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

Package-Manager: portage-2.2.8/cvs/Linux x86_64
Manifest-Sign-Key: 0x1F357D42

4 files changed, 33 insertions, 20 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/Manifest b/sci-biology/cufflinks/Manifest
index bc9149cf4941..a2396ffcac77 100644
--- a/sci-biology/cufflinks/Manifest
+++ b/sci-biology/cufflinks/Manifest
@@ -1,17 +1,21 @@
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 AUX cufflinks-1.3.0-boost.patch 52005 SHA256 4fc98a82bb1b283db0eb0b4064ac76237ddd1f5c329d76a4130ec09d7dc7983b SHA512 910c9d1b9b1635a4b3e30b0d377b1f2c192a20e482697da0346a9ecb99e0255ac50c906ff7be2d94446137ed04cfa7705c916dc892e1fc0c5c05c93e950e1d34 WHIRLPOOL a5fc395daccbf248fe819b1c21979fbd0f6168c7227d4774240fa70d58eb75dd479eb418bd181c5c470209f72d52c7913d0dea77d1b6d16716543841bd5a5984
 AUX cufflinks-1.3.0-gcc-4.7.patch 594 SHA256 9dcdde0e56b3ebb3f0325eaba05b0c8f80cab311519d3785956e32bb1c4e0b97 SHA512 fc8b3924af1f24cc57e5890bb22acc1123eb1704948ded6bdf2beb7500ccbe57c12ff3905c235f3ae47dfff19e4205ed266b94a6eef48ce1539cd2c260e37ac6 WHIRLPOOL 196255a59028cadfa6d0575230bb9f602c894db437b34e1f9efb573dbe5d9bdc9bc3f9ed573166aa9fbb070d7d506a447627369bb71d72040d1ab28b358c46fc
 DIST cufflinks-1.3.0.tar.gz 676660 SHA256 c1e194e30e6ba2e1cbbd35e5f92be59f9fdef95a12079b3141790efbbdbdfd86 SHA512 b493c06b00093958aa3bf4aefa6435b89aa3fa8f90b9adea955b38aaa0301fafe3f028321573855d2af9515f9792a8a9c3851bd9352846131658e54b5a6ac68a WHIRLPOOL 649ed7638bdc655cc38d9c0ec6c81bc464e648e6e684e31af955a424510ee4702e2cec8e3dbfa2d97859ed27e04ff45fe2e07cb0a548c87674337bb94f5352ce
-EBUILD cufflinks-1.3.0.ebuild 939 SHA256 258a7a6ff34e31b3b7d2f609661d73da405b402964078074d3e50b0459317b07 SHA512 5efbb88f99ae58bec80f7dbb9783582ff55076932221df02df30ab87368298f97abcdfe30adf8b293b0e751fd249d76ff673163f3b58cf02571283903b6d2219 WHIRLPOOL aa3caad2a764143ebd35a7105e03d5087c7bd16f6bf5a7873b47ade5a2ddbbe9bd75542502a32d5b6c83c32518f2b2d9e38c026490690e3dcccc2ec51b896197
-MISC ChangeLog 1027 SHA256 0e2ba40c7cfb482103068115e1d206bf476bd5aca60bde39470c60a0023079f9 SHA512 bb96d4cba91f42ca448b4a74cc7b5753fd77ed14a28e36acbf74f819e67aab0958338fc51a07b8b88b7e4c7bb0095cfdde2d8256b0de0d7ac952cd1bf5abe4b6 WHIRLPOOL 798e83837a1c57fe163f6dba373db80feee3deca2cd96407194d2068f6a64712b612b4048d1c7a29d8d5c0be0a78cf27e1da67624635915d5d7a548cb4f26d73
+EBUILD cufflinks-1.3.0-r1.ebuild 957 SHA256 9d5f642506fb3783081852b1ccefb3524f6dcfdaded577ca4c1b771033c71a8d SHA512 caf6cd751e25d490d86fcdb05e54596554ed76ad4c6c7acd4ff86ee3a179b25005159f0bcaa75104c8febbd22820a56039674e1b245a43538a0c66b378faf1d0 WHIRLPOOL 3668b9c1301ade0945c6ea5ad655890bd4d8be52bc357b0b84bfc640f8dd129370c74ecf4359dfcd556308ee73858a1b688a65c075339ccf90ada132b754481f
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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])