[med-svn] r22927 - in trunk/packages/R/r-bioc-rtracklayer/trunk/debian: . patches

Thu Oct 27 09:54:07 UTC 2016

Author: tille
Date: 2016-10-27 09:54:07 +0000 (Thu, 27 Oct 2016)
New Revision: 22927

Removed:
   trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/remove_broken_test.patch
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/delete_configure.patch
   trunk/packages/R/r-bioc-rtracklayer/trunk/debian/rules
Log:
  * New upstream version
  * Convert to dh-r
  * Generic BioConductor homepage



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

--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog	2016-10-27 09:33:50 UTC (rev 22926)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog	2016-10-27 09:54:07 UTC (rev 22927)
@@ -1,3 +1,11 @@
+r-bioc-rtracklayer (1.34.0-1) unstable; urgency=medium
+
+  * New upstream version
+  * Convert to dh-r
+  * Generic BioConductor homepage
+
+ -- Andreas Tille <tille at debian.org>  Thu, 27 Oct 2016 11:37:57 +0200
+
 r-bioc-rtracklayer (1.32.2-1) 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	2016-10-27 09:33:50 UTC (rev 22926)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control	2016-10-27 09:54:07 UTC (rev 22927)
@@ -4,7 +4,7 @@
 Section: gnu-r
 Priority: optional
 Build-Depends: debhelper (>= 9),
-               cdbs,
+               dh-r,
                r-base-dev (>= 3.3),
                r-cran-xml,
                r-cran-rcurl,
@@ -13,16 +13,15 @@
 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
+Homepage: https://bioconductor.org/packages/rtracklayer/
 
 Package: r-bioc-rtracklayer
 Architecture: any
 Depends: ${R:Depends},
          ${misc:Depends},
          ${shlibs:Depends},
-         r-cran-xml,
-         r-cran-rcurl,
-         r-bioc-genomicalignments (>= 1.6.0)
+Recommends: ${R:Recommends}
+Suggests: ${R:Suggests}
 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

Modified: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/copyright	2016-10-27 09:33:50 UTC (rev 22926)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/copyright	2016-10-27 09:54:07 UTC (rev 22927)
@@ -1,10 +1,10 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: rtracklayer
 Upstream-Contact: Michael Lawrence <michafla at gene.com> 
-Source: http://bioconductor.org/packages/release/bioc/html/rtracklayer.html
+Source: https://bioconductor.org/packages/rtracklayer/
 
 Files: *
-Copyright: © 2006-2014 Michael Lawrence, Vince Carey, Robert Gentleman 
+Copyright: © 2006-2016 Michael Lawrence, Vince Carey, Robert Gentleman 
 License: Artistic-2.0
 
 Files: src/ucsc/*
@@ -75,7 +75,7 @@
  that this is not the proper license but the license above applies.
 
 Files: debian/*
-Copyright: 2013-2014 Andreas Tille <tille at debian.org>
+Copyright: 2013-2016 Andreas Tille <tille at debian.org>
 License: Artistic-2.0
 
 License: Artistic-2.0

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	2016-10-27 09:33:50 UTC (rev 22926)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/delete_configure.patch	2016-10-27 09:54:07 UTC (rev 22927)
@@ -8,7 +8,7 @@
 
 --- a/configure
 +++ /dev/null
-@@ -1,3043 +0,0 @@
+@@ -1,3050 +0,0 @@
 -#! /bin/sh
 -# Guess values for system-dependent variables and create Makefiles.
 -# Generated by GNU Autoconf 2.69.
@@ -592,7 +592,6 @@
 -PACKAGE_BUGREPORT=
 -PACKAGE_URL=
 -
--ac_unique_file=""rtracklayer""
 -ac_subst_vars='LTLIBOBJS
 -LIBOBJS
 -SSL_CPPFLAGS
@@ -1891,6 +1890,14 @@
 -
 -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
 -
 -

Deleted: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/remove_broken_test.patch
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/remove_broken_test.patch	2016-10-27 09:33:50 UTC (rev 22926)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/remove_broken_test.patch	2016-10-27 09:54:07 UTC (rev 22927)
@@ -1,37 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 09 May 2016 12:46:31 +0200
-Description: Remove broken test from configure script
- Something like this was suggested by Dirk Eddelbuettel <edd at debian.org> at
-   https://lists.alioth.debian.org/pipermail/debian-med-packaging/2016-May/042034.html
- But this patch has not the effect that -DUSE_SSL is included in the
- compiler options and thus I'll stick to simply remove configure at all
- (see delete_configure.patch).
-
---- a/configure
-+++ b/configure
-@@ -1142,24 +1142,10 @@ $as_echo X"$as_myself" |
- 	  }
- 	  s/.*/./; q'`
-   srcdir=$ac_confdir
--  if test ! -r "$srcdir/$ac_unique_file"; then
--    srcdir=..
--  fi
- else
-   ac_srcdir_defaulted=no
- fi
--if test ! -r "$srcdir/$ac_unique_file"; then
--  test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .."
--  as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir"
--fi
--ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work"
--ac_abs_confdir=`(
--	cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg"
--	pwd)`
--# When building in place, set srcdir=.
--if test "$ac_abs_confdir" = "$ac_pwd"; then
--  srcdir=.
--fi
-+srcdir=.
- # Remove unnecessary trailing slashes from srcdir.
- # Double slashes in file names in object file debugging info
- # mess up M-x gdb in Emacs.

Modified: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/rules	2016-10-27 09:33:50 UTC (rev 22926)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/rules	2016-10-27 09:54:07 UTC (rev 22927)
@@ -1,4 +1,4 @@
 #!/usr/bin/make -f
 
-debRreposname=bioc
-include /usr/share/R/debian/r-cran.mk
+%:
+	dh $@ --buildsystem R


