[med-svn] r14880 - trunk/packages/R/r-bioc-genomicranges/trunk/debian

[Andreas Tille]

Author: tille
Date: 2013-10-18 08:34:54 +0000 (Fri, 18 Oct 2013)
New Revision: 14880

Added:
   trunk/packages/R/r-bioc-genomicranges/trunk/debian/README.source
Modified:
   trunk/packages/R/r-bioc-genomicranges/trunk/debian/changelog
Log:
Explain rationale for binary files in source package


Added: trunk/packages/R/r-bioc-genomicranges/trunk/debian/README.source
===================================================================
--- trunk/packages/R/r-bioc-genomicranges/trunk/debian/README.source	                        (rev 0)
+++ trunk/packages/R/r-bioc-genomicranges/trunk/debian/README.source	2013-10-18 08:34:54 UTC (rev 14880)
@@ -0,0 +1,33 @@
+Explanation for binary files inside source package according to
+  http://lists.debian.org/debian-devel/2013/09/msg00332.html
+
+Here is an extract of the response from upstream about
+  Files: GenomicRanges/inst/doc/precomputed_results/*.rda
+the full response can be read in the log of the ITP bug #721801.
+
+From: Hervé Pagès <hpages at fhcrc.org>
+ The objects in precomputed_results can be generated by running the
+ code in the OverlapEncodings.Rnw vignette. However running this code
+ takes a long time and would make 'R CMD check' take too much time to
+ complete, making the maintenance of the package very impractical.
+ .
+ So the trick is to have some of the more time-consuming code chunks
+ in the vignette set to eval=FALSE, and to load the precomputed results
+ instead. The loading is performed in a hidden code chunk and it also
+ performs some sanity checks to verify that the precomputed object that
+ was just loaded is in sync with other objects generated earlier in the
+ vignette.
+ 
+From: Martin Morgan <mtmorgan at fhcrc.org>
+ For precomputed_results above, it looks like these could be generated by a 
+ script, but the specific results depend on a web service query and the web 
+ service changes from time to time. So the script will become out-of-date, 
+ creating data that are no longer consistent with the illustrative puruposes of 
+ the vignette. Also, the time cost of generating data is not consistent  with our 
+ (nightly) build process; we will not generate this data on the fly, and it would 
+ be a mistake for your release process to generate data different from the data 
+ used in our release. These (expense of computation, consistency of external data 
+ sources) are typical reasons.
+
+ -- Andreas Tille <tille at debian.org>  Fri, 18 Oct 2013 10:34:02 +0200
+

Modified: trunk/packages/R/r-bioc-genomicranges/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-genomicranges/trunk/debian/changelog	2013-10-18 08:23:30 UTC (rev 14879)
+++ trunk/packages/R/r-bioc-genomicranges/trunk/debian/changelog	2013-10-18 08:34:54 UTC (rev 14880)
@@ -1,5 +1,6 @@
 r-bioc-genomicranges (1.12.4-1) unstable; urgency=low
 
   * Initial release (closes: #721801)
+  * Added README.source to document binary files in source tarball
 
  -- Andreas Tille <tille at debian.org>  Fri, 23 Aug 2013 09:23:02 +0200