[med-svn] r15073 - trunk/packages/R/r-bioc-rsamtools/trunk/debian

[Andreas Tille]

Author: tille
Date: 2013-10-31 22:06:44 +0000 (Thu, 31 Oct 2013)
New Revision: 15073

Added:
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/README.source
Modified:
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/copyright
Log:
Add information about binary files in Rsamtools


Added: trunk/packages/R/r-bioc-rsamtools/trunk/debian/README.source
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/README.source	                        (rev 0)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/README.source	2013-10-31 22:06:44 UTC (rev 15073)
@@ -0,0 +1,59 @@
+Explanation for binary files inside source package according to
+  http://lists.debian.org/debian-devel/2013/09/msg00332.html
+
+Upstream has provided information about the binary files inside the
+source package.  The complete answer is recorded in the ITP bug log at
+  http://bugs.debian.org/728285
+
+
+Files: inst/extdata/CaffeineTxdb.sqlite
+Description: stale; removed in future versions.
+  sqlite tables derived from querying a public data base ('biomart.org').
+
+Files: inst/extdata/ex1.bam
+Description: 
+  ex1.sam is the text representation of ex1.bam (using Rsamtools::asBam at the 
+  time of file creation); ex1.bam.bai is an index created on ex1.bam (using 
+  Rsamtools::indexBam at the time of file creation). ex1.sam is derived from files 
+  originally distributed with 'samtools' software under an MIT license, see 
+  Rsamtools/LICENSE
+
+Files: inst/extdata/ex1.bcf
+  ex1.bcf is a file hand created in antiquity, and used in unit tests and man pages.
+
+
+Files: inst/extdata/example.gtf.gz.*:
+  example.gtf.gz is gz-compressed text file used in unit tests and man pages, hand 
+  curated from public data sources, the .tbi variant is an index 
+  (Rsamtools::indexTabix)
+
+Files: inst/extdata/example_from_SAM_Spec*:
+  This is a file useful to the developer, hand-curated from the SAM spec at
+    http://samtools.sourceforge.net/SAMv1.pdf
+  although SAM.pdf did not historically include version numbers so the precise 
+  origin is unknown.
+
+Files: inst/extdata/olaps.Rda
+  The script for creating this file is in the vignette Rsamtools-Overiew.Rnw
+ .
+ <<readGAlignmentsFromBam, eval=FALSE>>=
+ library(parallel)
+ options(srapply_fapply="parallel", mc.cores=detectCores())
+ olaps <- readGAlignmentsFromBam(bv)
+ @
+
+Files: inst/unitTests/cases/ex1.sam.gz
+  Except of the first two lines this is a copy of file
+    inst/extdata/ex1.sam
+
+Files: inst/unitTests/cases/ex1_*.bam*
+  Files are derived from file
+    inst/extdata/ex1.sam
+  and just used for verification of the correctness of
+  Rsamtools.
+
+Files: inst/unitTests/cases/plp_refskip.bam*
+  This is a hand-crafted file used in a unit test
+
+
+ -- Andreas Tille <tille at debian.org>  Fri, 25 Oct 2013 08:53:18 +0200

Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog	2013-10-30 21:41:47 UTC (rev 15072)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog	2013-10-31 22:06:44 UTC (rev 15073)
@@ -1,5 +1,5 @@
 r-bioc-rsamtools (1.12.4-1) UNRELEASED; urgency=low
 
-  * Initial release (closes: #???)
+  * Initial release (closes: #728285)
 
  -- Andreas Tille <tille at debian.org>  Wed, 04 Sep 2013 11:11:22 +0200

Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/copyright	2013-10-30 21:41:47 UTC (rev 15072)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/copyright	2013-10-31 22:06:44 UTC (rev 15073)
@@ -1,6 +1,6 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: Rsamtools
-Upstream-Contact: Bioconductor Package Maintainer <maintainer at bioconductor.org> 
+Upstream-Contact: Bioconductor Package Maintainer <maintainer at bioconductor.org> 
 Source: http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html
 
 Files: *