Fri Mar 28 14:53:03 UTC 2025 I: starting to build ghmm/trixie/arm64 on jenkins on '2025-03-28 14:52'
Fri Mar 28 14:53:03 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_3/84339/console.log
Fri Mar 28 14:53:03 UTC 2025 I: Downloading source for trixie/ghmm=0.9~rc3-11
--2025-03-28 14:53:03-- http://deb.debian.org/debian/pool/main/g/ghmm/ghmm_0.9%7erc3-11.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 1709 (1.7K) [text/prs.lines.tag]
Saving to: ‘ghmm_0.9~rc3-11.dsc’
0K . 100% 260M=0s
2025-03-28 14:53:03 (260 MB/s) - ‘ghmm_0.9~rc3-11.dsc’ saved [1709/1709]
Fri Mar 28 14:53:03 UTC 2025 I: ghmm_0.9~rc3-11.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: ghmm
Binary: ghmm, libghmm-dev, libghmm1t64
Architecture: any
Version: 0.9~rc3-11
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>, Étienne Mollier <emollier@debian.org>
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
00c1b200261eab62a001e4df91fd7a089ebfad88 25200 ghmm_0.9~rc3-11.debian.tar.xz
Checksums-Sha256:
c42462ff4f87aadd5efe7bb6adb59657786ed71046ba924111bc28c7cbb588d0 770526 ghmm_0.9~rc3.orig.tar.gz
e3490ef0050c153878f44604a21efc64b68cbed07cbf4a1cfa2424dbe1688c92 25200 ghmm_0.9~rc3-11.debian.tar.xz
Files:
4e2db5a83bbd5b2a7cc6476657c0c4d7 770526 ghmm_0.9~rc3.orig.tar.gz
099470c5e79c6621c34edfdf992277d4 25200 ghmm_0.9~rc3-11.debian.tar.xz
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Fri Mar 28 14:53:03 UTC 2025 I: Checking whether the package is not for us
Fri Mar 28 14:53:03 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net.
Fri Mar 28 14:53:03 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net.
Fri Mar 28 14:54:10 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Thu Apr 30 09:16:05 -12 2026
I: pbuilder-time-stamp: 1777583765
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [ghmm_0.9~rc3-11.dsc]
I: copying [./ghmm_0.9~rc3.orig.tar.gz]
I: copying [./ghmm_0.9~rc3-11.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./ghmm_0.9~rc3-11.dsc: unsupported subcommand
dpkg-source: info: extracting ghmm in ghmm-0.9~rc3
dpkg-source: info: unpacking ghmm_0.9~rc3.orig.tar.gz
dpkg-source: info: unpacking ghmm_0.9~rc3-11.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix_imp_func_issue.patch
dpkg-source: info: applying buildError.patch
dpkg-source: info: applying pythonpaths.patch
dpkg-source: info: applying fix_libxml2_config.patch
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying python3_build_system.patch
dpkg-source: info: applying lapacke.patch
dpkg-source: info: applying python3_syntax.patch
dpkg-source: info: applying fix-test-mcmc.patch
dpkg-source: info: applying python3.12.patch
dpkg-source: info: applying gcc-14.patch
dpkg-source: info: applying python3.12-syntax.patch
dpkg-source: info: applying python3.13-build-fix.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/2994823/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='arm64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='arm64'
IFS='
'
INVOCATION_ID='92ae87c8853d43ec8ad8198f64631a2c'
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='2994823'
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.WjY6zqg6/pbuilderrc_DWrj --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WjY6zqg6/b1 --logfile b1/build.log ghmm_0.9~rc3-11.dsc'
SUDO_GID='109'
SUDO_UID='104'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.4:3128'
I: uname -a
Linux codethink03-arm64 6.1.0-32-cloud-arm64 #1 SMP Debian 6.1.129-1 (2025-03-06) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/2994823/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: arm64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), dh-sequence-python3, d-shlibs (>= 0.106~), python3-dev, python3-setuptools, pkgconf, libxml2-dev, libgsl-dev, liblapacke-dev, zlib1g-dev, swig
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19920 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however:
Package dh-sequence-python3 is not installed.
pbuilder-satisfydepends-dummy depends on d-shlibs (>= 0.106~); however:
Package d-shlibs is not installed.
pbuilder-satisfydepends-dummy depends on python3-dev; however:
Package python3-dev is not installed.
pbuilder-satisfydepends-dummy depends on python3-setuptools; however:
Package python3-setuptools is not installed.
pbuilder-satisfydepends-dummy depends on pkgconf; however:
Package pkgconf is not installed.
pbuilder-satisfydepends-dummy depends on libxml2-dev; however:
Package libxml2-dev is not installed.
pbuilder-satisfydepends-dummy depends on libgsl-dev; however:
Package libgsl-dev is not installed.
pbuilder-satisfydepends-dummy depends on liblapacke-dev; however:
Package liblapacke-dev is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on swig; however:
Package swig is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libicu-dev{a} libicu76{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack-dev{a} liblapack3{a} liblapacke{a} liblapacke-dev{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpkgconf3{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtmglib-dev{a} libtmglib3{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} libxml2-dev{a} m4{a} man-db{a} media-types{a} netbase{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} swig{a} tzdata{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl javascript-common libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 86 newly installed, 0 to remove and 0 not upgraded.
