Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

sci-biology/ncbi-tools++-9.0.0: put back in the --as-needed LDFLAG to yield hopefully smaller executables; recreating the patch so that it applies automatically

13 files changed, 84 insertions, 136 deletions

diff --git a/app-admin/eselect/ChangeLog b/app-admin/eselect/ChangeLog
index 6f71546ec..3b9e2fefd 100644
--- a/app-admin/eselect/ChangeLog
+++ b/app-admin/eselect/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for app-admin/eselect
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/app-admin/eselect/ChangeLog,v 1.179 2011/01/22 21:38:52 ulm Exp $
 
+*eselect-1.3.4-r100 (07 Jan 2013)
+
+  07 Jan 2013; Justin Lecher <jlec@gentoo.org> +eselect-1.3.4-r100.ebuild,
+  metadata.xml:
+  Version Bump
+
 *eselect-1.3.3-r100 (24 Oct 2012)
 
   24 Oct 2012; Justin Lecher <jlec@gentoo.org> -eselect-1.3.2-r1.ebuild,
diff --git a/app-admin/eselect/Manifest b/app-admin/eselect/Manifest
index 7af3cc6c3..d54be5e2e 100644
--- a/app-admin/eselect/Manifest
+++ b/app-admin/eselect/Manifest
@@ -1,2 +1,3 @@
 DIST eselect-1.3.2.tar.xz 164168 SHA256 8b3906133090229defd6c5017fac0049e14cc0a5185c479cb3e6155a71827a78 SHA512 3225ce8b4313ae15bc7be8f047b29a202976c4a8766005487b78031a0e11e6395da55d74a961b022685126b397f8811babd3ee6580e8ba94e1ddd117964207e5 WHIRLPOOL 94917cad340ab697a35d0b3d4e80e95a6d764829692d54e0ee17fdef84c847aa35da10174352b0d4ffd8f541bbf0280e4b63790a276789a66463d2c8a1a245b0
 DIST eselect-1.3.3.tar.xz 164872 SHA256 09132a0e7512da5c0e5907d04736445101c83b0dd0e6283374ebbc9d76bf6b74 SHA512 480c9c0cd844471b84b2e44440b23ab7538cb6ecb953648ea63057d65ac0f475f057294313f00d3c8cf4b1f1b4effb960cafdd636421302100b8ad7b82213114 WHIRLPOOL c91c91d5e52a9eeba0e8ef86a741838ce3dec2f5b0f0911ada3de3d51a5eba7b9addd9a4e4696171fa4ff3c71f7db494cd8f356d0d7b5daf943b0c24129ac2ea
+DIST eselect-1.3.4.tar.xz 165376 SHA256 9a2fc94d806ca04c20bd60034d3a1acc38caea49fbc66a027a0e9ef531991d33 SHA512 88c35ebee726fa75abe706a547f8ce9239e4bef04620368ae2ea66d7600bff2f17391e145f08e74284668f47a710bdfc427b958023c4f4c4df58bb058ba27a6a WHIRLPOOL b7e8d61218921b89d8cdfb9e42dc6b5401a86a191fe4e792c30fde3d54894e01d0e6c6d702f06a3b88bc7bf6a10d36a95917145b27bc4bcdc9a8968ed9035b45
diff --git a/app-admin/eselect/eselect-1.3.4-r100.ebuild b/app-admin/eselect/eselect-1.3.4-r100.ebuild
new file mode 100644
index 000000000..02d4c4308
--- /dev/null
+++ b/app-admin/eselect/eselect-1.3.4-r100.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/app-admin/eselect/eselect-1.3.4.ebuild,v 1.1 2013/01/06 19:10:44 ulm Exp $
+
+EAPI=4
+
+inherit autotools eutils bash-completion-r1
+
+DESCRIPTION="Gentoo's multi-purpose configuration and management tool"
+HOMEPAGE="http://www.gentoo.org/proj/en/eselect/"
+SRC_URI="mirror://gentoo/${P}.tar.xz"
+
+LICENSE="GPL-2+"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~m68k ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~ppc-aix ~amd64-fbsd ~sparc-fbsd ~x86-fbsd ~x64-freebsd ~x86-freebsd ~hppa-hpux ~ia64-hpux ~x86-interix ~amd64-linux ~ia64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~m68k-mint ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris"
+IUSE="doc"
+
+RDEPEND="sys-apps/sed
+	|| (
+		sys-apps/coreutils
+		sys-freebsd/freebsd-bin
+		app-misc/realpath
+	)"
+DEPEND="${RDEPEND}
+	app-arch/xz-utils
+	doc? ( dev-python/docutils )"
+RDEPEND="!app-admin/eselect-news
+	${RDEPEND}
+	sys-apps/file
+	sys-libs/ncurses"
+
+# Commented out: only few users of eselect will edit its source
+#PDEPEND="emacs? ( app-emacs/gentoo-syntax )
+#	vim-syntax? ( app-vim/eselect-syntax )"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PN}-alternatives.patch
