Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/g/ghmm/ghmm_0.9~rc3-4_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/ghmm-0.9~rc3-4agxe7mgs/ghmm_0.9~rc3-4_amd64.buildinfo Get source package info: ghmm=0.9~rc3-4 Source URL: http://snapshot.notset.fr/mr/package/ghmm/0.9~rc3-4/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 apt=2.1.18 autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-3 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.48 bash=5.1-2 binutils=2.35.1-7 binutils-common=2.35.1-7 binutils-x86-64-linux-gnu=2.35.1-7 bsdextrautils=2.36.1-6 bsdutils=1:2.36.1-6 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 d-shlibs=0.98 dash=0.5.11+git20200708+dd9ef66-5 debconf=1.5.74 debhelper=13.3.1 debian-archive-keyring=2019.1 debianutils=4.11.2 dh-autoreconf=19 dh-strip-nondeterminism=1.10.0-1 diffutils=1:3.7-5 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.13+20210118-1 file=1:5.39-3 findutils=4.8.0-1 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-3 gettext-base=0.21-3 gpgv=2.2.20-1 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 icu-devtools=67.1-6 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-9 libapt-pkg6.0=2.1.18 libarchive-zip-perl=1.68-1 libasan6=10.2.1-6 libatlas-base-dev=3.10.3-10 libatlas3-base=3.10.3-10 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.1-7 libblkid1=2.36.1-6 libbz2-1.0=1.0.8-4 libc-bin=2.31-9 libc-dev-bin=2.31-9 libc6=2.31-9 libc6-dev=2.31-9 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcom-err2=1.45.6-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-7 libctf0=2.35.1-7 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.256 libdebhelper-perl=13.3.1 libdpkg-perl=1.20.7.1 libelf1=0.182-3 libexpat1=2.2.10-1 libexpat1-dev=2.2.10-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.10.0-1 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-2 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgfortran5=10.2.1-6 libglib2.0-0=2.66.4-1 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.0-5 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgsl-dev=2.6+dfsg-2 libgsl25=2.6+dfsg-2 libgslcblas0=2.6+dfsg-2 libgssapi-krb5-2=1.18.3-4 libhogweed6=3.6-2 libicu-dev=67.1-6 libicu67=67.1-6 libidn2-0=2.3.0-5 libisl23=0.23-1 libitm1=10.2.1-6 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblapack-dev=3.9.0-3 liblapack3=3.9.0-3 liblsan0=10.2.1-6 liblz4-1=1.9.3-1 liblzma5=5.2.5-1.0 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-6 libmpc3=1.2.0-1 libmpdec3=2.5.1~rc1-2 libmpfr6=4.1.0-3 libncursesw6=6.2+20201114-2 libnettle8=3.6-2 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.23.22-1 libpam-modules=1.4.0-2 libpam-modules-bin=1.4.0-2 libpam-runtime=1.4.0-2 libpam0g=1.4.0-2 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.0-6 libpipeline1=1.5.3-1 libpython3-dev=3.9.1-1 libpython3-stdlib=3.9.1-1 libpython3.9=3.9.1-3 libpython3.9-dev=3.9.1-3 libpython3.9-minimal=3.9.1-3 libpython3.9-stdlib=3.9.1-3 libquadmath0=10.2.1-6 libreadline8=8.1-1 libseccomp2=2.5.1-1 libselinux1=3.1-2+b2 libsemanage-common=3.1-1 libsemanage1=3.1-1+b2 libsepol1=3.1-1 libsigsegv2=2.12-3 libsmartcols1=2.36.1-6 libsqlite3-0=3.34.1-1 libssl1.1=1.1.1i-2 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.2-5 libtasn1-6=4.16.0-2 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.2-5 libunistring2=0.9.10-4 libuuid1=2.36.1-6 libxml2=2.9.10+dfsg-6.3+b1 libxml2-dev=2.9.10+dfsg-6.3+b1 libxxhash0=0.8.0-2 libzstd1=1.4.8+dfsg-1 linux-libc-dev=5.10.5-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 mailcap=3.68 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 media-types=4.0.0 mime-support=3.66 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 passwd=1:4.8.1-1 patch=2.7.6-7 perl=5.32.0-6 perl-base=5.32.0-6 perl-modules-5.32=5.32.0-6 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 python3=3.9.1-1 python3-dev=3.9.1-1 python3-distutils=3.9.1-2 python3-lib2to3=3.9.1-2 python3-minimal=3.9.1-1 python3.9=3.9.1-3 python3.9-dev=3.9.1-3 python3.9-minimal=3.9.1-3 readline-common=8.1-1 sed=4.7-1 sensible-utils=0.0.14 swig=4.0.2-1 swig4.0=4.0.2-1 sysvinit-utils=2.96-5 tar=1.32+dfsg-1 tzdata=2020f-1 util-linux=2.36.1-6 xz-utils=5.2.5-1.0 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210121T144334Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d ghmm=0.9~rc3-4 && mkdir -p /build/ghmm-OJA2g2 && dpkg-source --no-check -x /*.dsc /build/ghmm-OJA2g2/ghmm-0.9-rc3 && chown -R builduser:builduser /build/ghmm-OJA2g2" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/ghmm-OJA2g2/ghmm-0.9-rc3 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1611516448" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/ghmm-OJA2g2 /tmp/ghmm-0.9~rc3-4agxe7mgs bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210121T144334Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.fdqxeZ6dxS as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.fdqxeZ6dxS Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-6). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210121T144334Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210121T144334Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1098 kB/s) Selecting previously unselected package libfakeroot: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 ... 4661 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-9) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210121T144334Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.fdqxeZ6dxS Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210121T144334Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 20s (1134 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.fdqxeZ6dxS I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d ghmm=0.9~rc3-4 && mkdir -p /build/ghmm-OJA2g2 && dpkg-source --no-check -x /*.dsc /build/ghmm-OJA2g2/ghmm-0.9-rc3 && chown -R builduser:builduser /build/ghmm-OJA2g2"' exec /tmp/mmdebstrap.fdqxeZ6dxS Reading package lists... NOTICE: 'ghmm' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/ghmm.git Please use: git clone https://salsa.debian.org/med-team/ghmm.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 790 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main ghmm 0.9~rc3-4 (dsc) [2136 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main ghmm 0.9~rc3-4 (tar) [771 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main ghmm 0.9~rc3-4 (diff) [17.6 kB] Fetched 790 kB in 1s (1164 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'ghmm_0.9~rc3-4.