Need to get 58.8 MB of archives. After unpacking 270 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.13-minimal arm64 3.13.2-2 [853 kB]
Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB]
Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.13-minimal arm64 3.13.2-2 [1995 kB]
Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.13.2-2 [27.1 kB]
Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 13.0.0 [29.3 kB]
Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.5 [12.4 kB]
Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2025b-1 [259 kB]
Get: 8 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.7-1 [21.2 kB]
Get: 9 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB]
Get: 10 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB]
Get: 11 http://deb.debian.org/debian trixie/main arm64 libpython3.13-stdlib arm64 3.13.2-2 [1888 kB]
Get: 12 http://deb.debian.org/debian trixie/main arm64 python3.13 arm64 3.13.2-2 [746 kB]
Get: 13 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.13.2-2 [10.1 kB]
Get: 14 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.13.2-2 [28.1 kB]
Get: 15 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get: 16 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get: 17 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get: 18 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get: 19 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB]
Get: 20 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB]
Get: 21 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB]
Get: 22 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB]
Get: 23 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get: 24 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get: 25 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-7 [285 kB]
Get: 26 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB]
Get: 27 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 28 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-4 [862 kB]
Get: 29 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB]
Get: 30 http://deb.debian.org/debian trixie/main arm64 d-shlibs all 0.109 [11.1 kB]
Get: 31 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 32 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-4 [539 kB]
Get: 33 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 34 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 35 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 36 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 37 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 38 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 39 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-2 [453 kB]
Get: 40 http://deb.debian.org/debian trixie/main arm64 libicu76 arm64 76.1-3 [9526 kB]
Get: 41 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.3+b1 [630 kB]
Get: 42 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB]
Get: 43 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 44 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 45 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB]
Get: 46 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20250308 [115 kB]
Get: 47 http://deb.debian.org/debian trixie/main arm64 icu-devtools arm64 76.1-3 [200 kB]
Get: 48 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.1-2 [104 kB]
Get: 49 http://deb.debian.org/debian trixie/main arm64 libblas-dev arm64 3.12.1-2 [111 kB]
Get: 50 http://deb.debian.org/debian trixie/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB]
Get: 51 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-19 [361 kB]
Get: 52 http://deb.debian.org/debian trixie/main arm64 libgslcblas0 arm64 2.8+dfsg-5 [84.1 kB]
Get: 53 http://deb.debian.org/debian trixie/main arm64 libgsl28 arm64 2.8+dfsg-5 [881 kB]
Get: 54 http://deb.debian.org/debian trixie/main arm64 libgsl-dev arm64 2.8+dfsg-5 [1118 kB]
Get: 55 http://deb.debian.org/debian trixie/main arm64 libicu-dev arm64 76.1-3 [10.6 MB]
Get: 56 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 57 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 58 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB]
Get: 59 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB]
Get: 60 http://deb.debian.org/debian trixie/main arm64 liblapack-dev arm64 3.12.1-2 [3726 kB]
Get: 61 http://deb.debian.org/debian trixie/main arm64 libtmglib3 arm64 3.12.1-2 [98.6 kB]
Get: 62 http://deb.debian.org/debian trixie/main arm64 liblapacke arm64 3.12.1-2 [338 kB]
Get: 63 http://deb.debian.org/debian trixie/main arm64 libtmglib-dev arm64 3.12.1-2 [103 kB]
Get: 64 http://deb.debian.org/debian trixie/main arm64 liblapacke-dev arm64 3.12.1-2 [353 kB]
Get: 65 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB]
Get: 66 http://deb.debian.org/debian trixie/main arm64 libpython3.13 arm64 3.13.2-2 [1972 kB]
Get: 67 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Get: 68 http://deb.debian.org/debian trixie/main arm64 libpython3.13-dev arm64 3.13.2-2 [4687 kB]
Get: 69 http://deb.debian.org/debian trixie/main arm64 libpython3-dev arm64 3.13.2-2 [10.3 kB]
Get: 70 http://deb.debian.org/debian trixie/main arm64 libxml2-dev arm64 2.12.7+dfsg+really2.9.14-0.3+b1 [751 kB]
Get: 71 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB]
Get: 72 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB]
Get: 73 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 74 http://deb.debian.org/debian trixie/main arm64 python3.13-dev arm64 3.13.2-2 [506 kB]
Get: 75 http://deb.debian.org/debian trixie/main arm64 python3-dev arm64 3.13.2-2 [26.1 kB]
Get: 76 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 77 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 78 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.4.2-1 [37.3 kB]
Get: 79 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 80 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 81 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 75.8.0-1 [222 kB]
Get: 82 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 83 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 84 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 75.8.0-1 [724 kB]
Get: 85 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B]
Get: 86 http://deb.debian.org/debian trixie/main arm64 swig arm64 4.3.0-1 [1406 kB]
Fetched 58.8 MB in 0s (164 MB/s)
Preconfiguring packages ...