+	AT_M4DIR="." eautoreconf
+}
+
+src_compile() {
+	emake
+	use doc && emake html
+}
+
+src_install() {
+	emake DESTDIR="${D}" install
+	newbashcomp misc/${PN}.bashcomp ${PN}
+	dodoc AUTHORS ChangeLog NEWS README TODO doc/*.txt
+	use doc && dohtml *.html doc/*
+
+	# needed by news module
+	keepdir /var/lib/gentoo/news
+	if ! use prefix; then
+		fowners root:portage /var/lib/gentoo/news
+		fperms g+w /var/lib/gentoo/news
+	fi
+
+	# band aid for prefix
+	if use prefix; then
+		cd "${ED}"/usr/share/eselect/libs
+		sed -i "s:ALTERNATIVESDIR_ROOTLESS=\"${EPREFIX}:ALTERNATIVESDIR_ROOTLESS=\":" alternatives.bash || die
+	fi
+}
+
+pkg_postinst() {
+	# fowners in src_install doesn't work for the portage group:
+	# merging changes the group back to root
+	if ! use prefix; then
+		chgrp portage "${EROOT}/var/lib/gentoo/news" \
+			&& chmod g+w "${EROOT}/var/lib/gentoo/news"
+	fi
+}
diff --git a/app-admin/eselect/metadata.xml b/app-admin/eselect/metadata.xml
index 8a4390ffe..33d01aa80 100644
--- a/app-admin/eselect/metadata.xml
+++ b/app-admin/eselect/metadata.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<maintainer>
-		<email>bicatali@gentoo.org</email>
-	</maintainer>
+  <maintainer>
+    <email>bicatali@gentoo.org</email>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-mathematics/petsc/files/petsc-3.2_p6-fix-afterimage.patch b/sci-mathematics/petsc/files/petsc-3.2_p6-fix-afterimage.patch
deleted file mode 100644
index 27f4d3b43..000000000
--- a/sci-mathematics/petsc/files/petsc-3.2_p6-fix-afterimage.patch
+++ /dev/null
@@ -1,71 +0,0 @@
-
-# HG changeset patch
-# User Jed Brown <jed@59A2.org>
-# Date 1330818004 21600
-# Node ID fb79e104b74267c74aa64f125e7eb6a64bce4b14
-# Parent  8242202a123dd2cbfea7a4a2a9a1797951306f8d
-Fixes for libAfterImage compilation, ImageMagick is still just a stub
-
-diff -r 8242202a123d -r fb79e104b742 config/PETSc/packages/afterimage.py
---- a/config/PETSc/packages/afterimage.py	Sat Mar 03 16:05:00 2012 -0600
-+++ b/config/PETSc/packages/afterimage.py	Sat Mar 03 17:40:04 2012 -0600
-@@ -9,6 +9,7 @@
-     self.includedir    = ''
-     self.libdir        = '../../lib'
-     self.double        = 0
-+    self.complex       = 1
- 
-   def setupDependencies(self, framework):
-     PETSc.package.NewPackage.setupDependencies(self, framework)
-diff -r 8242202a123d -r fb79e104b742 config/PETSc/packages/imagemagick.py
---- a/config/PETSc/packages/imagemagick.py	Sat Mar 03 16:05:00 2012 -0600
-+++ b/config/PETSc/packages/imagemagick.py	Sat Mar 03 17:40:04 2012 -0600
-@@ -4,8 +4,8 @@
-   def __init__(self, framework):
-     PETSc.package.NewPackage.__init__(self, framework)
-     self.functions     = ['IsMagickInstantiated']
--    self.includes      = ['MagicCore/MagickCore.h']
--    self.liblist       = [['libMagicCore.a']]
-+    self.includes      = ['magick/MagickCore.h']
-+    self.liblist       = [['libMagickCore.a']]
- 
- 
- 
-diff -r 8242202a123d -r fb79e104b742 src/sys/draw/impls/x/xinit.c
---- a/src/sys/draw/impls/x/xinit.c	Sat Mar 03 16:05:00 2012 -0600
-+++ b/src/sys/draw/impls/x/xinit.c	Sat Mar 03 17:40:04 2012 -0600
-@@ -291,7 +291,7 @@
- #include <afterimage.h>
- #undef __FUNCT__  
- #define __FUNCT__ "PetscDrawSave_X" 
--PetscErrorCode PetscDrawSave_X(PetscDraw draw,PetscViewer viewer)
-+PetscErrorCode PetscDrawSave_X(PetscDraw draw)
- {
-   PetscDraw_X              *drawx = (PetscDraw_X*)draw->data;
-   XImage                   *image;
-@@ -328,10 +328,10 @@
- void deflateEnd(void) {;}
- 
- #elif defined(PETSC_HAVE_IMAGEMAGICK)
--#include <MagicCore/MagickCore.h>
-+#include <magick/MagickCore.h>
