Sat May 20 14:01:45 UTC 2023 I: starting to build ghmm/bookworm/amd64 on jenkins on '2023-05-20 14:01' Sat May 20 14:01:45 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_15/11179/console.log Sat May 20 14:01:45 UTC 2023 I: Downloading source for bookworm/ghmm=0.9~rc3-4 --2023-05-20 14:01:45-- 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% 144M=0s 2023-05-20 14:01:45 (144 MB/s) - ‘ghmm_0.9~rc3-4.dsc’ saved [2136/2136] Sat May 20 14:01:45 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----- Sat May 20 14:01:45 UTC 2023 I: Checking whether the package is not for us Sat May 20 14:01:45 UTC 2023 I: Starting 1st build on remote node ionos11-amd64.debian.net. Sat May 20 14:01:45 UTC 2023 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Sat May 20 14:07:07 UTC 2023 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat May 20 02:01:48 -12 2023 I: pbuilder-time-stamp: 1684591308 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/3420017/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='047b87c5cef54d69a87990d6e6bb47af' 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='3420017' 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.jCTWwd3r/pbuilderrc_cZf3 --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.jCTWwd3r/b1 --logfile b1/build.log ghmm_0.9~rc3-4.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 09:23 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/3420017/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: 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 ... 19596 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 63.6 MB of archives. After unpacking 277 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 d-shlibs all 0.104 [18.6 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 icu-devtools amd64 72.1-3 [206 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libatlas3-base amd64 3.10.3-13 [3305 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libatlas-base-dev amd64 3.10.3-13 [3510 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libgslcblas0 amd64 2.7.1+dfsg-3+b1 [116 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libgsl27 amd64 2.7.1+dfsg-3+b1 [948 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libgsl-dev amd64 2.7.1+dfsg-3+b1 [1152 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libicu-dev amd64 72.1-3 [10.3 MB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 liblapack-dev amd64 3.11.0-2 [4631 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6 [1988 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6 [4738 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libxml2-dev amd64 2.9.14+dfsg-1.2 [781 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6 [615 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 swig4.0 amd64 4.1.0-0.2 [1388 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 swig all 4.1.0-0.2 [321 kB] Fetched 63.6 MB in 2s (36.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (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 ... 19912 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.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:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (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 ... 20346 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_amd64.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 ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. 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Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../27-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../32-icu-devtools_72.1-3_amd64.deb ... Unpacking icu-devtools (72.1-3) ... 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Unpacking libgsl27:amd64 (2.7.1+dfsg-3+b1) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../39-libgsl-dev_2.7.1+dfsg-3+b1_amd64.deb ... Unpacking libgsl-dev (2.7.1+dfsg-3+b1) ... Selecting previously unselected package libicu-dev:amd64. Preparing to unpack .../40-libicu-dev_72.1-3_amd64.deb ... Unpacking libicu-dev:amd64 (72.1-3) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../41-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../42-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../43-libjs-sphinxdoc_5.3.0-4_all.deb ... Unpacking libjs-sphinxdoc (5.3.0-4) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../44-liblapack3_3.11.0-2_amd64.deb ... Unpacking liblapack3:amd64 (3.11.0-2) ... Selecting previously unselected package liblapack-dev:amd64. Preparing to unpack .../45-liblapack-dev_3.11.0-2_amd64.deb ... Unpacking liblapack-dev:amd64 (3.11.0-2) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../46-libpkgconf3_1.8.1-1_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-1) ... Selecting previously unselected package libpython3.11:amd64. Preparing to unpack .../47-libpython3.11_3.11.2-6_amd64.deb ... Unpacking libpython3.11:amd64 (3.11.2-6) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../48-zlib1g-dev_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Selecting previously unselected package libpython3.11-dev:amd64. Preparing to unpack .../49-libpython3.11-dev_3.11.2-6_amd64.deb ... Unpacking libpython3.11-dev:amd64 (3.11.2-6) ... Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../50-libpython3-dev_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-dev:amd64 (3.11.2-1+b1) ... Selecting previously unselected package libxml2-dev:amd64. Preparing to unpack .../51-libxml2-dev_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2-dev:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../52-pkgconf-bin_1.8.1-1_amd64.deb ... Unpacking pkgconf-bin (1.8.1-1) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../53-pkgconf_1.8.1-1_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-1) ... Selecting previously unselected package pkg-config:amd64. Preparing to unpack .../54-pkg-config_1.8.1-1_amd64.deb ... Unpacking pkg-config:amd64 (1.8.1-1) ... Selecting previously unselected package python3.11-dev. Preparing to unpack .../55-python3.11-dev_3.11.2-6_amd64.deb ... Unpacking python3.11-dev (3.11.2-6) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../56-python3-lib2to3_3.11.2-3_all.deb ... Unpacking python3-lib2to3 (3.11.2-3) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../57-python3-distutils_3.11.2-3_all.deb ... Unpacking python3-distutils (3.11.2-3) ... Selecting previously unselected package python3-dev. Preparing to unpack .../58-python3-dev_3.11.2-1+b1_amd64.deb ... Unpacking python3-dev (3.11.2-1+b1) ... Selecting previously unselected package swig4.0. Preparing to unpack .../59-swig4.0_4.1.0-0.2_amd64.deb ... Unpacking swig4.0 (4.1.0-0.2) ... Selecting previously unselected package swig. Preparing to unpack .../60-swig_4.1.0-0.2_all.deb ... Unpacking swig (4.1.0-0.2) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libgslcblas0:amd64 (2.7.1+dfsg-3+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up libgsl27:amd64 (2.7.1+dfsg-3+b1) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:amd64 (1.8.1-1) ... Setting up libexpat1-dev:amd64 (2.5.0-1) ... Setting up autopoint (0.21-12) ... Setting up icu-devtools (72.1-3) ... Setting up d-shlibs (0.104) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up swig4.0 (4.1.0-0.2) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libicu-dev:amd64 (72.1-3) ... Setting up libxml2:amd64 (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:amd64 (3.10.3-13) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libtool (2.4.7-5) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libatlas-base-dev:amd64 (3.10.3-13) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/atlas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/atlas/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up pkgconf:amd64 (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libxml2-dev:amd64 (2.9.14+dfsg-1.2) ... Setting up pkg-config:amd64 (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:amd64 (3.11.0-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (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:amd64 (3.11.0-2) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libpython3.11:amd64 (3.11.2-6) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libpython3.11-dev:amd64 (3.11.2-6) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-distutils (3.11.2-3) ... Setting up libpython3-dev:amd64 (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 amd64 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=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-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... /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... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for 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... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/time.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gawk... (cached) mawk checking for doxygen... no checking for rm... /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) /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 /bin/rm: cannot remove 'libtoolT': No such file or directory make[1]: Leaving directory '/build/ghmm-0.9~rc3' dh_auto_build make -j15 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/x86_64-linux-gnu -I/usr/include/libxml2 -c -o rng.lo rng.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o randvar.lo randvar.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o matrixop.lo matrixop.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o gauss_tail.lo gauss_tail.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o mes.lo mes.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o ghmm_internals.lo ghmm_internals.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o mprintf.lo mprintf.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o vector.lo vector.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o matrix.lo matrix.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o scanner.lo scanner.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o linkedlist.lo linkedlist.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sequence.lo sequence.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o psequence.lo psequence.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o xmlreader.lo xmlreader.c /bin/bash ../libtool --tag=CC --mode=compile gcc -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/x86_64-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/x86_64-linux-gnu -I/usr/include/libxml2 -c rng.c -fPIC -DPIC -o .libs/rng.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c ghmm_internals.c -fPIC -DPIC -o .libs/ghmm_internals.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c matrixop.c -fPIC -DPIC -o .libs/matrixop.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c randvar.c -fPIC -DPIC -o .libs/randvar.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c gauss_tail.c -fPIC -DPIC -o .libs/gauss_tail.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c mes.c -fPIC -DPIC -o .libs/mes.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c mprintf.c -fPIC -DPIC -o .libs/mprintf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c vector.c -fPIC -DPIC -o .libs/vector.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sequence.c -fPIC -DPIC -o .libs/sequence.