Selecting previously unselected package libpython3.13-minimal:arm64.
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(Reading database ... 19920 files and directories currently installed.)
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Setting up python3-jaraco.functools (4.1.0-1) ...
Setting up python3-jaraco.context (6.0.1-1) ...
Setting up python3.13-dev (3.13.2-2) ...
Setting up python3-typeguard (4.4.2-1) ...
Setting up debhelper (13.24.1) ...
Setting up python3-inflect (7.3.1-2) ...
Setting up python3-jaraco.text (4.0.0-1) ...
Setting up python3-dev (3.13.2-2) ...
Setting up python3-pkg-resources (75.8.0-1) ...
Setting up python3-setuptools (75.8.0-1) ...
Processing triggers for libc-bin (2.41-6) ...
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_source.changes
dpkg-buildpackage: info: source package ghmm
dpkg-buildpackage: info: source version 0.9~rc3-11
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
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=aarch64-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/aarch64-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... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for file... file
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ranlib... ranlib
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for sys/time.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gawk... (cached) mawk
checking for doxygen... no
checking for rm... /usr/bin/rm
checking for pkg-config... /usr/bin/pkg-config
checking for expect... no
checking for runtest... no
configure: obsolete features disabled
configure: unsupported features disabled
checking for pthread_join in -lpthread... yes
checking for egrep... (cached) /usr/bin/grep -E
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for sqrt in -lm... yes
checking for exp in -lm... yes
checking for pow in -lm... yes
configure: "not using gsl"
checking for cos in -lm... yes
configure: "not using diagonal covariance matrix hack"
checking for lapacke with pkg-config... yes
configure: using internal Mersenne-Twister random number generator
checking for python3... /usr/bin/python3
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating ghmm/Makefile
config.status: creating ghmm/ghmmconfig.h
config.status: creating tools/Makefile
config.status: creating tests/Makefile
config.status: creating tests/data/Makefile
config.status: creating tools/ghmm-config
config.status: creating ghmmwrapper/Makefile
config.status: creating HMMEd/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
/usr/bin/rm: cannot remove 'libtoolT': No such file or directory
dh_auto_configure --buildsystem=pybuild --sourcedirectory=HMMEd
pybuild --configure -i python{version} -p 3.13 --dir HMMEd
I: pybuild base:311: python3.13 setup.py config
make[1]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3'
rm -f debian/ghmm.debhelper.log debian/libghmm-dev.debhelper.log debian/libghmm1t64.debhelper.log
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3'
dh_auto_build
make -j12
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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o sequence.lo sequence.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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c vector.c -fPIC -DPIC -o .libs/vector.o
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));
| ^
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c scanner.c -fPIC -DPIC -o .libs/scanner.o
sequence.c: In function 'ghmm_cseq_subseq_free':
sequence.c:715:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
715 | mes_check_ptr (sqd, return (-1));
| ^
sequence.c: In function 'ghmm_dseq_free':
sequence.c:1189:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
1189 | mes_check_ptr(sq, return -1);
| ^
sequence.c: In function 'ghmm_cseq_free':
sequence.c:1226:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
1226 | mes_check_ptr(sqd, return -1);
| ^
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c matrix.c -fPIC -DPIC -o .libs/matrix.o
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,
| ^~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c linkedlist.c -o linkedlist.o >/dev/null 2>&1
matrix.c: In function 'ighmm_cmatrix_stat_free':
matrix.c:176:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
176 | mes_check_ptr (matrix, return (-1));
| ^
matrix.c: In function 'ighmm_dmatrix_stat_free':
matrix.c:214:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
214 | mes_check_ptr (matrix, return (-1));
| ^
matrix.c: In function 'ighmm_cmatrix_3d_free':
matrix.c:270:35: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
270 | mes_check_ptr(matrix, return(-1));
| ^
matrix.c: In function 'ighmm_cmatrix_free':
matrix.c:285:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
285 | mes_check_ptr(matrix, return (-1));
| ^
matrix.c: In function 'ighmm_dmatrix_free':
matrix.c:343:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
343 | mes_check_ptr (matrix, return (-1));
| ^
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));
| ^
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c ghmm_internals.c -o ghmm_internals.o >/dev/null 2>&1
/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o psequence.lo psequence.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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c vector.c -o vector.o >/dev/null 2>&1
/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o xmlreader.lo xmlreader.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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o xmlwriter.lo xmlwriter.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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o model.lo model.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c matrix.c -o matrix.o >/dev/null 2>&1
/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o foba.lo foba.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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o viterbi.lo viterbi.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c randvar.c -o randvar.o >/dev/null 2>&1
psequence.c: In function 'ghmm_dpseq_free':
