[R-rtracklayer/f15] initial commit
Tom Callaway
spot at fedoraproject.org
Mon Nov 14 20:35:48 UTC 2011
commit 91e934207bf1720a97b2ed8981d43f3cffd6e1a2
Author: Tom "spot" Callaway <tcallawa at redhat.com>
Date: Mon Nov 14 15:35:45 2011 -0500
initial commit
R-rtracklayer-1.14.1-no-zlibbioc.patch | 24 +++++++
R-rtracklayer.spec | 73 ++++++++++++++++++++++
rtracklayer_jimkent_license.txt | 103 ++++++++++++++++++++++++++++++++
sources | 1 +
4 files changed, 201 insertions(+), 0 deletions(-)
---
diff --git a/R-rtracklayer-1.14.1-no-zlibbioc.patch b/R-rtracklayer-1.14.1-no-zlibbioc.patch
new file mode 100644
index 0000000..4e67d3e
--- /dev/null
+++ b/R-rtracklayer-1.14.1-no-zlibbioc.patch
@@ -0,0 +1,24 @@
+diff -up rtracklayer/DESCRIPTION.BAD rtracklayer/DESCRIPTION
+--- rtracklayer/DESCRIPTION.BAD 2011-11-11 08:54:26.799176456 -0500
++++ rtracklayer/DESCRIPTION 2011-11-11 08:54:41.422995212 -0500
+@@ -4,8 +4,7 @@ Version: 1.14.1
+ Author: Michael Lawrence, Vince Carey, Robert Gentleman
+ Depends: R (>= 2.7.0), methods, RCurl (>= 1.4-2)
+ Imports: XML (>= 1.98-0), IRanges (>= 1.11.34), GenomicRanges (>=
+- 1.5.42), Biostrings (>= 2.21.12), BSgenome (>= 1.15.17),
+- zlibbioc
++ 1.5.42), Biostrings (>= 2.21.12), BSgenome (>= 1.15.17)
+ Suggests: humanStemCell, microRNA (>= 1.1.1), genefilter, limma,
+ org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19,
+ TxDb.Hsapiens.UCSC.hg19.knownGene, hgu133plus2.db, Rsamtools
+diff -up rtracklayer/NAMESPACE.BAD rtracklayer/NAMESPACE
+--- rtracklayer/NAMESPACE.BAD 2011-11-11 08:57:40.729772933 -0500
++++ rtracklayer/NAMESPACE 2011-11-11 08:57:44.044731847 -0500
+@@ -1,7 +1,5 @@
+ useDynLib(rtracklayer, .registration = TRUE)
+
+-import(zlibbioc)
+-
+ import(RCurl, XML)
+
+ importFrom("stats", offset)
diff --git a/R-rtracklayer.spec b/R-rtracklayer.spec
new file mode 100644
index 0000000..45c20b9
--- /dev/null
+++ b/R-rtracklayer.spec
@@ -0,0 +1,73 @@
+%global packname rtracklayer
+
+Name: R-%{packname}
+Version: 1.14.1
+Release: 2%{?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
+
+%description
+Extensible framework for interacting with multiple genome browsers (currently
+UCSC built-in) and manipulating annotation tracks in various formats
+(currently GFF, BED, bedGraph, BED15, WIG, and BigWig built-in). The user may
+export/import tracks to/from the supported browsers, as well as query and
+modify the browser state, such as the current viewport.
+
+%prep
+%setup -c -q -n %{packname}
+%patch0 -p0 -b .no-zlibbioc
+# This email confirms that we have permission to use the Jim Kent
+# copyrighted files under the BSD license.
+cp %{SOURCE1} .
+
+%build
+
+%install
+mkdir -p %{buildroot}%{_libdir}/R/library
+%{_bindir}/R CMD INSTALL %{packname} -l %{buildroot}%{_libdir}/R/library
+# Clean up in advance of check
+test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)
+rm -rf %{buildroot}%{_libdir}/R/library/R.css
+
+# Zero file
+rm -rf %{buildroot}%{_libdir}/R/library/%{packname}/tests/quickload/T_species_Oct_2011/bedGraphData.bw
+
+%check
+# All sorts of missing Suggests prevents this from working.
