Running as unit: rb-build-amd64_28-72973.service; invocation ID: d95f1f405d4d4dad9dc3a76f6f4b2d71 ==================================================================================== Thu Sep 18 08:39:03 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_28) on jenkins, called using "ionos15-amd64 ionos11-amd64" as arguments. Thu Sep 18 08:39:03 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-n4mLVvXz" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 18 08:39:03 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Thu Sep 18 08:39:03 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-AhzICR' Thu Sep 18 08:39:03 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Thu Sep 18 08:39:03 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-mtYlTZ' ok, let's check if ghmm is building anywhere yet… ok, ghmm is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of ghmm in unstable on amd64 on jenkins now. 1st build will be done on ionos15-amd64.debian.net. 2nd build will be done on ionos11-amd64.debian.net. ============================================================================= Thu Sep 18 08:39:04 UTC 2025 I: starting to build ghmm/unstable/amd64 on jenkins on '2025-09-18 08:39' Thu Sep 18 08:39:04 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_28/72973/console.log 1758184744 amd64 unstable ghmm Thu Sep 18 08:39:04 UTC 2025 I: Downloading source for unstable/ghmm=0.9~rc3-11.1 --2025-09-18 08:39:04-- http://deb.debian.org/debian/pool/main/g/ghmm/ghmm_0.9%7erc3-11.1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2148 (2.1K) [text/prs.lines.tag] Saving to: ‘ghmm_0.9~rc3-11.1.dsc’ 0K .. 100% 12.2M=0s 2025-09-18 08:39:04 (12.2 MB/s) - ‘ghmm_0.9~rc3-11.1.dsc’ saved [2148/2148] --2025-09-18 08:39:04-- http://deb.debian.org/debian/pool/main/g/ghmm/ghmm_0.9%7erc3-11.1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2148 (2.1K) [text/prs.lines.tag] Saving to: ‘ghmm_0.9~rc3-11.1.dsc’ 0K .. 100% 12.2M=0s 2025-09-18 08:39:04 (12.2 MB/s) - ‘ghmm_0.9~rc3-11.1.dsc’ saved [2148/2148] Thu Sep 18 08:39:04 UTC 2025 I: ghmm_0.9~rc3-11.1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ghmm Binary: ghmm, libghmm-dev, libghmm1t64 Architecture: any Version: 0.9~rc3-11.1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Étienne Mollier Homepage: https://sourceforge.net/p/ghmm/wiki/Home/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/ghmm Vcs-Git: https://salsa.debian.org/med-team/ghmm.git Testsuite: autopkgtest Testsuite-Triggers: build-essential, liblapacke-dev Build-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 Package-List: ghmm deb science optional arch=any libghmm-dev deb libdevel optional arch=any libghmm1t64 deb libs optional arch=any Checksums-Sha1: c3f2be9c27010a6f82df6f136821673112ed41a5 770526 ghmm_0.9~rc3.orig.tar.gz ba166abe305d4d6da2b2dafe4707e46f5885e619 25256 ghmm_0.9~rc3-11.1.debian.tar.xz Checksums-Sha256: c42462ff4f87aadd5efe7bb6adb59657786ed71046ba924111bc28c7cbb588d0 770526 ghmm_0.9~rc3.orig.tar.gz 6a15b52afbe51b7a53696794986ef0d1fe598205752e1ceb537065afcff5e312 25256 ghmm_0.9~rc3-11.1.debian.tar.xz Files: 4e2db5a83bbd5b2a7cc6476657c0c4d7 770526 ghmm_0.9~rc3.orig.tar.gz 8525c30866aee7124331bef89804b0d3 25256 ghmm_0.9~rc3-11.1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQHEBAEBCgAuFiEEQGIgyLhVKAI3jM5BH1x6i0VWQxQFAmisl60QHGJhZ2VAZGVi aWFuLm9yZwAKCRAfXHqLRVZDFATQC/9uHyZ+jpQhWxQLEFwtW9t9v73QMd/b7Lhs cDWnIQcGm3bK87okll51LOSEifFzRtiPWS7+fQa6ppiEj1P80xBy3c2ekOnYD5lo g9rpZxYxy2+UT28S7OZOgrZnr+zrNFBXfcX/IG7NN3U+hDk5XRDXw5p0wEbwm9yZ hl+o5lOTl/5WwZt7RUbsi4kC1S1T3/eDzJ3m8Me1BQhYRc+NkDt/0ekkmF6bE0mT RrDFm4yd3TYQ8Xir6rQDuZr+IX2i0ZwMGMpMqFj2Kw7zFzjluEz5F1c0BmIMR9uc 4qu0A/tHTbei2Hwaj8gmfeoFmNWp/AP/Cm6re7ngiTzszWbOTFuQMn11jnTsMSbb PLFsiknWSak5ifUKDN8FkjfWzyBIoF8OiX6AxcYNzJ2kCfpguPpJ7FfW4IOLrhbH 6Q8AWL8HhqQF7icoLLyu8p+xc3JiyJjeDNRHXFPR6Mz7A+9pAs9P9GhBjrWVNfvJ PEYAFWTDo9t95nd0rH0o6x/2QWK9xlo= =Ee0x -----END PGP SIGNATURE----- Thu Sep 18 08:39:04 UTC 2025 I: Checking whether the package is not for us Thu Sep 18 08:39:04 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net. Thu Sep 18 08:39:04 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Thu Sep 18 08:39:04 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Thu Sep 18 08:39:04 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-zKN2Ac' ==================================================================================== Wed Oct 21 15:02:04 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "1 ghmm unstable /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4 0.9~rc3-11.1" as arguments. Wed Oct 21 15:02:04 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-V0jqSSia" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Oct 21 15:02:05 UTC 2026 I: Downloading source for unstable/ghmm=0.9~rc3-11.1 Reading package lists... NOTICE: 'ghmm' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/ghmm.git Please use: git clone https://salsa.debian.org/med-team/ghmm.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 798 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main ghmm 0.9~rc3-11.1 (dsc) [2148 B] Get:2 http://deb.debian.org/debian unstable/main ghmm 0.9~rc3-11.1 (tar) [771 kB] Get:3 http://deb.debian.org/debian unstable/main ghmm 0.9~rc3-11.1 (diff) [25.3 kB] Fetched 798 kB in 0s (22.9 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'ghmm' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/ghmm.git Please use: git clone https://salsa.debian.org/med-team/ghmm.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 798 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main ghmm 0.9~rc3-11.1 (dsc) [2148 B] Get:2 http://deb.debian.org/debian unstable/main ghmm 0.9~rc3-11.1 (tar) [771 kB] Get:3 http://deb.debian.org/debian unstable/main ghmm 0.9~rc3-11.1 (diff) [25.3 kB] Fetched 798 kB in 0s (22.9 MB/s) Download complete and in download only mode ============================================================================= Building ghmm in unstable on amd64 on ionos15-amd64 now. Date: Wed Oct 21 15:02:05 UTC 2026 Date UTC: Wed Oct 21 15:02:05 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Oct 21 03:02:05 -12 2026 I: pbuilder-time-stamp: 1792594925 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~rc3-11.1.dsc] I: copying [./ghmm_0.9~rc3.orig.tar.gz] I: copying [./ghmm_0.9~rc3-11.1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./ghmm_0.9~rc3-11.1.dsc: no acceptable signature found dpkg-source: info: extracting ghmm in ghmm-0.9~rc3 dpkg-source: info: unpacking ghmm_0.9~rc3.orig.tar.gz dpkg-source: info: unpacking ghmm_0.9~rc3-11.1.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/2894982/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='dd97bd738c2d4ae3a716f7df0596872f' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2894982' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/pbuilderrc_eoua --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/b1 --logfile b1/build.log ghmm_0.9~rc3-11.1.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2894982/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: 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 ... 19917 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} 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} libjs-sphinxdoc{a} liblapack-dev{a} liblapack3{a} liblapacke{a} liblapacke-dev{a} liblzma-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} libxml2-16{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 libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 82 newly installed, 0 to remove and 0 not upgraded. Need to get 44.7 MB of archives. After unpacking 195 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.2-1 [111 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 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 2.13.1-1 [1469 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [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 13.26 [91.8 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 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 1.15.0-1 [19.9 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 37 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-7 [229 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.2-1 [165 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5.1 [137 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5.1 [1068 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5.1 [1336 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.1-7 [5894 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libtmglib3 amd64 3.12.1-7 [143 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 liblapacke amd64 3.12.1-7 [441 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libtmglib-dev amd64 3.12.1-7 [148 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 liblapacke-dev amd64 3.12.1-7 [440 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1.1 [357 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.7-1 [2162 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.7-1 [5279 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.7-1 [10.5 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.14.5+dfsg-0.2 [744 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.7-1 [504 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.7-1 [26.1 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 82 http://deb.debian.org/debian unstable/main amd64 swig amd64 4.3.0-1 [1503 kB] Fetched 44.7 MB in 20s (2286 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.2-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../39-libjs-sphinxdoc_8.2.3-6_all.deb ... Unpacking libjs-sphinxdoc (8.2.3-6) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../40-liblapack3_3.12.1-7_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-7) ... Selecting previously unselected package liblapack-dev:amd64. Preparing to unpack .../41-liblapack-dev_3.12.1-7_amd64.deb ... Unpacking liblapack-dev:amd64 (3.12.1-7) ... Selecting previously unselected package libtmglib3:amd64. Preparing to unpack .../42-libtmglib3_3.12.1-7_amd64.deb ... Unpacking libtmglib3:amd64 (3.12.1-7) ... Selecting previously unselected package liblapacke:amd64. Preparing to unpack .../43-liblapacke_3.12.1-7_amd64.deb ... Unpacking liblapacke:amd64 (3.12.1-7) ... Selecting previously unselected package libtmglib-dev:amd64. Preparing to unpack .../44-libtmglib-dev_3.12.1-7_amd64.deb ... Unpacking libtmglib-dev:amd64 (3.12.1-7) ... Selecting previously unselected package liblapacke-dev:amd64. Preparing to unpack .../45-liblapacke-dev_3.12.1-7_amd64.deb ... Unpacking liblapacke-dev:amd64 (3.12.1-7) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../46-liblzma-dev_5.8.1-1.1_amd64.deb ... Unpacking liblzma-dev:amd64 (5.8.1-1.1) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../47-libpkgconf3_1.8.1-4_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-4) ... Selecting previously unselected package libpython3.13:amd64. Preparing to unpack .../48-libpython3.13_3.13.7-1_amd64.deb ... Unpacking libpython3.13:amd64 (3.13.7-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../49-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package libpython3.13-dev:amd64. Preparing to unpack .../50-libpython3.13-dev_3.13.7-1_amd64.deb ... Unpacking libpython3.13-dev:amd64 (3.13.7-1) ... Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../51-libpython3-dev_3.13.7-1_amd64.deb ... Unpacking libpython3-dev:amd64 (3.13.7-1) ... Selecting previously unselected package libxml2-dev:amd64. Preparing to unpack .../52-libxml2-dev_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-dev:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../53-pkgconf-bin_1.8.1-4_amd64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../54-pkgconf_1.8.1-4_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-4) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../55-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3.13-dev. 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Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../62-python3-jaraco.functools_4.1.0-1_all.deb ... Unpacking python3-jaraco.functools (4.1.0-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../63-python3-pkg-resources_78.1.1-0.1_all.deb ... Unpacking python3-pkg-resources (78.1.1-0.1) ... Selecting previously unselected package python3-jaraco.text. Preparing to unpack .../64-python3-jaraco.text_4.0.0-1_all.deb ... Unpacking python3-jaraco.text (4.0.0-1) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../65-python3-zipp_3.23.0-1_all.deb ... Unpacking python3-zipp (3.23.0-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../66-python3-setuptools_78.1.1-0.1_all.deb ... Unpacking python3-setuptools (78.1.1-0.1) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../67-python3-jaraco.context_6.0.1-1_all.deb ... Unpacking python3-jaraco.context (6.0.1-1) ... Selecting previously unselected package swig. Preparing to unpack .../68-swig_4.3.0-1_amd64.deb ... Unpacking swig (4.3.0-1) ... Setting up media-types (13.0.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up swig (4.3.0-1) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libgslcblas0:amd64 (2.8+dfsg-5.1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Oct 21 15:04:45 UTC 2026. Universal Time is now: Wed Oct 21 15:04:45 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libexpat1-dev:amd64 (2.7.2-1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up d-shlibs (0.109) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libjs-sphinxdoc (8.2.3-6) ... Setting up libgfortran5:amd64 (15.2.0-4) ... Setting up autoconf (2.72-3.1) ... Setting up liblzma-dev:amd64 (5.8.1-1.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up netbase (6.5) ... Setting up libgsl28:amd64 (2.8+dfsg-5.1) ... Setting up readline-common (8.3-3) ... Setting up libblas-dev:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up liblapack3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-2+b1) ... Setting up libgsl-dev (2.8+dfsg-5.1) ... Setting up libtool (2.5.4-5) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libxml2-dev:amd64 (2.14.5+dfsg-0.2) ... Setting up libtmglib3:amd64 (3.12.1-7) ... Setting up liblapack-dev:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up liblapacke:amd64 (3.12.1-7) ... Setting up libtmglib-dev:amd64 (3.12.1-7) ... Setting up libpython3.13-stdlib:amd64 (3.13.7-1) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up libpython3.13:amd64 (3.13.7-1) ... Setting up python3.13 (3.13.7-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.7-1) ... Setting up liblapacke-dev:amd64 (3.12.1-7) ... Setting up python3-zipp (3.23.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3.13-dev:amd64 (3.13.7-1) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.8.0-1) ... Setting up libpython3-dev:amd64 (3.13.7-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3.13-dev (3.13.7-1) ... Setting up python3-typeguard (4.4.4-1) ... Setting up debhelper (13.26) ... Setting up python3-inflect (7.5.0-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.7-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-setuptools (78.1.1-0.1) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/ghmm-0.9~rc3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../ghmm_0.9~rc3-11.1_source.changes dpkg-buildpackage: info: source package ghmm dpkg-buildpackage: info: source version 0.9~rc3-11.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Bastian Germann 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/x86_64-linux-gnu-ld checking if the linker (/usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-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/x86_64-linux-gnu-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 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 -j42 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/bash ../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/bash ../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/bash ../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 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-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 /bin/bash ../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 /bin/bash ../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 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 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 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 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 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 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 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 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 viterbi.c -fPIC -DPIC -o .libs/viterbi.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 cluster.c -fPIC -DPIC -o .libs/cluster.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 pviterbi.c -fPIC -DPIC -o .libs/pviterbi.