[R-rtracklayer/f18] R3

Mon Apr 22 17:10:38 UTC 2013

commit a6c57837b449481d3cf53ad2014a81eda7ba1404
Author: Tom Callaway <spot at fedoraproject.org>
Date:   Mon Apr 22 13:09:59 2013 -0400

    R3

 R-rtracklayer-1.20.0-no-zlibbioc.patch |   23 ++++++++++++++++++++++
 R-rtracklayer.spec                     |   33 ++++++++++++++++++++++---------
 sources                                |    2 +-
 3 files changed, 47 insertions(+), 11 deletions(-)
---

diff --git a/R-rtracklayer-1.20.0-no-zlibbioc.patch b/R-rtracklayer-1.20.0-no-zlibbioc.patch
new file mode 100644
index 0000000..26df6d5
--- /dev/null
+++ b/R-rtracklayer-1.20.0-no-zlibbioc.patch
@@ -0,0 +1,23 @@
+diff -up rtracklayer/rtracklayer/DESCRIPTION.no-zlibbioc rtracklayer/rtracklayer/DESCRIPTION
+--- rtracklayer/rtracklayer/DESCRIPTION.no-zlibbioc	2013-04-04 03:25:50.000000000 -0400
++++ rtracklayer/rtracklayer/DESCRIPTION	2013-04-11 15:02:37.849007738 -0400
+@@ -5,7 +5,7 @@ Author: Michael Lawrence, Vince Carey, R
+ 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
+diff -up rtracklayer/rtracklayer/NAMESPACE.no-zlibbioc rtracklayer/rtracklayer/NAMESPACE
+--- rtracklayer/rtracklayer/NAMESPACE.no-zlibbioc	2013-04-03 18:49:38.000000000 -0400
++++ rtracklayer/rtracklayer/NAMESPACE	2013-04-11 15:02:14.181008584 -0400
+@@ -1,7 +1,5 @@
+ useDynLib(rtracklayer, .registration = TRUE)
+ 
+-import(zlibbioc)
+-
+ importFrom("stats", offset)
+ 
+ importFrom("XML", getNodeSet, xmlValue, xmlAttrs, htmlTreeParse,
diff --git a/R-rtracklayer.spec b/R-rtracklayer.spec
index f1c0344..7a6fc27 100644
--- a/R-rtracklayer.spec
+++ b/R-rtracklayer.spec
@@ -1,21 +1,21 @@
 %global packname  rtracklayer
 
 Name:             R-%{packname}
-Version:          1.14.1
-Release:          4%{?dist}
+Version:          1.20.0
+Release:          1%{?dist}
 Summary:          R interface to genome browsers and their annotation tracks
 Group:            Applications/Productivity
 License:          Artistic 2.0 and BSD
 URL:              http://www.bioconductor.org/packages/release/bioc/html/rtracklayer.html
 Source0:          http://www.bioconductor.org/packages/2.9/bioc/src/contrib/%{packname}_%{version}.tar.gz
 Source1:          rtracklayer_jimkent_license.txt
-Patch0:           R-rtracklayer-1.14.1-no-zlibbioc.patch
-Requires:         R-core >= 2.7.0, texlive-latex, R-methods, R-RCurl >= 1.4.2, R-XML >= 1.98.0 
-Requires:         R-IRanges >= 1.11.34, R-GenomicRanges >= 1.5.42, R-Biostrings >= 2.21.12 
-Requires:         R-BSgenome >= 1.15.17
-BuildRequires:    R-devel >= 2.7.0, R-methods, R-RCurl >= 1.4.2, R-XML >= 1.98.0
-BuildRequires:    R-IRanges-devel >= 1.11.34, R-GenomicRanges >= 1.5.42, R-Biostrings-devel >= 2.21.12
-BuildRequires:    R-BSgenome >= 1.15.17, zlib-devel
+Patch0:           R-rtracklayer-1.20.0-no-zlibbioc.patch
+Requires:         R-core >= 3.0.0, texlive-latex, R-methods, R-RCurl >= 1.4.2, R-XML >= 1.98.0 
+Requires:         R-IRanges >= 1.11.34, R-GenomicRanges >= 1.9.6, R-Biostrings >= 2.21.12 
+Requires:         R-BSgenome >= 1.15.17, R-Rsamtools >= 1.7.3
+BuildRequires:    R-devel >= 3.0.0, R-methods, R-RCurl >= 1.4.2, R-XML >= 1.98.0
+BuildRequires:    R-IRanges-devel >= 1.11.34, R-GenomicRanges >= 1.9.6, R-Biostrings-devel >= 2.21.12
+BuildRequires:    R-BSgenome >= 1.15.17, R-Rsamtools-devel >= 1.7.3, zlib-devel
 
 %description
 Extensible framework for interacting with multiple genome browsers (currently 
@@ -26,7 +26,7 @@ modify the browser state, such as the current viewport.
 
 %prep
 %setup -c -q -n %{packname}
-%patch0 -p0 -b .no-zlibbioc
+%patch0 -p1 -b .no-zlibbioc
 # This email confirms that we have permission to use the Jim Kent 
 # copyrighted files under the BSD license.
 cp %{SOURCE1} .
@@ -50,7 +50,9 @@ rm -rf %{buildroot}%{_libdir}/R/library/%{packname}/tests/quickload/T_species_Oc
 %files
 %dir %{_libdir}/R/library/%{packname}
 %doc %{_libdir}/R/library/%{packname}/html
+%doc %{_libdir}/R/library/%{packname}/CITATION
 %doc %{_libdir}/R/library/%{packname}/DESCRIPTION
+%doc %{_libdir}/R/library/%{packname}/NEWS
 %doc %{_libdir}/R/library/%{packname}/doc/
 %doc rtracklayer_jimkent_license.txt
 %{_libdir}/R/library/%{packname}/INDEX
@@ -58,14 +60,25 @@ rm -rf %{buildroot}%{_libdir}/R/library/%{packname}/tests/quickload/T_species_Oc
 %{_libdir}/R/library/%{packname}/Meta
 %{_libdir}/R/library/%{packname}/R
 %{_libdir}/R/library/%{packname}/data/
+%{_libdir}/R/library/%{packname}/extdata/
 %{_libdir}/R/library/%{packname}/demo/
 %{_libdir}/R/library/%{packname}/help
 %{_libdir}/R/library/%{packname}/libs/
 %{_libdir}/R/library/%{packname}/notes/
 %{_libdir}/R/library/%{packname}/scripts/
 %{_libdir}/R/library/%{packname}/tests/
+%{_libdir}/R/library/%{packname}/unitTests/
 
 %changelog
+* Thu Apr 11 2013 Tom Callaway <spot at fedoraproject.org> - 1.20.0-1
+- update to 1.20.0
+
+* Fri Feb 22 2013 Tom Callaway <spot at fedoraproject.org> - 1.18.2-1
+- update to 1.18.2
+
+* Wed Feb 13 2013 Fedora Release Engineering <rel-eng at lists.fedoraproject.org> - 1.14.1-5
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
+
 * Wed Jul 18 2012 Fedora Release Engineering <rel-eng at lists.fedoraproject.org> - 1.14.1-4
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild
 
diff --git a/sources b/sources
index 45a315f..52a9302 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-130af70245801e131b0ebbda8fd83fde  rtracklayer_1.14.1.tar.gz
+c071febb7cee79fad7436f2762e93bc9  rtracklayer_1.20.0.tar.gz