+# %%{_bindir}/R CMD check %%{packname}
+
+%files
+%dir %{_libdir}/R/library/%{packname}
+%doc %{_libdir}/R/library/%{packname}/html
+%doc %{_libdir}/R/library/%{packname}/DESCRIPTION
+%doc %{_libdir}/R/library/%{packname}/doc/
+%doc rtracklayer_jimkent_license.txt
+%{_libdir}/R/library/%{packname}/INDEX
+%{_libdir}/R/library/%{packname}/NAMESPACE
+%{_libdir}/R/library/%{packname}/Meta
+%{_libdir}/R/library/%{packname}/R
+%{_libdir}/R/library/%{packname}/data/
+%{_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/
+
+%changelog
+* Mon Nov 14 2011 Tom Callaway <spot at fedoraproject.org> 1.14.1-2
+- update licensing with clarification from Jim Kent
+
+* Thu Nov 10 2011 Tom "spot" Callaway <tcallawa at redhat.com> 1.14.1-1
+- initial package for Fedora
diff --git a/rtracklayer_jimkent_license.txt b/rtracklayer_jimkent_license.txt
new file mode 100644
index 0000000..ea2344e
--- /dev/null
+++ b/rtracklayer_jimkent_license.txt
@@ -0,0 +1,103 @@
+Return-Path: kent at soe.ucsc.edu
+Received: from zmta02.collab.prod.int.phx2.redhat.com (LHLO
+ zmta02.collab.prod.int.phx2.redhat.com) (10.5.5.32) by
+ mail04.corp.redhat.com with LMTP; Sat, 12 Nov 2011 13:32:07 -0500 (EST)
+Received: from localhost (localhost.localdomain [127.0.0.1])
+ by zmta02.collab.prod.int.phx2.redhat.com (Postfix) with ESMTP id BE818129759
+ for <tcallawa at redhat.com>; Sat, 12 Nov 2011 13:32:07 -0500 (EST)
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+Content-Type: text/plain; charset=us-ascii
+Mime-Version: 1.0 (Apple Message framework v1084)
+Subject: Re: license for code in rtracklayer
+From: Jim Kent <kent at soe.ucsc.edu>
+In-Reply-To: <4EBDDC5B.2080603 at redhat.com>
+Date: Sat, 12 Nov 2011 10:32:06 -0800
+Content-Transfer-Encoding: quoted-printable
+Message-Id: <0490A007-6BAF-4B4E-970F-80E88CA9D24E at soe.ucsc.edu>
+References: <4EBD6A41.5070209 at redhat.com> <AA059DA7-4D44-4A57-B0EC-198A84F179FF at soe.ucsc.edu> <4EBDDC5B.2080603 at redhat.com>
+To: Tom Callaway <tcallawa at redhat.com>
+X-RedHat-Spam-Score: -1.201 (RP_MATCHES_RCVD)
+X-Scanned-By: MIMEDefang 2.67 on 10.5.11.12
+X-Scanned-By: MIMEDefang 2.68 on 10.5.110.18
+
+ps - if you want to stick the original BSD on to simplify your life =
+that's ok with me, but we don't actually require
+attribution, or the disclaimer.
+
+On Nov 11, 2011, at 6:39 PM, Tom Callaway wrote:
+
+> On 11/11/2011 09:14 PM, Jim Kent wrote:
+>> Could you give me the name of the source code modules you are =
+concerned about?
+>=20
+> Within the rtracklayer code, there is a directory under src labeled
+> "ucsc". The following files have your copyright statement:
+>=20
+> bits.c
+> bits.h
+> cheapcgi.h
+> common.c
+> common.h
+> dlist.c
+> dlist.h
+> dnaseq.c
+> dnaseq.h
+> dnautil.c
+> dnautil.h
+> dystring.c
+> dystring.h
+> errabort.c
+> errabort.h
+> hash.c
+> hash.h
+> hmmstats.c
+> hmmstats.h
+> htmshell.h
+> linefile.c
+> linefile.h
+> localmem.c
+> localmem.h
+> memalloc.c
+> memalloc.h
+> net.c
+> net.h
+> obscure.c
+> obscure.h
+> options.h
+> osunix.c
+> oswin9x.c
+> portable.h
+> portimpl.h
+> sig.h
+> sqlNum.c
+> sqlNum.h
+> wildcmp.c
+>=20
+> The rtracklayer source can be found here:
+> =
+http://www.bioconductor.org/packages/release/bioc/html/rtracklayer.html
+>=20
+> Thanks,
+>=20
+> ~tom
+>=20
+> =3D=3D
+> Fedora Project
+
diff --git a/sources b/sources
index e69de29..45a315f 100644
--- a/sources
+++ b/sources
@@ -0,0 +1 @@
+130af70245801e131b0ebbda8fd83fde rtracklayer_1.14.1.tar.gz
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