Revision bump: EAPI 5, add subslot to Boost dependency, fix compatibility with Automake 1.14, wrt bug #499046. Drop old revision

(Portage version: 2.2.8/cvs/Linux x86_64, signed Manifest commit with key 0x1F357D42)

3 files changed, 22 insertions, 13 deletions

diff --git a/sci-biology/cufflinks/ChangeLog b/sci-biology/cufflinks/ChangeLog
index ec3408a0e2c4..e2625dc6420f 100644
--- a/sci-biology/cufflinks/ChangeLog
+++ b/sci-biology/cufflinks/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/cufflinks
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/cufflinks/ChangeLog,v 1.5 2013/03/11 15:00:28 jlec Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cufflinks/ChangeLog,v 1.6 2014/02/05 08:16:11 pinkbyte Exp $
+
+*cufflinks-1.3.0-r1 (05 Feb 2014)
+
+  05 Feb 2014; Sergey Popov <pinkbyte@gentoo.org> -cufflinks-1.3.0.ebuild,
+  +cufflinks-1.3.0-r1.ebuild, files/cufflinks-1.3.0-autotools.patch:
+  Revision bump: EAPI 5, add subslot to Boost dependency, fix compatibility
+  with Automake 1.14, wrt bug #499046. Drop old revision
 
   11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
diff --git a/sci-biology/cufflinks/cufflinks-1.3.0.ebuild b/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild
index 49a29ded8165..0fd23209329c 100644
--- a/sci-biology/cufflinks/cufflinks-1.3.0.ebuild
+++ b/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/cufflinks/cufflinks-1.3.0.ebuild,v 1.3 2012/11/10 10:58:55 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild,v 1.1 2014/02/05 08:16:11 pinkbyte Exp $
 
-EAPI=4
+EAPI=5
 
 AUTOTOOLS_AUTORECONF=yes
 
@@ -18,8 +18,8 @@ IUSE="debug"
 KEYWORDS="~amd64 ~x86"
 
 DEPEND="
-	sci-biology/samtools
-	dev-libs/boost"
+	>=sci-biology/samtools-0.1.18
+	dev-libs/boost:="
 RDEPEND="${DEPEND}"
 
 PATCHES=(
diff --git a/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch b/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch
index 72c643900ec4..73e52b4343a0 100644
--- a/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch
+++ b/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch
@@ -1,8 +1,3 @@
- configure.ac | 7 ++++---
- 1 file changed, 4 insertions(+), 3 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index b8a0b9b..b0a4635 100755
 --- a/configure.ac
 +++ b/configure.ac
 @@ -27,6 +27,7 @@ AC_PROG_AWK
@@ -22,7 +17,7 @@ index b8a0b9b..b0a4635 100755
  ext_CFLAGS=""
  debug_CFLAGS=""
  #echo "${host_cpu}-${host_os}"
-@@ -99,9 +100,9 @@ AC_ARG_ENABLE(profiling,      [  --enable-profiling        enable profiling with
+@@ -99,15 +100,15 @@ AC_ARG_ENABLE(profiling,      [  --enable-profiling        enable profiling with
  	  [ext_LDFLAGS="-lprofiler -ltcmalloc"], [])
  	  
  CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}"
@@ -34,3 +29,10 @@ index b8a0b9b..b0a4635 100755
  
  # Checks for structures/functions that can be used to determine system memory
  AC_CHECK_MEMBERS([struct sysinfo.totalram], [], [], [#include <sys/sysinfo.h>])
+ AC_CHECK_DECLS([sysctl, CTL_HW, HW_PHYSMEM], [], [], [#include <sys/sysctl.h>])
+ 
+-AM_INIT_AUTOMAKE([-Wall -Werror tar-pax foreign])
++AM_INIT_AUTOMAKE([-Wall tar-pax foreign subdir-objects])
+ 
+ AC_CONFIG_FILES([Makefile				 
+ 				 src/Makefile])