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting ghmm in /build/ghmm-OJA2g2/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: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/ghmm-OJA2g2/ghmm-0.9-rc3 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1611516448" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.fdqxeZ6dxS 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-OJA2g2/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-OJA2g2/ghmm-0.9-rc3' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a 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' 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-OJA2g2/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 thread-safe 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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... 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 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 how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.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 ANSI C header files... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether time.h and sys/time.h may both be included... 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-OJA2g2/ghmm-0.9-rc3' dh_auto_build -a make -j4 make[1]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3' make all-recursive make[2]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3' Making all in ghmm make[3]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/ghmm' Making all in . make[4]: Entering directory '/build/ghmm-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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 libtool: compile: 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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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 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:410:14: note: in a call to function ‘initstate’ declared here 410 | 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-OJA2g2/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-OJA2g2/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 libtool: compile: 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-OJA2g2/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 /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-OJA2g2/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-OJA2g2/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 libtool: compile: 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-OJA2g2/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-OJA2g2/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 /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-OJA2g2/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 libtool: compile: 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-OJA2g2/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-OJA2g2/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 In file included from /usr/include/string.h:495, from ghmm_internals.c:44: In function ‘strncpy’, inlined from ‘process_external_log’ at ghmm_internals.c:68:17, inlined from ‘ighmm_log_out’ at ghmm_internals.c:83:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ghmm_internals.c: In function ‘ighmm_log_out’: ghmm_internals.c:63:18: note: length computed here 63 | int proc_len = strlen(proc); | ^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from ghmm_internals.c:44: In function ‘strncat’, inlined from ‘process_external_log’ at ghmm_internals.c:69:17, inlined from ‘ighmm_log_out’ at ghmm_internals.c:83:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ghmm_internals.c: In function ‘ighmm_log_out’: ghmm_internals.c:64:14: note: length computed here 64 | int slen = strlen(error_str); | ^~~~~~~~~~~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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 /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-OJA2g2/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 libtool: compile: 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-OJA2g2/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-OJA2g2/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 libtool: compile: 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-OJA2g2/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-OJA2g2/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 matrix.c: In function ‘ighmm_cmatrix_stat_free’: matrix.c:176:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 176 | mes_check_ptr (matrix, return (-1)); | ^ matrix.c: In function ‘ighmm_dmatrix_stat_free’: matrix.c:214:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 214 | mes_check_ptr (matrix, return (-1)); | ^ matrix.c: In function ‘ighmm_cmatrix_3d_free’: matrix.c:270:35: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 270 | mes_check_ptr(matrix, return(-1)); | ^ matrix.c: In function ‘ighmm_cmatrix_free’: matrix.c:285:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 285 | mes_check_ptr(matrix, return (-1)); | ^ matrix.c: In function ‘ighmm_dmatrix_free’: matrix.c:343:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 343 | mes_check_ptr (matrix, return (-1)); | ^ matrix.c: In function ‘ighmm_dmatrix_3d_free’: matrix.c:378:35: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 378 | mes_check_ptr(matrix, return(-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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-OJA2g2/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-OJA2g2/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 libtool: compile: 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-OJA2g2/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 /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-OJA2g2/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 libtool: compile: 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-OJA2g2/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-OJA2g2/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 /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-OJA2g2/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 libtool: compile: 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-OJA2g2/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-OJA2g2/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 /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-OJA2g2/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 libtool: compile: 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-OJA2g2/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 /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-OJA2g2/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 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)); | ^ sequence.c: In function ‘ghmm_dseq_free’: sequence.c:1189:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1189 | mes_check_ptr(sq, return -1); | ^ sequence.c: In function ‘ghmm_cseq_free’: sequence.c:1226:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1226 | mes_check_ptr(sqd, return -1); | ^ /bin/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-OJA2g2/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-OJA2g2/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 psequence.c: In function ‘ghmm_dpseq_free’: psequence.c:78:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 78 | mes_check_ptr(seq, return(-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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-OJA2g2/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-OJA2g2/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 /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-OJA2g2/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 libtool: compile: 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-OJA2g2/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 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;); | ^ libtool: compile: 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-OJA2g2/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 libtool: compile: 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-OJA2g2/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-OJA2g2/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 /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-OJA2g2/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 /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-OJA2g2/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 libtool: compile: 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-OJA2g2/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 libtool: compile: 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-OJA2g2/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); | ^ 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-OJA2g2/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 libtool: compile: 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-OJA2g2/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 /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-OJA2g2/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 libtool: compile: 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-OJA2g2/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 reestimate.c: In function ‘reestimate_free’: reestimate.c:79:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 79 | mes_check_ptr (r, return (-1)); | ^ reestimate.c: In function ‘reestimate_setlambda’: reestimate.c:306:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 306 | mes_check_0 (r->pi_denom, goto STOP); | ^ /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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 libtool: compile: 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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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 /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-OJA2g2/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-OJA2g2/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 /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-OJA2g2/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-OJA2g2/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 modelutil.c: In function ‘topo_free’: modelutil.c:89:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 89 | mes_check_ptr (v, return (-1)); | ^ /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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 libtool: compile: 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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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 libtool: compile: 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-OJA2g2/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 /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-OJA2g2/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 /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-OJA2g2/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-OJA2g2/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 libtool: compile: 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-OJA2g2/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 /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-OJA2g2/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 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-OJA2g2/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 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)); | ^ libtool: compile: 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-OJA2g2/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-OJA2g2/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 /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-OJA2g2/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 /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-OJA2g2/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 libtool: compile: 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-OJA2g2/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 libtool: compile: 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-OJA2g2/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-OJA2g2/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 /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-OJA2g2/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 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-OJA2g2/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-OJA2g2/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-OJA2g2/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 libtool: compile: 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-OJA2g2/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 libtool: compile: 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-OJA2g2/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 /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-OJA2g2/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 libtool: compile: 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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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 /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-OJA2g2/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 libtool: compile: 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-OJA2g2/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 sdmodel.c: In function ‘ghmm_dsmodel_free’: sdmodel.c:211:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 211 | mes_check_ptr (mo, return (-1)); | ^ /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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-OJA2g2/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 