[med-svn] r21909 - in trunk/packages/R/r-bioc-rtracklayer/trunk/debian: . patches

Mon May 9 08:45:32 UTC 2016

Author: tille
Date: 2016-05-09 08:45:31 +0000 (Mon, 09 May 2016)
New Revision: 21909

Modified:
   trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog
   trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control
   trunk/packages/R/r-bioc-rtracklayer/trunk/debian/copyright
   trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/use_debian_packaged_zlib.patch
Log:
New upstream version, overworked d/copyright, asked on GitHub for clarification of license


Modified: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog
===================================================================

--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog	2016-05-09 07:34:44 UTC (rev 21908)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog	2016-05-09 08:45:31 UTC (rev 21909)
@@ -1,3 +1,15 @@
+r-bioc-rtracklayer (1.32.0-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * cme fix dpkg-control
+  * debian/copyright: Clarify license of files in src/ucsc/*
+    TODO: four remaining files containing explicit non-free licensing
+          statement (see #807580) but probably due to an error.  Asked
+          for clarification on GitHub
+             https://github.com/jstjohn/KentLib/issues/2
+
+ -- Andreas Tille <tille at debian.org>  Mon, 09 May 2016 09:49:03 +0200
+
 r-bioc-rtracklayer (1.30.1-1) unstable; urgency=medium
 
   * New upstream version

Modified: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control	2016-05-09 07:34:44 UTC (rev 21908)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control	2016-05-09 08:45:31 UTC (rev 21909)
@@ -9,8 +9,8 @@
                r-cran-xml,
                r-cran-rcurl,
                r-bioc-genomicalignments (>= 1.6.0)
-Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-rtracklayer/trunk/
+Standards-Version: 3.9.8
+Vcs-Browser: https://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/
 Homepage: http://bioconductor.org/packages/release/bioc/html/rtracklayer.html
 

Modified: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/copyright	2016-05-09 07:34:44 UTC (rev 21908)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/copyright	2016-05-09 08:45:31 UTC (rev 21909)
@@ -7,7 +7,67 @@
 Copyright: © 2006-2014 Michael Lawrence, Vince Carey, Robert Gentleman 
 License: Artistic-2.0
 
+Files: src/ucsc/*
+Copyright: 2011-2014 The Regents of the University of California
+License: all_use_kentlib
+ *** TEXT FROM ORIGINAL KENT SOURCE LIB README ***
+ This directory contains general purpose, web oriented,
+ and computational biology oriented modules,  as well
+ as some less general stuff associated with the Intronerator
+ web site.  Initially this library was created by Jim
+ Kent from 1999 to 2001.  Since then other programmers have
+ also added to it.  Jim continues to make substantial
+ contributions.
+ .
+ With the exception of the gifcomp.c module, all 
+ modules here are free for all use - public, private,
+ or commercial. The gifcomp.c module contains code
+ originally distributed by CompuServe under a similar
+ "free for all" license.  However this uses the LZW
+ patented by UniSys, which UniSys started enforcing
+ several years after CompuServe released this module.
+ The last I heard UniSys did not require a license
+ for non-commercial purposes, but did require a
+ license for commercial purposes. This may change
+ in the future, though the patent is nearing it's
+ expiration date in any case.  Commercial users
+ are advised to either get a license for LZW, or
+ to switch from GIF to PNG.
 
+Files: src/ucsc/bits.*
+       src/ucsc/common.*
+       src/ucsc/dirlist.* 
+       src/ucsc/dnaseq.* 
+       src/ucsc/dnautil.* 
+       src/ucsc/dystring.* 
+       src/ucsc/errAbort.* 
+       src/ucsc/hash.* 
+       src/ucsc/hmmstats.c
+       src/ucsc/htmshell.h
+       src/ucsc/linefile.*
+       src/ucsc/localmem.*
+       src/ucsc/memalloc.*
+       src/ucsc/net.*
+       src/ucsc/obscure.*
+       src/ucsc/options.h
+       src/ucsc/os*x.c
+       src/ucsc/portable.h
+       src/ucsc/sqlNum.*
+       src/ucsc/wildcmp.c
+Copyright: 2000-2005 Jim Kent
+License: all_use
+ license is hereby granted for all use - public, private or commercial
+
+Files: src/ucsc/cheapcgi.h
+       src/ucsc/hmmstats.h
+       src/ucsc/portimpl.h
+       src/ucsc/sig.h
+Copyright: 2000 Jim Kent
+License: non_commercial
+ Source code may be freely used
+ for personal, academic, and non-profit purposes.  Commercial use
+ permitted only by explicit agreement with Jim Kent (jim_kent at pacbell.net)
+
 Files: debian/*
 Copyright: 2013-2014 Andreas Tille <tille at debian.org>
 License: Artistic-2.0

Modified: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/use_debian_packaged_zlib.patch
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/use_debian_packaged_zlib.patch	2016-05-09 07:34:44 UTC (rev 21908)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/use_debian_packaged_zlib.patch	2016-05-09 08:45:31 UTC (rev 21909)
@@ -16,9 +16,9 @@
 --- a/DESCRIPTION
 +++ b/DESCRIPTION
 @@ -5,7 +5,7 @@ Author: Michael Lawrence, Vince Carey, R
- Depends: R (>= 2.10), methods, GenomicRanges (>= 1.21.20)
+ Depends: R (>= 3.3), methods, GenomicRanges (>= 1.21.20)
  Imports: XML (>= 1.98-0), BiocGenerics (>= 0.13.8), S4Vectors (>=
-         0.7.11), IRanges (>= 2.3.7), XVector (>= 0.9.4), GenomeInfoDb
+         0.9.33), IRanges (>= 2.3.7), XVector (>= 0.9.4), GenomeInfoDb
 -        (>= 1.3.14), Biostrings (>= 2.37.1), zlibbioc, RCurl (>=
 +        (>= 1.3.14), Biostrings (>= 2.37.1), RCurl (>=
          1.4-2), Rsamtools (>= 1.17.8), GenomicAlignments (>= 1.5.4),