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c scanner.c -fPIC -DPIC -o .libs/scanner.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c matrix.c -fPIC -DPIC -o .libs/matrix.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c linkedlist.c -fPIC -DPIC -o .libs/linkedlist.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c xmlreader.c -fPIC -DPIC -o .libs/xmlreader.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c psequence.c -fPIC -DPIC -o .libs/psequence.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c xmlwriter.c -fPIC -DPIC -o .libs/xmlwriter.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c scanner.c -o scanner.o >/dev/null 2>&1 ghmm_internals.c: In function 'ighmm_log_out': ghmm_internals.c:69:17: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] 69 | message = strncat(message, error_str, slen); | ^ In function 'process_external_log', inlined from 'ighmm_log_out' at ghmm_internals.c:83:5: ghmm_internals.c:64:14: note: length computed here 64 | int slen = strlen(error_str); | ^~~~~~~~~~~~~~~~~ /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/x86_64-linux-gnu -I/usr/include/libxml2 -c -o model.lo model.c 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_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)); | ^ 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': libtool: compile: 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/x86_64-linux-gnu -I/usr/include/libxml2 -c ghmm_internals.c -o ghmm_internals.o >/dev/null 2>&1 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_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); | ^ 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/x86_64-linux-gnu -I/usr/include/libxml2 -c rng.c -o rng.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c linkedlist.c -o linkedlist.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c gauss_tail.c -o gauss_tail.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c psequence.c -o psequence.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c vector.c -o vector.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c model.c -fPIC -DPIC -o .libs/model.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-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/x86_64-linux-gnu -I/usr/include/libxml2 -c -o foba.lo foba.c 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;); | ^ /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/x86_64-linux-gnu -I/usr/include/libxml2 -c -o viterbi.lo viterbi.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/x86_64-linux-gnu -I/usr/include/libxml2 -c -o reestimate.lo reestimate.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/x86_64-linux-gnu -I/usr/include/libxml2 -c -o gradescent.lo gradescent.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/x86_64-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/x86_64-linux-gnu -I/usr/include/libxml2 -c foba.c -fPIC -DPIC -o .libs/foba.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/x86_64-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/x86_64-linux-gnu -I/usr/include/libxml2 -c matrix.c -o matrix.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c mes.c -o mes.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/x86_64-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/x86_64-linux-gnu -I/usr/include/libxml2 -c randvar.c -o randvar.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c viterbi.c -fPIC -DPIC -o .libs/viterbi.o 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); | ^ libtool: compile: 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/x86_64-linux-gnu -I/usr/include/libxml2 -c gradescent.c -fPIC -DPIC -o .libs/gradescent.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c reestimate.c -fPIC -DPIC -o .libs/reestimate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c discrime.c -fPIC -DPIC -o .libs/discrime.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c kbest.c -fPIC -DPIC -o .libs/kbest.o viterbi.c: In function 'viterbi_free': viterbi.c:71:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 71 | mes_check_ptr(v, return -1); | ^ libtool: compile: 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/x86_64-linux-gnu -I/usr/include/libxml2 -c modelutil.c -fPIC -DPIC -o .libs/modelutil.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); | ^ modelutil.c: In function 'topo_free': modelutil.c:89:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 89 | mes_check_ptr (v, return (-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c mprintf.c -o mprintf.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/x86_64-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/x86_64-linux-gnu -I/usr/include/libxml2 -c -o root_finder.lo root_finder.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c modelutil.c -o modelutil.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c viterbi.c -o viterbi.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c cluster.c -fPIC -DPIC -o .libs/cluster.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c cluster.c -o cluster.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o smodel.lo smodel.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-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/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sfoba.lo sfoba.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c gradescent.c -o gradescent.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c xmlwriter.c -o xmlwriter.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c root_finder.c -o root_finder.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c smodel.c -fPIC -DPIC -o .libs/smodel.