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -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 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 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 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)); | ^ 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)); | ^ ghmm_internals.c: In function 'ighmm_log_out': ghmm_internals.c:69:17: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] 69 | message = strncat(message, error_str, slen); | ^ In function 'process_external_log', inlined from 'ighmm_log_out' at ghmm_internals.c:83:5: ghmm_internals.c:64:14: note: length computed here 64 | int slen = strlen(error_str); | ^~~~~~~~~~~~~~~~~ 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)); | ^ reestimate.c: In function 'reestimate_free': matrix.c: In function 'ighmm_cmatrix_3d_free': matrix.c:270:35: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 270 | mes_check_ptr(matrix, return(-1)); | ^ reestimate.c:79:32: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 79 | mes_check_ptr (r, return (-1)); | ^ matrix.c: In function 'ighmm_cmatrix_free': matrix.c:285:36: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 285 | mes_check_ptr(matrix, return (-1)); | ^ matrix.c: In function 'ighmm_dmatrix_free': matrix.c:343:37: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 343 | mes_check_ptr (matrix, return (-1)); | ^ sequence.c: In function 'ghmm_dseq_subseq_free': sequence.c:685:33: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 685 | mes_check_ptr (sq, return (-1)); | ^ foba.c: In function 'ghmm_dmodel_backward': 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)); | ^ foba.c:286:37: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 286 | mes_check_0 (scale[t], goto STOP); | ^ viterbi.c: In function 'viterbi_free': viterbi.c:71:31: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 71 | mes_check_ptr(v, return -1); | ^ 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)); | ^ 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)); | ^ 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); | ^ 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)); | ^ 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); | ^ foba.c: In function 'ghmm_dmodel_label_backward': foba.c:848:37: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 848 | mes_check_0 (scale[t], goto STOP); | ^ 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); | ^ pmodel.c: In function 'ghmm_dpmodel_free': pmodel.c:127:31: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 127 | mes_check_ptr(mo, return(-1)); | ^ sdfoba.c: In function 'ghmm_dsmodel_backward': sdfoba.c:336:37: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 336 | mes_check_0 (scale[t], goto STOP); | ^ 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;); | ^ 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)); | ^ 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)); | ^ 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)); | ^ 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, | ^~~~~~~~~ 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 scanner.c -o scanner.o >/dev/null 2>&1 pviterbi_propagate.c: In function 'pviterbi_propagate_free': pviterbi_propagate.c:255:30: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 255 | mes_check_ptr(v, return(-1)); | ^ xmlwriter.c: In function 'ghmm_xmlfile_write': xmlwriter.c:1106:5: warning: 'xmlSubstituteEntitiesDefault' is deprecated [-Wdeprecated-declarations] 1106 | xmlSubstituteEntitiesDefault(1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from xmlwriter.c:45: /usr/include/libxml2/libxml/parser.h:1106:17: note: declared here 1106 | xmlSubstituteEntitiesDefault(int val); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ xmlwriter.c:1171:3: warning: 'xmlMemoryDump' is deprecated [-Wdeprecated-declarations] 1171 | xmlMemoryDump(); | ^~~~~~~~~~~~~ In file included from /usr/include/libxml2/libxml/tree.h:28, from /usr/include/libxml2/libxml/xmlIO.h:18, from /usr/include/libxml2/libxml/xmlwriter.h:18, from xmlwriter.c:44: /usr/include/libxml2/libxml/xmlmemory.h:161:9: note: declared here 161 | xmlMemoryDump (void); | ^~~~~~~~~~~~~ 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)); | ^ sdviterbi.c: In function 'sdviterbi_free': sdviterbi.c:111:32: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 111 | mes_check_ptr (v, return (-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 rng.c -o rng.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 sviterbi.c -o sviterbi.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -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 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 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 modelutil.c -o modelutil.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -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 matrixop.c -o matrixop.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 randvar.c -o randvar.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 mprintf.c -o mprintf.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 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 reestimate.c -o reestimate.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -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 xmlwriter.c -o xmlwriter.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 sequence.c -o sequence.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 model.c -o model.o >/dev/null 2>&1 /bin/bash ../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" ) make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/ghmm' make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/ghmm' Making all in tools make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tools' make all-recursive make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tools' Making all in . make[6]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tools' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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/bash ../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 cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 /bin/bash ../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 scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 make[6]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tools' make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tools' make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tools' Making all in tests make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests' Making all in data make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' Making all in . make[6]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[6]: Nothing to be done for 'all-am'. make[6]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 /bin/bash ../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 root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 test_gsl_ran_gaussian_tail test_gsl_ran_gaussian_tail.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 /bin/bash ../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 libxml-test libxml-test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 shmm_viterbi_test shmm_viterbi_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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_test sequences_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 two_states_three_symbols two_states_three_symbols.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 chmm chmm.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 randvar_test randvar_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 chmm_test chmm_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 coin_toss_test coin_toss_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 read_fa read_fa.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 mcmc mcmc.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 /bin/bash ../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 label_higher_order_test label_higher_order_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 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 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 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 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 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 mcmc mcmc.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 '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: 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; | ^ 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/bash ../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/bash ../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:90: 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:90: 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:90: 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:90: 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:90: 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/ \ --override s/libxml2-16-dev/libxml2-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/ghmm/usr/share/doc/ghmm install -p -m0644 debian/.debhelper/generated/ghmm/dh_installchangelogs.dch.trimmed debian/ghmm/usr/share/doc/ghmm/changelog.Debian install -m0755 -d debian/libghmm-dev/usr/share/doc/libghmm-dev install -p -m0644 debian/.debhelper/generated/libghmm-dev/dh_installchangelogs.dch.trimmed debian/libghmm-dev/usr/share/doc/libghmm-dev/changelog.Debian 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: 6.20250414 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: 3.13 (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/probdist): cannot parse binary file D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/scluster): cannot parse binary file D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/ghmm-config): doesn't look like a shebang: #! /bin/sh I: dh_python3 tools:114: replacing shebang in debian/ghmm/usr/bin/HMMEd D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/ghmm-cluster): cannot parse binary file D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/smix_hmm): cannot parse binary file D: dh_python3 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:any', 'python3 (>= 3.13~)', '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/libghmm-dev/changelog.Debian chmod a-x usr/share/doc/libghmm1t64/changelog.Debian gzip -9nf usr/share/doc/ghmm/changelog.Debian gzip -9nf usr/share/doc/libghmm-dev/changelog.Debian gzip -9nf usr/share/doc/libghmm1t64/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 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/chmm_test.c' retained as 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/coin_toss_test.c' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/label_higher_order_test.c' retained as 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/libxml-test.c' retained as 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/mcmc.c' retained as 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/randvar_test.c' retained as 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/read_fa.c' retained as 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/root_finder_test.c' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/sequences_old_format.c' retained as 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/sequences_test.c' retained as 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/shmm_viterbi_test.c' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/test_gsl_ran_gaussian_tail.c' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/two_states_three_symbols.c' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--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/ghmm/usr/share/doc -type f -a -true -a ! -regex 'debian/ghmm/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libghmm1t64/usr/share/doc -type f -a -true -a ! -regex 'debian/libghmm1t64/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libghmm-dev/usr/share/doc -type 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/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 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/usr/share/lintian/overrides -type f -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/ghmm/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x 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/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/libghmm-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing dh_dwz -a dwz -- debian/libghmm1t64/usr/lib/x86_64-linux-gnu/libghmm.so.1.0.0 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 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/e1 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/e1/9fcc4852056bd9c0d652fb90feabe3b9edda60.debug install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/84 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/84/2b08744923da9c31974766926f2bfd7745f545.debug chmod 0644 -- debian/.debhelper/libghmm1t64/dbgsym-root/usr/lib/debug/.build-id/e1/9fcc4852056bd9c0d652fb90feabe3b9edda60.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/e1/9fcc4852056bd9c0d652fb90feabe3b9edda60.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/84/2b08744923da9c31974766926f2bfd7745f545.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/84/2b08744923da9c31974766926f2bfd7745f545.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/ed objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/probdist debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ed/84709dfdd3ffbedb5de77ef616c5b6fd02e635.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ed/84709dfdd3ffbedb5de77ef616c5b6fd02e635.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/ed/84709dfdd3ffbedb5de77ef616c5b6fd02e635.debug debian/ghmm/usr/bin/probdist install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ac objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/scluster debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ac/c90fa15a95b8c46f557624776a1e6b4136fb77.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ac/c90fa15a95b8c46f557624776a1e6b4136fb77.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/ac/c90fa15a95b8c46f557624776a1e6b4136fb77.debug debian/ghmm/usr/bin/scluster install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/19 objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/ghmm-cluster debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/19/e49a4c9880d3424e8d05686e519def4b6e2008.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/19/e49a4c9880d3424e8d05686e519def4b6e2008.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/19/e49a4c9880d3424e8d05686e519def4b6e2008.debug debian/ghmm/usr/bin/ghmm-cluster install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/9a objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/smix_hmm debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/9a/40d14ae8e2994380db9574fdfb98caf2e3dba3.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/9a/40d14ae8e2994380db9574fdfb98caf2e3dba3.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/9a/40d14ae8e2994380db9574fdfb98caf2e3dba3.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/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-313-x86_64-linux-gnu.so debian/ghmm/usr/bin/probdist debian/ghmm/usr/bin/scluster debian/ghmm/usr/bin/ghmm-cluster debian/ghmm/usr/bin/smix_hmm 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/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=19e49a4c9880d3424e8d05686e519def4b6e2008 842b08744923da9c31974766926f2bfd7745f545 9a40d14ae8e2994380db9574fdfb98caf2e3dba3 acc90fa15a95b8c46f557624776a1e6b4136fb77 ed84709dfdd3ffbedb5de77ef616c5b6fd02e635" -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 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=e19fcc4852056bd9c0d652fb90feabe3b9edda60 -DSection=debug -UMulti-Arch -UReplaces -UBreaks 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/.debhelper/libghmm1t64/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibghmm1t64 -ldebian/changelog -Tdebian/libghmm1t64.substvars -cdebian/control -Pdebian/libghmm1t64 chmod 0644 -- debian/libghmm-dev/DEBIAN/control chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/DEBIAN/control dpkg-gencontrol -pghmm -ldebian/changelog -Tdebian/ghmm.substvars -cdebian/control -Pdebian/ghmm chmod 0644 -- debian/libghmm1t64/DEBIAN/control chmod 0644 -- debian/ghmm/DEBIAN/control dh_md5sums install -m0755 -d debian/ghmm/DEBIAN install -m0755 -d debian/libghmm-dev/DEBIAN install -m0755 -d debian/libghmm1t64/DEBIAN cd debian/ghmm >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libghmm-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libghmm1t64 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libghmm1t64/DEBIAN/md5sums install -m0755 -d debian/.debhelper/libghmm1t64/dbgsym-root/DEBIAN chmod 0644 -- debian/libghmm-dev/DEBIAN/md5sums chmod 0644 -- debian/ghmm/DEBIAN/md5sums install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/DEBIAN cd debian/.debhelper/libghmm1t64/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/.debhelper/ghmm/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libghmm1t64/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/ghmm .. dpkg-deb --root-owner-group --build debian/.debhelper/ghmm/dbgsym-root .. dpkg-deb --root-owner-group --build debian/libghmm-dev .. dpkg-deb --root-owner-group --build debian/libghmm1t64 .. dpkg-deb --root-owner-group --build debian/.debhelper/libghmm1t64/dbgsym-root .. dpkg-deb: building package 'ghmm-dbgsym' in '../ghmm-dbgsym_0.9~rc3-11.1_amd64.deb'. dpkg-deb: building package 'ghmm' in '../ghmm_0.9~rc3-11.1_amd64.deb'. dpkg-deb: building package 'libghmm-dev' in '../libghmm-dev_0.9~rc3-11.1_amd64.deb'. dpkg-deb: building package 'libghmm1t64' in '../libghmm1t64_0.9~rc3-11.1_amd64.deb'. dpkg-deb: building package 'libghmm1t64-dbgsym' in '../libghmm1t64-dbgsym_0.9~rc3-11.1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../ghmm_0.9~rc3-11.1_amd64.buildinfo dpkg-genchanges --build=binary -O../ghmm_0.9~rc3-11.1_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: 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/2894982 and its subdirectories I: Current time: Wed Oct 21 03:05:31 -12 2026 I: pbuilder-time-stamp: 1792595131 Wed Oct 21 15:05:31 UTC 2026 I: Signing ./b1/ghmm_0.9~rc3-11.1_amd64.buildinfo as ghmm_0.9~rc3-11.1_amd64.buildinfo.asc Wed Oct 21 15:05:31 UTC 2026 I: Signed ./b1/ghmm_0.9~rc3-11.1_amd64.buildinfo as ./b1/ghmm_0.9~rc3-11.1_amd64.buildinfo.asc Wed Oct 21 15:05:31 UTC 2026 - build #1 for ghmm/unstable/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Wed Oct 21 15:05:31 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-V0jqSSia, removing. /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 08:42 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 08:39 b2 -rw-rw-r-- 1 jenkins jenkins 2148 Aug 25 17:19 ghmm_0.9~rc3-11.1.dsc -rw------- 1 jenkins jenkins 3257 Sep 18 08:39 rbuildlog.8BxGUCj /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/b1: total 1520 -rw-r--r-- 1 jenkins jenkins 188578 Sep 18 08:42 build.log -rw-r--r-- 1 jenkins jenkins 457468 Sep 18 08:42 ghmm-dbgsym_0.9~rc3-11.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 25256 Sep 18 08:42 ghmm_0.9~rc3-11.1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2148 Sep 18 08:42 ghmm_0.9~rc3-11.1.dsc -rw-r--r-- 1 jenkins jenkins 7698 Sep 18 08:42 ghmm_0.9~rc3-11.1_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 8580 Sep 18 08:42 ghmm_0.9~rc3-11.1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2465 Sep 18 08:42 ghmm_0.9~rc3-11.1_amd64.changes -rw-r--r-- 1 jenkins jenkins 156324 Sep 18 08:42 ghmm_0.9~rc3-11.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1304 Sep 18 08:42 ghmm_0.9~rc3-11.1_source.changes -rw-r--r-- 1 jenkins jenkins 189896 Sep 18 08:42 libghmm-dev_0.9~rc3-11.