Wed May 31 08:22:03 UTC 2023 I: starting to build ghmm/bookworm/arm64 on jenkins on '2023-05-31 08:21' Wed May 31 08:22:03 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_14/8/console.log Wed May 31 08:22:03 UTC 2023 I: Downloading source for bookworm/ghmm=0.9~rc3-4 --2023-05-31 08:22:03-- http://cdn-fastly.deb.debian.org/debian/pool/main/g/ghmm/ghmm_0.9%7erc3-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2136 (2.1K) [text/prs.lines.tag] Saving to: ‘ghmm_0.9~rc3-4.dsc’ 0K .. 100% 119M=0s 2023-05-31 08:22:03 (119 MB/s) - ‘ghmm_0.9~rc3-4.dsc’ saved [2136/2136] Wed May 31 08:22:03 UTC 2023 I: ghmm_0.9~rc3-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: ghmm Binary: ghmm, libghmm-dev, libghmm1 Architecture: any Version: 0.9~rc3-4 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Homepage: https://sourceforge.net/p/ghmm/wiki/Home/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/ghmm Vcs-Git: https://salsa.debian.org/med-team/ghmm.git Build-Depends: debhelper-compat (= 13), d-shlibs, python3-dev, pkg-config, libxml2-dev, libgsl-dev, libatlas-base-dev, liblapack-dev, zlib1g-dev, swig Package-List: ghmm deb science optional arch=any libghmm-dev deb libdevel optional arch=any libghmm1 deb libs optional arch=any Checksums-Sha1: c3f2be9c27010a6f82df6f136821673112ed41a5 770526 ghmm_0.9~rc3.orig.tar.gz c059e52d31ca04dfc89ee8ef2f13251ba22e1630 17608 ghmm_0.9~rc3-4.debian.tar.xz Checksums-Sha256: c42462ff4f87aadd5efe7bb6adb59657786ed71046ba924111bc28c7cbb588d0 770526 ghmm_0.9~rc3.orig.tar.gz 5001881369d69ed4f31735baed771cca32a09e4c51ca1b0aa9231c20e2ccc962 17608 ghmm_0.9~rc3-4.debian.tar.xz Files: 4e2db5a83bbd5b2a7cc6476657c0c4d7 770526 ghmm_0.9~rc3.orig.tar.gz 227ea4dd4bfbbd9caba9856961187854 17608 ghmm_0.9~rc3-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmANyvQRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHfehAAkFIlkE3G4M8BSCIgl0y0Rq6aIND0pTte b7Npcqo7kunWAvb0XrDZXsJ7DSnbinJuMXyUMRhRZl2pWhOtY65Ix4/TD/XplzmP 4O/w0mHxv5ELooEC6CoXLA4myDzH7Z+4sxPTzRZeQU8Rdq7l6uHNkRnrWyWfXzMF 7DsauMuhrHcwfkZ/pRuUMJGWVan6FIL/UfT5IbtXt6bP7qgGkwZL7mL5ERlA7zWj 0zzFHtN2edw4hbCMaQnDbAgPlPFyuMIIe2FbYkjAp12EP79NpEYX6qRXLZVw6+tg wt9vtcBxU5Sz0g4nfD4674Jee5ATJktt8nA/MHLjbMo+i014r7l8drg41vz/lBx7 FTfPQIOUEsmBvrdIaSWBe7/iDsI8UAnJHkCiD4xt8SJoWGwcxmua5OgPdeOpPaCO NmhyJxoS4rT/PGBK890BJw2uB5mbHTuRy1ePciBh5Xf7U0D5NDbkl4gikgJLUqz3 ZqWXx8JKpAem5ZIIvmRKOFYVixOZ8i7GXYiFOG8wInKxYye08CrGlNRNLUB+CBn+ BBqj7yb3TalEEvxAw74q/clJLVoYq/E592Oo4TGpbqBd0fLffi3ImblsYlxAh5Oi bOpCMB7sywLhWcRav6krf+o70wYpLVZq+zMTEQXSGvMvhVhR4LjBW+o6zxBhwYm3 OHkgTFncPH0= =wuBS -----END PGP SIGNATURE----- Wed May 31 08:22:03 UTC 2023 I: Checking whether the package is not for us Wed May 31 08:22:03 UTC 2023 I: Starting 1st build on remote node codethink12-arm64.debian.net. Wed May 31 08:22:03 UTC 2023 I: Preparing to do remote build '1' on codethink12-arm64.debian.net. Wed May 31 08:26:16 UTC 2023 I: Deleting $TMPDIR on codethink12-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 30 20:22:09 -12 2023 I: pbuilder-time-stamp: 1685521329 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [ghmm_0.9~rc3-4.dsc] I: copying [./ghmm_0.9~rc3.orig.tar.gz] I: copying [./ghmm_0.9~rc3-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Jan 24 07:31:00 2021 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./ghmm_0.9~rc3-4.dsc: no acceptable signature found dpkg-source: info: extracting ghmm in ghmm-0.9~rc3 dpkg-source: info: unpacking ghmm_0.9~rc3.orig.tar.gz dpkg-source: info: unpacking ghmm_0.9~rc3-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying buildError.patch dpkg-source: info: applying pythonpaths.patch dpkg-source: info: applying fix_libxml2_config.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying python3_build_system.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3119/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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=8 ' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='3119' 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.bDHQOm0o/pbuilderrc_hZD9 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bDHQOm0o/b1 --logfile b1/build.log ghmm_0.9~rc3-4.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink12-arm64 4.15.0-211-generic #222-Ubuntu SMP Tue Apr 18 18:58:27 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 26 22:26 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3119/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 Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), d-shlibs, python3-dev, pkg-config, libxml2-dev, libgsl-dev, libatlas-base-dev, liblapack-dev, zlib1g-dev, swig dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19611 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libxml2-dev; however: Package libxml2-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on libatlas-base-dev; however: Package libatlas-base-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on swig; however: Package swig is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libatlas-base-dev{a} libatlas3-base{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libicu-dev{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack-dev{a} liblapack3{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpkgconf3{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libxml2-dev{a} m4{a} man-db{a} media-types{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} swig{a} swig4.0{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 71 newly installed, 0 to remove and 0 not upgraded. Need to get 57.5 MB of archives. After unpacking 266 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B] Get: 11 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 d-shlibs all 0.104 [18.6 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 35 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 icu-devtools arm64 72.1-3 [192 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 libgfortran5 arm64 12.2.0-14 [340 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 libatlas3-base arm64 3.10.3-13 [2537 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 libatlas-base-dev arm64 3.10.3-13 [2655 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libexpat1-dev arm64 2.5.0-1 [135 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libgslcblas0 arm64 2.7.1+dfsg-3+b1 [82.3 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 libgsl27 arm64 2.7.1+dfsg-3+b1 [824 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libgsl-dev arm64 2.7.1+dfsg-3+b1 [1035 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libicu-dev arm64 72.1-3 [10.2 MB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 liblapack3 arm64 3.11.0-2 [1664 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 liblapack-dev arm64 3.11.0-2 [3065 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 libpkgconf3 arm64 1.8.1-1 [35.3 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libpython3.11 arm64 3.11.2-6 [1841 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-dev arm64 3.11.2-6 [4395 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 libpython3-dev arm64 3.11.2-1+b1 [9564 B] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libxml2-dev arm64 2.9.14+dfsg-1.2 [740 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 pkgconf-bin arm64 1.8.1-1 [28.9 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 pkgconf arm64 1.8.1-1 [25.9 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 python3.11-dev arm64 3.11.2-6 [617 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 python3-distutils all 3.11.2-3 [131 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 python3-dev arm64 3.11.2-1+b1 [26.2 kB] Get: 70 http://deb.debian.org/debian bookworm/main arm64 swig4.0 arm64 4.1.0-0.2 [1299 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 swig all 4.1.0-0.2 [321 kB] Fetched 57.5 MB in 3s (21.