psequence.c:78:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
78 | mes_check_ptr(seq, return(-1));
| ^
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c mprintf.c -o mprintf.o >/dev/null 2>&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));
| ^
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c psequence.c -o psequence.o >/dev/null 2>&1
model.c: In function 'ghmm_dstate_clean':
model.c:1758:35: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
1758 | mes_check_ptr (my_state, return;);
| ^
/bin/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o reestimate.lo reestimate.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c viterbi.c -fPIC -DPIC -o .libs/viterbi.o
/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o gradescent.lo gradescent.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c foba.c -fPIC -DPIC -o .libs/foba.o
viterbi.c: In function 'viterbi_free':
viterbi.c:71:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
71 | mes_check_ptr(v, return -1);
| ^
/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o kbest.lo kbest.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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o discrime.lo discrime.c
foba.c: In function 'ghmm_dmodel_backward':
foba.c:286:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
286 | mes_check_0 (scale[t], goto STOP);
| ^
foba.c: In function 'ghmm_dmodel_label_backward':
foba.c:848:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
848 | mes_check_0 (scale[t], goto STOP);
| ^
/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o modelutil.lo modelutil.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c gradescent.c -fPIC -DPIC -o .libs/gradescent.o
reestimate.c: In function 'reestimate_free':
reestimate.c:79:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
79 | mes_check_ptr (r, return (-1));
| ^
reestimate.c: In function 'reestimate_setlambda':
reestimate.c:306:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
306 | mes_check_0 (r->pi_denom, goto STOP);
| ^
/bin/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o cluster.lo cluster.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c modelutil.c -fPIC -DPIC -o .libs/modelutil.o
/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o root_finder.lo root_finder.c
modelutil.c: In function 'topo_free':
modelutil.c:89:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
89 | mes_check_ptr (v, return (-1));
| ^
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c reestimate.c -o reestimate.o >/dev/null 2>&1
/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o smodel.lo smodel.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c cluster.c -o cluster.o >/dev/null 2>&1
/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o sfoba.lo sfoba.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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o sviterbi.lo sviterbi.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c root_finder.c -o root_finder.o >/dev/null 2>&1
/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o sreestimate.lo sreestimate.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c model.c -o model.o >/dev/null 2>&1
/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o scluster.lo scluster.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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c sfoba.c -fPIC -DPIC -o .libs/sfoba.o
/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o sgenerate.lo sgenerate.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c smodel.c -fPIC -DPIC -o .libs/smodel.o
smodel.c: In function 'ghmm_cmodel_free':
smodel.c:765:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
765 | mes_check_ptr (smo, return (-1));
| ^
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c sreestimate.c -fPIC -DPIC -o .libs/sreestimate.o
/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o smixturehmm.lo smixturehmm.c
sviterbi.c: In function 'sviterbi_free':
sviterbi.c:89:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
89 | mes_check_ptr (v, return (-1));
| ^
sreestimate.c: In function 'sreestimate_free':
sreestimate.c:174:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
174 | mes_check_ptr (r, return (-1));
| ^
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c scluster.c -fPIC -DPIC -o .libs/scluster.o
/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o smap_classify.lo smap_classify.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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o sdmodel.lo sdmodel.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c sviterbi.c -o sviterbi.o >/dev/null 2>&1
/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o sdfoba.lo sdfoba.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c smixturehmm.c -o smixturehmm.o >/dev/null 2>&1
/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o sdviterbi.lo sdviterbi.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c sdmodel.c -fPIC -DPIC -o .libs/sdmodel.o
/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o pmodel.lo pmodel.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c smap_classify.c -o smap_classify.o >/dev/null 2>&1
/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o pviterbi.lo pviterbi.c
sdmodel.c: In function 'ghmm_dsmodel_free':
sdmodel.c:211:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
211 | mes_check_ptr (mo, return (-1));
| ^
/bin/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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o pviterbi_propagate.lo pviterbi_propagate.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c sdviterbi.c -fPIC -DPIC -o .libs/sdviterbi.o
sdfoba.c: In function 'ghmm_dsmodel_backward':
sdfoba.c:336:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
336 | mes_check_0 (scale[t], goto STOP);
| ^
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c pviterbi.c -fPIC -DPIC -o .libs/pviterbi.o
sdviterbi.c: In function 'sdviterbi_free':
sdviterbi.c:111:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
111 | mes_check_ptr (v, return (-1));
| ^
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c sgenerate.c -o sgenerate.o >/dev/null 2>&1