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 345868 Sep 18 08:42 libghmm1t64-dbgsym_0.9~rc3-11.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 142112 Sep 18 08:42 libghmm1t64_0.9~rc3-11.1_amd64.deb /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/b2: total 0 Thu Sep 18 08:42:31 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Oct 21 03:02:05 -12 2026 I: pbuilder-time-stamp: 1792594925 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~rc3-11.1.dsc] I: copying [./ghmm_0.9~rc3.orig.tar.gz] I: copying [./ghmm_0.9~rc3-11.1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./ghmm_0.9~rc3-11.1.dsc: no acceptable signature found dpkg-source: info: extracting ghmm in ghmm-0.9~rc3 dpkg-source: info: unpacking ghmm_0.9~rc3.orig.tar.gz dpkg-source: info: unpacking ghmm_0.9~rc3-11.1.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/2894982/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='dd97bd738c2d4ae3a716f7df0596872f' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2894982' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/pbuilderrc_eoua --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/b1 --logfile b1/build.log ghmm_0.9~rc3-11.1.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2894982/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: 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 ... 19917 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} 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} libjs-sphinxdoc{a} liblapack-dev{a} liblapack3{a} liblapacke{a} liblapacke-dev{a} liblzma-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} libxml2-16{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 libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 82 newly installed, 0 to remove and 0 not upgraded. Need to get 44.7 MB of archives. After unpacking 195 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.2-1 [111 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 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 2.13.1-1 [1469 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [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 13.26 [91.8 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 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 1.15.0-1 [19.9 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 37 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-7 [229 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.2-1 [165 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5.1 [137 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5.1 [1068 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5.1 [1336 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.1-7 [5894 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libtmglib3 amd64 3.12.1-7 [143 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 liblapacke amd64 3.12.1-7 [441 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libtmglib-dev amd64 3.12.1-7 [148 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 liblapacke-dev amd64 3.12.1-7 [440 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1.1 [357 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.7-1 [2162 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.7-1 [5279 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.7-1 [10.5 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.14.5+dfsg-0.2 [744 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.7-1 [504 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.7-1 [26.1 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 82 http://deb.debian.org/debian unstable/main amd64 swig amd64 4.3.0-1 [1503 kB] Fetched 44.7 MB in 20s (2286 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.2-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_amd64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:amd64 (3.13.7-1) ... Setting up libexpat1:amd64 (2.7.2-1) ... Setting up python3.13-minimal (3.13.7-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20251 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21266 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../16-d-shlibs_0.109_all.deb ... Unpacking d-shlibs (0.109) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../23-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../25-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../26-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Selecting previously unselected package dh-python. Preparing to unpack .../31-dh-python_6.20250414_all.deb ... Unpacking dh-python (6.20250414) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../32-libblas3_3.12.1-7_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-7) ... Selecting previously unselected package libblas-dev:amd64. Preparing to unpack .../33-libblas-dev_3.12.1-7_amd64.deb ... Unpacking libblas-dev:amd64 (3.12.1-7) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../34-libexpat1-dev_2.7.2-1_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.7.2-1) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../35-libgfortran5_15.2.0-4_amd64.deb ... Unpacking libgfortran5:amd64 (15.2.0-4) ... Selecting previously unselected package libgslcblas0:amd64. Preparing to unpack .../36-libgslcblas0_2.8+dfsg-5.1_amd64.deb ... Unpacking libgslcblas0:amd64 (2.8+dfsg-5.1) ... Selecting previously unselected package libgsl28:amd64. Preparing to unpack .../37-libgsl28_2.8+dfsg-5.1_amd64.deb ... Unpacking libgsl28:amd64 (2.8+dfsg-5.1) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../38-libgsl-dev_2.8+dfsg-5.1_amd64.deb ... Unpacking libgsl-dev (2.8+dfsg-5.1) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../39-libjs-sphinxdoc_8.2.3-6_all.deb ... Unpacking libjs-sphinxdoc (8.2.3-6) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../40-liblapack3_3.12.1-7_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-7) ... Selecting previously unselected package liblapack-dev:amd64. Preparing to unpack .../41-liblapack-dev_3.12.1-7_amd64.deb ... Unpacking liblapack-dev:amd64 (3.12.1-7) ... Selecting previously unselected package libtmglib3:amd64. Preparing to unpack .../42-libtmglib3_3.12.1-7_amd64.deb ... Unpacking libtmglib3:amd64 (3.12.1-7) ... Selecting previously unselected package liblapacke:amd64. Preparing to unpack .../43-liblapacke_3.12.1-7_amd64.deb ... Unpacking liblapacke:amd64 (3.12.1-7) ... Selecting previously unselected package libtmglib-dev:amd64. Preparing to unpack .../44-libtmglib-dev_3.12.1-7_amd64.deb ... Unpacking libtmglib-dev:amd64 (3.12.1-7) ... Selecting previously unselected package liblapacke-dev:amd64. Preparing to unpack .../45-liblapacke-dev_3.12.1-7_amd64.deb ... Unpacking liblapacke-dev:amd64 (3.12.1-7) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../46-liblzma-dev_5.8.1-1.1_amd64.deb ... Unpacking liblzma-dev:amd64 (5.8.1-1.1) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../47-libpkgconf3_1.8.1-4_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-4) ... Selecting previously unselected package libpython3.13:amd64. Preparing to unpack .../48-libpython3.13_3.13.7-1_amd64.deb ... Unpacking libpython3.13:amd64 (3.13.7-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../49-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package libpython3.13-dev:amd64. Preparing to unpack .../50-libpython3.13-dev_3.13.7-1_amd64.deb ... Unpacking libpython3.13-dev:amd64 (3.13.7-1) ... Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../51-libpython3-dev_3.13.7-1_amd64.deb ... Unpacking libpython3-dev:amd64 (3.13.7-1) ... Selecting previously unselected package libxml2-dev:amd64. Preparing to unpack .../52-libxml2-dev_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-dev:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../53-pkgconf-bin_1.8.1-4_amd64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../54-pkgconf_1.8.1-4_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-4) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../55-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3.13-dev. 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Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../62-python3-jaraco.functools_4.1.0-1_all.deb ... Unpacking python3-jaraco.functools (4.1.0-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../63-python3-pkg-resources_78.1.1-0.1_all.deb ... Unpacking python3-pkg-resources (78.1.1-0.1) ... Selecting previously unselected package python3-jaraco.text. Preparing to unpack .../64-python3-jaraco.text_4.0.0-1_all.deb ... Unpacking python3-jaraco.text (4.0.0-1) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../65-python3-zipp_3.23.0-1_all.deb ... Unpacking python3-zipp (3.23.0-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../66-python3-setuptools_78.1.1-0.1_all.deb ... Unpacking python3-setuptools (78.1.1-0.1) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../67-python3-jaraco.context_6.0.1-1_all.deb ... Unpacking python3-jaraco.context (6.0.1-1) ... Selecting previously unselected package swig. Preparing to unpack .../68-swig_4.3.0-1_amd64.deb ... Unpacking swig (4.3.0-1) ... Setting up media-types (13.0.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up swig (4.3.0-1) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libgslcblas0:amd64 (2.8+dfsg-5.1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Oct 21 15:04:45 UTC 2026. Universal Time is now: Wed Oct 21 15:04:45 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libexpat1-dev:amd64 (2.7.2-1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up d-shlibs (0.109) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libjs-sphinxdoc (8.2.3-6) ... Setting up libgfortran5:amd64 (15.2.0-4) ... Setting up autoconf (2.72-3.1) ... Setting up liblzma-dev:amd64 (5.8.1-1.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up netbase (6.5) ... Setting up libgsl28:amd64 (2.8+dfsg-5.1) ... Setting up readline-common (8.3-3) ... Setting up libblas-dev:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up liblapack3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-2+b1) ... Setting up libgsl-dev (2.8+dfsg-5.1) ... Setting up libtool (2.5.4-5) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libxml2-dev:amd64 (2.14.5+dfsg-0.2) ... Setting up libtmglib3:amd64 (3.12.1-7) ... Setting up liblapack-dev:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up liblapacke:amd64 (3.12.1-7) ... Setting up libtmglib-dev:amd64 (3.12.1-7) ... Setting up libpython3.13-stdlib:amd64 (3.13.7-1) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up libpython3.13:amd64 (3.13.7-1) ... Setting up python3.13 (3.13.7-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.7-1) ... Setting up liblapacke-dev:amd64 (3.12.1-7) ... Setting up python3-zipp (3.23.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3.13-dev:amd64 (3.13.7-1) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.8.0-1) ... Setting up libpython3-dev:amd64 (3.13.7-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3.13-dev (3.13.7-1) ... Setting up python3-typeguard (4.4.4-1) ... Setting up debhelper (13.26) ... Setting up python3-inflect (7.5.0-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.7-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-setuptools (78.1.1-0.1) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/ghmm-0.9~rc3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../ghmm_0.9~rc3-11.1_source.changes dpkg-buildpackage: info: source package ghmm dpkg-buildpackage: info: source version 0.9~rc3-11.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Bastian Germann 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/x86_64-linux-gnu-ld checking if the linker (/usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-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/x86_64-linux-gnu-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 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 -j42 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/bash ../libtool --tag=CC 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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/bash ../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/bash ../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 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--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 /bin/bash ../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/bash ../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 /bin/bash ../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 /bin/bash ../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 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 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 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 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 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 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 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 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 viterbi.c -fPIC -DPIC -o .libs/viterbi.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 cluster.c -fPIC -DPIC -o .libs/cluster.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 pviterbi.c -fPIC -DPIC -o .libs/pviterbi.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -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 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 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 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)); | ^ 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)); | ^ ghmm_internals.c: In function 'ighmm_log_out': ghmm_internals.c:69:17: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] 69 | message = strncat(message, error_str, slen); | ^ In function 'process_external_log', inlined from 'ighmm_log_out' at ghmm_internals.c:83:5: ghmm_internals.c:64:14: note: length computed here 64 | int slen = strlen(error_str); | ^~~~~~~~~~~~~~~~~ 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)); | ^ reestimate.c: In function 'reestimate_free': matrix.c: In function 'ighmm_cmatrix_3d_free': matrix.c:270:35: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 270 | mes_check_ptr(matrix, return(-1)); | ^ reestimate.c:79:32: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 79 | mes_check_ptr (r, return (-1)); | ^ matrix.c: In function 'ighmm_cmatrix_free': matrix.c:285:36: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 285 | mes_check_ptr(matrix, return (-1)); | ^ matrix.c: In function 'ighmm_dmatrix_free': matrix.c:343:37: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 343 | mes_check_ptr (matrix, return (-1)); | ^ sequence.c: In function 'ghmm_dseq_subseq_free': sequence.c:685:33: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 685 | mes_check_ptr (sq, return (-1)); | ^ foba.c: In function 'ghmm_dmodel_backward': 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)); | ^ foba.c:286:37: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 286 | mes_check_0 (scale[t], goto STOP); | ^ viterbi.c: In function 'viterbi_free': viterbi.c:71:31: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 71 | mes_check_ptr(v, return -1); | ^ 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)); | ^ 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)); | ^ 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); | ^ 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)); | ^ 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); | ^ foba.c: In function 'ghmm_dmodel_label_backward': foba.c:848:37: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 848 | mes_check_0 (scale[t], goto STOP); | ^ 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); | ^ pmodel.c: In function 'ghmm_dpmodel_free': pmodel.c:127:31: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 127 | mes_check_ptr(mo, return(-1)); | ^ sdfoba.c: In function 'ghmm_dsmodel_backward': sdfoba.c:336:37: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 336 | mes_check_0 (scale[t], goto STOP); | ^ 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;); | ^ 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)); | ^ 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)); | ^ 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)); | ^ 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, | ^~~~~~~~~ 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 scanner.c -o scanner.o >/dev/null 2>&1 pviterbi_propagate.c: In function 'pviterbi_propagate_free': pviterbi_propagate.c:255:30: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 255 | mes_check_ptr(v, return(-1)); | ^ xmlwriter.c: In function 'ghmm_xmlfile_write': xmlwriter.c:1106:5: warning: 'xmlSubstituteEntitiesDefault' is deprecated [-Wdeprecated-declarations] 1106 | xmlSubstituteEntitiesDefault(1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from xmlwriter.c:45: /usr/include/libxml2/libxml/parser.h:1106:17: note: declared here 1106 | xmlSubstituteEntitiesDefault(int val); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ xmlwriter.c:1171:3: warning: 'xmlMemoryDump' is deprecated [-Wdeprecated-declarations] 1171 | xmlMemoryDump(); | ^~~~~~~~~~~~~ In file included from /usr/include/libxml2/libxml/tree.h:28, from /usr/include/libxml2/libxml/xmlIO.h:18, from /usr/include/libxml2/libxml/xmlwriter.h:18, from xmlwriter.c:44: /usr/include/libxml2/libxml/xmlmemory.h:161:9: note: declared here 161 | xmlMemoryDump (void); | ^~~~~~~~~~~~~ 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)); | ^ sdviterbi.c: In function 'sdviterbi_free': sdviterbi.c:111:32: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 111 | mes_check_ptr (v, return (-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 rng.c -o rng.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 sviterbi.c -o sviterbi.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -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 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 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 modelutil.c -o modelutil.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -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 matrixop.c -o matrixop.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 randvar.c -o randvar.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 mprintf.c -o mprintf.