[med-svn] r14815 - in trunk/packages/R: r-bioc-altcdfenvs/trunk/debian r-bioc-biovizbase/trunk/debian r-bioc-bsgenome/trunk/debian r-bioc-genomicfeatures/trunk/debian r-bioc-gviz/trunk/debian r-bioc-rsamtools/trunk/debian r-bioc-rtracklayer/trunk/debian
Andreas Tille
tille at alioth.debian.org
Fri Oct 11 17:41:35 UTC 2013
Author: tille
Date: 2013-10-11 17:41:35 +0000 (Fri, 11 Oct 2013)
New Revision: 14815
Modified:
trunk/packages/R/r-bioc-altcdfenvs/trunk/debian/changelog
trunk/packages/R/r-bioc-altcdfenvs/trunk/debian/control
trunk/packages/R/r-bioc-biovizbase/trunk/debian/changelog
trunk/packages/R/r-bioc-biovizbase/trunk/debian/control
trunk/packages/R/r-bioc-bsgenome/trunk/debian/changelog
trunk/packages/R/r-bioc-bsgenome/trunk/debian/control
trunk/packages/R/r-bioc-bsgenome/trunk/debian/copyright
trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/changelog
trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/control
trunk/packages/R/r-bioc-gviz/trunk/debian/changelog
trunk/packages/R/r-bioc-gviz/trunk/debian/control
trunk/packages/R/r-bioc-gviz/trunk/debian/copyright
trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog
trunk/packages/R/r-bioc-rsamtools/trunk/debian/control
trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog
trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control
Log:
r-bioc-biostrings is available in unstable
Modified: trunk/packages/R/r-bioc-altcdfenvs/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-altcdfenvs/trunk/debian/changelog 2013-10-11 17:32:58 UTC (rev 14814)
+++ trunk/packages/R/r-bioc-altcdfenvs/trunk/debian/changelog 2013-10-11 17:41:35 UTC (rev 14815)
@@ -4,7 +4,6 @@
TODO: Dependencies:
affy: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-affy/trunk/ (uploaded to new)
makecdfenv: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-makecdfenv/trunk/
- Biostrings: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-biostrings/trunk (uploaded to new)
hypergraph: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-hypergraph/trunk (uploaded to new)
-- Andreas Tille <tille at debian.org> Fri, 23 Aug 2013 09:23:02 +0200
Modified: trunk/packages/R/r-bioc-altcdfenvs/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-altcdfenvs/trunk/debian/control 2013-10-11 17:32:58 UTC (rev 14814)
+++ trunk/packages/R/r-bioc-altcdfenvs/trunk/debian/control 2013-10-11 17:41:35 UTC (rev 14815)
@@ -7,7 +7,8 @@
cdbs,
r-base-dev,
r-bioc-biobase,
- r-bioc-biocgenerics
+ r-bioc-biocgenerics,
+ r-bioc-biostrings
Standards-Version: 3.9.4
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-altcdfenvs/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-altcdfenvs/trunk/
@@ -18,7 +19,8 @@
Depends: ${R:Depends},
${misc:Depends},
r-bioc-biobase,
- r-bioc-biocgenerics
+ r-bioc-biocgenerics,
+ r-bioc-biostrings
Description: BioConductor alternative CDF environments
This BioConductor module provides alternative CDF environments (aka
probeset mappings) which are Convenience data structures and functions
Modified: trunk/packages/R/r-bioc-biovizbase/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-biovizbase/trunk/debian/changelog 2013-10-11 17:32:58 UTC (rev 14814)
+++ trunk/packages/R/r-bioc-biovizbase/trunk/debian/changelog 2013-10-11 17:41:35 UTC (rev 14815)
@@ -3,7 +3,6 @@
* Initial release (closes: #???)
TODO: Dependencies
GenomicRanges: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicranges/trunk/ (uploaded to new)
- Biostrings: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-biostrings/trunk/ (uploaded to new)
Rsamtools: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rsamtools/trunk/
GenomicFeatures: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicfeatures/trunk/
Modified: trunk/packages/R/r-bioc-biovizbase/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-biovizbase/trunk/debian/control 2013-10-11 17:32:58 UTC (rev 14814)
+++ trunk/packages/R/r-bioc-biovizbase/trunk/debian/control 2013-10-11 17:41:35 UTC (rev 14815)
@@ -11,7 +11,8 @@
r-cran-rcolorbrewer,
r-cran-scales,
r-bioc-biobase,
- r-bioc-iranges
+ r-bioc-iranges,
+ r-bioc-biostrings
Standards-Version: 3.9.4
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-biovizbase/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-biovizbase/trunk/
@@ -26,7 +27,8 @@
r-cran-rcolorbrewer,
r-cran-scales,
r-bioc-biobase,
- r-bioc-iranges
+ r-bioc-iranges,
+ r-bioc-biostrings
Description: GNU R basic graphic utilities for visualization of genomic data
The biovizBase package is designed to provide a set of utilities, color
schemes and conventions for genomic data. It serves as the base for
Modified: trunk/packages/R/r-bioc-bsgenome/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-bsgenome/trunk/debian/changelog 2013-10-11 17:32:58 UTC (rev 14814)
+++ trunk/packages/R/r-bioc-bsgenome/trunk/debian/changelog 2013-10-11 17:41:35 UTC (rev 14815)
@@ -3,6 +3,5 @@
* Initial release (closes: #?????)