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19611 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_arm64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:arm64 (3.11.2-6) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19927 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_arm64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../3-libreadline8_8.2-1.3_arm64.deb ... Unpacking libreadline8:arm64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_arm64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20361 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_arm64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... 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Setting up readline-common (8.2-1.3) ... Setting up libicu-dev:arm64 (72.1-3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libgsl-dev (2.7.1+dfsg-3+b1) ... Setting up swig (4.1.0-0.2) ... Setting up libatlas3-base:arm64 (3.10.3-13) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/atlas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/atlas/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libtool (2.4.7-5) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up libatlas-base-dev:arm64 (3.10.3-13) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/atlas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/atlas/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up pkgconf:arm64 (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libxml2-dev:arm64 (2.9.14+dfsg-1.2) ... Setting up pkg-config:arm64 (1.8.1-1) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up liblapack3:arm64 (3.11.0-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up liblapack-dev:arm64 (3.11.0-2) ... Setting up libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libpython3.11:arm64 (3.11.2-6) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libpython3.11-dev:arm64 (3.11.2-6) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-distutils (3.11.2-3) ... Setting up libpython3-dev:arm64 (3.11.2-1+b1) ... Setting up python3.11-dev (3.11.2-6) ... Setting up python3-dev (3.11.2-1+b1) ... Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/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~rc3-4_source.changes dpkg-buildpackage: info: source package ghmm dpkg-buildpackage: info: source version 0.9~rc3-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/ghmm-0.9~rc3' if [ -r Makefile ]; then /usr/bin/make clean; fi find . -name Makefile -delete find . \( -name "*.o" -o -name "*.lo" \) -delete rm -f ghmmwrapper/ghmmwrapper.py ghmmwrapper/ghmmwrapper_wrap.c rm -rf HMMEd/build/ ghmmwrapper/build/ rm -f config.h config.log config.status rm -f libtool stamp-h1 tests/chmm_test.2JNcXz rm -f tools/ghmm-config rm -rf ghmm/.deps/ tests/.deps/ tools/.deps/ make[1]: Leaving directory '/build/ghmm-0.9~rc3' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.in, libtoolize: and rerunning libtoolize and aclocal. libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am. aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:47: warning: 'AM_CONFIG_HEADER': this macro is obsolete. configure.in:47: You should use the 'AC_CONFIG_HEADERS' macro instead. ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:9833: AM_CONFIG_HEADER is expanded from... configure.in:47: the top level configure.in:63: warning: The macro `AM_PROG_LIBTOOL' is obsolete. configure.in:63: You should run autoupdate. aclocal.m4:123: AM_PROG_LIBTOOL is expanded from... configure.in:63: the top level configure.in:75: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:75: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.in:75: the top level configure.in:93: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:93: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.in:93: the top level configure.in:104: warning: The macro `AC_LANG_C' is obsolete. configure.in:104: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... configure.in:104: the top level configure.in:111: warning: The macro `AC_HEADER_STDC' is obsolete. configure.in:111: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.in:111: the top level configure.in:117: warning: The macro `AC_HEADER_TIME' is obsolete. configure.in:117: You should run autoupdate. ./lib/autoconf/headers.m4:743: AC_HEADER_TIME is expanded from... configure.in:117: the top level configure.in:136: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:136: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.in:136: the top level configure.in:135: warning: The macro `AC_TRY_RUN' is obsolete. configure.in:135: You should run autoupdate. ./lib/autoconf/general.m4:2997: AC_TRY_RUN is expanded from... acinclude.m4:10: AM_PATH_GSL is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.in:135: the top level configure.in:135: warning: The macro `AC_TRY_LINK' is obsolete. configure.in:135: You should run autoupdate. ./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from... acinclude.m4:10: AM_PATH_GSL is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.in:135: the top level configure.in:135: warning: The macro `AC_TRY_COMPILE' is obsolete. configure.in:135: You should run autoupdate. ./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.in:135: the top level configure.in:135: warning: The macro `AC_TRY_LINK' is obsolete. configure.in:135: You should run autoupdate. ./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.in:135: the top level configure.in:194: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:194: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.in:194: the top level configure.in:207: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:207: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.in:207: the top level configure.in:206: warning: The macro `AC_TRY_COMPILE' is obsolete. configure.in:206: You should run autoupdate. ./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.in:206: the top level configure.in:323: warning: The macro `AC_HELP_STRING' is obsolete. configure.in:323: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1553: AC_ARG_WITH is expanded from... configure.in:323: the top level configure.in:354: warning: AC_OUTPUT should be used without arguments. configure.in:354: You should run autoupdate. autoheader: warning: autoconf input should be named 'configure.ac', not 'configure.in' automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:62: installing './compile' configure.in:49: installing './missing' ghmm/Makefile.am:77: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' ghmm/Makefile.am: installing './depcomp' tests/Makefile.am:51: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') parallel-tests: installing './test-driver' tools/Makefile.am:48: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') debian/rules override_dh_auto_configure make[1]: Entering directory '/build/ghmm-0.9~rc3' dh_auto_configure -- --enable-atlas ./configure --build=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-atlas checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking build system type... 