From e2ac8a70d97efb41401aef1ba7efccdf924d05f1 Mon Sep 17 00:00:00 2001 From: =?utf8?q?Jan=20R=C4=99korajski?= Date: Wed, 17 Oct 2012 14:53:29 +0200 Subject: [PATCH 1/1] - new, based on fedora --- R-affy.spec | 67 ++++++++++++++++++++++++++++++++++++++++++++++++ bogus-deps.patch | 34 ++++++++++++++++++++++++ 2 files changed, 101 insertions(+) create mode 100644 R-affy.spec create mode 100644 bogus-deps.patch 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 , John Zhang + Maintainer: Rafael A. Irizarry + 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) -- 2.43.0