu/libghmm.so
	rm -f debian/libghmm1t64/usr/lib/x86_64-linux-gnu/libghmm.so.1
	ln -s libghmm.so.1.0.0 debian/libghmm1t64/usr/lib/x86_64-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/ghmm/changelog.Debian
	chmod a-x usr/share/doc/libghmm1t64/changelog.Debian
	gzip -9nf usr/share/doc/ghmm/changelog.Debian
	chmod a-x usr/share/doc/libghmm-dev/changelog.Debian
	gzip -9nf usr/share/doc/libghmm1t64/changelog.Debian
	gzip -9nf usr/share/doc/libghmm-dev/changelog.Debian
	cd '/build/reproducible-path/ghmm-0.9~rc3'
	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/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/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/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/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/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/libghmm1t64/usr/share/lintian/overrides -type f -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/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/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/libghmm1t64/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
	find debian/ghmm/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
	find debian/libghmm-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
	find debian/ghmm/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
   dh_missing
   dh_dwz -a
	install -m0755 -d debian/ghmm/usr/lib/debug/.dwz/x86_64-linux-gnu
	dwz -mdebian/ghmm/usr/lib/debug/.dwz/x86_64-linux-gnu/ghmm.debug -M/usr/lib/debug/.dwz/x86_64-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-313-x86_64-linux-gnu.so
	dwz -- debian/libghmm1t64/usr/lib/x86_64-linux-gnu/libghmm.so.1.0.0
	objcopy --compress-debug-sections debian/ghmm/usr/lib/debug/.dwz/x86_64-linux-gnu/ghmm.debug
	chmod 0644 -- debian/ghmm/usr/lib/debug/.dwz/x86_64-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/x86_64-linux-gnu/libghmm.a
	install -m0755 -d debian/.debhelper/libghmm1t64/dbgsym-root/usr/lib/debug/.build-id/fd
	objcopy --only-keep-debug --compress-debug-sections debian/libghmm1t64/usr/lib/x86_64-linux-gnu/libghmm.so.1.0.0 debian/.debhelper/libghmm1t64/dbgsym-root/usr/lib/debug/.build-id/fd/2ce6d34d3227a0b46909f0fa454afda3cbbf55.debug
	install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/a7
	objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-313-x86_64-linux-gnu.so debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/a7/3ed646309c02fd57e167c0fa318fc252907931.debug
	chmod 0644 -- debian/.debhelper/libghmm1t64/dbgsym-root/usr/lib/debug/.build-id/fd/2ce6d34d3227a0b46909f0fa454afda3cbbf55.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libghmm1t64/usr/lib/x86_64-linux-gnu/libghmm.so.1.0.0
	objcopy --add-gnu-debuglink debian/.debhelper/libghmm1t64/dbgsym-root/usr/lib/debug/.build-id/fd/2ce6d34d3227a0b46909f0fa454afda3cbbf55.debug debian/libghmm1t64/usr/lib/x86_64-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/a7/3ed646309c02fd57e167c0fa318fc252907931.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/ghmm/usr/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-313-x86_64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/a7/3ed646309c02fd57e167c0fa318fc252907931.debug debian/ghmm/usr/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-313-x86_64-linux-gnu.so
	install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/29
	objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/ghmm-cluster debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/29/c041b40adb358703e5e196c2f20289c5bc7a9b.debug
	chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/29/c041b40adb358703e5e196c2f20289c5bc7a9b.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/29/c041b40adb358703e5e196c2f20289c5bc7a9b.debug debian/ghmm/usr/bin/ghmm-cluster
	install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/0a
	objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/scluster debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/0a/c7504ffd9044e283c813bc12c1a7a29ff64509.debug
	chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/0a/c7504ffd9044e283c813bc12c1a7a29ff64509.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/0a/c7504ffd9044e283c813bc12c1a7a29ff64509.debug debian/ghmm/usr/bin/scluster
	install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/82
	objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/probdist debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/82/988538e2e883a8d192862feb96e16399726885.debug
	chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/82/988538e2e883a8d192862feb96e16399726885.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/82/988538e2e883a8d192862feb96e16399726885.debug debian/ghmm/usr/bin/probdist
	install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/96
	objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/smix_hmm debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/96/19d59eac967f2e84343ecaa54c30854cc10f26.debug
	chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/96/19d59eac967f2e84343ecaa54c30854cc10f26.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/96/19d59eac967f2e84343ecaa54c30854cc10f26.debug debian/ghmm/usr/bin/smix_hmm
	install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.dwz
	cp --reflink=auto -a debian/ghmm/usr/lib/debug/.dwz/x86_64-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/x86_64-linux-gnu/libghmm.so.1.0.0
	install -m0755 -d debian/ghmm/DEBIAN
	dpkg-shlibdeps -Tdebian/ghmm.substvars debian/ghmm/usr/bin/ghmm-cluster debian/ghmm/usr/bin/scluster debian/ghmm/usr/bin/probdist debian/ghmm/usr/bin/smix_hmm debian/ghmm/usr/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-313-x86_64-linux-gnu.so
   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/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=fd2ce6d34d3227a0b46909f0fa454afda3cbbf55 -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=0ac7504ffd9044e283c813bc12c1a7a29ff64509 29c041b40adb358703e5e196c2f20289c5bc7a9b 82988538e2e883a8d192862feb96e16399726885 9619d59eac967f2e84343ecaa54c30854cc10f26 a73ed646309c02fd57e167c0fa318fc252907931" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
	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
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/.debhelper/libghmm1t64/dbgsym-root/DEBIAN/control
	dpkg-gencontrol -plibghmm1t64 -ldebian/changelog -Tdebian/libghmm1t64.substvars -cdebian/control -Pdebian/libghmm1t64
	chmod 0644 -- debian/ghmm/DEBIAN/control
	chmod 0644 -- debian/libghmm1t64/DEBIAN/control
   dh_md5sums
	install -m0755 -d debian/libghmm1t64/DEBIAN
	install -m0755 -d debian/ghmm/DEBIAN
	cd debian/libghmm1t64 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	cd debian/ghmm >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	install -m0755 -d debian/libghmm-dev/DEBIAN
	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
	cd debian/.debhelper/libghmm1t64/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/ghmm/DEBIAN/md5sums
	install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/DEBIAN
	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/libghmm-dev/DEBIAN/md5sums
	chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/DEBIAN/md5sums
   dh_builddeb
	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/ghmm ..
	dpkg-deb --root-owner-group --build debian/libghmm1t64 ..
	dpkg-deb --root-owner-group --build debian/.debhelper/libghmm1t64/dbgsym-root ..
dpkg-deb: building package 'libghmm1t64-dbgsym' in '../libghmm1t64-dbgsym_0.9~rc3-11_amd64.deb'.
dpkg-deb: building package 'libghmm-dev' in '../libghmm-dev_0.9~rc3-11_amd64.deb'.
dpkg-deb: building package 'libghmm1t64' in '../libghmm1t64_0.9~rc3-11_amd64.deb'.
dpkg-deb: building package 'ghmm' in '../ghmm_0.9~rc3-11_amd64.deb'.
dpkg-deb: building package 'ghmm-dbgsym' in '../ghmm-dbgsym_0.9~rc3-11_amd64.deb'.
 dpkg-genbuildinfo --build=binary -O../ghmm_0.9~rc3-11_amd64.buildinfo
 dpkg-genchanges --build=binary -O../ghmm_0.9~rc3-11_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/140055/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/140055/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/140055 and its subdirectories
I: Current time: Wed Feb 12 16:21:50 +14 2025
I: pbuilder-time-stamp: 1739326910