pviterbi.c: In function 'pviterbi_free':
pviterbi.c:151:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
151 | mes_check_ptr(v, return(-1));
| ^
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));
| ^
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c pviterbi_propagate.c -fPIC -DPIC -o .libs/pviterbi_propagate.o
pviterbi_propagate.c: In function 'pviterbi_propagate_free':
pviterbi_propagate.c:255:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
255 | mes_check_ptr(v, return(-1));
| ^
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c sdviterbi.c -o sdviterbi.o >/dev/null 2>&1
/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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c cfbgibbs.c -o cfbgibbs.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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -version-info 1:0:0 -Wl,-z,relro -Wl,-z,now -o libghmm.la -rpath /usr/lib/aarch64-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 -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libghmm.so.1 -o .libs/libghmm.so.1.0.0
libtool: link: (cd ".libs" && rm -f "libghmm.so.1" && ln -s "libghmm.so.1.0.0" "libghmm.so.1")
libtool: link: (cd ".libs" && rm -f "libghmm.so" && ln -s "libghmm.so.1.0.0" "libghmm.so")
libtool: link: ar cr .libs/libghmm.a rng.o randvar.o matrixop.o gauss_tail.o mes.o ghmm_internals.o mprintf.o vector.o matrix.o scanner.o linkedlist.o sequence.o psequence.o xmlreader.o xmlwriter.o model.o foba.o viterbi.o reestimate.o gradescent.o kbest.o discrime.o modelutil.o cluster.o root_finder.o smodel.o sfoba.o sviterbi.o sreestimate.o scluster.o sgenerate.o smixturehmm.o smap_classify.o sdmodel.o sdfoba.o sdviterbi.o pmodel.o pviterbi.o pviterbi_propagate.o fbgibbs.o cfbgibbs.o
libtool: link: ranlib .libs/libghmm.a
libtool: link: ( cd ".libs" && rm -f "libghmm.la" && ln -s "../libghmm.la" "libghmm.la" )
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gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o smix_hmm.o smix_hmm.c
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libtool: link: gcc -g -O2 -Werror=implicit-function-declaration "-ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=." -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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
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gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ghmm-0.9~rc3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o mcmc.o mcmc.c
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/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 -mbranch-protection=standard -I/usr/include/aarch64-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
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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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
/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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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
/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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-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 -mbranch-protection=standard -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o mcmc mcmc.o ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2
make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests'
make[4]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/tests'
Making all in ghmmwrapper
make[4]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/ghmmwrapper'
Making all in .
make[5]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3/ghmmwrapper'
make[5]: Nothing to be done for 'all-am'.
make[5]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3/ghmmwrapper'
/usr/bin/python3 setup.py build
file ghmmwrapper.py (for module ghmmwrapper) not found
file ghmmwrapper.py (for module ghmmwrapper) not found
ghmmwrapper_wrap.c: In function '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/aarch64-linux-gnu'
/bin/bash ../libtool --mode=install /usr/bin/install -c libghmm.la '/build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/aarch64-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/aarch64-linux-gnu/libghmm.so.1.0.0
libtool: install: (cd /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libghmm.la
libtool: install: /usr/bin/install -c .libs/libghmm.a /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/aarch64-linux-gnu/libghmm.a
libtool: install: chmod 644 /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/aarch64-linux-gnu/libghmm.a
libtool: install: ranlib /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/aarch64-linux-gnu/libghmm.a
libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-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:79: 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:79: 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-aarch64/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-aarch64.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:79: 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:79: 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:79: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!
********************************************************************************
Please avoid running ``setup.py`` directly.
Instead, use pypa/build, pypa/installer or other
standards-based tools.
See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
********************************************************************************
!!
self.initialize_options()
make[1]: Leaving directory '/build/reproducible-path/ghmm-0.9~rc3'
rm -f debian/ghmm.debhelper.log debian/libghmm-dev.debhelper.log debian/libghmm1t64.debhelper.log
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/ghmm-0.9~rc3'
d-shlibmove --commit \
--t64 \
--multiarch \
--devunversioned \
--exclude-la \
--override s/libgsl23-dev/libgsl-dev/ \
--override s/liblapacke3-dev/liblapacke-dev/ \
--movedev debian/tmp/usr/include usr \
debian/tmp/usr/lib/*/*.so
Library package automatic movement utility
--> liblapacke-dev package exists.
