rpms/ghmm/devel ghmm-config.patch, NONE, 1.1 ghmm-make-check.patch, NONE, 1.1 ghmm.spec, NONE, 1.1 import.log, NONE, 1.1 .cvsignore, 1.1, 1.2 sources, 1.1, 1.2
mycae
mycae at fedoraproject.org
Thu Oct 29 09:34:20 UTC 2009
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Author: mycae
Update of /cvs/pkgs/rpms/ghmm/devel
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv20074/devel
Modified Files:
.cvsignore sources
Added Files:
ghmm-config.patch ghmm-make-check.patch ghmm.spec import.log
Log Message:
*Initial commit
ghmm-config.patch:
ghmm-config.in | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
--- NEW FILE ghmm-config.patch ---
--- tools/ghmm-config.in 2003-11-10 01:47:43.000000000 +1100
+++ tools/ghmm-config.in.new 2009-09-12 20:57:28.000000000 +1000
@@ -54,10 +54,10 @@
echo @VERSION@
;;
--cflags)
- echo @CFLAGS@ -I${prefix}/include
+ echo -n " @CFLAGS@ -I${prefix}/include"
;;
--libs)
- echo -L${prefix}/lib -lghmm @LIBS@
+ echo -n " -L${prefix}/lib -lghmm @LIBS@"
;;
--lib-prefix)
echo ${prefix}/lib
@@ -75,3 +75,5 @@
shift
done
+echo
+
ghmm-make-check.patch:
Makefile.am | 1 -
1 file changed, 1 deletion(-)
--- NEW FILE ghmm-make-check.patch ---
--- ghmmwrapper/Makefile.am 2009-08-23 11:54:16.000000000 +1000
+++ ghmmwrapper/Makefile.am.new 2009-08-23 11:54:36.000000000 +1000
@@ -51,7 +51,6 @@
testdata/multiple_hmmer.hmm \
testdata/tiny.smo \
testdata/xml_cont_multiple.xml \
- testdata/es_discrete_testwrite.seq \
testdata/test10.sqd \
testdata/test2.xml \
testdata/model_label.xml \
--- NEW FILE ghmm.spec ---
%{!?python_sitelib: %global python_sitelib %(%{__python} -c "from distutils.sysconfig import get_python_lib; print get_python_lib()")}
%{!?python_sitearch: %define python_sitearch %(%{__python} -c "from distutils.sysconfig import get_python_lib; print get_python_lib(1)")}
%define svnver 2286
#Need to fix this package. The latest spec is in koji...
# http://koji.fedoraproject.org/koji/taskinfo?taskID=1672945
#Upstream has been notified of exit() calls.
#https://sourceforge.net/tracker/?func=detail&aid=2842844&group_id=67094&atid=516866
#Upstream has been notified of licencing issues
#https://sourceforge.net/tracker/?func=detail&aid=2842854&group_id=67094&atid=516866
#Upstream has been notfied of unit test problems
#https://sourceforge.net/tracker/?func=detail&aid=2842847&group_id=67094&atid=516867
Name: ghmm
Version: 0.7
Release: 4.svn%{svnver}%{?dist}
Summary: A library with data structures and algorithms for Hidden Markov Models
Group: Development/Libraries
License: LGPLv2+
URL: http://ghmm.sourceforge.net/
# The source for this package was pulled from upstream's vcs. Use the
# following commands to generate the tarball:
# export LANG=en_US.utf8; export TZ=+0000;
# svn export -r2286 https://ghmm.svn.sourceforge.net/svnroot/ghmm/trunk/ghmm ghmm
# tar -cjf ghmm.tar.bz2 ghmm/
# MD5 sum should be : 24d1829f2562d04115b7f028e0399f0f ghmm.tar.bz2
Source0: %{name}.tar.bz2
#Disable single broken test
Patch0: %{name}-make-check.patch
#Fix ghmm-config output
Patch1: %{name}-config.patch
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
BuildRequires: gsl-devel
BuildRequires: libtool
BuildRequires: libxml2-devel
BuildRequires: pkgconfig
BuildRequires: python-devel
BuildRequires: swig
BuildRequires: atlas-devel
Requires: tkinter
%description
The General Hidden Markov Model library (GHMM) is a freely available
LGPL-ed C library implementing efficient data structures and algorithms
for basic and extended HMMs.
It is developed by the Algorithmics group at the Max Planck Institute
for Molecular Genetics.
Features:
* Discrete and continuous emissions
* Mixtures of PDFs for continuous emissions
* Non-homogenous Markov chains
* Pair HMMs (contributed by Genoscope)
* Clustering and mixture modelling for HMMs
* Graphical Editor HMMEd
* Python bindings
* XML-based file format
%package static
Summary: Static libraries for %{name}
Group: Development/Libraries
Requires: %{name}-devel = %{version}-%{release}
%description static
Static libraries for developing with %{name}.