TODO: Dependencies
GenomicRanges: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicranges/trunk/ (uploaded to new)
- Biostrings: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-biostrings/trunk/ (uploaded to new)
-- Andreas Tille <tille at debian.org> Fri, 23 Aug 2013 09:23:02 +0200
Modified: trunk/packages/R/r-bioc-bsgenome/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-bsgenome/trunk/debian/control 2013-10-11 17:32:58 UTC (rev 14814)
+++ trunk/packages/R/r-bioc-bsgenome/trunk/debian/control 2013-10-11 17:41:35 UTC (rev 14815)
@@ -6,18 +6,20 @@
Build-Depends: debhelper (>= 9),
cdbs,
r-base-dev,
- r-bioc-iranges
+ r-bioc-iranges,
+ r-bioc-biostrings
Standards-Version: 3.9.4
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-bsgenome/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-bsgenome/trunk/
-Homepage: http://bioconductor.org/packages/2.12/bioc/html/bsgenome.html
+Homepage: http://bioconductor.org/packages/release/bioc/html/BSgenome.html
Package: r-bioc-bsgenome
Architecture: any
Depends: ${R:Depends},
${shlibs:Depends},
${misc:Depends},
- r-bioc-iranges
+ r-bioc-iranges,
+ r-bioc-biostrings
Description: BioConductor infrastructure for Biostrings-based genome data packages
This BioConductor module provides some basic infrastructure for
Biostrings-based genome data packages.
Modified: trunk/packages/R/r-bioc-bsgenome/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-bsgenome/trunk/debian/copyright 2013-10-11 17:32:58 UTC (rev 14814)
+++ trunk/packages/R/r-bioc-bsgenome/trunk/debian/copyright 2013-10-11 17:41:35 UTC (rev 14815)
@@ -1,7 +1,7 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: BSgenome
Upstream-Contact: H. Pages <hpages at fhcrc.org>
-Source: http://www.bioconductor.org/packages/2.12/bioc/html/BSgenome.html
+Source: http://bioconductor.org/packages/release/bioc/html/BSgenome.html
Files: *
Copyright: © 2006-2013 Herve Pages
Modified: trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/changelog 2013-10-11 17:32:58 UTC (rev 14814)
+++ trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/changelog 2013-10-11 17:41:35 UTC (rev 14815)
@@ -2,7 +2,6 @@
* Initial release (closes: #???)
TODO: Dependencies
- Biostrings: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-biostrings/trunk (uploaded to new)
GenomicRanges: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicranges/trunk/ (uploaded to new)
rtracklayer: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rtracklayer/trunk/
biomaRt: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-biomart/trunk/
Modified: trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/control 2013-10-11 17:32:58 UTC (rev 14814)
+++ trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/control 2013-10-11 17:41:35 UTC (rev 14815)
@@ -9,7 +9,8 @@
r-cran-dbi,
r-cran-rsqlite,
r-bioc-biobase,
- r-bioc-iranges
+ r-bioc-iranges,
+ r-bioc-biostrings
Standards-Version: 3.9.4
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-genomicfeatures/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicfeatures/trunk/
@@ -21,7 +22,8 @@
${misc:Depends},
r-cran-rsqlite,
r-bioc-biobase,
- r-bioc-iranges
+ r-bioc-iranges,
+ r-bioc-biostrings
Description: GNU R tools for making and manipulating transcript centric annotations
A set of tools and methods for making and manipulating transcript
centric annotations. With these tools the user can easily download the
Modified: trunk/packages/R/r-bioc-gviz/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-gviz/trunk/debian/changelog 2013-10-11 17:32:58 UTC (rev 14814)
+++ trunk/packages/R/r-bioc-gviz/trunk/debian/changelog 2013-10-11 17:41:35 UTC (rev 14815)
@@ -4,7 +4,6 @@
The following preconditions are needed but missing in Debian
rtracklayer: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rtracklayer/trunk/
GenomicRanges: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicranges/trunk/ (uploaded to new)
- Biostrings: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-biostrings/trunk/ (uploaded to new)
BSgenome: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-bsgenome/trunk/
Rsamtools: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rsamtools/trunk/
biomaRt: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-biomart/trunk/
Modified: trunk/packages/R/r-bioc-gviz/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-gviz/trunk/debian/control 2013-10-11 17:32:58 UTC (rev 14814)