libtool: compile: 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-OJA2g2/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-OJA2g2/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 sdfoba.c: In function ‘ghmm_dsmodel_backward’: sdfoba.c:336:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 336 | mes_check_0 (scale[t], goto STOP); | ^ /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-OJA2g2/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 sdviterbi.c: In function ‘sdviterbi_free’: sdviterbi.c:111:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 111 | mes_check_ptr (v, return (-1)); | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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 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-OJA2g2/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 libtool: compile: 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-OJA2g2/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-OJA2g2/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-OJA2g2/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 /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-OJA2g2/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 /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-OJA2g2/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-OJA2g2/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 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-OJA2g2/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 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-OJA2g2/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 libtool: compile: 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-OJA2g2/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 /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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/ghmm-0.9-rc3/ghmm' make[3]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/ghmm' Making all in tools make[3]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tools' make all-recursive make[4]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tools' Making all in . make[5]: Entering directory '/build/ghmm-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/ghmm-0.9-rc3=. -fstack-protector-strong -Wformat 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-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-OJA2g2/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 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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 libtool: link: gcc -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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-OJA2g2/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-OJA2g2/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 libtool: link: gcc -g -O2 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directory '/build/ghmm-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/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 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-OJA2g2/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-OJA2g2/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 libtool: link: gcc -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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-OJA2g2/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 libtool: link: gcc -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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-OJA2g2/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 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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 libtool: link: gcc -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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-OJA2g2/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-OJA2g2/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 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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-OJA2g2/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 libtool: link: gcc -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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 libtool: link: gcc -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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-OJA2g2/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 libtool: link: gcc -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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-OJA2g2/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 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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-OJA2g2/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 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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-OJA2g2/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 libtool: link: gcc -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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-OJA2g2/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 libtool: link: gcc -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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 make[4]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tests' make[3]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tests' Making all in ghmmwrapper make[3]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/ghmmwrapper' Making all in . make[4]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/ghmmwrapper' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/ghmmwrapper' /usr/bin/python3 setup.py build running build running build_py file ghmmwrapper.py (for module ghmmwrapper) not found creating build creating build/lib.linux-x86_64-3.9 copying ghmm.py -> build/lib.linux-x86_64-3.9 copying ghmmhelper.py -> build/lib.linux-x86_64-3.9 copying modhmmer.py -> build/lib.linux-x86_64-3.9 copying class_change.py -> build/lib.linux-x86_64-3.9 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_64-3.9 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/ghmm-OJA2g2/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/python3.9 -c ghmmwrapper_wrap.c -o build/temp.linux-x86_64-3.9/ghmmwrapper_wrap.o -O2 -pipe -Wall ghmmwrapper_wrap.c: In function ‘PythonCallBack’: ghmmwrapper_wrap.c:3057:9: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 3057 | PyEval_CallObject(func, arglist); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/python3.9/Python.h:145, from ghmmwrapper_wrap.c:154: /usr/include/python3.9/ceval.h:17:43: note: declared here 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ghmmwrapper_wrap.c: In function ‘delete_ghmm_alphabet’: ghmmwrapper_wrap.c:3258:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3258 | for(i=0; isize; ++i) | ^ ghmmwrapper_wrap.c: In function ‘ghmm_cmodel_getStateName’: ghmmwrapper_wrap.c:3511:43: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 3511 | if((self->s + index) && index < self->N) return (self->s + index)->desc; | ^ ghmmwrapper_wrap.c: In function ‘ghmm_dbackground_setName’: ghmmwrapper_wrap.c:3544:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 3544 | if(index < self->n){ | ^ ghmmwrapper_wrap.c: In function ‘ghmm_dmodel_getStateName’: ghmmwrapper_wrap.c:3592:43: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 3592 | if((self->s + index) && index < self->N) return (self->s + index)->desc; | ^ ghmmwrapper_wrap.c: In function ‘int_matrix_alloc’: ghmmwrapper_wrap.c:3703:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 3703 | for (i=0; i build/lib copying ObjectHMM.py -> build/lib copying HMMEditingContext.py -> build/lib running build_scripts creating build/scripts-3.9 copying and adjusting HMMEd -> build/scripts-3.9 changing mode of build/scripts-3.9/HMMEd from 644 to 755 make[3]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/HMMEd' make[3]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3' make[3]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3' make[2]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3' make[1]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3' debian/rules override_dh_auto_test make[1]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3' /usr/bin/make --directory=tests make[2]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tests' Making all in data make[3]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tests/data' Making all in . make[4]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tests/data' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tests/data' make[3]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tests/data' make[3]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tests' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tests' make[2]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tests' make[1]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install -a make -j1 install DESTDIR=/build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3' Making install in ghmm make[2]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/ghmm' Making install in . make[3]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/ghmm' make[4]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/ghmm' /bin/mkdir -p '/build/ghmm-OJA2g2/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-OJA2g2/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-OJA2g2/ghmm-0.9-rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.so.1.0.0 libtool: install: (cd /build/ghmm-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/ghmm-0.9-rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.a libtool: install: chmod 644 /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp/usr/lib/x86_64-linux-gnu/libghmm.a libtool: install: ranlib /build/ghmm-OJA2g2/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-OJA2g2/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-OJA2g2/ghmm-0.9-rc3/debian/tmp/usr/include/ghmm' make[4]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/ghmm' make[3]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/ghmm' make[2]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/ghmm' Making install in tools make[2]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tools' make install-recursive make[3]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tools' Making install in . make[4]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tools' make[5]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tools' /bin/mkdir -p '/build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c probdist cluster scluster smix_hmm '/build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp/usr/bin' libtool: install: /usr/bin/install -c probdist /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp/usr/bin/probdist libtool: install: /usr/bin/install -c cluster /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp/usr/bin/cluster libtool: install: /usr/bin/install -c scluster /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp/usr/bin/scluster libtool: install: /usr/bin/install -c smix_hmm /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp/usr/bin/smix_hmm /bin/mkdir -p '/build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp/usr/bin' /usr/bin/install -c ghmm-config '/build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp/usr/bin' make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tools' make[4]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tools' make[3]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tools' make[2]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tools' Making install in tests make[2]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tests' Making install in data make[3]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tests/data' Making install in . make[4]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tests/data' make[5]: Entering directory '/build/ghmm-OJA2g2/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-OJA2g2/ghmm-0.9-rc3/tests/data' make[4]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tests/data' make[3]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tests/data' make[3]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tests' make[4]: Entering directory '/build/ghmm-OJA2g2/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-OJA2g2/ghmm-0.9-rc3/tests' make[3]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tests' make[2]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/tests' Making install in ghmmwrapper make[2]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/ghmmwrapper' Making all in . make[3]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/ghmmwrapper' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/ghmmwrapper' /usr/bin/python3 setup.py build running build running build_py copying ghmmwrapper.py -> build/lib.linux-x86_64-3.9 running build_ext /usr/bin/python3 setup.py install --prefix=/build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr running install running build running build_py running build_ext running install_lib creating /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp/usr/lib/python3.9 creating /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp/usr/lib/python3.9/site-packages copying build/lib.linux-x86_64-3.9/class_change.py -> /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages copying build/lib.linux-x86_64-3.9/_ghmmwrapper.cpython-39-x86_64-linux-gnu.so -> /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages copying build/lib.linux-x86_64-3.9/ghmmwrapper.py -> /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages copying build/lib.linux-x86_64-3.9/ghmm.py -> /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages copying build/lib.linux-x86_64-3.9/modhmmer.py -> /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages copying build/lib.linux-x86_64-3.9/ghmmhelper.py -> /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages byte-compiling /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/class_change.py to class_change.cpython-39.pyc byte-compiling /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/ghmmwrapper.py to ghmmwrapper.cpython-39.pyc byte-compiling /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/ghmm.py to ghmm.cpython-39.pyc /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/ghmm.py:1358: SyntaxWarning: "is" with a literal. Did you mean "=="? if emission_domain is 'd': /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/ghmm.py:2868: SyntaxWarning: "is" with a literal. Did you mean "=="? if R is -1: byte-compiling /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/modhmmer.py to modhmmer.cpython-39.pyc byte-compiling /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/ghmmhelper.py to ghmmhelper.cpython-39.pyc running install_egg_info Writing /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/ghmmwrapper-0.8-py3.9.egg-info make[2]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/ghmmwrapper' Making install in HMMEd make[2]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/HMMEd' /usr/bin/python3 setup.py install --prefix=/build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr running install running build running build_py running build_scripts running install_lib copying build/lib/HMMEditor.py -> /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages copying build/lib/ObjectHMM.py -> /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages copying build/lib/HMMEditingContext.py -> /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages byte-compiling /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/HMMEditor.py to HMMEditor.cpython-39.pyc /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/HMMEditor.py:436: SyntaxWarning: "is" with a literal. Did you mean "=="? if file is "": /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/HMMEditor.py:471: SyntaxWarning: "is not" with a literal. Did you mean "!="? if file is not "": byte-compiling /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/ObjectHMM.py to ObjectHMM.cpython-39.pyc /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/ObjectHMM.py:648: SyntaxWarning: "is" with a literal. Did you mean "=="? if name is "emission": /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/ObjectHMM.py:650: SyntaxWarning: "is" with a literal. Did you mean "=="? elif name is "name": /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/ObjectHMM.py:665: SyntaxWarning: "is" with a literal. Did you mean "=="? if name is "emission": /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/ObjectHMM.py:667: SyntaxWarning: "is" with a literal. Did you mean "=="? elif name is "name": /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/ObjectHMM.py:1053: SyntaxWarning: "is" with a literal. Did you mean "=="? if name is "p": /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/ObjectHMM.py:1060: SyntaxWarning: "is" with a literal. Did you mean "=="? if name is "p": byte-compiling /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/HMMEditingContext.py to HMMEditingContext.cpython-39.pyc /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/HMMEditingContext.py:42: SyntaxWarning: "is" with a literal. Did you mean "=="? if parameter.CDataType is "int": /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/HMMEditingContext.py:45: SyntaxWarning: "is" with a literal. Did you mean "=="? elif parameter.CDataType is "double": running install_scripts copying build/scripts-3.9/HMMEd -> /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/bin changing mode of /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/bin/HMMEd to 755 running install_egg_info Writing /build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp//usr/lib/python3.9/site-packages/HMMEd-0.8-py3.9.egg-info make[2]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3/HMMEd' make[2]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3' make[3]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp/usr/share/ghmm' /usr/bin/install -c -m 644 doc/ghmm.dtd.1.0 '/build/ghmm-OJA2g2/ghmm-0.9-rc3/debian/tmp/usr/share/ghmm' make[3]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3' make[2]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3' make[1]: Leaving directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3' debian/rules override_dh_install make[1]: Entering directory '/build/ghmm-OJA2g2/ghmm-0.9-rc3' dh_install find /build/ghmm-OJA2g2/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-OJA2g2/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-OJA2g2/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-OJA2g2/ghmm-0.9-rc3/debian/ghmm/usr/bin/ && mv cluster ghmm-cluster sed -i -e 's@ [^ ]*-f\(file\|debug\)-prefix-map=[^ ]*@@g' \ /build/ghmm-OJA2g2/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-OJA2g2/ghmm-0.9-rc3' dh_installdocs -a dh_installchangelogs -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a 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 -a dh_builddeb -a 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-dbgsym' in '../libghmm1-dbgsym_0.9~rc3-4_amd64.deb'. dpkg-deb: building package 'libghmm1' in '../libghmm1_0.9~rc3-4_amd64.deb'. dpkg-deb: building package 'ghmm-dbgsym' in '../ghmm-dbgsym_0.9~rc3-4_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../ghmm_0.9~rc3-4_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/ghmm-OJA2g2 /tmp/ghmm-0.9~rc3-4agxe7mgs I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.fdqxeZ6dxS... I: success in 458.6596 seconds md5: ghmm-dbgsym_0.9~rc3-4_amd64.deb: OK md5: ghmm_0.9~rc3-4_amd64.deb: OK md5: libghmm-dev_0.9~rc3-4_amd64.deb: OK md5: libghmm1-dbgsym_0.9~rc3-4_amd64.deb: OK md5: libghmm1_0.9~rc3-4_amd64.deb: OK sha1: ghmm-dbgsym_0.9~rc3-4_amd64.deb: OK sha1: ghmm_0.9~rc3-4_amd64.deb: OK sha1: libghmm-dev_0.9~rc3-4_amd64.deb: OK sha1: libghmm1-dbgsym_0.9~rc3-4_amd64.deb: OK sha1: libghmm1_0.9~rc3-4_amd64.deb: OK sha256: ghmm-dbgsym_0.9~rc3-4_amd64.deb: OK sha256: ghmm_0.9~rc3-4_amd64.deb: OK sha256: libghmm-dev_0.9~rc3-4_amd64.deb: OK sha256: libghmm1-dbgsym_0.9~rc3-4_amd64.deb: OK sha256: libghmm1_0.9~rc3-4_amd64.deb: OK Checksums: OK