- new

diff --git a/R-Rsamtools.spec b/R-Rsamtools.spec
new file mode 100644 (file)
index 0000000..48ff706
--- /dev/null
+++ b/R-Rsamtools.spec
@@ -0,0 +1,78 @@
+%define                packname        Rsamtools
+
+Summary:       Binary alignment (BAM), variant call (BCF), or tabix file import
+Name:          R-%{packname}
+Version:       1.12.2
+Release:       1
+License:       Artistic 2.0
+Group:         Applications/Math
+Source0:       http://www.bioconductor.org/packages/release/bioc/src/contrib/%{packname}_%{version}.tar.gz
+# Source0-md5: 4ff6113fe8b925cf7586e1331da1ec23
+Patch0:                bogus-deps.patch
+URL:           http://www.bioconductor.org/packages/2.12/bioc/html/Rsamtools.html
+BuildRequires: R
+BuildRequires: R-IRanges-devel >= 1.15.35
+BuildRequires: R-GenomicRanges >= 1.11.38
+BuildRequires: R-Biostrings-devel >= 2.25.6
+BuildRequires: texlive-latex
+Requires:      R
+Requires:      R-IRanges >= 1.17.33
+Requires:      R-GenomicRanges >= 1.11.38
+Requires:      R-Biostrings >= 2.25.6
+BuildRoot:     %{tmpdir}/%{name}-%{version}-root-%(id -u -n)
+
+%description
+This package provides an interface to the 'samtools', 'bcftools',
+and 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence
+Alignment / Map), binary variant call (BCF) and compressed indexed
+tab-delimited (tabix) files.
+
+%package        devel
+Summary:        Development files for %{name}
+Group:          Development/Libraries
+Requires:       %{name} = %{version}-%{release}
+
+%description    devel
+The %{name}-devel package contains libraries and header files for
+developing applications that use %{name}.
+
+%prep
+%setup -q -c -n %{packname}
+%patch0 -p1
+
+%build
+# circular dep on R-Rsamtools
+#{_bindir}/R CMD build %{packname}
+
+%install
+rm -rf $RPM_BUILD_ROOT
+install -d $RPM_BUILD_ROOT%{_libdir}/R/library
+
+%{_bindir}/R CMD INSTALL -l $RPM_BUILD_ROOT%{_libdir}/R/library %{packname}
+
+%clean
+rm -rf $RPM_BUILD_ROOT
+
+%files
+%defattr(644,root,root,755)
+%dir %{_libdir}/R/library/%{packname}/
+%doc %{_libdir}/R/library/%{packname}/doc/
+%doc %{_libdir}/R/library/%{packname}/html/
+%doc %{_libdir}/R/library/%{packname}/DESCRIPTION
+%doc %{_libdir}/R/library/%{packname}/LICENSE
+%doc %{_libdir}/R/library/%{packname}/NEWS
+%{_libdir}/R/library/%{packname}/INDEX
+%{_libdir}/R/library/%{packname}/NAMESPACE
+%{_libdir}/R/library/%{packname}/Meta/
+%{_libdir}/R/library/%{packname}/R/
+%{_libdir}/R/library/%{packname}/extdata/
+%{_libdir}/R/library/%{packname}/help/
+%{_libdir}/R/library/%{packname}/scripts/
+%{_libdir}/R/library/%{packname}/unitTests/
+%{_libdir}/R/library/%{packname}/libs/
+
+%files devel
+%defattr(644,root,root,755)
+%{_libdir}/R/library/%{packname}/include
+%{_libdir}/R/library/%{packname}/usretc
+%{_libdir}/R/library/%{packname}/usrlib

diff --git a/bogus-deps.patch b/bogus-deps.patch
new file mode 100644 (file)
index 0000000..5b575c5
--- /dev/null
+++ b/bogus-deps.patch
@@ -0,0 +1,21 @@
+--- Rsamtools/Rsamtools/DESCRIPTION~   2013-04-18 07:46:40.000000000 +0200
++++ Rsamtools/Rsamtools/DESCRIPTION    2013-05-10 14:30:55.269037518 +0200
+@@ -14,7 +14,7 @@
+ LazyLoad: yes
+ Depends: methods, IRanges (>= 1.15.35), GenomicRanges (>= 1.11.38),
+         Biostrings (>= 2.25.6)
+-Imports: methods, utils, IRanges, GenomicRanges, Biostrings, zlibbioc,
++Imports: methods, utils, IRanges, GenomicRanges, Biostrings,
+         bitops, BiocGenerics (>= 0.1.3)
+ Suggests: ShortRead (>= 1.13.19), GenomicFeatures,
+         TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, pasillaBamSubset,
+--- Rsamtools/Rsamtools/NAMESPACE~     2013-04-04 00:15:29.000000000 +0200
++++ Rsamtools/Rsamtools/NAMESPACE      2013-05-10 14:31:12.692547009 +0200
+@@ -1,7 +1,5 @@
+ useDynLib(Rsamtools, .registration=TRUE)
+ 
+-import(zlibbioc)
+-
+ importFrom(bitops, bitAnd)
+ 
+ importFrom(utils, read.table)           # normalizePath --> base in R-2.13