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 ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/time.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gawk... (cached) mawk checking for doxygen... no checking for rm... /usr/bin/rm checking for pkg-config... /usr/bin/pkg-config checking for expect... no checking for runtest... no configure: obsolete features disabled configure: unsupported features disabled checking for pthread_join in -lpthread... yes checking for egrep... (cached) /usr/bin/grep -E checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for sqrt in -lm... yes checking for exp in -lm... yes checking for pow in -lm... yes configure: "not using gsl" checking for cos in -lm... yes configure: "not using diagonal covariance matrix hack" checking for lapack with pkg-config... yes checking for clapack_dgetrf in -llapack... yes checking for clapack_dgetri in -llapack... yes checking for clapack_dpotrf in -llapack... yes configure: using internal Mersenne-Twister random number generator checking for python3... /usr/bin/python3 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating ghmm/Makefile config.status: creating ghmm/ghmmconfig.h config.status: creating tools/Makefile config.status: creating tests/Makefile config.status: creating tests/data/Makefile config.status: creating tools/ghmm-config config.status: creating ghmmwrapper/Makefile config.status: creating HMMEd/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands /usr/bin/rm: cannot remove 'libtoolT': No such file or directory make[1]: Leaving directory '/build/ghmm-0.9~rc3' dh_auto_build make -j8 make[1]: Entering directory '/build/ghmm-0.9~rc3' make all-recursive make[2]: Entering directory '/build/ghmm-0.9~rc3' Making all in ghmm make[3]: Entering directory '/build/ghmm-0.9~rc3/ghmm' Making all in . make[4]: Entering directory '/build/ghmm-0.9~rc3/ghmm' /bin/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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o vector.lo vector.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c vector.c -fPIC -DPIC -o .libs/vector.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c mes.c -fPIC -DPIC -o .libs/mes.o ghmm_internals.c: In function 'ighmm_log_out': ghmm_internals.c:69:17: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] 69 | message = strncat(message, error_str, slen); | ^ In function 'process_external_log', inlined from 'ighmm_log_out' at ghmm_internals.c:83:5: ghmm_internals.c:64:14: note: length computed here 64 | int slen = strlen(error_str); | ^~~~~~~~~~~~~~~~~ rng.c: In function 'ghmm_rng_init': rng.c:67:3: warning: argument 2 null where non-null expected [-Wnonnull] 67 | initstate(1, ighmm_rng_state, sizeof(ghmm_rng_state_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from rng.c:40: /usr/include/stdlib.h:411:14: note: in a call to function 'initstate' declared 'nonnull' 411 | extern char *initstate (unsigned int __seed, char *__statebuf, | ^~~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c ghmm_internals.c -o ghmm_internals.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c vector.c -o vector.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c matrixop.c -o matrixop.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o sequence.lo sequence.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c matrix.c -fPIC -DPIC -o .libs/matrix.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c scanner.c -fPIC -DPIC -o .libs/scanner.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c randvar.c -o randvar.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c psequence.c -fPIC -DPIC -o .libs/psequence.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o xmlreader.lo xmlreader.c matrix.c: In function 'ighmm_cmatrix_stat_free': matrix.c:176:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 176 | mes_check_ptr (matrix, return (-1)); | ^ matrix.c: In function 'ighmm_dmatrix_stat_free': matrix.c:214:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 214 | mes_check_ptr (matrix, return (-1)); | ^ matrix.c: In function 'ighmm_cmatrix_3d_free': 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)); | ^ sequence.c: In function 'ghmm_dseq_subseq_free': sequence.c:685:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 685 | mes_check_ptr (sq, return (-1)); | ^ sequence.c: In function 'ghmm_cseq_subseq_free': sequence.c:715:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 715 | mes_check_ptr (sqd, return (-1)); | ^ psequence.c: In function 'ghmm_dpseq_free': psequence.c:78:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 78 | mes_check_ptr(seq, return(-1)); | ^ sequence.c: 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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c linkedlist.c -o linkedlist.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c psequence.c -o psequence.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o xmlwriter.lo xmlwriter.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c mprintf.c -o mprintf.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c matrix.c -o matrix.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c xmlwriter.c -fPIC -DPIC -o .libs/xmlwriter.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o model.lo model.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o foba.lo foba.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c foba.c -fPIC -DPIC -o .libs/foba.o 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)); | ^ model.c: In function 'ghmm_dstate_clean': model.c:1758:35: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1758 | mes_check_ptr (my_state, return;); | ^ foba.c: 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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o reestimate.lo reestimate.c viterbi.c: In function 'viterbi_free': viterbi.c:71:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 71 | mes_check_ptr(v, return -1); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c reestimate.c -fPIC -DPIC -o .libs/reestimate.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c gradescent.c -fPIC -DPIC -o .libs/gradescent.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c gradescent.c -o gradescent.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o kbest.lo kbest.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o discrime.lo discrime.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c modelutil.c -fPIC -DPIC -o .libs/modelutil.o modelutil.c: In function 'topo_free': modelutil.c:89:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 89 | mes_check_ptr (v, return (-1)); | ^ /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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o cluster.lo cluster.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o root_finder.lo root_finder.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c modelutil.c -o modelutil.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c cluster.c -o cluster.