From: Jan Rękorajski <baggins@pld-linux.org>
Date: Fri, 10 May 2013 12:36:28 +0000 (+0200)
Subject: - new
X-Git-Tag: auto/th/R-Rsamtools-1.12.2-1
X-Git-Url: http://git.pld-linux.org/?p=packages%2FR-Rsamtools.git;a=commitdiff_plain;h=93cd0b930913509b3376d9a37cd234277268abf5

- new
---

93cd0b930913509b3376d9a37cd234277268abf5
diff --git a/R-Rsamtools.spec b/R-Rsamtools.spec
new file mode 100644
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
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