%package devel
Summary: Development headers and libraries for %{name}
Group: Development/Libraries
Requires: %{name} = %{version}-%{release}
%description devel
Headers and libraries for developing with %{name}.
%prep
%setup -q -n %{name}
sed -i \
-e 's|$(PYTHON) setup.py install.*$|$(PYTHON) setup.py install -O1 --skip-build --root ${RPM_BUILD_ROOT}|' \
ghmmwrapper/Makefile.am HMMEd/Makefile.am
sed -i -e '1,1d' \
ghmmwrapper/ghmm_gato/{xmlutil,HMMEd,EditObjectAttributesDialog}.py \
ghmmwrapper/ghmm.py HMMEd/{HMMEditor,ObjectHMM,HMMEditingContext}.py
find . -type f -name '*.c' | xargs chmod -x
find . -type f -name '*.h' | xargs chmod -x
find . -type f -name '*.txt' | xargs chmod -x
#convert to UTF-8
chmod 644 AUTHORS
for i in AUTHORS
do
iconv -f iso8859-1 -t utf-8 $i > $i.new && \
touch -r $i $i.new && \
mv $i.new $i
done
\
%patch0
%patch1
%build
# Docs aren't build because Fedora doesn't have doc++
./autogen.sh
export CFLAGS="${CFLAGS} -I/usr/include/atlas"
%configure --enable-gsl --enable-experimental --enable-unsupported --enable-atlas
make %{?_smp_mflags}
%install
rm -rf $RPM_BUILD_ROOT
make install DESTDIR=$RPM_BUILD_ROOT
rm -f $RPM_BUILD_ROOT%{_libdir}/*.la
pushd $RPM_BUILD_ROOT%{_bindir}
for bin in cluster probdist scluster smix_hmm smo2xml; do
mv ${bin} %{name}-${bin}
done
popd
%check
pushd ghmmwrapper
# Currently their unit tests fail.
# make check
popd
%post -p /sbin/ldconfig
%postun -p /sbin/ldconfig
%clean
rm -rf $RPM_BUILD_ROOT
%files
%defattr(-,root,root,-)
%doc COPYRIGHT.txt LGPL.txt AUTHORS
%if "%{python_sitearch}" != "%{python_sitelib}"
%{python_sitearch}/*
%endif
%{python_sitelib}/*
%{_libdir}/lib%{name}.so.*
%{_bindir}/HMMEd
%{_bindir}/%{name}-*
%exclude %{_bindir}/%{name}-config
%{_datadir}/%{name}
%files static
%defattr(-,root,root,-)
%{_libdir}/lib%{name}.a
%files devel
%defattr(-,root,root,-)
%{_includedir}/ghmm
%{_libdir}/lib%{name}.so
%{_bindir}/%{name}-config
%changelog
* Sat Oct 24 2009 D Haley <mycae(a!t)yahoo.com> - 0.7-4.svn2286
- Modify CFLAGS again
- Fix permissions on AUTHORS file
* Sat Oct 24 2009 D Haley <mycae(a!t)yahoo.com> - 0.7-3.svn2286
- Enabled atlas build
- Use CFLAGS export
* Sat Oct 10 2009 D Haley <mycae(a!t)yahoo.com> - 0.7-2.svn2286
- Remove GSL Requires (should be found by RPM)
- Patched non-executing make check, but test results indicate a few fails. Upstream notified
- Fixed -config script output via patch
* Sat Mar 21 2009 Conrad Meyer <konrad at tylerc.org> - 0.7-1.svn2251
- Initial package.
--- NEW FILE import.log ---
ghmm-0_7-4_svn2286_fc10:HEAD:ghmm-0.7-4.svn2286.fc10.src.rpm:1256808891
Index: .cvsignore
===================================================================
RCS file: /cvs/pkgs/rpms/ghmm/devel/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -p -r1.1 -r1.2
--- .cvsignore 29 Oct 2009 00:12:32 -0000 1.1
+++ .cvsignore 29 Oct 2009 09:34:20 -0000 1.2
@@ -0,0 +1 @@
+ghmm.tar.bz2
Index: sources
===================================================================
RCS file: /cvs/pkgs/rpms/ghmm/devel/sources,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -p -r1.1 -r1.2
--- sources 29 Oct 2009 00:12:34 -0000 1.1
+++ sources 29 Oct 2009 09:34:20 -0000 1.2
@@ -0,0 +1 @@
+24d1829f2562d04115b7f028e0399f0f ghmm.tar.bz2
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