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/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sviterbi.lo sviterbi.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sfoba.c -fPIC -DPIC -o .libs/sfoba.o smodel.c: In function 'ghmm_cmodel_free': smodel.c:765:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 765 | mes_check_ptr (smo, return (-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sequence.c -o sequence.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/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sreestimate.lo sreestimate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c kbest.c -o kbest.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sviterbi.c -fPIC -DPIC -o .libs/sviterbi.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/x86_64-linux-gnu -I/usr/include/libxml2 -c -o scluster.lo scluster.c sviterbi.c: In function 'sviterbi_free': sviterbi.c:89:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 89 | mes_check_ptr (v, return (-1)); | ^ /bin/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/x86_64-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/x86_64-linux-gnu -I/usr/include/libxml2 -c sreestimate.c -fPIC -DPIC -o .libs/sreestimate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c foba.c -o foba.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sfoba.c -o sfoba.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c scluster.c -fPIC -DPIC -o .libs/scluster.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/x86_64-linux-gnu -I/usr/include/libxml2 -c scluster.c -o scluster.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sviterbi.c -o sviterbi.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-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/x86_64-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/x86_64-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/x86_64-linux-gnu -I/usr/include/libxml2 -c sgenerate.c -fPIC -DPIC -o .libs/sgenerate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c xmlreader.c -o xmlreader.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c smap_classify.c -fPIC -DPIC -o .libs/smap_classify.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c smixturehmm.c -fPIC -DPIC -o .libs/smixturehmm.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c smap_classify.c -o smap_classify.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c smixturehmm.c -o smixturehmm.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sdmodel.lo sdmodel.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/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sdfoba.lo sdfoba.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/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sdviterbi.lo sdviterbi.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/x86_64-linux-gnu -I/usr/include/libxml2 -c -o pmodel.lo pmodel.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sdmodel.c -fPIC -DPIC -o .libs/sdmodel.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sdfoba.c -fPIC -DPIC -o .libs/sdfoba.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sdviterbi.c -fPIC -DPIC -o .libs/sdviterbi.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c model.c -o model.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile 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/x86_64-linux-gnu -I/usr/include/libxml2 -c -o pviterbi.lo pviterbi.c sdfoba.c: In function 'ghmm_dsmodel_backward': libtool: compile: 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/x86_64-linux-gnu -I/usr/include/libxml2 -c sgenerate.c -o sgenerate.o >/dev/null 2>&1 sdfoba.c:336:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 336 | mes_check_0 (scale[t], goto STOP); | ^ sdmodel.c: In function 'ghmm_dsmodel_free': sdmodel.c:211:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 211 | mes_check_ptr (mo, return (-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c pmodel.c -fPIC -DPIC -o .libs/pmodel.o sdviterbi.c: In function 'sdviterbi_free': sdviterbi.c:111:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 111 | mes_check_ptr (v, return (-1)); | ^ 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/x86_64-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/x86_64-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/x86_64-linux-gnu -I/usr/include/libxml2 -c sdfoba.c -o sdfoba.o >/dev/null 2>&1 pviterbi.c: In function 'pviterbi_free': pviterbi.c:151:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 151 | mes_check_ptr(v, return(-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sreestimate.c -o sreestimate.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c pmodel.c -o pmodel.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c pviterbi_propagate.c -fPIC -DPIC -o .libs/pviterbi_propagate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c smodel.c -o smodel.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/x86_64-linux-gnu -I/usr/include/libxml2 -c -o fbgibbs.lo fbgibbs.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o cfbgibbs.lo cfbgibbs.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sdviterbi.c -o sdviterbi.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c discrime.c -o discrime.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c fbgibbs.c -fPIC -DPIC -o .libs/fbgibbs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c cfbgibbs.c -fPIC -DPIC -o .libs/cfbgibbs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c sdmodel.c -o sdmodel.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c pviterbi.c -o pviterbi.