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 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 reestimate.c -o reestimate.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -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 xmlwriter.c -o xmlwriter.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 sequence.c -o sequence.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 model.c -o model.o >/dev/null 2>&1 /bin/bash ../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" ) make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/ghmm' make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/ghmm' Making all in tools make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tools' make all-recursive make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tools' Making all in . make[6]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tools' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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/bash ../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 cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 /bin/bash ../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 scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 make[6]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tools' make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tools' make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tools' Making all in tests make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests' Making all in data make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' Making all in . make[6]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[6]: Nothing to be done for 'all-am'. make[6]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 /bin/bash ../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 root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 test_gsl_ran_gaussian_tail test_gsl_ran_gaussian_tail.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 /bin/bash ../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 libxml-test libxml-test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 shmm_viterbi_test shmm_viterbi_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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_test sequences_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 two_states_three_symbols two_states_three_symbols.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 chmm chmm.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 randvar_test randvar_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 chmm_test chmm_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 coin_toss_test coin_toss_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 read_fa read_fa.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/bash ../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 mcmc mcmc.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 /bin/bash ../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 label_higher_order_test label_higher_order_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 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 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 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 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 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 mcmc mcmc.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 '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: 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; | ^ 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/bash ../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/bash ../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:90: 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:90: 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:90: 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:90: 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:90: 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/ \ --override s/libxml2-16-dev/libxml2-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/ghmm/usr/share/doc/ghmm install -p -m0644 debian/.debhelper/generated/ghmm/dh_installchangelogs.dch.trimmed debian/ghmm/usr/share/doc/ghmm/changelog.Debian install -m0755 -d debian/libghmm-dev/usr/share/doc/libghmm-dev install -p -m0644 debian/.debhelper/generated/libghmm-dev/dh_installchangelogs.dch.trimmed debian/libghmm-dev/usr/share/doc/libghmm-dev/changelog.Debian 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: 6.20250414 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: 3.13 (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/probdist): cannot parse binary file D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/scluster): cannot parse binary file D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/ghmm-config): doesn't look like a shebang: #! /bin/sh I: dh_python3 tools:114: replacing shebang in debian/ghmm/usr/bin/HMMEd D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/ghmm-cluster): cannot parse binary file D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/smix_hmm): cannot parse binary file D: dh_python3 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:any', 'python3 (>= 3.13~)', '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/libghmm-dev/changelog.Debian chmod a-x usr/share/doc/libghmm1t64/changelog.Debian gzip -9nf usr/share/doc/ghmm/changelog.Debian gzip -9nf usr/share/doc/libghmm-dev/changelog.Debian gzip -9nf usr/share/doc/libghmm1t64/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 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/chmm_test.c' retained as 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/coin_toss_test.c' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/label_higher_order_test.c' retained as 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/libxml-test.c' retained as 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/mcmc.c' retained as 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/randvar_test.c' retained as 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/read_fa.c' retained as 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/root_finder_test.c' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/sequences_old_format.c' retained as 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/sequences_test.c' retained as 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/shmm_viterbi_test.c' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/test_gsl_ran_gaussian_tail.c' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of 'debian/ghmm/usr/share/doc/ghmm/examples/two_states_three_symbols.c' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--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/ghmm/usr/share/doc -type f -a -true -a ! -regex 'debian/ghmm/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libghmm1t64/usr/share/doc -type f -a -true -a ! -regex 'debian/libghmm1t64/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libghmm-dev/usr/share/doc -type 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/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 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/usr/share/lintian/overrides -type f -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/ghmm/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x 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/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/libghmm-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing dh_dwz -a dwz -- debian/libghmm1t64/usr/lib/x86_64-linux-gnu/libghmm.so.1.0.0 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 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/e1 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/e1/9fcc4852056bd9c0d652fb90feabe3b9edda60.debug install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/84 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/84/2b08744923da9c31974766926f2bfd7745f545.debug chmod 0644 -- debian/.debhelper/libghmm1t64/dbgsym-root/usr/lib/debug/.build-id/e1/9fcc4852056bd9c0d652fb90feabe3b9edda60.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/e1/9fcc4852056bd9c0d652fb90feabe3b9edda60.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/84/2b08744923da9c31974766926f2bfd7745f545.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/84/2b08744923da9c31974766926f2bfd7745f545.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/ed objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/probdist debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ed/84709dfdd3ffbedb5de77ef616c5b6fd02e635.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ed/84709dfdd3ffbedb5de77ef616c5b6fd02e635.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/ed/84709dfdd3ffbedb5de77ef616c5b6fd02e635.debug debian/ghmm/usr/bin/probdist install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ac objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/scluster debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ac/c90fa15a95b8c46f557624776a1e6b4136fb77.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ac/c90fa15a95b8c46f557624776a1e6b4136fb77.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/ac/c90fa15a95b8c46f557624776a1e6b4136fb77.debug debian/ghmm/usr/bin/scluster install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/19 objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/ghmm-cluster debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/19/e49a4c9880d3424e8d05686e519def4b6e2008.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/19/e49a4c9880d3424e8d05686e519def4b6e2008.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/19/e49a4c9880d3424e8d05686e519def4b6e2008.debug debian/ghmm/usr/bin/ghmm-cluster install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/9a objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/smix_hmm debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/9a/40d14ae8e2994380db9574fdfb98caf2e3dba3.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/9a/40d14ae8e2994380db9574fdfb98caf2e3dba3.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/9a/40d14ae8e2994380db9574fdfb98caf2e3dba3.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/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-313-x86_64-linux-gnu.so debian/ghmm/usr/bin/probdist debian/ghmm/usr/bin/scluster debian/ghmm/usr/bin/ghmm-cluster debian/ghmm/usr/bin/smix_hmm 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/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=19e49a4c9880d3424e8d05686e519def4b6e2008 842b08744923da9c31974766926f2bfd7745f545 9a40d14ae8e2994380db9574fdfb98caf2e3dba3 acc90fa15a95b8c46f557624776a1e6b4136fb77 ed84709dfdd3ffbedb5de77ef616c5b6fd02e635" -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 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=e19fcc4852056bd9c0d652fb90feabe3b9edda60 -DSection=debug -UMulti-Arch -UReplaces -UBreaks 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/.debhelper/libghmm1t64/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibghmm1t64 -ldebian/changelog -Tdebian/libghmm1t64.substvars -cdebian/control -Pdebian/libghmm1t64 chmod 0644 -- debian/libghmm-dev/DEBIAN/control chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/DEBIAN/control dpkg-gencontrol -pghmm -ldebian/changelog -Tdebian/ghmm.substvars -cdebian/control -Pdebian/ghmm chmod 0644 -- debian/libghmm1t64/DEBIAN/control chmod 0644 -- debian/ghmm/DEBIAN/control dh_md5sums install -m0755 -d debian/ghmm/DEBIAN install -m0755 -d debian/libghmm-dev/DEBIAN install -m0755 -d debian/libghmm1t64/DEBIAN cd debian/ghmm >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libghmm-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libghmm1t64 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libghmm1t64/DEBIAN/md5sums install -m0755 -d debian/.debhelper/libghmm1t64/dbgsym-root/DEBIAN chmod 0644 -- debian/libghmm-dev/DEBIAN/md5sums chmod 0644 -- debian/ghmm/DEBIAN/md5sums install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/DEBIAN cd debian/.debhelper/libghmm1t64/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/.debhelper/ghmm/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libghmm1t64/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/ghmm .. dpkg-deb --root-owner-group --build debian/.debhelper/ghmm/dbgsym-root .. dpkg-deb --root-owner-group --build debian/libghmm-dev .. dpkg-deb --root-owner-group --build debian/libghmm1t64 .. dpkg-deb --root-owner-group --build debian/.debhelper/libghmm1t64/dbgsym-root .. dpkg-deb: building package 'ghmm-dbgsym' in '../ghmm-dbgsym_0.9~rc3-11.1_amd64.deb'. dpkg-deb: building package 'ghmm' in '../ghmm_0.9~rc3-11.1_amd64.deb'. dpkg-deb: building package 'libghmm-dev' in '../libghmm-dev_0.9~rc3-11.1_amd64.deb'. dpkg-deb: building package 'libghmm1t64' in '../libghmm1t64_0.9~rc3-11.1_amd64.deb'. dpkg-deb: building package 'libghmm1t64-dbgsym' in '../libghmm1t64-dbgsym_0.9~rc3-11.1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../ghmm_0.9~rc3-11.1_amd64.buildinfo dpkg-genchanges --build=binary -O../ghmm_0.9~rc3-11.1_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: 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/2894982 and its subdirectories I: Current time: Wed Oct 21 03:05:31 -12 2026 I: pbuilder-time-stamp: 1792595131 Thu Sep 18 08:42:32 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Thu Sep 18 08:42:32 UTC 2025 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Thu Sep 18 08:42:32 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Thu Sep 18 08:42:32 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-1wK5WT' ==================================================================================== Thu Sep 18 08:42:32 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos11-amd64, called using "2 ghmm unstable /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4 0.9~rc3-11.1" as arguments. Thu Sep 18 08:42:32 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-nI89SrSN" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 18 08:42:32 UTC 2025 I: Downloading source for unstable/ghmm=0.9~rc3-11.1 Reading package lists... NOTICE: 'ghmm' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/ghmm.git Please use: git clone https://salsa.debian.org/med-team/ghmm.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 798 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main ghmm 0.9~rc3-11.1 (dsc) [2148 B] Get:2 http://deb.debian.org/debian unstable/main ghmm 0.9~rc3-11.1 (tar) [771 kB] Get:3 http://deb.debian.org/debian unstable/main ghmm 0.9~rc3-11.1 (diff) [25.3 kB] Fetched 798 kB in 0s (22.4 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'ghmm' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/ghmm.git Please use: git clone https://salsa.debian.org/med-team/ghmm.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 798 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main ghmm 0.9~rc3-11.1 (dsc) [2148 B] Get:2 http://deb.debian.org/debian unstable/main ghmm 0.9~rc3-11.1 (tar) [771 kB] Get:3 http://deb.debian.org/debian unstable/main ghmm 0.9~rc3-11.1 (diff) [25.3 kB] Fetched 798 kB in 0s (22.4 MB/s) Download complete and in download only mode ============================================================================= Re-Building ghmm in unstable on amd64 on ionos11-amd64 now. Date: Thu Sep 18 08:42:33 UTC 2025 Date UTC: Thu Sep 18 08:42:33 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4 + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/pbuilderrc_Av26 + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' ghmm = debian-installer -o ghmm = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' ghmm = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo 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.dJrJz6X4/pbuilderrc_Av26 --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.dJrJz6X4/b2 --logfile b2/build.log ghmm_0.9~rc3-11.1.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 18 22:42:33 +14 2025 I: pbuilder-time-stamp: 1758184953 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~rc3-11.1.dsc] I: copying [./ghmm_0.9~rc3.orig.tar.gz] I: copying [./ghmm_0.9~rc3-11.1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./ghmm_0.9~rc3-11.1.dsc: no acceptable signature found dpkg-source: info: extracting ghmm in ghmm-0.9~rc3 dpkg-source: info: unpacking ghmm_0.9~rc3.orig.tar.gz dpkg-source: info: unpacking ghmm_0.9~rc3-11.1.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/513057/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-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 Sep 18 08:43 /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/513057/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/513057/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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(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=40 ' 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=d414b8d2150341aabb5522b60b56bc92 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=513057 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.dJrJz6X4/pbuilderrc_Av26 --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.dJrJz6X4/b2 --logfile b2/build.log ghmm_0.9~rc3-11.1.dsc' SUDO_GID=111 SUDO_HOME=/var/lib/jenkins SUDO_UID=106 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 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/513057/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: 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 ... 