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c root_finder.c -fPIC -DPIC -o .libs/root_finder.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c smodel.c -fPIC -DPIC -o .libs/smodel.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c sfoba.c -fPIC -DPIC -o .libs/sfoba.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c root_finder.c -o root_finder.o >/dev/null 2>&1 smodel.c: In function 'ghmm_cmodel_free': smodel.c:765:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 765 | mes_check_ptr (smo, return (-1)); | ^ sviterbi.c: In function 'sviterbi_free': sviterbi.c:89:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 89 | mes_check_ptr (v, return (-1)); | ^ /bin/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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o sreestimate.lo sreestimate.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c sreestimate.c -fPIC -DPIC -o .libs/sreestimate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c scluster.c -fPIC -DPIC -o .libs/scluster.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c scluster.c -o scluster.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c sviterbi.c -o sviterbi.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c sgenerate.c -fPIC -DPIC -o .libs/sgenerate.o sreestimate.c: In function 'sreestimate_free': sreestimate.c:174:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 174 | mes_check_ptr (r, return (-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c sfoba.c -o sfoba.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o smixturehmm.lo smixturehmm.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o smap_classify.lo smap_classify.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c smixturehmm.c -o smixturehmm.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c smap_classify.c -fPIC -DPIC -o .libs/smap_classify.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c sdmodel.c -fPIC -DPIC -o .libs/sdmodel.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c sdfoba.c -fPIC -DPIC -o .libs/sdfoba.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o sdviterbi.lo sdviterbi.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)); | ^ sdfoba.c: In function 'ghmm_dsmodel_backward': sdfoba.c:336:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 336 | mes_check_0 (scale[t], goto STOP); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c sdviterbi.c -fPIC -DPIC -o .libs/sdviterbi.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c sgenerate.c -o sgenerate.o >/dev/null 2>&1 sdviterbi.c: In function 'sdviterbi_free': sdviterbi.c:111:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 111 | mes_check_ptr (v, return (-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c sreestimate.c -o sreestimate.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o pviterbi.lo pviterbi.c pmodel.c: In function 'ghmm_dpmodel_free': pmodel.c:127:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 127 | mes_check_ptr(mo, return(-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c pviterbi.c -fPIC -DPIC -o .libs/pviterbi.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c pviterbi_propagate.c -fPIC -DPIC -o .libs/pviterbi_propagate.o pviterbi.c: In function 'pviterbi_free': pviterbi.c:151:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 151 | mes_check_ptr(v, return(-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c sdmodel.c -o sdmodel.o >/dev/null 2>&1 pviterbi_propagate.c: In function 'pviterbi_propagate_free': pviterbi_propagate.c:255:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 255 | mes_check_ptr(v, return(-1)); | ^ /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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o fbgibbs.lo fbgibbs.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c fbgibbs.c -fPIC -DPIC -o .libs/fbgibbs.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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -version-info 1:0:0 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o libghmm.la -rpath /usr/lib/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 -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -shared -fPIC -DPIC .libs/rng.o .libs/randvar.o .libs/matrixop.o .libs/gauss_tail.o .libs/mes.o .libs/ghmm_internals.o .libs/mprintf.o .libs/vector.o .libs/matrix.o .libs/scanner.o .libs/linkedlist.o .libs/sequence.o .libs/psequence.o .libs/xmlreader.o .libs/xmlwriter.o .libs/model.o .libs/foba.o .libs/viterbi.o .libs/reestimate.o .libs/gradescent.o .libs/kbest.o .libs/discrime.o .libs/modelutil.o .libs/cluster.o .libs/root_finder.o .libs/smodel.o .libs/sfoba.o .libs/sviterbi.o .libs/sreestimate.o .libs/scluster.o .libs/sgenerate.o .libs/smixturehmm.o .libs/smap_classify.o .libs/sdmodel.o .libs/sdfoba.o .libs/sdviterbi.o .libs/pmodel.o .libs/pviterbi.o .libs/pviterbi_propagate.o .libs/fbgibbs.o .libs/cfbgibbs.o -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -Wl,-soname -Wl,libghmm.so.1 -o .libs/libghmm.so.1.0.0 libtool: link: (cd ".libs" && rm -f "libghmm.so.1" && ln -s "libghmm.so.1.0.0" "libghmm.so.1") libtool: link: (cd ".libs" && rm -f "libghmm.so" && ln -s "libghmm.so.1.0.0" "libghmm.so") libtool: link: ar cr .libs/libghmm.a rng.o randvar.o matrixop.o gauss_tail.o mes.o ghmm_internals.o mprintf.o vector.o matrix.o scanner.o linkedlist.o sequence.o psequence.o xmlreader.o xmlwriter.o model.o foba.o viterbi.o reestimate.o gradescent.o kbest.o discrime.o modelutil.o cluster.o root_finder.o smodel.o sfoba.o sviterbi.o sreestimate.o scluster.o sgenerate.o smixturehmm.o smap_classify.o sdmodel.o sdfoba.o sdviterbi.o pmodel.o pviterbi.o pviterbi_propagate.o fbgibbs.o cfbgibbs.o libtool: link: ranlib .libs/libghmm.a libtool: link: ( cd ".libs" && rm -f "libghmm.la" && ln -s "../libghmm.la" "libghmm.la" ) make[4]: Leaving directory '/build/ghmm-0.9~rc3/ghmm' make[3]: Leaving directory '/build/ghmm-0.9~rc3/ghmm' Making all in tools make[3]: Entering directory '/build/ghmm-0.9~rc3/tools' make all-recursive make[4]: Entering directory '/build/ghmm-0.9~rc3/tools' Making all in . make[5]: Entering directory '/build/ghmm-0.9~rc3/tools' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o smix_hmm.o smix_hmm.c /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o smix_hmm smix_hmm.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 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'/build/ghmm-0.9~rc3/tests/data' Making all in . make[5]: Entering directory '/build/ghmm-0.9~rc3/tests/data' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/build/ghmm-0.9~rc3/tests/data' make[4]: Leaving directory '/build/ghmm-0.9~rc3/tests/data' make[4]: Entering directory '/build/ghmm-0.9~rc3/tests' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong 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sequences_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -c -o mcmc.o mcmc.c /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o randvar_test randvar_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o two_states_three_symbols two_states_three_symbols.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o libxml-test libxml-test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o chmm chmm.