--> libxml2-dev package exists.
set -e
install -d -m 755 debian/libghmm-dev/usr/lib/aarch64-linux-gnu
install -d -m 755 debian/libghmm1t64/usr/lib/aarch64-linux-gnu
mv debian/tmp/usr/lib/aarch64-linux-gnu/libghmm.a debian/libghmm-dev/usr/lib/aarch64-linux-gnu
mv debian/tmp/usr/lib/aarch64-linux-gnu/libghmm.so debian/libghmm-dev/usr/lib/aarch64-linux-gnu
mv /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/aarch64-linux-gnu/libghmm.so.1 debian/libghmm1t64/usr/lib/aarch64-linux-gnu
mv /build/reproducible-path/ghmm-0.9~rc3/debian/tmp/usr/lib/aarch64-linux-gnu/libghmm.so.1.0.0 debian/libghmm1t64/usr/lib/aarch64-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: 6.20250308
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/ghmm-config): doesn't look like a shebang: #! /bin/sh
D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/ghmm-cluster): cannot parse binary file
D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/smix_hmm): cannot parse binary file
D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/scluster): cannot parse binary file
D: dh_python3 tools:101: fix_shebang (debian/ghmm/usr/bin/probdist): 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/aarch64-linux-gnu/libghmm.so
ln -s libghmm.so.1.0.0 debian/libghmm-dev/usr/lib/aarch64-linux-gnu/libghmm.so
rm -f debian/libghmm1t64/usr/lib/aarch64-linux-gnu/libghmm.so.1
ln -s libghmm.so.1.0.0 debian/libghmm1t64/usr/lib/aarch64-linux-gnu/libghmm.so.1
dh_strip_nondeterminism
dh_compress
cd debian/ghmm
chmod a-x usr/share/doc/ghmm/changelog.Debian
gzip -9nf usr/share/doc/ghmm/changelog.Debian
cd '/build/reproducible-path/ghmm-0.9~rc3'
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
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'
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/libghmm-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/libghmm1t64 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/ghmm ! -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/ghmm/usr/share/doc -type f -a -true -a ! -regex 'debian/ghmm/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libghmm-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libghmm-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/ghmm/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/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/libghmm1t64/usr/share/lintian/overrides -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/libghmm-dev/usr/include -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/libghmm-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
find debian/libghmm1t64/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
find debian/ghmm/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
dh_missing
dh_dwz -a
dwz -- debian/libghmm1t64/usr/lib/aarch64-linux-gnu/libghmm.so.1.0.0
install -m0755 -d debian/ghmm/usr/lib/debug/.dwz/aarch64-linux-gnu
dwz -mdebian/ghmm/usr/lib/debug/.dwz/aarch64-linux-gnu/ghmm.debug -M/usr/lib/debug/.dwz/aarch64-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-aarch64-linux-gnu.so
objcopy --compress-debug-sections debian/ghmm/usr/lib/debug/.dwz/aarch64-linux-gnu/ghmm.debug
chmod 0644 -- debian/ghmm/usr/lib/debug/.dwz/aarch64-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/aarch64-linux-gnu/libghmm.a
install -m0755 -d debian/.debhelper/libghmm1t64/dbgsym-root/usr/lib/debug/.build-id/65
objcopy --only-keep-debug --compress-debug-sections debian/libghmm1t64/usr/lib/aarch64-linux-gnu/libghmm.so.1.0.0 debian/.debhelper/libghmm1t64/dbgsym-root/usr/lib/debug/.build-id/65/e8a37cc32bcb505ff49eade8b65262157cc482.debug
install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/3a
objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-313-aarch64-linux-gnu.so debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/3a/4d5d651107569af987ccb0e1e9c59faadc082e.debug
chmod 0644 -- debian/.debhelper/libghmm1t64/dbgsym-root/usr/lib/debug/.build-id/65/e8a37cc32bcb505ff49eade8b65262157cc482.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libghmm1t64/usr/lib/aarch64-linux-gnu/libghmm.so.1.0.0
objcopy --add-gnu-debuglink debian/.debhelper/libghmm1t64/dbgsym-root/usr/lib/debug/.build-id/65/e8a37cc32bcb505ff49eade8b65262157cc482.debug debian/libghmm1t64/usr/lib/aarch64-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/3a/4d5d651107569af987ccb0e1e9c59faadc082e.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/ghmm/usr/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-313-aarch64-linux-gnu.so
objcopy --add-gnu-debuglink debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/3a/4d5d651107569af987ccb0e1e9c59faadc082e.debug debian/ghmm/usr/lib/python3/dist-packages/ghmm/_ghmmwrapper.cpython-313-aarch64-linux-gnu.so
install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/7b
objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/smix_hmm debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/7b/be3cc689c1d0df5d569f41a871b3264cc89993.debug
chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/7b/be3cc689c1d0df5d569f41a871b3264cc89993.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/7b/be3cc689c1d0df5d569f41a871b3264cc89993.debug debian/ghmm/usr/bin/smix_hmm
install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/22
objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/probdist debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/22/5362e105cf046dce77ddc57de3a4c0044856a8.debug
chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/22/5362e105cf046dce77ddc57de3a4c0044856a8.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/22/5362e105cf046dce77ddc57de3a4c0044856a8.debug debian/ghmm/usr/bin/probdist
install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/14
objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/scluster debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/14/6e6fcb80aaa966baa0917470d0d657528808a4.debug
chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/14/6e6fcb80aaa966baa0917470d0d657528808a4.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/14/6e6fcb80aaa966baa0917470d0d657528808a4.debug debian/ghmm/usr/bin/scluster
install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/85
objcopy --only-keep-debug --compress-debug-sections debian/ghmm/usr/bin/ghmm-cluster debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/85/d8191b4afdd8885a2eb8e953474a84809d2533.debug
chmod 0644 -- debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.build-id/85/d8191b4afdd8885a2eb8e953474a84809d2533.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/85/d8191b4afdd8885a2eb8e953474a84809d2533.debug debian/ghmm/usr/bin/ghmm-cluster
install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/usr/lib/debug/.dwz
cp --reflink=auto -a debian/ghmm/usr/lib/debug/.dwz/aarch64-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/aarch64-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-aarch64-linux-gnu.so debian/ghmm/usr/bin/smix_hmm debian/ghmm/usr/bin/probdist debian/ghmm/usr/bin/scluster debian/ghmm/usr/bin/ghmm-cluster
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
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=146e6fcb80aaa966baa0917470d0d657528808a4 225362e105cf046dce77ddc57de3a4c0044856a8 3a4d5d651107569af987ccb0e1e9c59faadc082e 7bbe3cc689c1d0df5d569f41a871b3264cc89993 85d8191b4afdd8885a2eb8e953474a84809d2533" -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=65e8a37cc32bcb505ff49eade8b65262157cc482 -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/libghmm-dev/DEBIAN/control
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
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
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
install -m0755 -d debian/libghmm1t64/DEBIAN
chmod 0644 -- debian/libghmm-dev/DEBIAN/md5sums
cd debian/libghmm1t64 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/ghmm/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/ghmm/dbgsym-root/DEBIAN
chmod 0644 -- debian/libghmm1t64/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/libghmm1t64/dbgsym-root/DEBIAN
cd debian/.debhelper/libghmm1t64/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
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/libghmm-dev ..
dpkg-deb --root-owner-group --build debian/.debhelper/ghmm/dbgsym-root ..
dpkg-deb --root-owner-group --build debian/.debhelper/libghmm1t64/dbgsym-root ..
dpkg-deb --root-owner-group --build debian/ghmm ..
dpkg-deb: building package 'libghmm-dev' in '../libghmm-dev_0.9~rc3-11_arm64.deb'.
dpkg-deb: building package 'ghmm' in '../ghmm_0.9~rc3-11_arm64.deb'.
dpkg-deb: building package 'libghmm1t64-dbgsym' in '../libghmm1t64-dbgsym_0.9~rc3-11_arm64.deb'.
dpkg-deb --root-owner-group --build debian/libghmm1t64 ..
dpkg-deb: building package 'libghmm1t64' in '../libghmm1t64_0.9~rc3-11_arm64.deb'.
dpkg-deb: building package 'ghmm-dbgsym' in '../ghmm-dbgsym_0.9~rc3-11_arm64.deb'.
dpkg-genbuildinfo --build=binary -O../ghmm_0.9~rc3-11_arm64.buildinfo
dpkg-genchanges --build=binary -O../ghmm_0.9~rc3-11_arm64.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/2994823 and its subdirectories
I: Current time: Thu Apr 30 09:17:08 -12 2026
I: pbuilder-time-stamp: 1777583828
Fri Mar 28 14:54:11 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net.
Fri Mar 28 14:54:11 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net.
Fri Mar 28 14:55:30 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net.
Fri Mar 28 14:55:31 UTC 2025 I: ghmm_0.9~rc3-11_arm64.changes:
Format: 1.8
Date: Tue, 14 Jan 2025 18:47:58 +0530
Source: ghmm
Binary: ghmm ghmm-dbgsym libghmm-dev libghmm1t64 libghmm1t64-dbgsym
Architecture: arm64
Version: 0.9~rc3-11
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Description:
ghmm - General Hidden-Markov-Model library - tools
libghmm-dev - General Hidden-Markov-Model library - header files
libghmm1t64 - General Hidden-Markov-Model library
Closes: 1092058
Changes:
ghmm (0.9~rc3-11) unstable; urgency=medium
.