19917 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} 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} libjs-sphinxdoc{a} liblapack-dev{a} liblapack3{a} liblapacke{a} liblapacke-dev{a} liblzma-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} libxml2-16{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 libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 82 newly installed, 0 to remove and 0 not upgraded. Need to get 44.7 MB of archives. After unpacking 195 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.2-1 [111 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 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 2.13.1-1 [1469 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [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 13.26 [91.8 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 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 1.15.0-1 [19.9 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 37 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-7 [229 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.2-1 [165 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5.1 [137 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5.1 [1068 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5.1 [1336 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.1-7 [5894 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libtmglib3 amd64 3.12.1-7 [143 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 liblapacke amd64 3.12.1-7 [441 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libtmglib-dev amd64 3.12.1-7 [148 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 liblapacke-dev amd64 3.12.1-7 [440 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1.1 [357 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.7-1 [2162 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.7-1 [5279 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.7-1 [10.5 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.14.5+dfsg-0.2 [744 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.7-1 [504 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.7-1 [26.1 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 82 http://deb.debian.org/debian unstable/main amd64 swig amd64 4.3.0-1 [1503 kB] Fetched 44.7 MB in 17s (2599 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.2-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_amd64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:amd64 (3.13.7-1) ... Setting up libexpat1:amd64 (2.7.2-1) ... Setting up python3.13-minimal (3.13.7-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20251 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21266 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package sensible-utils. 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Selecting previously unselected package libblas-dev:amd64. Preparing to unpack .../33-libblas-dev_3.12.1-7_amd64.deb ... Unpacking libblas-dev:amd64 (3.12.1-7) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../34-libexpat1-dev_2.7.2-1_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.7.2-1) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../35-libgfortran5_15.2.0-4_amd64.deb ... Unpacking libgfortran5:amd64 (15.2.0-4) ... Selecting previously unselected package libgslcblas0:amd64. Preparing to unpack .../36-libgslcblas0_2.8+dfsg-5.1_amd64.deb ... Unpacking libgslcblas0:amd64 (2.8+dfsg-5.1) ... Selecting previously unselected package libgsl28:amd64. Preparing to unpack .../37-libgsl28_2.8+dfsg-5.1_amd64.deb ... Unpacking libgsl28:amd64 (2.8+dfsg-5.1) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../38-libgsl-dev_2.8+dfsg-5.1_amd64.deb ... Unpacking libgsl-dev (2.8+dfsg-5.1) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../39-libjs-sphinxdoc_8.2.3-6_all.deb ... Unpacking libjs-sphinxdoc (8.2.3-6) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../40-liblapack3_3.12.1-7_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-7) ... Selecting previously unselected package liblapack-dev:amd64. Preparing to unpack .../41-liblapack-dev_3.12.1-7_amd64.deb ... Unpacking liblapack-dev:amd64 (3.12.1-7) ... Selecting previously unselected package libtmglib3:amd64. Preparing to unpack .../42-libtmglib3_3.12.1-7_amd64.deb ... Unpacking libtmglib3:amd64 (3.12.1-7) ... Selecting previously unselected package liblapacke:amd64. Preparing to unpack .../43-liblapacke_3.12.1-7_amd64.deb ... Unpacking liblapacke:amd64 (3.12.1-7) ... Selecting previously unselected package libtmglib-dev:amd64. Preparing to unpack .../44-libtmglib-dev_3.12.1-7_amd64.deb ... Unpacking libtmglib-dev:amd64 (3.12.1-7) ... Selecting previously unselected package liblapacke-dev:amd64. Preparing to unpack .../45-liblapacke-dev_3.12.1-7_amd64.deb ... Unpacking liblapacke-dev:amd64 (3.12.1-7) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../46-liblzma-dev_5.8.1-1.1_amd64.deb ... Unpacking liblzma-dev:amd64 (5.8.1-1.1) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../47-libpkgconf3_1.8.1-4_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-4) ... Selecting previously unselected package libpython3.13:amd64. Preparing to unpack .../48-libpython3.13_3.13.7-1_amd64.deb ... Unpacking libpython3.13:amd64 (3.13.7-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../49-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package libpython3.13-dev:amd64. Preparing to unpack .../50-libpython3.13-dev_3.13.7-1_amd64.deb ... Unpacking libpython3.13-dev:amd64 (3.13.7-1) ... Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../51-libpython3-dev_3.13.7-1_amd64.deb ... Unpacking libpython3-dev:amd64 (3.13.7-1) ... Selecting previously unselected package libxml2-dev:amd64. Preparing to unpack .../52-libxml2-dev_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-dev:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../53-pkgconf-bin_1.8.1-4_amd64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../54-pkgconf_1.8.1-4_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-4) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../55-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3.13-dev. Preparing to unpack .../56-python3.13-dev_3.13.7-1_amd64.deb ... Unpacking python3.13-dev (3.13.7-1) ... Selecting previously unselected package python3-dev. Preparing to unpack .../57-python3-dev_3.13.7-1_amd64.deb ... Unpacking python3-dev (3.13.7-1) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../58-python3-more-itertools_10.8.0-1_all.deb ... Unpacking python3-more-itertools (10.8.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../59-python3-typing-extensions_4.15.0-1_all.deb ... Unpacking python3-typing-extensions (4.15.0-1) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../60-python3-typeguard_4.4.4-1_all.deb ... Unpacking python3-typeguard (4.4.4-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../61-python3-inflect_7.5.0-1_all.deb ... Unpacking python3-inflect (7.5.0-1) ... Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../62-python3-jaraco.functools_4.1.0-1_all.deb ... Unpacking python3-jaraco.functools (4.1.0-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../63-python3-pkg-resources_78.1.1-0.1_all.deb ... Unpacking python3-pkg-resources (78.1.1-0.1) ... Selecting previously unselected package python3-jaraco.text. Preparing to unpack .../64-python3-jaraco.text_4.0.0-1_all.deb ... Unpacking python3-jaraco.text (4.0.0-1) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../65-python3-zipp_3.23.0-1_all.deb ... Unpacking python3-zipp (3.23.0-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../66-python3-setuptools_78.1.1-0.1_all.deb ... Unpacking python3-setuptools (78.1.1-0.1) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../67-python3-jaraco.context_6.0.1-1_all.deb ... Unpacking python3-jaraco.context (6.0.1-1) ... Selecting previously unselected package swig. Preparing to unpack .../68-swig_4.3.0-1_amd64.deb ... Unpacking swig (4.3.0-1) ... Setting up media-types (13.0.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up swig (4.3.0-1) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libgslcblas0:amd64 (2.8+dfsg-5.1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Sep 18 08:46:04 UTC 2025. Universal Time is now: Thu Sep 18 08:46:04 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libexpat1-dev:amd64 (2.7.2-1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up d-shlibs (0.109) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libjs-sphinxdoc (8.2.3-6) ... Setting up libgfortran5:amd64 (15.2.0-4) ... Setting up autoconf (2.72-3.1) ... Setting up liblzma-dev:amd64 (5.8.1-1.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up netbase (6.5) ... Setting up libgsl28:amd64 (2.8+dfsg-5.1) ... Setting up readline-common (8.3-3) ... Setting up libblas-dev:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up liblapack3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-2+b1) ... Setting up libgsl-dev (2.8+dfsg-5.1) ... Setting up libtool (2.5.4-5) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libxml2-dev:amd64 (2.14.5+dfsg-0.2) ... Setting up libtmglib3:amd64 (3.12.1-7) ... Setting up liblapack-dev:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up liblapacke:amd64 (3.12.1-7) ... Setting up libtmglib-dev:amd64 (3.12.1-7) ... Setting up libpython3.13-stdlib:amd64 (3.13.7-1) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up libpython3.13:amd64 (3.13.7-1) ... Setting up python3.13 (3.13.7-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.7-1) ... Setting up liblapacke-dev:amd64 (3.12.1-7) ... Setting up python3-zipp (3.23.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3.13-dev:amd64 (3.13.7-1) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.8.0-1) ... Setting up libpython3-dev:amd64 (3.13.7-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3.13-dev (3.13.7-1) ... Setting up python3-typeguard (4.4.4-1) ... Setting up debhelper (13.26) ... Setting up python3-inflect (7.5.0-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.7-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-setuptools (78.1.1-0.1) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/513057/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/513057/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~rc3-11.1_source.changes dpkg-buildpackage: info: source package ghmm dpkg-buildpackage: info: source version 0.9~rc3-11.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Bastian Germann 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/x86_64-linux-gnu-ld checking if the linker (/usr/bin/x86_64-linux-gnu-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/x86_64-linux-gnu-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/x86_64-linux-gnu-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 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 -j40 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 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-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 /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 /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 /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 /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 /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 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 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 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 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 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 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 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 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 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 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 viterbi.c -fPIC -DPIC -o .libs/viterbi.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 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 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 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 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 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 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 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 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 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 pviterbi.c -fPIC -DPIC -o .libs/pviterbi.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -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 cluster.c -fPIC -DPIC -o .libs/cluster.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 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 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 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 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 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 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 pviterbi_propagate.c -fPIC -DPIC -o .libs/pviterbi_propagate.o ghmm_internals.c: In function 'ighmm_log_out': ghmm_internals.c:69:17: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] 69 | message = strncat(message, error_str, slen); | ^ In function 'process_external_log', inlined from 'ighmm_log_out' at ghmm_internals.c:83:5: ghmm_internals.c:64:14: note: length computed here 64 | int slen = strlen(error_str); | ^~~~~~~~~~~~~~~~~ rng.c: In function 'ghmm_rng_init': rng.c:67:3: warning: argument 2 null where non-null expected [-Wnonnull] 67 | initstate(1, ighmm_rng_state, sizeof(ghmm_rng_state_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from rng.c:40: /usr/include/stdlib.h:530:14: note: in a call to function 'initstate' declared 'nonnull' 530 | extern char *initstate (unsigned int __seed, char *__statebuf, | ^~~~~~~~~ modelutil.c: In function 'topo_free': 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)); | ^ modelutil.c:89:32: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 89 | mes_check_ptr (v, return (-1)); | ^ psequence.c: In function 'ghmm_dpseq_free': psequence.c:78:32: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 78 | mes_check_ptr(seq, return(-1)); | ^ 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)); | ^ 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)); | ^ 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)); | ^ matrix.c: In function 'ighmm_cmatrix_stat_free': matrix.c:176:37: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 176 | mes_check_ptr (matrix, return (-1)); | ^ matrix.c: In function 'ighmm_dmatrix_stat_free': matrix.c:214:37: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 214 | mes_check_ptr (matrix, return (-1)); | ^ matrix.c: In function 'ighmm_cmatrix_3d_free': matrix.c:270:35: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 270 | mes_check_ptr(matrix, return(-1)); | ^ viterbi.c: In function 'viterbi_free': 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)); | ^ viterbi.c:71:31: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 71 | mes_check_ptr(v, return -1); | ^ matrix.c: In function 'ighmm_dmatrix_free': matrix.c:343:37: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 343 | mes_check_ptr (matrix, return (-1)); | ^ 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); | ^ 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)); | ^ 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); | ^ sequence.c: In function 'ghmm_dseq_subseq_free': sequence.c:685:33: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 685 | mes_check_ptr (sq, return (-1)); | ^ sequence.c: In function 'ghmm_cseq_subseq_free': sequence.c:715:34: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 715 | mes_check_ptr (sqd, return (-1)); | ^ 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); | ^ sviterbi.c: In function 'sviterbi_free': sequence.c: In function 'ghmm_dseq_free': sviterbi.c:89:32: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 89 | mes_check_ptr (v, return (-1)); | ^ 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); | ^ foba.c: In function 'ghmm_dmodel_label_backward': foba.c:848:37: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 848 | mes_check_0 (scale[t], goto STOP); | ^ 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;); | ^ 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)); | ^ 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)); | ^ 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)); | ^ xmlwriter.c: In function 'ghmm_xmlfile_write': xmlwriter.c:1106:5: warning: 'xmlSubstituteEntitiesDefault' is deprecated [-Wdeprecated-declarations] 1106 | xmlSubstituteEntitiesDefault(1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from xmlwriter.c:45: /usr/include/libxml2/libxml/parser.h:1106:17: note: declared here 1106 | xmlSubstituteEntitiesDefault(int val); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ xmlwriter.c:1171:3: warning: 'xmlMemoryDump' is deprecated [-Wdeprecated-declarations] 1171 | xmlMemoryDump(); | ^~~~~~~~~~~~~ In file included from /usr/include/libxml2/libxml/tree.h:28, from /usr/include/libxml2/libxml/xmlIO.h:18, from /usr/include/libxml2/libxml/xmlwriter.h:18, from xmlwriter.c:44: /usr/include/libxml2/libxml/xmlmemory.h:161:9: note: declared here 161 | xmlMemoryDump (void); | ^~~~~~~~~~~~~ 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 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 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 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 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 rng.c -o rng.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 modelutil.c -o modelutil.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -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 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 smixturehmm.c -o smixturehmm.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 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 scluster.c -o scluster.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 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 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 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 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 matrixop.c -o matrixop.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 mprintf.c -o mprintf.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 randvar.c -o randvar.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 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 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 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 reestimate.c -o reestimate.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -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 xmlwriter.c -o xmlwriter.