+++ trunk/packages/R/r-bioc-gviz/trunk/debian/control 2013-10-11 17:41:35 UTC (rev 14815)
@@ -11,11 +11,12 @@
r-bioc-biobase,
r-bioc-biocgenerics,
r-bioc-iranges,
- r-bioc-annotationdbi
+ r-bioc-annotationdbi,
+ r-bioc-biostrings
Standards-Version: 3.9.4
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-gviz/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-gviz/trunk/
-Homepage: http://bioconductor.org/packages/2.12/bioc/html/gviz.html
+Homepage: http://bioconductor.org/packages/release/bioc/html/Gviz.html
Package: r-bioc-gviz
Architecture: all
@@ -26,7 +27,8 @@
r-bioc-biobase,
r-bioc-biocgenerics,
r-bioc-iranges,
- r-bioc-annotationdbi
+ r-bioc-annotationdbi,
+ r-bioc-biostrings
Description: Plotting data and annotation information along genomic coordinates
Genomic data analyses requires integrated visualization of known
genomic information and new experimental data. Gviz uses the biomaRt and
Modified: trunk/packages/R/r-bioc-gviz/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-gviz/trunk/debian/copyright 2013-10-11 17:32:58 UTC (rev 14814)
+++ trunk/packages/R/r-bioc-gviz/trunk/debian/copyright 2013-10-11 17:41:35 UTC (rev 14815)
@@ -1,7 +1,7 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: Gviz
Upstream-Contact: Florian Hahne <florian.hahne at novartis.com>
-Source: http://www.bioconductor.org/packages/2.12/bioc/html/Gviz.html
+Source: http://bioconductor.org/packages/release/bioc/html/Gviz.html
Files: *
Copyright: © 2006-2013 Florian Hahne, Steffen Durinck,
Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog 2013-10-11 17:32:58 UTC (rev 14814)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog 2013-10-11 17:41:35 UTC (rev 14815)
@@ -2,7 +2,6 @@
* Initial release (closes: #???)
TODO: Depends:
- Biostrings: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-biostrings/trunk/ (uploaded to new)
GenomicRanges: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicranges/trunk/ (uploaded to new)
-- Andreas Tille <tille at debian.org> Wed, 04 Sep 2013 11:11:22 +0200
Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/control 2013-10-11 17:32:58 UTC (rev 14814)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/control 2013-10-11 17:41:35 UTC (rev 14815)
@@ -8,7 +8,8 @@
r-base-dev,
r-cran-bitops,
r-bioc-biocgenerics,
- r-bioc-iranges
+ r-bioc-iranges,
+ r-bioc-biostrings
Standards-Version: 3.9.4
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-rsamtools/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rsamtools/trunk/
@@ -20,7 +21,8 @@
${misc:Depends},
r-cran-bitops,
r-bioc-biocgenerics,
- r-bioc-iranges
+ r-bioc-iranges,
+ r-bioc-biostrings
Description: GNU R binary alignment (BAM), variant call (BCF), or tabix file import
This package provides an interface to the 'samtools', 'bcftools', and
'tabix' utilities for manipulating SAM (Sequence Alignment / Map),
Modified: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog 2013-10-11 17:32:58 UTC (rev 14814)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog 2013-10-11 17:41:35 UTC (rev 14815)
@@ -3,7 +3,6 @@
* Initial release (closes: #???).
The following preconditions are needed but missing in Debian
GenomicRanges: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicranges/trunk/ (uploaded to new)
- Biostrings: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-biostrings/trunk/ (uploaded to new)
BSgenome: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-bsgenome/trunk/
RCurl: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-rcurl/trunk/ (Uploaded to new)
Rsamtools: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rsamtools/trunk/
Modified: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control 2013-10-11 17:32:58 UTC (rev 14814)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control 2013-10-11 17:41:35 UTC (rev 14815)
@@ -8,7 +8,8 @@
r-base-dev,
r-cran-xml,
r-bioc-biocgenerics,
- r-bioc-iranges
+ r-bioc-iranges,
+ r-bioc-biostrings
Standards-Version: 3.9.4
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-rtracklayer/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rtracklayer/trunk/
@@ -20,7 +21,8 @@
${misc:Depends},
r-cran-xml,
r-bioc-biocgenerics,
- r-bioc-iranges
+ r-bioc-iranges,
+ r-bioc-biostrings
Description: GNU R interface to genome browsers and their annotation tracks
Extensible framework for interacting with multiple genome browsers
(currently UCSC built-in) and manipulating annotation tracks in various
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