[med-svn] r23919 - in trunk/packages/R/r-bioc-rtracklayer/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2017-08-23 18:21:47 +0000 (Wed, 23 Aug 2017)
New Revision: 23919

Removed:
   trunk/packages/R/r-bioc-rtracklayer/trunk/debian/lintian-overrides
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/patches/delete_configure.patch
   trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/use_debian_packaged_zlib.patch
Log:
New upstream version


Modified: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog	2017-08-23 08:15:04 UTC (rev 23918)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog	2017-08-23 18:21:47 UTC (rev 23919)
@@ -1,3 +1,12 @@
+r-bioc-rtracklayer (1.36.4-1) unstable; urgency=medium
+
+  * New upstream version
+    Closes: #871333
+  * Standards-Version: 4.0.1 (no changes needed)
+  * Remove unused lintian override
+
+ -- Andreas Tille <tille at debian.org>  Wed, 23 Aug 2017 19:43:41 +0200
+
 r-bioc-rtracklayer (1.34.1-1) 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	2017-08-23 08:15:04 UTC (rev 23918)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control	2017-08-23 18:21:47 UTC (rev 23919)
@@ -11,7 +11,7 @@
                r-bioc-genomicalignments (>= 1.6.0),
                libssl-dev,
                pkg-config
-Standards-Version: 3.9.8
+Standards-Version: 4.0.1
 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: https://bioconductor.org/packages/rtracklayer/
@@ -20,7 +20,7 @@
 Architecture: any
 Depends: ${R:Depends},
          ${misc:Depends},
-         ${shlibs:Depends},
+         ${shlibs:Depends}
 Recommends: ${R:Recommends}
 Suggests: ${R:Suggests}
 Description: GNU R interface to genome browsers and their annotation tracks

Deleted: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/lintian-overrides
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/lintian-overrides	2017-08-23 08:15:04 UTC (rev 23918)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/lintian-overrides	2017-08-23 18:21:47 UTC (rev 23919)
@@ -1,2 +0,0 @@
-# The gzip files are simply taken over from upstream source into binary package
-r-bioc-rtracklayer: package-contains-timestamped-gzip usr/lib/R/site-library/rtracklayer/extdata/demo.narrowPeak.gz
\ No newline at end of file

Modified: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/delete_configure.patch
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/delete_configure.patch	2017-08-23 08:15:04 UTC (rev 23918)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/delete_configure.patch	2017-08-23 18:21:47 UTC (rev 23919)
@@ -8,7 +8,7 @@
 
 --- a/configure
 +++ /dev/null
-@@ -1,3050 +0,0 @@
+@@ -1,3048 +0,0 @@
 -#! /bin/sh
 -# Guess values for system-dependent variables and create Makefiles.
 -# Generated by GNU Autoconf 2.69.
@@ -1696,6 +1696,11 @@
 -
 -
 -
+-case "$OSTYPE" in "darwin"*)
+-  BREWDIR=`brew --prefix`
+-  export PKG_CONFIG_PATH=$BREWDIR/opt/openssl/lib/pkgconfig
+-  ;;
+-esac
 -
 -
 -
@@ -1703,6 +1708,7 @@
 -
 -
 -
+-
 -if test "x$ac_cv_env_PKG_CONFIG_set" != "xset"; then
 -	if test -n "$ac_tool_prefix"; then
 -  # Extract the first word of "${ac_tool_prefix}pkg-config", so it can be a program name with args.
@@ -1890,14 +1896,6 @@
 -
 -if test "${OPENSSL}" != "no"; then
 -  SSL_CPPFLAGS="-DUSE_SSL"
--else
--  case "$OSTYPE" in "darwin"*)
--  BREWDIR=`brew --prefix`
--  OPENSSL_CFLAGS="-I$BREWDIR/opt/openssl/include"
--  OPENSSL_LIBS="-L$BREWDIR/opt/openssl/lib -lssl -lcrypto"
--  SSL_CPPFLAGS="-DUSE_SSL"
--  ;;
--  esac
 -fi
 -
 -

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	2017-08-23 08:15:04 UTC (rev 23918)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/use_debian_packaged_zlib.patch	2017-08-23 18:21:47 UTC (rev 23919)
@@ -18,9 +18,9 @@
 @@ -5,7 +5,7 @@ Author: Michael Lawrence, Vince Carey, R
  Depends: R (>= 3.3), methods, GenomicRanges (>= 1.21.20)
  Imports: XML (>= 1.98-0), BiocGenerics (>= 0.13.8), S4Vectors (>=
-         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 (>=
+         0.13.13), IRanges (>= 2.3.7), XVector (>= 0.9.4), GenomeInfoDb
+-        (>= 1.3.14), Biostrings (>= 2.43.7), zlibbioc, RCurl (>=
++        (>= 1.3.14), Biostrings (>= 2.43.7), RCurl (>=
          1.4-2), Rsamtools (>= 1.17.8), GenomicAlignments (>= 1.5.4),
          tools
  Suggests: BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1),