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 cfbgibbs.c -o cfbgibbs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 /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" ) make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/ghmm' make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/ghmm' Making all in tools make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tools' make all-recursive make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tools' Making all in . make[6]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tools' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 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 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 cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 make[6]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tools' make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tools' make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tools' Making all in tests make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests' Making all in data make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' Making all in . make[6]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[6]: Nothing to be done for 'all-am'. make[6]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests/data' make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/tests' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 /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 root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 libxml-test libxml-test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 chmm chmm.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 chmm_test chmm_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 shmm_viterbi_test shmm_viterbi_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 test_gsl_ran_gaussian_tail test_gsl_ran_gaussian_tail.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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_test sequences_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 /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 label_higher_order_test label_higher_order_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 read_fa read_fa.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 mcmc mcmc.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 randvar_test randvar_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 coin_toss_test coin_toss_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 two_states_three_symbols two_states_three_symbols.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 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 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 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 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 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 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 root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 coin_toss_test coin_toss_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests' make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests' Making all in ghmmwrapper make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/ghmmwrapper' Making all in . make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/ghmmwrapper' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/ghmmwrapper' /usr/bin/python3 setup.py build file ghmmwrapper.py (for module ghmmwrapper) not found file ghmmwrapper.py (for module ghmmwrapper) not found ghmmwrapper_wrap.c: In function '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: 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; | ^ 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:90: 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:90: 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:90: 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:90: 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:90: 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/ \ --override s/libxml2-16-dev/libxml2-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/libghmm1t64/usr/share/doc/libghmm1t64 install -p -m0644 debian/.debhelper/generated/libghmm1t64/dh_installchangelogs.dch.trimmed debian/libghmm1t64/usr/share/doc/libghmm1t64/changelog.Debian install -m0755 -d debian/ghmm/usr/share/doc/ghmm install -p -m0644 debian/.debhelper/generated/ghmm/dh_installchangelogs.dch.trimmed debian/ghmm/usr/share/doc/ghmm/changelog.Debian install -m0755 -d debian/libghmm-dev/usr/share/doc/libghmm-dev install -p -m0644 debian/.debhelper/generated/libghmm-dev/dh_installchangelogs.dch.trimmed debian/libghmm-dev/usr/share/doc/libghmm-dev/changelog.Debian dh_installexamples install -m0755 -d debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./debian/tests/ghmm_test.py debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./debian/tests/autopkgtest.mk debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/chmm.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/chmm_test.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/coin_toss_test.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/label_higher_order_test.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/libxml-test.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/mcmc.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/randvar_test.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/read_fa.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/root_finder_test.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/sequences_old_format.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/sequences_test.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/shmm_viterbi_test.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/test_gsl_ran_gaussian_tail.c debian/ghmm/usr/share/doc/ghmm/examples cp --reflink=auto -a ./tests/two_states_three_symbols.c debian/ghmm/usr/share/doc/ghmm/examples rm -f debian/ghmm.debhelper.log debian/libghmm-dev.debhelper.log debian/libghmm1t64.debhelper.log debian/rules execute_after_dh_installexamples make[1]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3' # convert sequences_test.c from its national encoding iconv -f ISO-8859-1 -t UTF-8 tests/sequences_test.c \ -o debian/ghmm/usr/share/doc/ghmm/examples/sequences_test.c make[1]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3' debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3' # We do not provide a package python3-HMMEd thus copy the pybuild installed files over to ghmm mv debian/python3-HMMEd/usr/bin/* debian/ghmm/usr/bin mv debian/python3-HMMEd/usr/lib debian/ghmm/usr dh_python3 -p ghmm D: dh_python3 dh_python3:180: version: 6.20250414 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: 3.13 (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/probdist): cannot parse binary file I: dh_python3 tools:114: replacing shebang in debian/ghmm/usr/bin/HMMEd 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/scluster): 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/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 (<< 3.14)', 'python3 (>= 3.13~)', 'python3:any'}; 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/libghmm-dev/changelog.Debian chmod a-x usr/share/doc/libghmm1t64/changelog.Debian chmod a-x usr/share/doc/ghmm/changelog.Debian gzip -9nf usr/share/doc/libghmm1t64/changelog.Debian gzip -9nf usr/share/doc/libghmm-dev/changelog.Debian gzip -9nf usr/share/doc/ghmm/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/libghmm1t64/usr/share/doc -type f -a -true -a ! -regex 'debian/libghmm1t64/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libghmm-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libghmm-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/ghmm/usr/share/doc -type f -a -true -a ! -regex 'debian/ghmm/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libghmm1t64/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libghmm-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/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/ghmm/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x 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/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/libghmm-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing dh_dwz -a dwz -- debian/libghmm1t64/usr/lib/x86_64-linux-gnu/libghmm.so.1.0.0 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 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/e1 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/e1/9fcc4852056bd9c0d652fb90feabe3b9edda60.debug install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/84 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/84/2b08744923da9c31974766926f2bfd7745f545.debug chmod 0644 -- debian/.debhelper/libghmm1t64/dbgsym-root/usr/lib/debug/.build-id/e1/9fcc4852056bd9c0d652fb90feabe3b9edda60.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libghmm1t64/usr/lib/x86_64-linux-gnu/libghmm.so.1.0.0 chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/84/2b08744923da9c31974766926f2bfd7745f545.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/84/2b08744923da9c31974766926f2bfd7745f545.debug debian/ghmm/usr/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-313-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/libghmm1t64/dbgsym-root/usr/lib/debug/.build-id/e1/9fcc4852056bd9c0d652fb90feabe3b9edda60.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 install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ed objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/probdist debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ed/84709dfdd3ffbedb5de77ef616c5b6fd02e635.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ed/84709dfdd3ffbedb5de77ef616c5b6fd02e635.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/ed/84709dfdd3ffbedb5de77ef616c5b6fd02e635.debug debian/ghmm/usr/bin/probdist install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/19 objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/ghmm-cluster debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/19/e49a4c9880d3424e8d05686e519def4b6e2008.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/19/e49a4c9880d3424e8d05686e519def4b6e2008.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/19/e49a4c9880d3424e8d05686e519def4b6e2008.debug debian/ghmm/usr/bin/ghmm-cluster install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ac objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/scluster debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ac/c90fa15a95b8c46f557624776a1e6b4136fb77.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ac/c90fa15a95b8c46f557624776a1e6b4136fb77.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/ac/c90fa15a95b8c46f557624776a1e6b4136fb77.debug debian/ghmm/usr/bin/scluster install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/9a objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/smix_hmm debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/9a/40d14ae8e2994380db9574fdfb98caf2e3dba3.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/9a/40d14ae8e2994380db9574fdfb98caf2e3dba3.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/9a/40d14ae8e2994380db9574fdfb98caf2e3dba3.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/ghmm/DEBIAN dpkg-shlibdeps -Tdebian/ghmm.substvars debian/ghmm/usr/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-313-x86_64-linux-gnu.so debian/ghmm/usr/bin/probdist debian/ghmm/usr/bin/ghmm-cluster debian/ghmm/usr/bin/scluster debian/ghmm/usr/bin/smix_hmm install -m0755 -d debian/libghmm1t64/DEBIAN dpkg-shlibdeps -Tdebian/libghmm1t64.substvars debian/libghmm1t64/usr/lib/x86_64-linux-gnu/libghmm.so.1.0.0 dh_installdeb install -m0755 -d debian/ghmm/DEBIAN printf '#!/bin/sh\nset -e\n' > debian/ghmm/DEBIAN/postinst cat debian/ghmm.postinst.debhelper >> debian/ghmm/DEBIAN/postinst chmod 0755 -- debian/ghmm/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/ghmm/DEBIAN/prerm cat debian/ghmm.prerm.debhelper >> debian/ghmm/DEBIAN/prerm chmod 0755 -- debian/ghmm/DEBIAN/prerm install -m0755 -d debian/libghmm-dev/DEBIAN install -m0755 -d debian/libghmm1t64/DEBIAN install -p -m0644 debian/.debhelper/generated/libghmm1t64/triggers debian/libghmm1t64/DEBIAN/triggers dh_gencontrol install -m0755 -d debian/libghmm-dev/DEBIAN echo misc:Depends= >> debian/libghmm-dev.substvars echo misc:Pre-Depends= >> debian/libghmm-dev.substvars dpkg-gencontrol -plibghmm-dev -ldebian/changelog -Tdebian/libghmm-dev.substvars -cdebian/control -Pdebian/libghmm-dev install -m0755 -d debian/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=19e49a4c9880d3424e8d05686e519def4b6e2008 842b08744923da9c31974766926f2bfd7745f545 9a40d14ae8e2994380db9574fdfb98caf2e3dba3 acc90fa15a95b8c46f557624776a1e6b4136fb77 ed84709dfdd3ffbedb5de77ef616c5b6fd02e635" -DSection=debug -UMulti-Arch -UReplaces -UBreaks 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=e19fcc4852056bd9c0d652fb90feabe3b9edda60 -DSection=debug -UMulti-Arch -UReplaces -UBreaks dpkg-gencontrol: warning: Depends field of package libghmm-dev: substitution variable ${shlibs:Depends} used, but is not defined chmod 0644 -- debian/.debhelper/libghmm1t64/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibghmm1t64 -ldebian/changelog -Tdebian/libghmm1t64.substvars -cdebian/control -Pdebian/libghmm1t64 chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/DEBIAN/control dpkg-gencontrol -pghmm -ldebian/changelog -Tdebian/ghmm.substvars -cdebian/control -Pdebian/ghmm dpkg-gencontrol: warning: package libghmm-dev: substitution variable ${devlibs:Depends} unused, but is defined chmod 0644 -- debian/libghmm-dev/DEBIAN/control chmod 0644 -- debian/libghmm1t64/DEBIAN/control chmod 0644 -- debian/ghmm/DEBIAN/control dh_md5sums install -m0755 -d debian/ghmm/DEBIAN install -m0755 -d debian/libghmm-dev/DEBIAN install -m0755 -d debian/libghmm1t64/DEBIAN cd debian/libghmm-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libghmm1t64 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/ghmm >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libghmm-dev/DEBIAN/md5sums chmod 0644 -- debian/libghmm1t64/DEBIAN/md5sums install -m0755 -d debian/.debhelper/libghmm1t64/dbgsym-root/DEBIAN chmod 0644 -- debian/ghmm/DEBIAN/md5sums install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/DEBIAN cd debian/.debhelper/libghmm1t64/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/.debhelper/ghmm/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libghmm1t64/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/ghmm .. dpkg-deb --root-owner-group --build debian/.debhelper/ghmm/dbgsym-root .. dpkg-deb --root-owner-group --build debian/libghmm-dev .. dpkg-deb --root-owner-group --build debian/libghmm1t64 .. dpkg-deb --root-owner-group --build debian/.debhelper/libghmm1t64/dbgsym-root .. dpkg-deb: building package 'ghmm-dbgsym' in '../ghmm-dbgsym_0.9~rc3-11.1_amd64.deb'. dpkg-deb: building package 'ghmm' in '../ghmm_0.9~rc3-11.1_amd64.deb'. dpkg-deb: building package 'libghmm-dev' in '../libghmm-dev_0.9~rc3-11.1_amd64.deb'. dpkg-deb: building package 'libghmm1t64' in '../libghmm1t64_0.9~rc3-11.1_amd64.deb'. dpkg-deb: building package 'libghmm1t64-dbgsym' in '../libghmm1t64-dbgsym_0.9~rc3-11.1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../ghmm_0.9~rc3-11.1_amd64.buildinfo dpkg-genchanges --build=binary -O../ghmm_0.9~rc3-11.1_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/513057/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/513057/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/513057 and its subdirectories I: Current time: Thu Sep 18 22:48:02 +14 2025 I: pbuilder-time-stamp: 1758185282 + false + set +x Thu Sep 18 08:48:02 UTC 2025 I: Signing ./b2/ghmm_0.9~rc3-11.1_amd64.buildinfo as ghmm_0.9~rc3-11.1_amd64.buildinfo.asc Thu Sep 18 08:48:02 UTC 2025 I: Signed ./b2/ghmm_0.9~rc3-11.1_amd64.buildinfo as ./b2/ghmm_0.9~rc3-11.1_amd64.buildinfo.asc Thu Sep 18 08:48:02 UTC 2025 - build #2 for ghmm/unstable/amd64 on ionos11-amd64 done. Starting cleanup. All cleanup done. Thu Sep 18 08:48:02 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-nI89SrSN, removing. /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4: total 204 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 08:42 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 08:48 b2 -rw-rw-r-- 1 jenkins jenkins 2148 Aug 25 17:19 ghmm_0.9~rc3-11.1.dsc -rw------- 1 jenkins jenkins 192124 Sep 18 08:42 rbuildlog.8BxGUCj /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/b1: total 1544 -rw-r--r-- 1 jenkins jenkins 188578 Sep 18 08:42 build.log -rw-r--r-- 1 jenkins jenkins 457468 Sep 18 08:42 ghmm-dbgsym_0.9~rc3-11.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 25256 Sep 18 08:42 ghmm_0.9~rc3-11.1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2148 Sep 18 08:42 ghmm_0.9~rc3-11.1.dsc -rw-r--r-- 1 jenkins jenkins 7698 Sep 18 08:42 ghmm_0.9~rc3-11.1_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 8580 Sep 18 08:42 ghmm_0.9~rc3-11.1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2465 Sep 18 08:42 ghmm_0.9~rc3-11.1_amd64.changes -rw-r--r-- 1 jenkins jenkins 156324 Sep 18 08:42 ghmm_0.9~rc3-11.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1304 Sep 18 08:42 ghmm_0.9~rc3-11.1_source.changes -rw-r--r-- 1 jenkins jenkins 189896 Sep 18 08:42 libghmm-dev_0.9~rc3-11.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 345868 Sep 18 08:42 libghmm1t64-dbgsym_0.9~rc3-11.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 142112 Sep 18 08:42 libghmm1t64_0.9~rc3-11.1_amd64.deb /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/b2: total 1520 -rw-rw-r-- 1 jenkins jenkins 190370 Sep 18 08:48 build.log -rw-r--r-- 1 jenkins jenkins 457468 Sep 18 08:48 ghmm-dbgsym_0.9~rc3-11.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 25256 Sep 18 08:48 ghmm_0.9~rc3-11.1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2148 Sep 18 08:48 ghmm_0.9~rc3-11.1.dsc -rw-rw-r-- 1 jenkins jenkins 7698 Sep 18 08:48 ghmm_0.9~rc3-11.1_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 8580 Sep 18 08:48 ghmm_0.9~rc3-11.1_amd64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 2465 Sep 18 08:48 ghmm_0.9~rc3-11.1_amd64.changes -rw-r--r-- 1 jenkins jenkins 156324 Sep 18 08:48 ghmm_0.9~rc3-11.1_amd64.deb -rw-rw-r-- 1 jenkins jenkins 1304 Sep 18 08:48 ghmm_0.9~rc3-11.1_source.changes -rw-r--r-- 1 jenkins jenkins 189896 Sep 18 08:48 libghmm-dev_0.9~rc3-11.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 345868 Sep 18 08:48 libghmm1t64-dbgsym_0.9~rc3-11.