rpms/ghmm/F-11 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]

Author: mycae

Update of /cvs/pkgs/rpms/ghmm/F-11
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv22168/F-11

Modified Files:
	.cvsignore sources 
Added Files:
	ghmm-config.patch ghmm-make-check.patch ghmm.spec import.log 
Log Message:
*Initial commmit

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:F-11:ghmm-0.7-4.svn2286.fc10.src.rpm:1256809203


Index: .cvsignore
===================================================================
RCS file: /cvs/pkgs/rpms/ghmm/F-11/.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 09:40:29 -0000	1.2
@@ -0,0 +1 @@
+ghmm.tar.bz2


Index: sources
===================================================================
RCS file: /cvs/pkgs/rpms/ghmm/F-11/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 09:40:29 -0000	1.2
@@ -0,0 +1 @@
+24d1829f2562d04115b7f028e0399f0f  ghmm.tar.bz2