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 mcmc.c: In function 'main': mcmc.c:144:3: warning: implicit declaration of function 'init_priors' [-Wimplicit-function-declaration] 144 | init_priors(mo, &pA, &pB, &pPi); | ^~~~~~~~~~~ mcmc.c:146:15: warning: implicit declaration of function 'ghmm_dmodel_cfbgibbs'; did you mean 'ghmm_dmodel_logp'? [-Wimplicit-function-declaration] 146 | int * Q = ghmm_dmodel_cfbgibbs(mo, my_output, | ^~~~~~~~~~~~~~~~~~~~ | ghmm_dmodel_logp mcmc.c:146:15: warning: initialization of 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] mcmc.c:148:108: warning: passing argument 4 of 'ghmm_dmodel_viterbi_logp' makes pointer from integer without a cast [-Wint-conversion] 148 | printf("viterbi prob mcmc%f \n", ghmm_dmodel_viterbi_logp(mo, my_output->seq[0], my_output->seq_len[0], Q[0])); | ~^~~ | | | int In file included from mcmc.c:13: ../ghmm/viterbi.h:75:76: note: expected 'int *' but argument is of type 'int' 75 | double ghmm_dmodel_viterbi_logp (ghmm_dmodel * mo, int *o, int len, int *state_seq); | ~~~~~^~~~~~~~~ libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o randvar_test randvar_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o libxml-test libxml-test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o two_states_three_symbols two_states_three_symbols.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o chmm_test chmm_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o shmm_viterbi_test shmm_viterbi_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o chmm chmm.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o test_gsl_ran_gaussian_tail test_gsl_ran_gaussian_tail.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sequences_test sequences_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sequences_old_format sequences_old_format.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o chmm_test chmm_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o test_gsl_ran_gaussian_tail test_gsl_ran_gaussian_tail.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o shmm_viterbi_test shmm_viterbi_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o sequences_test sequences_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o label_higher_order_test label_higher_order_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o read_fa read_fa.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o mcmc mcmc.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o sequences_old_format sequences_old_format.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o coin_toss_test coin_toss_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o read_fa read_fa.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o label_higher_order_test label_higher_order_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o coin_toss_test coin_toss_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 libtool: link: gcc -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o mcmc mcmc.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/aarch64-linux-gnu/atlas -llapack -lxml2 make[4]: Leaving directory '/build/ghmm-0.9~rc3/tests' make[3]: Leaving directory '/build/ghmm-0.9~rc3/tests' Making all in ghmmwrapper make[3]: Entering directory '/build/ghmm-0.9~rc3/ghmmwrapper' Making all in . make[4]: Entering directory '/build/ghmm-0.9~rc3/ghmmwrapper' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/ghmm-0.9~rc3/ghmmwrapper' /usr/bin/python3 setup.py build /build/ghmm-0.9~rc3/ghmmwrapper/setup.py:38: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup,Extension running build running build_py file ghmmwrapper.py (for module ghmmwrapper) not found creating build creating build/lib.linux-aarch64-3.11 copying ghmm.py -> build/lib.linux-aarch64-3.11 copying ghmmhelper.py -> build/lib.linux-aarch64-3.11 copying modhmmer.py -> build/lib.linux-aarch64-3.11 copying class_change.py -> build/lib.linux-aarch64-3.11 file ghmmwrapper.py (for module ghmmwrapper) not found running build_ext building '_ghmmwrapper' extension swigging ghmmwrapper.i to ghmmwrapper_wrap.c swig -python -o ghmmwrapper_wrap.c ghmmwrapper.i creating build/temp.linux-aarch64-3.11 aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I.. -I/usr/include/python3.11 -c ghmmwrapper_wrap.c -o build/temp.linux-aarch64-3.11/ghmmwrapper_wrap.o -O2 -pipe -Wall ghmmwrapper_wrap.c: In function 'PythonCallBack': ghmmwrapper_wrap.c:3366:9: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] 3366 | PyEval_CallObject(func, arglist); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/python3.11/Python.h:95, from ghmmwrapper_wrap.c:168: /usr/include/python3.11/ceval.h:27:43: note: declared here 27 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ghmmwrapper_wrap.c: In function 'delete_ghmm_alphabet': ghmmwrapper_wrap.c:3567:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 3567 | for(i=0; isize; ++i) | ^ ghmmwrapper_wrap.c: In function 'ghmm_cmodel_getStateName': ghmmwrapper_wrap.c:3820:16: warning: the comparison will always evaluate as 'true' for the pointer operand in 'self->s + (sizetype)(index * 96)' must not be NULL [-Waddress] 3820 | if((self->s + index) && index < self->N) return (self->s + index)->desc; | ^ ghmmwrapper_wrap.c:3820:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3820 | if((self->s + index) && index < self->N) return (self->s + index)->desc; | ^ ghmmwrapper_wrap.c: In function 'ghmm_dbackground_setName': ghmmwrapper_wrap.c:3853:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3853 | if(index < self->n){ | ^ ghmmwrapper_wrap.c: In function 'ghmm_dmodel_getStateName': ghmmwrapper_wrap.c:3901:16: warning: the comparison will always evaluate as 'true' for the pointer operand in 'self->s + (sizetype)(index * 80)' must not be NULL [-Waddress] 3901 | if((self->s + index) && index < self->N) return (self->s + index)->desc; | ^ ghmmwrapper_wrap.c:3901:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3901 | if((self->s + index) && index < self->N) return (self->s + index)->desc; | ^ ghmmwrapper_wrap.c: In function 'int_matrix_alloc': ghmmwrapper_wrap.c:4012:28: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 4012 | for (i=0; iseq_index = seq_index; | ^~ pclasschange.c:96:10: note: object of size 8 allocated by 'calloc' 96 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:98:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 98 | td->threshold = threshold; | ^~ pclasschange.c:96:10: note: object of size 8 allocated by 'calloc' 96 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:99:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 99 | td->offset_x = offset_x; | ^~ pclasschange.c:96:10: note: object of size 8 allocated by 'calloc' 96 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:100:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 100 | td->offset_y = offset_y; | ^~ pclasschange.c:96:10: note: object of size 8 allocated by 'calloc' 96 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c: In function 'set_to_gt_sum': pclasschange.c:112:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 112 | td->seq_index = seq_index; | ^~ pclasschange.c:111:10: note: object of size 8 allocated by 'calloc' 111 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:113:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 113 | td->threshold = threshold; | ^~ pclasschange.c:111:10: note: object of size 8 allocated by 'calloc' 111 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:114:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 114 | td->offset_x = offset_x; | ^~ pclasschange.c:111:10: note: object of size 8 allocated by 'calloc' 111 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:115:7: warning: array subscript 'threshold_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 115 | td->offset_y = offset_y; | ^~ pclasschange.c:111:10: note: object of size 8 allocated by 'calloc' 111 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c: In function 'set_to_boolean_and': pclasschange.c:127:7: warning: array subscript 'boolean_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 127 | td->seq_index = seq_index; | ^~ pclasschange.c:126:10: note: object of size 8 allocated by 'calloc' 126 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:128:7: warning: array subscript 'boolean_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 128 | td->offset_x = offset_x; | ^~ pclasschange.c:126:10: note: object of size 8 allocated by 'calloc' 126 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:129:7: warning: array subscript 'boolean_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 129 | td->offset_y = offset_y; | ^~ pclasschange.c:126:10: note: object of size 8 allocated by 'calloc' 126 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c: In function 'set_to_boolean_or': pclasschange.c:141:7: warning: array subscript 'boolean_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 141 | td->seq_index = seq_index; | ^~ pclasschange.c:140:10: note: object of size 8 allocated by 'calloc' 140 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:142:7: warning: array subscript 'boolean_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 142 | td->offset_x = offset_x; | ^~ pclasschange.c:140:10: note: object of size 8 allocated by 'calloc' 140 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ pclasschange.c:143:7: warning: array subscript 'boolean_user_data[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 143 | td->offset_y = offset_y; | ^~ pclasschange.c:140:10: note: object of size 8 allocated by 'calloc' 140 | td = calloc (1, sizeof (td)); | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I.. -I/usr/include/python3.11 -c sclass_change.c -o build/temp.linux-aarch64-3.11/sclass_change.o -O2 -pipe -Wall sclass_change.c: In function 'python_class_change': sclass_change.c:98:14: warning: implicit declaration of function 'PyString_FromString'; did you mean 'PyLong_FromString'? [-Wimplicit-function-declaration] 98 | pName = PyString_FromString(ModuleName); | ^~~~~~~~~~~~~~~~~~~ | PyLong_FromString sclass_change.c:98:12: warning: assignment to 'PyObject *' {aka 'struct _object *'} from 'int' makes pointer from integer without a cast [-Wint-conversion] 98 | pName = PyString_FromString(ModuleName); | ^ sclass_change.c:133:13: warning: implicit declaration of function 'PyInt_FromLong'; did you mean 'PyLong_FromLong'? [-Wimplicit-function-declaration] 133 | pValue = PyInt_FromLong((long)k); | ^~~~~~~~~~~~~~ | PyLong_FromLong sclass_change.c:133:11: warning: assignment to 'PyObject *' {aka 'struct _object *'} from 'int' makes pointer from integer without a cast [-Wint-conversion] 133 | pValue = PyInt_FromLong((long)k); | ^ sclass_change.c:136:11: warning: assignment to 'PyObject *' {aka 'struct _object *'} from 'int' makes pointer from integer without a cast [-Wint-conversion] 136 | pValue = PyInt_FromLong((long)t); | ^ sclass_change.c:142:12: warning: implicit declaration of function 'PyInt_AsLong'; did you mean 'PyLong_AsLong'? [-Wimplicit-function-declaration] 142 | class = PyInt_AsLong(pValue); | ^~~~~~~~~~~~ | PyLong_AsLong sclass_change.c: In function 'executePythonCallback': sclass_change.c:214:11: warning: assignment to 'PyObject *' {aka 'struct _object *'} from 'int' makes pointer from integer without a cast [-Wint-conversion] 214 | pValue = PyInt_FromLong((long)k); | ^ sclass_change.c:217:11: warning: assignment to 'PyObject *' {aka 'struct _object *'} from 'int' makes pointer from integer without a cast [-Wint-conversion] 217 | pValue = PyInt_FromLong((long)t); | ^ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/aarch64-linux-gnu -I/usr/include/libxml2 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.11/ghmmwrapper_wrap.o build/temp.linux-aarch64-3.11/gql.o build/temp.linux-aarch64-3.11/pclasschange.o build/temp.linux-aarch64-3.11/sclass_change.o -L../ghmm/.libs -lghmm -lm -lpthread -lxml2 -lz -o build/lib.linux-aarch64-3.11/_ghmmwrapper.cpython-311-aarch64-linux-gnu.so make[3]: Leaving directory '/build/ghmm-0.9~rc3/ghmmwrapper' Making all in HMMEd make[3]: Entering directory '/build/ghmm-0.9~rc3/HMMEd' Making all in . make[4]: Entering directory '/build/ghmm-0.9~rc3/HMMEd' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/ghmm-0.9~rc3/HMMEd' /usr/bin/python3 setup.py build /build/ghmm-0.9~rc3/HMMEd/setup.py:38: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup,Extension running build running build_py creating build creating build/lib copying HMMEditor.py -> build/lib copying ObjectHMM.py -> build/lib copying HMMEditingContext.py -> build/lib running build_scripts creating build/scripts-3.11 copying and adjusting HMMEd -> build/scripts-3.11 changing mode of build/scripts-3.11/HMMEd from 644 to 755 make[3]: Leaving directory '/build/ghmm-0.9~rc3/HMMEd' make[3]: Entering directory '/build/ghmm-0.9~rc3' make[3]: Leaving directory '/build/ghmm-0.9~rc3' make[2]: Leaving directory '/build/ghmm-0.9~rc3' make[1]: Leaving directory '/build/ghmm-0.9~rc3' debian/rules override_dh_auto_test make[1]: Entering directory '/build/ghmm-0.9~rc3' /usr/bin/make --directory=tests make[2]: Entering directory '/build/ghmm-0.9~rc3/tests' Making all in data make[3]: Entering directory '/build/ghmm-0.9~rc3/tests/data' Making all in . make[4]: Entering directory '/build/ghmm-0.9~rc3/tests/data' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/ghmm-0.9~rc3/tests/data' make[3]: Leaving directory '/build/ghmm-0.9~rc3/tests/data' make[3]: Entering directory '/build/ghmm-0.9~rc3/tests' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/ghmm-0.9~rc3/tests' make[2]: Leaving directory '/build/ghmm-0.9~rc3/tests' make[1]: Leaving directory '/build/ghmm-0.9~rc3' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j1 install DESTDIR=/build/ghmm-0.9\~rc3/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/ghmm-0.9~rc3' Making install in ghmm make[2]: Entering directory '/build/ghmm-0.9~rc3/ghmm' Making install in . make[3]: Entering directory '/build/ghmm-0.9~rc3/ghmm' make[4]: Entering directory '/build/ghmm-0.9~rc3/ghmm' /usr/bin/mkdir -p '/build/ghmm-0.9~rc3/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libghmm.la '/build/ghmm-0.9~rc3/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libghmm.so.1.0.0 /build/ghmm-0.9~rc3/debian/tmp/usr/lib/aarch64-linux-gnu/libghmm.so.1.0.0 libtool: install: (cd /build/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/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/ghmm-0.9~rc3/debian/tmp/usr/lib/aarch64-linux-gnu/libghmm.la libtool: install: /usr/bin/install -c .libs/libghmm.a /build/ghmm-0.9~rc3/debian/tmp/usr/lib/aarch64-linux-gnu/libghmm.a libtool: install: chmod 644 /build/ghmm-0.9~rc3/debian/tmp/usr/lib/aarch64-linux-gnu/libghmm.a libtool: install: ranlib /build/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/ghmm-0.9~rc3/debian/tmp/usr/include/ghmm' /usr/bin/install -c -m 644 ghmm.h ghmmconfig.h sequence.h psequence.h xmlreader.h xmlwriter.h model.h foba.h viterbi.h gradescent.h kbest.h discrime.h cluster.h scluster.h reestimate.h sfoba.h sviterbi.h smodel.h sdmodel.h sdfoba.h sreestimate.h sgenerate.h smixturehmm.h smap_classify.h pmodel.h pviterbi.h pviterbi_propagate.h rng.h scanner.h obsolete.h unsupported.h fbgibbs.h cfbgibbs.h '/build/ghmm-0.9~rc3/debian/tmp/usr/include/ghmm' make[4]: Leaving directory '/build/ghmm-0.9~rc3/ghmm' make[3]: Leaving directory '/build/ghmm-0.9~rc3/ghmm' make[2]: Leaving directory '/build/ghmm-0.9~rc3/ghmm' Making install in tools make[2]: Entering directory '/build/ghmm-0.9~rc3/tools' make install-recursive make[3]: Entering directory '/build/ghmm-0.9~rc3/tools' Making install in . make[4]: Entering directory '/build/ghmm-0.9~rc3/tools' make[5]: Entering directory '/build/ghmm-0.9~rc3/tools' /usr/bin/mkdir -p '/build/ghmm-0.9~rc3/debian/tmp/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c probdist cluster scluster smix_hmm '/build/ghmm-0.9~rc3/debian/tmp/usr/bin' libtool: install: /usr/bin/install -c probdist /build/ghmm-0.9~rc3/debian/tmp/usr/bin/probdist libtool: install: /usr/bin/install -c cluster /build/ghmm-0.9~rc3/debian/tmp/usr/bin/cluster libtool: install: /usr/bin/install -c scluster /build/ghmm-0.9~rc3/debian/tmp/usr/bin/scluster libtool: install: /usr/bin/install -c smix_hmm /build/ghmm-0.9~rc3/debian/tmp/usr/bin/smix_hmm /usr/bin/mkdir -p '/build/ghmm-0.9~rc3/debian/tmp/usr/bin' /usr/bin/install -c ghmm-config '/build/ghmm-0.9~rc3/debian/tmp/usr/bin' make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/build/ghmm-0.9~rc3/tools' make[4]: Leaving directory '/build/ghmm-0.9~rc3/tools' make[3]: Leaving directory '/build/ghmm-0.9~rc3/tools' make[2]: Leaving directory '/build/ghmm-0.9~rc3/tools' Making install in tests make[2]: Entering directory '/build/ghmm-0.9~rc3/tests' Making install in data make[3]: Entering directory '/build/ghmm-0.9~rc3/tests/data' Making install in . make[4]: Entering directory '/build/ghmm-0.9~rc3/tests/data' make[5]: Entering directory '/build/ghmm-0.9~rc3/tests/data' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/build/ghmm-0.9~rc3/tests/data' make[4]: Leaving directory '/build/ghmm-0.9~rc3/tests/data' make[3]: Leaving directory '/build/ghmm-0.9~rc3/tests/data' make[3]: Entering directory '/build/ghmm-0.9~rc3/tests' make[4]: Entering directory '/build/ghmm-0.9~rc3/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/ghmm-0.9~rc3/tests' make[3]: Leaving directory '/build/ghmm-0.9~rc3/tests' make[2]: Leaving directory '/build/ghmm-0.9~rc3/tests' Making install in ghmmwrapper make[2]: Entering directory '/build/ghmm-0.9~rc3/ghmmwrapper' Making all in . make[3]: Entering directory '/build/ghmm-0.9~rc3/ghmmwrapper' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/ghmm-0.9~rc3/ghmmwrapper' /usr/bin/python3 setup.py build /build/ghmm-0.9~rc3/ghmmwrapper/setup.py:38: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup,Extension running build running build_py copying ghmmwrapper.py -> build/lib.linux-aarch64-3.11 running build_ext /usr/bin/python3 setup.py install --prefix=/build/ghmm-0.9~rc3/debian/tmp//usr /build/ghmm-0.9~rc3/ghmmwrapper/setup.py:38: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup,Extension running install running build running build_py running build_ext running install_lib creating /build/ghmm-0.9~rc3/debian/tmp/usr/lib/python3.11 creating /build/ghmm-0.9~rc3/debian/tmp/usr/lib/python3.11/site-packages copying build/lib.linux-aarch64-3.11/ghmmwrapper.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib.linux-aarch64-3.11/_ghmmwrapper.cpython-311-aarch64-linux-gnu.so -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib.linux-aarch64-3.11/class_change.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib.linux-aarch64-3.11/modhmmer.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib.linux-aarch64-3.11/ghmmhelper.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib.linux-aarch64-3.11/ghmm.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages byte-compiling /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ghmmwrapper.py to ghmmwrapper.cpython-311.pyc byte-compiling /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/class_change.py to class_change.cpython-311.pyc byte-compiling /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/modhmmer.py to modhmmer.cpython-311.pyc byte-compiling /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ghmmhelper.py to ghmmhelper.cpython-311.pyc byte-compiling /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ghmm.py to ghmm.cpython-311.pyc /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ghmm.py:1358: SyntaxWarning: "is" with a literal. Did you mean "=="? if emission_domain is 'd': /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ghmm.py:2868: SyntaxWarning: "is" with a literal. Did you mean "=="? if R is -1: running install_egg_info Writing /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ghmmwrapper-0.8-py3.11.egg-info make[2]: Leaving directory '/build/ghmm-0.9~rc3/ghmmwrapper' Making install in HMMEd make[2]: Entering directory '/build/ghmm-0.9~rc3/HMMEd' /usr/bin/python3 setup.py install --prefix=/build/ghmm-0.9~rc3/debian/tmp//usr /build/ghmm-0.9~rc3/HMMEd/setup.py:38: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup,Extension running install running build running build_py running build_scripts running install_lib copying build/lib/HMMEditingContext.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib/ObjectHMM.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib/HMMEditor.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages byte-compiling /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/HMMEditingContext.py to HMMEditingContext.cpython-311.pyc /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/HMMEditingContext.py:42: SyntaxWarning: "is" with a literal. Did you mean "=="? if parameter.CDataType is "int": /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/HMMEditingContext.py:45: SyntaxWarning: "is" with a literal. Did you mean "=="? elif parameter.CDataType is "double": byte-compiling /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ObjectHMM.py to ObjectHMM.cpython-311.pyc /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ObjectHMM.py:648: SyntaxWarning: "is" with a literal. Did you mean "=="? if name is "emission": /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ObjectHMM.py:650: SyntaxWarning: "is" with a literal. Did you mean "=="? elif name is "name": /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ObjectHMM.py:665: SyntaxWarning: "is" with a literal. Did you mean "=="? if name is "emission": /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ObjectHMM.py:667: SyntaxWarning: "is" with a literal. Did you mean "=="? elif name is "name": /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ObjectHMM.py:1053: SyntaxWarning: "is" with a literal. Did you mean "=="? if name is "p": /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/ObjectHMM.py:1060: SyntaxWarning: "is" with a literal. Did you mean "=="? if name is "p": byte-compiling /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/HMMEditor.py to HMMEditor.cpython-311.pyc /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/HMMEditor.py:436: SyntaxWarning: "is" with a literal. Did you mean "=="? if file is "": /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/HMMEditor.py:471: SyntaxWarning: "is not" with a literal. Did you mean "!