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 142112 Sep 18 08:48 libghmm1t64_0.9~rc3-11.1_amd64.deb Thu Sep 18 08:48:02 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Thu Sep 18 08:48:02 UTC 2025 I: ghmm_0.9~rc3-11.1_amd64.changes: Format: 1.8 Date: Mon, 25 Aug 2025 17:03:09 +0200 Source: ghmm Binary: ghmm ghmm-dbgsym libghmm-dev libghmm1t64 libghmm1t64-dbgsym Architecture: amd64 Version: 0.9~rc3-11.1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Bastian Germann Description: ghmm - General Hidden-Markov-Model library - tools libghmm-dev - General Hidden-Markov-Model library - header files libghmm1t64 - General Hidden-Markov-Model library Closes: 1106611 Changes: ghmm (0.9~rc3-11.1) unstable; urgency=medium . * Non-maintainer upload. * Add override to d-shlibmove call due to changed libxml2 file name. (Closes: #1106611) Checksums-Sha1: e90df62359993b6f847b68382be930ee57e2a013 457468 ghmm-dbgsym_0.9~rc3-11.1_amd64.deb f286ab608f9cbc3930518718fcf2403e29050928 7698 ghmm_0.9~rc3-11.1_amd64.buildinfo 7b52cd987e14a46a5175b01d4f443b0a096062ad 156324 ghmm_0.9~rc3-11.1_amd64.deb 170a1bf01992887c3f731da05d8b7cb1302c9b26 189896 libghmm-dev_0.9~rc3-11.1_amd64.deb 6270ec2c0e41d57c22b1ba58f6ce56fc04ef1b79 345868 libghmm1t64-dbgsym_0.9~rc3-11.1_amd64.deb f6b211e31436802e3a4c1cd8a85e5495a309edd7 142112 libghmm1t64_0.9~rc3-11.1_amd64.deb Checksums-Sha256: e2567f68295427bfd93c0ed83151f456783360ea7d2d4916b54b9909182c9f30 457468 ghmm-dbgsym_0.9~rc3-11.1_amd64.deb 4b9e181cbf5c886fe4e44ac03aa9c9a55e57e14ef973a85cc1d796158c386b2a 7698 ghmm_0.9~rc3-11.1_amd64.buildinfo a0b243d35bcf69bebd42015fa4b680ba3c5ce7678577794b26b485e366cc8789 156324 ghmm_0.9~rc3-11.1_amd64.deb 30914507fdf1594dca981190bf99559facf067a9946b9bf5b5ad790b3aab9304 189896 libghmm-dev_0.9~rc3-11.1_amd64.deb 63986afc33b66625d80d7ba062d4433c0777b1c0296b156fb89598a7f62b9b41 345868 libghmm1t64-dbgsym_0.9~rc3-11.1_amd64.deb f498e919aaac8f33cb024e382cd788c392ca480f79eba5bac213c9dd0d11bf30 142112 libghmm1t64_0.9~rc3-11.1_amd64.deb Files: 7627ce855045f967bd7ee15edaf9397b 457468 debug optional ghmm-dbgsym_0.9~rc3-11.1_amd64.deb 49883e0fe1aa5611c91c7cfaca453317 7698 science optional ghmm_0.9~rc3-11.1_amd64.buildinfo 496005b5d95d68745757f864a5589e99 156324 science optional ghmm_0.9~rc3-11.1_amd64.deb 6109dd32c6b9043bd2b124e08587ebd7 189896 libdevel optional libghmm-dev_0.9~rc3-11.1_amd64.deb 55dc42e8dd9be76be501d4a9182e3dfb 345868 debug optional libghmm1t64-dbgsym_0.9~rc3-11.1_amd64.deb 14eca0548983753fee5df10449429d07 142112 libs optional libghmm1t64_0.9~rc3-11.1_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/ghmm_0.9~rc3-11.1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/ghmm_0.9~rc3-11.1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/ghmm_0.9~rc3-11.1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/ghmm_0.9~rc3-11.1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/ghmm_0.9~rc3-11.1_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/ghmm_0.9~rc3-11.1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-09-18 08:42:31.753635859 +0000 +++ b2/build.log 2025-09-18 08:48:02.710046899 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Oct 21 03:02:05 -12 2026 -I: pbuilder-time-stamp: 1792594925 +I: Current time: Thu Sep 18 22:42:33 +14 2025 +I: pbuilder-time-stamp: 1758184953 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -36,53 +36,85 @@ 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/2894982/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/513057/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 Sep 18 08:43 /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/513057/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/513057/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(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=40 ' + 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='dd97bd738c2d4ae3a716f7df0596872f' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2894982' - PS1='# ' - PS2='> ' + INVOCATION_ID=d414b8d2150341aabb5522b60b56bc92 + 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=513057 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/pbuilderrc_eoua --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/b1 --logfile b1/build.log ghmm_0.9~rc3-11.1.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/pbuilderrc_Av26 --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.dJrJz6X4/b2 --logfile b2/build.log ghmm_0.9~rc3-11.1.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + 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 ionos15-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2894982/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/513057/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -220,7 +252,7 @@ Get: 80 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 82 http://deb.debian.org/debian unstable/main amd64 swig amd64 4.3.0-1 [1503 kB] -Fetched 44.7 MB in 20s (2286 kB/s) +Fetched 44.7 MB in 17s (2599 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) @@ -496,8 +528,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Oct 21 15:04:45 UTC 2026. -Universal Time is now: Wed Oct 21 15:04:45 UTC 2026. +Local time is now: Thu Sep 18 08:46:04 UTC 2025. +Universal Time is now: Thu Sep 18 08:46:04 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -579,7 +611,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/ghmm-0.9~rc3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../ghmm_0.9~rc3-11.1_source.changes +I: user script /srv/workspace/pbuilder/513057/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/513057/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~rc3-11.1_source.changes dpkg-buildpackage: info: source package ghmm dpkg-buildpackage: info: source version 0.9~rc3-11.1 dpkg-buildpackage: info: source distribution unstable @@ -851,7 +887,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3' dh_auto_build - make -j42 + make -j40 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' @@ -859,96 +895,86 @@ 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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../libtool --tag=CC --mode=compile gcc 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-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 +/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 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 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 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 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 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 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 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 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 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 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 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 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 viterbi.c -fPIC -DPIC -o .libs/viterbi.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 pviterbi.c -fPIC -DPIC -o .libs/pviterbi.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -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 cluster.c -fPIC -DPIC -o .libs/cluster.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 sdviterbi.c -fPIC -DPIC -o .libs/sdviterbi.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 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 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 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 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 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 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 pviterbi.c -fPIC -DPIC -o .libs/pviterbi.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -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 +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 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 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 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 pviterbi_propagate.c -fPIC -DPIC -o .libs/pviterbi_propagate.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 -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)); - | ^ -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)); - | ^ ghmm_internals.c: In function 'ighmm_log_out': ghmm_internals.c:69:17: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] 69 | message = strncat(message, error_str, slen); @@ -958,6 +984,38 @@ ghmm_internals.c:64:14: note: length computed here 64 | int slen = strlen(error_str); | ^~~~~~~~~~~~~~~~~ +rng.c: In function 'ghmm_rng_init': +rng.c:67:3: warning: argument 2 null where non-null expected [-Wnonnull] + 67 | initstate(1, ighmm_rng_state, sizeof(ghmm_rng_state_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from rng.c:40: +/usr/include/stdlib.h:530:14: note: in a call to function 'initstate' declared 'nonnull' + 530 | extern char *initstate (unsigned int __seed, char *__statebuf, + | ^~~~~~~~~ +modelutil.c: In function 'topo_free': +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)); + | ^ +modelutil.c:89:32: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] + 89 | mes_check_ptr (v, return (-1)); + | ^ +psequence.c: In function 'ghmm_dpseq_free': +psequence.c:78:32: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] + 78 | mes_check_ptr(seq, return(-1)); + | ^ +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)); + | ^ +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)); + | ^ +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)); + | ^ 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)); @@ -966,50 +1024,42 @@ matrix.c:214:37: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 214 | mes_check_ptr (matrix, return (-1)); | ^ -reestimate.c: In function 'reestimate_free': matrix.c: In function 'ighmm_cmatrix_3d_free': matrix.c:270:35: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 270 | mes_check_ptr(matrix, return(-1)); | ^ -reestimate.c:79:32: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] - 79 | mes_check_ptr (r, return (-1)); - | ^ +viterbi.c: In function 'viterbi_free': 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)); | ^ +viterbi.c:71:31: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] + 71 | mes_check_ptr(v, return -1); + | ^ matrix.c: In function 'ighmm_dmatrix_free': matrix.c:343:37: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 343 | mes_check_ptr (matrix, return (-1)); | ^ -sequence.c: In function 'ghmm_dseq_subseq_free': -sequence.c:685:33: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] - 685 | mes_check_ptr (sq, return (-1)); - | ^ -foba.c: In function 'ghmm_dmodel_backward': +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); + | ^ 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)); | ^ -foba.c:286:37: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] - 286 | mes_check_0 (scale[t], goto STOP); +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); | ^ -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); - | ^ +sequence.c: In function 'ghmm_dseq_subseq_free': +sequence.c:685:33: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] + 685 | mes_check_ptr (sq, return (-1)); + | ^ sequence.c: In function 'ghmm_cseq_subseq_free': sequence.c:715:34: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 715 | mes_check_ptr (sqd, return (-1)); | ^ -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)); - | ^ -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); - | ^ 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)); @@ -1017,25 +1067,25 @@ 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); + | ^ +sviterbi.c: In function 'sviterbi_free': sequence.c: In function 'ghmm_dseq_free': +sviterbi.c:89:32: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] + 89 | mes_check_ptr (v, return (-1)); + | ^ sequence.c:1189:30: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 1189 | mes_check_ptr(sq, return -1); | ^ -foba.c: In function 'ghmm_dmodel_label_backward': -foba.c:848:37: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] - 848 | mes_check_0 (scale[t], goto STOP); - | ^ 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); | ^ -pmodel.c: In function 'ghmm_dpmodel_free': -pmodel.c:127:31: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] - 127 | mes_check_ptr(mo, return(-1)); - | ^ -sdfoba.c: In function 'ghmm_dsmodel_backward': -sdfoba.c:336:37: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] - 336 | mes_check_0 (scale[t], goto STOP); +foba.c: In function 'ghmm_dmodel_label_backward': +foba.c:848:37: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] + 848 | mes_check_0 (scale[t], goto STOP); | ^ model.c: In function 'ghmm_dstate_clean': model.c:1758:35: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] @@ -1049,20 +1099,6 @@ sdmodel.c:211:33: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 211 | mes_check_ptr (mo, return (-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)); - | ^ -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, - | ^~~~~~~~~ -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 scanner.c -o scanner.o >/dev/null 2>&1 pviterbi_propagate.c: In function 'pviterbi_propagate_free': pviterbi_propagate.c:255:30: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 255 | mes_check_ptr(v, return(-1)); @@ -1085,54 +1121,54 @@ /usr/include/libxml2/libxml/xmlmemory.h:161:9: note: declared here 161 | xmlMemoryDump (void); | ^~~~~~~~~~~~~ -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)); - | ^ -sdviterbi.c: In function 'sdviterbi_free': -sdviterbi.c:111:32: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] - 111 | mes_check_ptr (v, return (-1)); - | ^ -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 -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 -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 rng.c -o rng.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 +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 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 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 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 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 sviterbi.c -o sviterbi.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -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 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 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 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 modelutil.c -o modelutil.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -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 +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 smixturehmm.c -o smixturehmm.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 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 scluster.c -o scluster.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 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 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 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 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 matrixop.c -o matrixop.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 randvar.c -o randvar.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 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 mprintf.c -o mprintf.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 randvar.c -o randvar.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 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 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 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 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 reestimate.c -o reestimate.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -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 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 xmlwriter.c -o xmlwriter.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 -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 sequence.c -o sequence.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 cfbgibbs.c -o cfbgibbs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 -/bin/bash ../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 +/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") @@ -1151,14 +1187,14 @@ 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/bash ../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 cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 -/bin/bash ../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 -/bin/bash ../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 scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 -/bin/bash ../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 probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 -libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 -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 +/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 cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 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 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 cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 +libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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' @@ -1186,34 +1222,34 @@ 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 -/bin/bash ../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 root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 -/bin/bash ../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 test_gsl_ran_gaussian_tail test_gsl_ran_gaussian_tail.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 -/bin/bash ../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 -/bin/bash ../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 libxml-test libxml-test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 -/bin/bash ../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 shmm_viterbi_test shmm_viterbi_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 -/bin/bash ../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_test sequences_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 -/bin/bash ../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 two_states_three_symbols two_states_three_symbols.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 -/bin/bash ../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 chmm chmm.