* Team Upload.
* Fixup build with python 3.13 (Closes: #1092058)
Checksums-Sha1:
a56b00460b36e4060334d37c5a6c1edcbe29e426 449424 ghmm-dbgsym_0.9~rc3-11_arm64.deb
3d51f1f98fc3592ab80908b8a1e129333303f7ae 7811 ghmm_0.9~rc3-11_arm64.buildinfo
022e270182282a43bfbf4d57f5dfca97dd3d6ec9 153836 ghmm_0.9~rc3-11_arm64.deb
c553ce3ee56c1bd1987649b7be692fbb892308c3 181232 libghmm-dev_0.9~rc3-11_arm64.deb
598e1e1e0ed8202bf009ebc764b0edee866566ec 328724 libghmm1t64-dbgsym_0.9~rc3-11_arm64.deb
6f25551bc6ac2f442d099a7de20d15f5247885a6 135892 libghmm1t64_0.9~rc3-11_arm64.deb
Checksums-Sha256:
643e296fda509bd72d7d6a1a9736250f44d001ff51aaa38f655b8c964b890b4d 449424 ghmm-dbgsym_0.9~rc3-11_arm64.deb
7980ae043a7719b7cfc2bac53b6511548bc1634b202dbcdd0473d842662ab62e 7811 ghmm_0.9~rc3-11_arm64.buildinfo
c298cd421b838d44954f6639f3599c3a7288032f37318f1f8aede296bc6f35f6 153836 ghmm_0.9~rc3-11_arm64.deb
2f5510080e5c394ce805f6584b6a2e03e916dfd78204cacf226274e8d5e702fe 181232 libghmm-dev_0.9~rc3-11_arm64.deb
6f03e95ce2489667cb5c26f25544ab6541339942c7e3178a7da28d61e6b16a05 328724 libghmm1t64-dbgsym_0.9~rc3-11_arm64.deb
99835b935e66ad17ba84287512cb054968fd375b31bb2dcbf284a6bc0f22267c 135892 libghmm1t64_0.9~rc3-11_arm64.deb
Files:
074399dacf192a9dd45ed630b6a585a0 449424 debug optional ghmm-dbgsym_0.9~rc3-11_arm64.deb
4c260ec6b4d3b2bbffe699e28653c904 7811 science optional ghmm_0.9~rc3-11_arm64.buildinfo
4836e4f4a4a33809b1f55a8d152b14eb 153836 science optional ghmm_0.9~rc3-11_arm64.deb
9e55a34f54b5b1d7c8d3c46f869724ac 181232 libdevel optional libghmm-dev_0.9~rc3-11_arm64.deb
663a18f8c7f40fd83c3a0ca6005be243 328724 debug optional libghmm1t64-dbgsym_0.9~rc3-11_arm64.deb
40919e998b5255bd9b97056139f01a53 135892 libs optional libghmm1t64_0.9~rc3-11_arm64.deb
Fri Mar 28 14:55:32 UTC 2025 I: diffoscope 291 will be used to compare the two builds:
Running as unit: rb-diffoscope-arm64_3-84339.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.WjY6zqg6/ghmm_0.9~rc3-11.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.WjY6zqg6/ghmm_0.9~rc3-11.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.WjY6zqg6/ghmm_0.9~rc3-11.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.WjY6zqg6/b1/ghmm_0.9~rc3-11_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.WjY6zqg6/b2/ghmm_0.9~rc3-11_arm64.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
Service runtime: 227ms
CPU time consumed: 227ms
Fri Mar 28 14:55:34 UTC 2025 I: diffoscope 291 found no differences in the changes files, and a .buildinfo file also exists.
Fri Mar 28 14:55:34 UTC 2025 I: ghmm from trixie built successfully and reproducibly on arm64.
Fri Mar 28 14:55:35 UTC 2025 I: Submitting .buildinfo files to external archives:
Fri Mar 28 14:55:35 UTC 2025 I: Submitting 12K b1/ghmm_0.9~rc3-11_arm64.buildinfo.asc
Fri Mar 28 14:55:36 UTC 2025 I: Submitting 12K b2/ghmm_0.9~rc3-11_arm64.buildinfo.asc
Fri Mar 28 14:55:37 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Fri Mar 28 14:55:37 UTC 2025 I: Done submitting .buildinfo files.
Fri Mar 28 14:55:37 UTC 2025 I: Removing signed ghmm_0.9~rc3-11_arm64.buildinfo.asc files:
removed './b1/ghmm_0.9~rc3-11_arm64.buildinfo.asc'
removed './b2/ghmm_0.9~rc3-11_arm64.buildinfo.asc'