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c fbgibbs.c -o fbgibbs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c pviterbi_propagate.c -o pviterbi_propagate.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-ffile-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-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/x86_64-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/x86_64-linux-gnu rng.lo randvar.lo matrixop.lo gauss_tail.lo mes.lo ghmm_internals.lo mprintf.lo vector.lo matrix.lo scanner.lo linkedlist.lo sequence.lo psequence.lo xmlreader.lo xmlwriter.lo model.lo foba.lo viterbi.lo reestimate.lo gradescent.lo kbest.lo discrime.lo modelutil.lo cluster.lo root_finder.lo smodel.lo sfoba.lo sviterbi.lo sreestimate.lo scluster.lo sgenerate.lo smixturehmm.lo smap_classify.lo sdmodel.lo sdfoba.lo sdviterbi.lo pmodel.lo pviterbi.lo pviterbi_propagate.lo fbgibbs.lo cfbgibbs.lo -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-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/x86_64-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/x86_64-linux-gnu -I/usr/include/libxml2 -c -o probdist.o probdist.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o cluster.o cluster.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o scluster.o scluster.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o smix_hmm.o smix_hmm.c /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/lib/x86_64-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/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-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/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o smix_hmm smix_hmm.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-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/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-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/x86_64-linux-gnu -I/usr/include/libxml2 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/lib/x86_64-linux-gnu/atlas -llapack -lxml2 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' Making all in tests make[3]: Entering directory '/build/ghmm-0.9~rc3/tests' Making all in data make[4]: Entering directory '/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/x86_64-linux-gnu -I/usr/include/libxml2 -c -o randvar_test.o randvar_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o root_finder_test.o root_finder_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o coin_toss_test.o coin_toss_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o two_states_three_symbols.o two_states_three_symbols.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o libxml-test.o libxml-test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o chmm.o chmm.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o chmm_test.o chmm_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o shmm_viterbi_test.o shmm_viterbi_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o test_gsl_ran_gaussian_tail.o test_gsl_ran_gaussian_tail.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sequences_test.o sequences_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o sequences_old_format.o sequences_old_format.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o label_higher_order_test.o label_higher_order_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o read_fa.o read_fa.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c -o mcmc.o mcmc.c /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-0.9~rc3=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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); | ~~~~~^~~~~~~~~ /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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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-x86_64-3.11 copying ghmm.py -> build/lib.linux-x86_64-3.11 copying ghmmhelper.py -> build/lib.linux-x86_64-3.11 copying modhmmer.py -> build/lib.linux-x86_64-3.11 copying class_change.py -> build/lib.linux-x86_64-3.11 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-x86_64-3.11 x86_64-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/x86_64-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-x86_64-3.11/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)); | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-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/x86_64-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-x86_64-3.11/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); | ^ x86_64-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/x86_64-linux-gnu -I/usr/include/libxml2 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.11/ghmmwrapper_wrap.o build/temp.linux-x86_64-3.11/gql.o build/temp.linux-x86_64-3.11/pclasschange.o build/temp.linux-x86_64-3.11/sclass_change.o -L../ghmm/.libs -lghmm -lm -lpthread -lxml2 -lz -o build/lib.linux-x86_64-3.11/_ghmmwrapper.cpython-311-x86_64-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' /bin/mkdir -p '/build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libghmm.la '/build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libghmm.so.1.0.0 /build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.so.1.0.0 libtool: install: (cd /build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libghmm.so.1.0.0 libghmm.so.1 || { rm -f libghmm.so.1 && ln -s libghmm.so.1.0.0 libghmm.so.1; }; }) libtool: install: (cd /build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libghmm.so.1.0.0 libghmm.so || { rm -f libghmm.so && ln -s libghmm.so.1.0.0 libghmm.so; }; }) libtool: install: /usr/bin/install -c .libs/libghmm.lai /build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.la libtool: install: /usr/bin/install -c .libs/libghmm.a /build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.a libtool: install: chmod 644 /build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.a libtool: install: ranlib /build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /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' /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 /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-x86_64-3.11 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-x86_64-3.11/ghmmwrapper.