From 27c0f5b4cfeba9697437b337140a3156588cb44a Mon Sep 17 00:00:00 2001
From: =?utf8?q?Jan=20R=C4=99korajski?= <baggins@pld-linux.org>
Date: Fri, 10 May 2013 14:43:29 +0200
Subject: [PATCH] - new

---
 R-rtracklayer.spec | 68 ++++++++++++++++++++++++++++++++++++++++++++++
 bogus-deps.patch   | 21 ++++++++++++++
 2 files changed, 89 insertions(+)
 create mode 100644 R-rtracklayer.spec
 create mode 100644 bogus-deps.patch

diff --git a/R-rtracklayer.spec b/R-rtracklayer.spec
new file mode 100644
index 0000000..98949c9
--- /dev/null
+++ b/R-rtracklayer.spec
@@ -0,0 +1,68 @@
+%define		packname	rtracklayer
+
+Summary:	R interface to genome browsers and their annotation tracks
+Name:		R-%{packname}
+Version:	1.20.2
+Release:	1
+License:	Artistic 2.0
+Group:		Applications/Engineering
+Source0:	http://www.bioconductor.org/packages/release/bioc/src/contrib/%{packname}_%{version}.tar.gz
+# Source0-md5:	04d4c40bba7adb50721c6ad256c854a7
+Patch0:		bogus-deps.patch
+URL:		http://www.bioconductor.org/packages/2.12/bioc/html/rtracklayer.html
+BuildRequires:	R
+BuildRequires:	R-GenomicRanges >= 1.11.12
+BuildRequires:	R-BSgenome
+BuildRequires:	R-Rsamtools-devel >= 1.7.3
+BuildRequires:	texlive-latex
+Requires:	R
+Requires:	R-GenomicRanges >= 1.11.12
+Requires:	R-BSgenome
+Requires:	R-Rsamtools >= 1.7.3
+BuildRoot:	%{tmpdir}/%{name}-%{version}-root-%(id -u -n)
+
+%description
+Extensible framework for interacting with multiple genome browsers
+(currently UCSC built-in) and manipulating annotation tracks in
+various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig
+and 2bit built-in). The user may export/import tracks to/from
+the supported browsers, as well as query and modify the browser
+state, such as the current viewport.
+
+%prep
+%setup -q -c -n %{packname}
+%patch0 -p1
+
+%build
+
+%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)
+%doc %{_libdir}/R/library/%{packname}/DESCRIPTION
+%doc %{_libdir}/R/library/%{packname}/CITATION
+%doc %{_libdir}/R/library/%{packname}/NEWS
+%doc %{_libdir}/R/library/%{packname}/doc
+%doc %{_libdir}/R/library/%{packname}/html
+%doc %{_libdir}/R/library/%{packname}/notes
+%dir %{_libdir}/R/library/%{packname}
+%{_libdir}/R/library/%{packname}/Meta
+%{_libdir}/R/library/%{packname}/NAMESPACE
+%{_libdir}/R/library/%{packname}/INDEX
+%{_libdir}/R/library/%{packname}/R
+%{_libdir}/R/library/%{packname}/help
+%{_libdir}/R/library/%{packname}/data
+%{_libdir}/R/library/%{packname}/demo
+%{_libdir}/R/library/%{packname}/tests
+%{_libdir}/R/library/%{packname}/unitTests
+%{_libdir}/R/library/%{packname}/scripts
+%{_libdir}/R/library/%{packname}/extdata
+%dir %{_libdir}/R/library/%{packname}/libs
+%attr(755,root,root) %{_libdir}/R/library/%{packname}/libs/%{packname}.so
diff --git a/bogus-deps.patch b/bogus-deps.patch
new file mode 100644
index 0000000..9bf0a49
--- /dev/null
+++ b/bogus-deps.patch
@@ -0,0 +1,21 @@
+--- rtracklayer/rtracklayer/DESCRIPTION~	2013-05-04 06:57:13.000000000 +0200
++++ rtracklayer/rtracklayer/DESCRIPTION	2013-05-10 14:37:24.622975892 +0200
+@@ -5,7 +5,7 @@
+ Depends: R (>= 2.10), methods, GenomicRanges (>= 1.11.12)
+ Imports: XML (>= 1.98-0), BiocGenerics (>= 0.1.0), IRanges (>=
+         1.15.37), GenomicRanges, Biostrings (>= 2.25.6), BSgenome (>=
+-        1.23.1), zlibbioc, RCurl (>= 1.4-2), Rsamtools (>= 1.7.3)
++        1.23.1), RCurl (>= 1.4-2), Rsamtools (>= 1.7.3)
+ Suggests: humanStemCell, microRNA (>= 1.1.1), genefilter, limma,
+         org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19,
+         TxDb.Hsapiens.UCSC.hg19.knownGene, hgu133plus2.db
+--- rtracklayer/rtracklayer/NAMESPACE~	2013-05-04 02:02:40.000000000 +0200
++++ rtracklayer/rtracklayer/NAMESPACE	2013-05-10 14:37:38.086445477 +0200
+@@ -1,7 +1,5 @@
+ useDynLib(rtracklayer, .registration = TRUE)
+ 
+-import(zlibbioc)
+-
+ importFrom("stats", offset)
+ 
+ importFrom("XML", getNodeSet, xmlValue, xmlAttrs, htmlTreeParse,
-- 
2.43.0