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 -/bin/bash ../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 randvar_test randvar_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 -/bin/bash ../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 chmm_test chmm_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 -/bin/bash ../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 coin_toss_test coin_toss_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 -/bin/bash ../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 read_fa read_fa.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 -/bin/bash ../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 mcmc mcmc.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 -libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 +/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 root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 libxml-test libxml-test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 chmm chmm.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 chmm_test chmm_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 shmm_viterbi_test shmm_viterbi_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 test_gsl_ran_gaussian_tail test_gsl_ran_gaussian_tail.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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_test sequences_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 +/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 label_higher_order_test label_higher_order_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 read_fa read_fa.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 mcmc mcmc.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 randvar_test randvar_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 coin_toss_test coin_toss_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -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 two_states_three_symbols two_states_three_symbols.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 -/bin/bash ../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 label_higher_order_test label_higher_order_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -llapacke -lxml2 -libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 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 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 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 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 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 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 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 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 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 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 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 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 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 root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -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 -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 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 coin_toss_test coin_toss_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2 make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests' make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests' Making all in ghmmwrapper @@ -1371,7 +1407,7 @@ 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/bash ../libtool --mode=install /usr/bin/install -c libghmm.la '/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; }; }) @@ -1393,7 +1429,7 @@ 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/bash ../libtool --mode=install /usr/bin/install -c probdist cluster scluster smix_hmm '/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 @@ -1640,12 +1676,12 @@ install -m0755 -d debian/libghmm1t64/usr/share/doc/libghmm1t64 install -p -m0644 debian/copyright debian/libghmm1t64/usr/share/doc/libghmm1t64/copyright dh_installchangelogs + install -m0755 -d debian/libghmm1t64/usr/share/doc/libghmm1t64 + install -p -m0644 debian/.debhelper/generated/libghmm1t64/dh_installchangelogs.dch.trimmed debian/libghmm1t64/usr/share/doc/libghmm1t64/changelog.Debian install -m0755 -d debian/ghmm/usr/share/doc/ghmm install -p -m0644 debian/.debhelper/generated/ghmm/dh_installchangelogs.dch.trimmed debian/ghmm/usr/share/doc/ghmm/changelog.Debian install -m0755 -d debian/libghmm-dev/usr/share/doc/libghmm-dev install -p -m0644 debian/.debhelper/generated/libghmm-dev/dh_installchangelogs.dch.trimmed debian/libghmm-dev/usr/share/doc/libghmm-dev/changelog.Debian - 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 @@ -1685,14 +1721,14 @@ 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/probdist): cannot parse binary file -D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/scluster): cannot parse binary file -D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/ghmm-config): doesn't look like a shebang: #! /bin/sh I: dh_python3 tools:114: replacing shebang in debian/ghmm/usr/bin/HMMEd 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/scluster): 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/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:any', 'python3 (>= 3.13~)', 'python3 (<< 3.14)'}; R=[]; S=[]; E=[], B=[]; RT=[] +D: dh_python3 depends:253: D={'python3 (<< 3.14)', 'python3 (>= 3.13~)', 'python3:any'}; 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 @@ -1711,12 +1747,12 @@ 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/libghmm-dev/changelog.Debian chmod a-x usr/share/doc/libghmm1t64/changelog.Debian - gzip -9nf usr/share/doc/ghmm/changelog.Debian - gzip -9nf usr/share/doc/libghmm-dev/changelog.Debian + chmod a-x usr/share/doc/ghmm/changelog.Debian gzip -9nf usr/share/doc/libghmm1t64/changelog.Debian + gzip -9nf usr/share/doc/libghmm-dev/changelog.Debian + gzip -9nf usr/share/doc/ghmm/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' @@ -1724,34 +1760,34 @@ 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 0755 (rwxr-xr-x) to 0644 (rw-r--r--) -mode of 'debian/ghmm/usr/share/doc/ghmm/examples/chmm_test.c' retained as 0644 (rw-r--r--) -mode of 'debian/ghmm/usr/share/doc/ghmm/examples/coin_toss_test.c' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) -mode of 'debian/ghmm/usr/share/doc/ghmm/examples/label_higher_order_test.c' retained as 0644 (rw-r--r--) -mode of 'debian/ghmm/usr/share/doc/ghmm/examples/libxml-test.c' retained as 0644 (rw-r--r--) -mode of 'debian/ghmm/usr/share/doc/ghmm/examples/mcmc.c' retained as 0644 (rw-r--r--) -mode of 'debian/ghmm/usr/share/doc/ghmm/examples/randvar_test.c' retained as 0644 (rw-r--r--) -mode of 'debian/ghmm/usr/share/doc/ghmm/examples/read_fa.c' retained as 0644 (rw-r--r--) -mode of 'debian/ghmm/usr/share/doc/ghmm/examples/root_finder_test.c' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) -mode of 'debian/ghmm/usr/share/doc/ghmm/examples/sequences_old_format.c' retained as 0644 (rw-r--r--) -mode of 'debian/ghmm/usr/share/doc/ghmm/examples/sequences_test.c' retained as 0644 (rw-r--r--) -mode of 'debian/ghmm/usr/share/doc/ghmm/examples/shmm_viterbi_test.c' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) -mode of 'debian/ghmm/usr/share/doc/ghmm/examples/test_gsl_ran_gaussian_tail.c' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) -mode of 'debian/ghmm/usr/share/doc/ghmm/examples/two_states_three_symbols.c' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) +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/libghmm1t64/usr/share/doc -type f -a -true -a ! -regex 'debian/libghmm1t64/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libghmm-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libghmm-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/ghmm/usr/share/doc -type f -a -true -a ! -regex 'debian/ghmm/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libghmm1t64/usr/share/doc -type f -a -true -a ! -regex 'debian/libghmm1t64/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/libghmm1t64/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libghmm-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/ghmm/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/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/usr/share/lintian/overrides -type f -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/ghmm/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x @@ -1773,28 +1809,28 @@ 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/84/2b08744923da9c31974766926f2bfd7745f545.debug chmod 0644 -- debian/.debhelper/libghmm1t64/dbgsym-root/usr/lib/debug/.build-id/e1/9fcc4852056bd9c0d652fb90feabe3b9edda60.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libghmm1t64/usr/lib/x86_64-linux-gnu/libghmm.so.1.0.0 + chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/84/2b08744923da9c31974766926f2bfd7745f545.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/84/2b08744923da9c31974766926f2bfd7745f545.debug debian/ghmm/usr/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-313-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/libghmm1t64/dbgsym-root/usr/lib/debug/.build-id/e1/9fcc4852056bd9c0d652fb90feabe3b9edda60.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/84/2b08744923da9c31974766926f2bfd7745f545.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/84/2b08744923da9c31974766926f2bfd7745f545.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/ed objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/probdist debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ed/84709dfdd3ffbedb5de77ef616c5b6fd02e635.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ed/84709dfdd3ffbedb5de77ef616c5b6fd02e635.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/ed/84709dfdd3ffbedb5de77ef616c5b6fd02e635.debug debian/ghmm/usr/bin/probdist - install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ac - objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/scluster debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ac/c90fa15a95b8c46f557624776a1e6b4136fb77.debug - chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ac/c90fa15a95b8c46f557624776a1e6b4136fb77.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/ac/c90fa15a95b8c46f557624776a1e6b4136fb77.debug debian/ghmm/usr/bin/scluster install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/19 objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/ghmm-cluster debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/19/e49a4c9880d3424e8d05686e519def4b6e2008.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/19/e49a4c9880d3424e8d05686e519def4b6e2008.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/19/e49a4c9880d3424e8d05686e519def4b6e2008.debug debian/ghmm/usr/bin/ghmm-cluster + install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ac + objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/scluster debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ac/c90fa15a95b8c46f557624776a1e6b4136fb77.debug + chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/ac/c90fa15a95b8c46f557624776a1e6b4136fb77.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/ac/c90fa15a95b8c46f557624776a1e6b4136fb77.debug debian/ghmm/usr/bin/scluster install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/9a objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/smix_hmm debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/9a/40d14ae8e2994380db9574fdfb98caf2e3dba3.debug chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/9a/40d14ae8e2994380db9574fdfb98caf2e3dba3.debug @@ -1817,10 +1853,10 @@ 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/ghmm/DEBIAN + dpkg-shlibdeps -Tdebian/ghmm.substvars debian/ghmm/usr/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-313-x86_64-linux-gnu.so debian/ghmm/usr/bin/probdist debian/ghmm/usr/bin/ghmm-cluster debian/ghmm/usr/bin/scluster debian/ghmm/usr/bin/smix_hmm 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/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-313-x86_64-linux-gnu.so debian/ghmm/usr/bin/probdist debian/ghmm/usr/bin/scluster debian/ghmm/usr/bin/ghmm-cluster debian/ghmm/usr/bin/smix_hmm dh_installdeb install -m0755 -d debian/ghmm/DEBIAN printf '#!/bin/sh\nset -e\n' > debian/ghmm/DEBIAN/postinst @@ -1833,39 +1869,39 @@ install -m0755 -d debian/libghmm1t64/DEBIAN install -p -m0644 debian/.debhelper/generated/libghmm1t64/triggers debian/libghmm1t64/DEBIAN/triggers dh_gencontrol + install -m0755 -d debian/libghmm-dev/DEBIAN + echo misc:Depends= >> debian/libghmm-dev.substvars + echo misc:Pre-Depends= >> debian/libghmm-dev.substvars + dpkg-gencontrol -plibghmm-dev -ldebian/changelog -Tdebian/libghmm-dev.substvars -cdebian/control -Pdebian/libghmm-dev install -m0755 -d debian/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=19e49a4c9880d3424e8d05686e519def4b6e2008 842b08744923da9c31974766926f2bfd7745f545 9a40d14ae8e2994380db9574fdfb98caf2e3dba3 acc90fa15a95b8c46f557624776a1e6b4136fb77 ed84709dfdd3ffbedb5de77ef616c5b6fd02e635" -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 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=e19fcc4852056bd9c0d652fb90feabe3b9edda60 -DSection=debug -UMulti-Arch -UReplaces -UBreaks 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/.debhelper/libghmm1t64/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibghmm1t64 -ldebian/changelog -Tdebian/libghmm1t64.substvars -cdebian/control -Pdebian/libghmm1t64 - 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 +dpkg-gencontrol: warning: package libghmm-dev: substitution variable ${devlibs:Depends} unused, but is defined + chmod 0644 -- debian/libghmm-dev/DEBIAN/control chmod 0644 -- debian/libghmm1t64/DEBIAN/control chmod 0644 -- debian/ghmm/DEBIAN/control dh_md5sums install -m0755 -d debian/ghmm/DEBIAN install -m0755 -d debian/libghmm-dev/DEBIAN install -m0755 -d debian/libghmm1t64/DEBIAN - cd debian/ghmm >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libghmm-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums 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 + chmod 0644 -- debian/libghmm-dev/DEBIAN/md5sums chmod 0644 -- debian/libghmm1t64/DEBIAN/md5sums install -m0755 -d debian/.debhelper/libghmm1t64/dbgsym-root/DEBIAN - chmod 0644 -- debian/libghmm-dev/DEBIAN/md5sums chmod 0644 -- debian/ghmm/DEBIAN/md5sums install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/DEBIAN cd debian/.debhelper/libghmm1t64/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums @@ -1890,12 +1926,14 @@ 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/513057/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/513057/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/2894982 and its subdirectories -I: Current time: Wed Oct 21 03:05:31 -12 2026 -I: pbuilder-time-stamp: 1792595131 +I: removing directory /srv/workspace/pbuilder/513057 and its subdirectories +I: Current time: Thu Sep 18 22:48:02 +14 2025 +I: pbuilder-time-stamp: 1758185282 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/ghmm_0.9~rc3-11.1.diff: 93.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/ghmm_0.9~rc3-11.1.diff.gz b2/build.log: 88.0% -- replaced with stdout Compressing the 1st log... b1/build.log: 88.2% -- replaced with stdout Thu Sep 18 08:48:03 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_ghmm_unstable_amd64_1758185283 + touch /var/log/reproducible-builds/diffoscope_stamp_ghmm_unstable_amd64_1758185283 + RESULT=0 + systemd-run '--description=diffoscope on ghmm/0.9~rc3-11.1 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_28-72973 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4 --run-session -c jenkins-reproducible-unstable-diffoscope-5888849b-f733-444e-8914-b031d6ad890a -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/dbd-tmp-h3Eid7A ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/ghmm_0.9~rc3-11.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/ghmm_0.9~rc3-11.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/ghmm_0.9~rc3-11.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/b1/ghmm_0.9~rc3-11.1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/b2/ghmm_0.9~rc3-11.1_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_28-72973.service; invocation ID: cb8dbe5d186b4367a2806505fa0c9365 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/ghmm_0.9~rc3-11.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/ghmm_0.9~rc3-11.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/ghmm_0.9~rc3-11.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/b1/ghmm_0.9~rc3-11.1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.dJrJz6X4/b2/ghmm_0.9~rc3-11.1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 219ms CPU time consumed: 168ms Memory peak: 18M (swap: 0B) _ __ _| |__ _ __ ___ _ __ ___ / _` | '_ \| '_ ` _ \| '_ ` _ \ | (_| | | | | | | | | | | | | | | \__, |_| |_|_| |_| |_|_| |_| |_| |___/ Thu Sep 18 08:48:04 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Thu Sep 18 08:48:04 UTC 2025 I: ghmm from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-18 08:48:04] INFO: Starting at 2025-09-18 08:48:04.472488 [2025-09-18 08:48:04] INFO: Generating the pages of 1 package(s) [2025-09-18 08:48:04] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/ghmm didn't produce a buildlog, even though it has been built. [2025-09-18 08:48:04] INFO: Finished at 2025-09-18 08:48:04.727739, took: 0:00:00.255255 Thu Sep 18 08:48:04 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/ghmm.html Thu Sep 18 08:48:04 UTC 2025 I: Removing signed ghmm_0.9~rc3-11.1_amd64.buildinfo.asc files: removed './b1/ghmm_0.9~rc3-11.1_amd64.buildinfo.asc' removed './b2/ghmm_0.9~rc3-11.1_amd64.buildinfo.asc' 1758185284 amd64 unstable ghmm Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/ghmm_0.9~rc3-11.1.rbuild.log: 87.0% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/ghmm_0.9~rc3-11.1.rbuild.log.gz [2025-09-18 08:48:05] INFO: Starting at 2025-09-18 08:48:05.051339 [2025-09-18 08:48:05] INFO: Generating the pages of 1 package(s) [2025-09-18 08:48:05] INFO: Finished at 2025-09-18 08:48:05.303759, took: 0:00:00.252423 All cleanup done. Thu Sep 18 08:48:05 UTC 2025 - total duration: 0h 9m 1s. Thu Sep 18 08:48:05 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-n4mLVvXz, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 9min 2.293s CPU time consumed: 3.196s Memory peak: 43.1M (swap: 0B)