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib.linux-x86_64-3.11/_ghmmwrapper.cpython-311-x86_64-linux-gnu.so -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib.linux-x86_64-3.11/class_change.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib.linux-x86_64-3.11/modhmmer.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib.linux-x86_64-3.11/ghmmhelper.py -> /build/ghmm-0.9~rc3/debian/tmp//usr/lib/python3.11/site-packages copying build/lib.linux-x86_64-3.11/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'. /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/x86_64-linux-gnu install -d -m 755 debian/libghmm1/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.a debian/libghmm-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.so debian/libghmm-dev/usr/lib/x86_64-linux-gnu mv /build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.so.1 debian/libghmm1/usr/lib/x86_64-linux-gnu mv /build/ghmm-0.9~rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.so.1.0.0 debian/libghmm1/usr/lib/x86_64-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-dbgsym' in '../ghmm-dbgsym_0.9~rc3-4_amd64.deb'. dpkg-deb: building package 'ghmm' in '../ghmm_0.9~rc3-4_amd64.deb'. dpkg-deb: building package 'libghmm-dev' in '../libghmm-dev_0.9~rc3-4_amd64.deb'. dpkg-deb: building package 'libghmm1' in '../libghmm1_0.9~rc3-4_amd64.deb'. dpkg-deb: building package 'libghmm1-dbgsym' in '../libghmm1-dbgsym_0.9~rc3-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../ghmm_0.9~rc3-4_amd64.buildinfo dpkg-genchanges --build=binary -O../ghmm_0.9~rc3-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3420017 and its subdirectories I: Current time: Sat May 20 02:07:06 -12 2023 I: pbuilder-time-stamp: 1684591626 Sat May 20 14:07:07 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Sat May 20 14:07:07 UTC 2023 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Sat May 20 14:08:44 UTC 2023 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Sat May 20 14:08:45 UTC 2023 I: ghmm_0.9~rc3-4_amd64.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: amd64 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: 5a743990c0a9f94ea0bae4c90a709005d9c51bc5 491768 ghmm-dbgsym_0.9~rc3-4_amd64.deb 07ddab44e02b23ae67dd1042901034a7a6d6b3f8 7606 ghmm_0.9~rc3-4_amd64.buildinfo 6df03824e0ef5f82db6c4b72ff431925a855d709 142236 ghmm_0.9~rc3-4_amd64.deb 60fccbd0135cc59164622a3ed5250371c0f2c49a 182232 libghmm-dev_0.9~rc3-4_amd64.deb 1e6ccb1d58455ff7fc4f25b584fb32dca9aeee65 335776 libghmm1-dbgsym_0.9~rc3-4_amd64.deb 9a854ab7c140f8838c66800054202130ddf26bf9 138828 libghmm1_0.9~rc3-4_amd64.deb Checksums-Sha256: d5fbb24b78517a7582f2c64c3a3f1150d7546a346ac3a57f47c5acbc38ee2bdf 491768 ghmm-dbgsym_0.9~rc3-4_amd64.deb ba7228467fa64195f299c0453f82a54356b6580e334b3ad01c41913594eafb95 7606 ghmm_0.9~rc3-4_amd64.buildinfo f1d11437eb3148c48cbeda3d20ad2c20a7721310a25ffac0fa066f0ca9f684ba 142236 ghmm_0.9~rc3-4_amd64.deb 55917316967b3b327d94f55f758848c5a07cbab7e6ca56c2cf20317efc420330 182232 libghmm-dev_0.9~rc3-4_amd64.deb 9a1d43aee5df09d2ecb049ade25db7301fbf1cb344e68ebc87bd36fd4aa5dc92 335776 libghmm1-dbgsym_0.9~rc3-4_amd64.deb 3d8884b8d9cd0bfeb3032c8dcb861565039043103d2c6d349f518ca35235d02d 138828 libghmm1_0.9~rc3-4_amd64.deb Files: f8f33bd66efc964ca56e50183875f027 491768 debug optional ghmm-dbgsym_0.9~rc3-4_amd64.deb 00147adc474e57d600e2a2a97097ffd7 7606 science optional ghmm_0.9~rc3-4_amd64.buildinfo 3998936ecfe91b36ce90916b02d6f879 142236 science optional ghmm_0.9~rc3-4_amd64.deb 22c08c8390c25d7d959a9d1e3e4de6e2 182232 libdevel optional libghmm-dev_0.9~rc3-4_amd64.deb a55eb6822213c10a875f676890095584 335776 debug optional libghmm1-dbgsym_0.9~rc3-4_amd64.deb b7c3b75204b80d0d283718306f093adb 138828 libs optional libghmm1_0.9~rc3-4_amd64.deb Sat May 20 14:08:49 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.jCTWwd3r/ghmm_0.9~rc3-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.jCTWwd3r/ghmm_0.9~rc3-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.jCTWwd3r/ghmm_0.9~rc3-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.jCTWwd3r/b1/ghmm_0.9~rc3-4_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.jCTWwd3r/b2/ghmm_0.9~rc3-4_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 4.249s) 4.249s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.248s) 0.247s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Sat May 20 14:08:54 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Sat May 20 14:08:54 UTC 2023 I: ghmm from bookworm built successfully and reproducibly on amd64. Sat May 20 14:08:55 UTC 2023 I: Submitting .buildinfo files to external archives: Sat May 20 14:08:55 UTC 2023 I: Submitting 12K b1/ghmm_0.9~rc3-4_amd64.buildinfo.asc Sat May 20 14:08:56 UTC 2023 I: Submitting 12K b2/ghmm_0.9~rc3-4_amd64.buildinfo.asc Sat May 20 14:08:57 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat May 20 14:08:57 UTC 2023 I: Done submitting .buildinfo files. Sat May 20 14:08:57 UTC 2023 I: Removing signed ghmm_0.9~rc3-4_amd64.buildinfo.asc files: removed './b1/ghmm_0.9~rc3-4_amd64.buildinfo.asc' removed './b2/ghmm_0.9~rc3-4_amd64.buildinfo.asc'