- new, based on fedora

diff --git a/R-affy.spec b/R-affy.spec
new file mode 100644 (file)
index 0000000..f3f3a57
--- /dev/null
+++ b/R-affy.spec
@@ -0,0 +1,67 @@
+%define                packname        affy
+
+Summary:       Methods for Affymetrix Oligonucleotide Arrays
+Name:          R-%{packname}
+Version:       1.36.0
+Release:       1
+License:       LGPL v2+
+Group:         Applications/Engineering
+Source0:       http://bioconductor.org/packages/release/bioc/src/contrib/%{packname}_%{version}.tar.gz
+# Source0-md5: 92dbab4b79c79f07c2db8ed3a40b9a8f
+Patch0:                bogus-deps.patch
+URL:           http://bioconductor.org/packages/release/bioc/html/%{packname}.html
+BuildRequires: R
+BuildRequires: R-Biobase
+BuildRequires: R-BiocGenerics
+BuildRequires: R-affyio
+BuildRequires: R-preprocessCore-devel
+BuildRequires: R-tkWidgets
+BuildRequires: texlive-latex
+BuildRequires: zlib-devel
+Requires:      R
+Requires:      R-Biobase
+Requires:      R-BiocGenerics
+Requires:      R-affyio
+Requires:      R-preprocessCore
+Suggests:      R-tkWidgets
+BuildRoot:     %{tmpdir}/%{name}-%{version}-root-%(id -u -n)
+
+%description
+The package contains functions for exploratory oligonucleotide array
+analysis.
+
+The dependancy to tkWidgets only concerns few convenience functions.
+'affy' is fully functional without it.
+
+%prep
+%setup -q -c -n %{packname}
+%patch0 -p1
+
+%build
+
+%install
+rm -rf $RPM_BUILD_ROOT
+install -d $RPM_BUILD_ROOT%{_libdir}/R/library
+
+R CMD INSTALL %{packname} -l $RPM_BUILD_ROOT%{_libdir}/R/library
+
+%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}/NEWS
+%doc %{_libdir}/R/library/%{packname}/CITATION
+%{_libdir}/R/library/%{packname}/INDEX
+%{_libdir}/R/library/%{packname}/NAMESPACE
+%{_libdir}/R/library/%{packname}/Meta
+%{_libdir}/R/library/%{packname}/R
+%{_libdir}/R/library/%{packname}/help
+%{_libdir}/R/library/%{packname}/data
+%{_libdir}/R/library/%{packname}/libs
+%{_libdir}/R/library/%{packname}/demo
+%{_libdir}/R/library/%{packname}/tests

diff --git a/bogus-deps.patch b/bogus-deps.patch
new file mode 100644 (file)
index 0000000..6d4fad5
--- /dev/null
+++ b/bogus-deps.patch
@@ -0,0 +1,34 @@
+--- affy/affy/DESCRIPTION.orig 2012-10-17 14:49:59.956583161 +0200
++++ affy/affy/DESCRIPTION      2012-10-17 14:51:23.219913557 +0200
+@@ -12,9 +12,8 @@
+         Christopher Workman <workman@cbs.dtu.dk>, John Zhang
+ Maintainer: Rafael A. Irizarry <rafa@jhu.edu>
+ Depends: R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5)
+-Imports: BiocGenerics, Biobase, affyio (>= 1.13.3), BiocInstaller,
+-        graphics, grDevices, methods, preprocessCore, stats, utils,
+-        zlibbioc
++Imports: BiocGenerics, Biobase, affyio (>= 1.13.3),
++        graphics, grDevices, methods, preprocessCore, stats, utils
+ Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools
+ LinkingTo: preprocessCore
+ Description: The package contains functions for exploratory
+--- affy/affy/NAMESPACE.orig   2012-10-02 00:51:49.000000000 +0200
++++ affy/affy/NAMESPACE        2012-10-17 14:50:58.656581090 +0200
+@@ -4,8 +4,6 @@
+ 
+ import(affyio)
+ 
+-import(zlibbioc)
+-
+ importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, MIAME,
+                   Versioned, VersionedBiobase, Versions)
+ 
+@@ -28,8 +26,6 @@
+            assayDataNew, multiassign, read.AnnotatedDataFrame,
+            read.MIAME, testBioCConnection)
+ 
+-importFrom(BiocInstaller, biocinstallRepos)
+-
+ importFrom(graphics, abline, axis, barplot, frame, hist,
+            lines, matplot, mtext, pairs, par, plot, points,
+            smoothScatter, text)