="? if file is not "": running install_scripts copying build/scripts-3.11/HMMEd -> /build/ghmm-0.9~rc3/debian/tmp//usr/bin changing mode of /build/ghmm-0.9~rc3/debian/tmp//usr/bin/HMMEd to 755 running install_egg_info Writing /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages/HMMEd-0.8-py3.11.egg-info make[2]: Leaving directory '/build/ghmm-0.9~rc3/HMMEd' make[2]: Entering directory '/build/ghmm-0.9~rc3' make[3]: Entering directory '/build/ghmm-0.9~rc3' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/ghmm-0.9~rc3/debian/tmp/usr/share/ghmm' /usr/bin/install -c -m 644 doc/ghmm.dtd.1.0 '/build/ghmm-0.9~rc3/debian/tmp/usr/share/ghmm' make[3]: Leaving directory '/build/ghmm-0.9~rc3' make[2]: Leaving directory '/build/ghmm-0.9~rc3' make[1]: Leaving directory '/build/ghmm-0.9~rc3' debian/rules override_dh_install make[1]: Entering directory '/build/ghmm-0.9~rc3' dh_install find /build/ghmm-0.9~rc3/debian/tmp -name "*.pyc" -delete d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --override s/libgsl23-dev/libgsl-dev/ \ --movedev debian/tmp/usr/include usr \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility --> liblapack-dev package exists. --> libxml2-dev package exists. set -e install -d -m 755 debian/libghmm-dev/usr/lib/aarch64-linux-gnu install -d -m 755 debian/libghmm1/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/ghmm-0.9~rc3/debian/tmp/usr/lib/aarch64-linux-gnu/libghmm.so.1 debian/libghmm1/usr/lib/aarch64-linux-gnu mv /build/ghmm-0.9~rc3/debian/tmp/usr/lib/aarch64-linux-gnu/libghmm.so.1.0.0 debian/libghmm1/usr/lib/aarch64-linux-gnu PKGDEV=libghmm-dev PKGSHL=libghmm1 install -d -m 755 debian/libghmm-dev/usr mv debian/tmp/usr/include debian/libghmm-dev/usr cd /build/ghmm-0.9~rc3/debian/ghmm/usr/bin/ && mv cluster ghmm-cluster sed -i -e 's@ [^ ]*-f\(file\|debug\)-prefix-map=[^ ]*@@g' \ /build/ghmm-0.9~rc3/debian/ghmm/usr/bin/ghmm-config find debian -name __pycache__ | xargs rm -rf find debian -name libghmm.la -delete make[1]: Leaving directory '/build/ghmm-0.9~rc3' dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libghmm-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package libghmm-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'ghmm' in '../ghmm_0.9~rc3-4_arm64.deb'. dpkg-deb: building package 'ghmm-dbgsym' in '../ghmm-dbgsym_0.9~rc3-4_arm64.deb'. dpkg-deb: building package 'libghmm1-dbgsym' in '../libghmm1-dbgsym_0.9~rc3-4_arm64.deb'. dpkg-deb: building package 'libghmm-dev' in '../libghmm-dev_0.9~rc3-4_arm64.deb'. dpkg-deb: building package 'libghmm1' in '../libghmm1_0.9~rc3-4_arm64.deb'. dpkg-genbuildinfo --build=binary -O../ghmm_0.9~rc3-4_arm64.buildinfo dpkg-genchanges --build=binary -O../ghmm_0.9~rc3-4_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/3119 and its subdirectories I: Current time: Tue May 30 20:26:14 -12 2023 I: pbuilder-time-stamp: 1685521574 Wed May 31 08:26:17 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink11-arm64.debian.net. Wed May 31 08:26:17 UTC 2023 I: Preparing to do remote build '2' on codethink11-arm64.debian.net. Wed May 31 08:30:23 UTC 2023 I: Deleting $TMPDIR on codethink11-arm64.debian.net. Wed May 31 08:30:23 UTC 2023 I: ghmm_0.9~rc3-4_arm64.changes: Format: 1.8 Date: Sun, 24 Jan 2021 20:27:28 +0100 Source: ghmm Binary: ghmm ghmm-dbgsym libghmm-dev libghmm1 libghmm1-dbgsym Architecture: arm64 Version: 0.9~rc3-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: ghmm - General Hidden-Markov-Model library - tools libghmm-dev - General Hidden-Markov-Model library - header files libghmm1 - General Hidden-Markov-Model library Closes: 980934 Changes: ghmm (0.9~rc3-4) unstable; urgency=medium . * Team upload. * Fix homepage Closes: #980934 Checksums-Sha1: d1594428f140db7df951a9b8aa7bf6ab8e9302e1 498796 ghmm-dbgsym_0.9~rc3-4_arm64.deb 477612c041244315367f6d35ee53e9bd48edff16 7628 ghmm_0.9~rc3-4_arm64.buildinfo 443b2bcc56488b49fe115baef32e12785381988f 138724 ghmm_0.9~rc3-4_arm64.deb 0af30ca89835dcf6e6584a75375596370386d7c7 171188 libghmm-dev_0.9~rc3-4_arm64.deb 852898e78e723d523ec4dc9d66acbecac7eb30cb 326164 libghmm1-dbgsym_0.9~rc3-4_arm64.deb 3fe8dcaefe138d76b5fcfef60d59f1646935c88f 130432 libghmm1_0.9~rc3-4_arm64.deb Checksums-Sha256: b5c2d970964ab31bd2dee996a261fb2f0e96d978fa3ccef11872e7b88821afbf 498796 ghmm-dbgsym_0.9~rc3-4_arm64.deb f7db80ec6ab34822d0ba31a7de61bae63a0834e2e6fb1dfc90811db9c11f71b4 7628 ghmm_0.9~rc3-4_arm64.buildinfo 7ab83c22dadf45dc10eea8028de7865747b0c9d71d63da7f9641e5154b5b0020 138724 ghmm_0.9~rc3-4_arm64.deb be9b37966380d82318bcd0e3c96b2d9a0080601578b1a00232220d13f76c8b34 171188 libghmm-dev_0.9~rc3-4_arm64.deb 4488cc735dcdb848e789c9559907e1dd11c9ff559c23c178640bf90afd21c881 326164 libghmm1-dbgsym_0.9~rc3-4_arm64.deb 7335a356543585d9deb935cf44558d0323112eefc699d1d2bb9c8a56190c9ae6 130432 libghmm1_0.9~rc3-4_arm64.deb Files: 84acc4498e4e7b9d62e2d7f7ac3a3a0e 498796 debug optional ghmm-dbgsym_0.9~rc3-4_arm64.deb 71e1842598858a6f32908643e5374c24 7628 science optional ghmm_0.9~rc3-4_arm64.buildinfo 78c20a118fb82da8a682a831b30fbe4b 138724 science optional ghmm_0.9~rc3-4_arm64.deb 876a2fdf9372321549be930ed8c35e56 171188 libdevel optional libghmm-dev_0.9~rc3-4_arm64.deb ddf50f58ddeeccfeb0b0496a7256a783 326164 debug optional libghmm1-dbgsym_0.9~rc3-4_arm64.deb 906afe0ce45cab92e4dd7e8593980939 130432 libs optional libghmm1_0.9~rc3-4_arm64.deb Wed May 31 08:30:24 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.bDHQOm0o/ghmm_0.9~rc3-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.bDHQOm0o/ghmm_0.9~rc3-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.bDHQOm0o/ghmm_0.9~rc3-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.bDHQOm0o/b1/ghmm_0.9~rc3-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.bDHQOm0o/b2/ghmm_0.9~rc3-4_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 abc.DotChangesFile ## main (total time: 0.338s) 0.338s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.030s) 0.030s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Wed May 31 08:30:27 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Wed May 31 08:30:27 UTC 2023 I: ghmm from bookworm built successfully and reproducibly on arm64. Wed May 31 08:30:28 UTC 2023 I: Submitting .buildinfo files to external archives: Wed May 31 08:30:28 UTC 2023 I: Submitting 12K b1/ghmm_0.9~rc3-4_arm64.buildinfo.asc Wed May 31 08:30:29 UTC 2023 I: Submitting 12K b2/ghmm_0.9~rc3-4_arm64.buildinfo.asc Wed May 31 08:30:31 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed May 31 08:30:31 UTC 2023 I: Done submitting .buildinfo files. Wed May 31 08:30:31 UTC 2023 I: Removing signed ghmm_0.9~rc3-4_arm64.buildinfo.asc files: removed './b1/ghmm_0.9~rc3-4_arm64.buildinfo.asc' removed './b2/ghmm_0.9~rc3-4_arm64.buildinfo.asc'