[packages/R-affy] - new, based on fedora

[baggins]

commit e2ac8a70d97efb41401aef1ba7efccdf924d05f1
Author: Jan Rękorajski <baggins at pld-linux.org>
Date:   Wed Oct 17 14:53:29 2012 +0200

    - new, based on fedora

 R-affy.spec      | 67 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 bogus-deps.patch | 34 ++++++++++++++++++++++++++++
 2 files changed, 101 insertions(+)
---
diff --git a/R-affy.spec b/R-affy.spec
new file mode 100644
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
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 at cbs.dtu.dk>, John Zhang
+ Maintainer: Rafael A. Irizarry <rafa at 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)
================================================================

---- gitweb:

http://git.pld-linux.org/gitweb.cgi/packages/R-affy.git/commitdiff/e2ac8a70d97efb41401aef1ba7efccdf924d05f1