diff --git a/.gitignore b/.gitignore index 10e142f..b6e0c96 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ /rtracklayer_1.14.1.tar.gz /rtracklayer_1.18.2.tar.gz +/rtracklayer_1.20.0.tar.gz 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 6f27149..7a6fc27 100644 --- a/R-rtracklayer.spec +++ b/R-rtracklayer.spec @@ -1,7 +1,7 @@ %global packname rtracklayer Name: R-%{packname} -Version: 1.18.2 +Version: 1.20.0 Release: 1%{?dist} Summary: R interface to genome browsers and their annotation tracks Group: Applications/Productivity @@ -9,11 +9,11 @@ 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-1.18.2-no-zlibbioc.patch -Requires: R-core >= 2.10.0, texlive-latex, R-methods, R-RCurl >= 1.4.2, R-XML >= 1.98.0 +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 >= 2.10.0, R-methods, R-RCurl >= 1.4.2, R-XML >= 1.98.0 +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 @@ -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} . @@ -60,6 +60,7 @@ 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/ @@ -69,6 +70,9 @@ rm -rf %{buildroot}%{_libdir}/R/library/%{packname}/tests/quickload/T_species_Oc %{_libdir}/R/library/%{packname}/unitTests/ %changelog +* Thu Apr 11 2013 Tom Callaway - 1.20.0-1 +- update to 1.20.0 + * Fri Feb 22 2013 Tom Callaway - 1.18.2-1 - update to 1.18.2 diff --git a/sources b/sources index bcda77f..52a9302 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -fc691eb429941ca2cd4fa41e2260ba03 rtracklayer_1.18.2.tar.gz +c071febb7cee79fad7436f2762e93bc9 rtracklayer_1.20.0.tar.gz