- #undef __FUNCT__  
- #define __FUNCT__ "PetscDrawSave_X" 
--PetscErrorCode PetscDrawSave_X(PetscDraw draw,PetscViewer viewer)
-+PetscErrorCode PetscDrawSave_X(PetscDraw draw)
- {
-   PetscDraw_X  *drawx = (PetscDraw_X*)draw->data;
-   Image        *image;
-diff -r 8242202a123d -r fb79e104b742 src/sys/draw/impls/x/xops.c
---- a/src/sys/draw/impls/x/xops.c	Sat Mar 03 16:05:00 2012 -0600
-+++ b/src/sys/draw/impls/x/xops.c	Sat Mar 03 17:40:04 2012 -0600
-@@ -551,7 +551,7 @@
-   PetscFunctionReturn(0);
- }
- 
--PetscErrorCode PetscDrawSave_X(PetscDraw,PetscViewer);
-+PetscErrorCode PetscDrawSave_X(PetscDraw);
- PetscErrorCode PetscDrawSetSave_X(PetscDraw,const char*);
- 
- static struct _PetscDrawOps DvOps = { PetscDrawSetDoubleBuffer_X,
-
diff --git a/sci-mathematics/petsc/files/petsc-3.2_p6-fix-imagemagick.patch b/sci-mathematics/petsc/files/petsc-3.2_p6-fix-imagemagick.patch
deleted file mode 100644
index 0e17f8945..000000000
--- a/sci-mathematics/petsc/files/petsc-3.2_p6-fix-imagemagick.patch
+++ /dev/null
@@ -1,24 +0,0 @@
---- config/PETSc/packages/imagemagick.py.orig	2012-01-22 17:25:36.440142627 +0000
-+++ config/PETSc/packages/imagemagick.py	2012-01-22 17:26:26.091417306 +0000
-@@ -4,8 +4,8 @@
-   def __init__(self, framework):
-     PETSc.package.NewPackage.__init__(self, framework)
-     self.functions     = ['IsMagickInstantiated']
--    self.includes      = ['MagicCore/MagickCore.h']
--    self.liblist       = [['libMagicCore.a']]
-+    self.includes      = ['MagickCore/MagickCore.h']
-+    self.liblist       = [['libMagickCore.a']]
- 
- 
- 
---- src/sys/draw/impls/x/xinit.c.orig	2012-01-22 17:25:46.230393969 +0000
-+++ src/sys/draw/impls/x/xinit.c	2012-01-22 17:26:26.091417306 +0000
-@@ -328,7 +328,7 @@
- void deflateEnd(void) {;}
- 
- #elif defined(PETSC_HAVE_IMAGEMAGICK)
--#include <MagicCore/MagickCore.h>
-+#include <MagickCore/MagickCore.h>
- #undef __FUNCT__  
- #define __FUNCT__ "PetscDrawSave_X" 
- PetscErrorCode PetscDrawSave_X(PetscDraw draw,PetscViewer viewer)
diff --git a/sci-mathematics/petsc/files/petsc-3.2_p6-fix-xops.patch b/sci-mathematics/petsc/files/petsc-3.2_p6-fix-xops.patch
deleted file mode 100644
index cd2edeb68..000000000
--- a/sci-mathematics/petsc/files/petsc-3.2_p6-fix-xops.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-
-# HG changeset patch
-# User Jed Brown <jed@59A2.org>
-# Date 1330812300 21600
-# Node ID 8242202a123dd2cbfea7a4a2a9a1797951306f8d
-# Parent  759927945bb3cdd30ff4265c043264db5286d263
-Fix declaration of PetscDrawSave_X()
-
-diff -r 759927945bb3 -r 8242202a123d src/sys/draw/impls/x/xops.c
---- a/src/sys/draw/impls/x/xops.c	Fri Mar 02 11:10:34 2012 -0600
-+++ b/src/sys/draw/impls/x/xops.c	Sat Mar 03 16:05:00 2012 -0600
-@@ -551,7 +551,7 @@
-   PetscFunctionReturn(0);
- }
- 
--PetscErrorCode PetscDrawSave_X(PetscDraw);
-+PetscErrorCode PetscDrawSave_X(PetscDraw,PetscViewer);
- PetscErrorCode PetscDrawSetSave_X(PetscDraw,const char*);
- 
- static struct _PetscDrawOps DvOps = { PetscDrawSetDoubleBuffer_X,
-
diff --git a/sci-mathematics/petsc/files/petsc-3.2_p6-configure-pic.patch b/sci-mathematics/petsc/files/petsc-3.2_p7-configure-pic.patch
index bbfdae1c8..bbfdae1c8 100644
--- a/sci-mathematics/petsc/files/petsc-3.2_p6-configure-pic.patch
+++ b/sci-mathematics/petsc/files/petsc-3.2_p7-configure-pic.patch
diff --git a/sci-mathematics/petsc/files/petsc-3.2_p6-disable-env-warnings.patch b/sci-mathematics/petsc/files/petsc-3.2_p7-disable-env-warnings.patch
index d2ee44e1d..d2ee44e1d 100644
--- a/sci-mathematics/petsc/files/petsc-3.2_p6-disable-env-warnings.patch
+++ b/sci-mathematics/petsc/files/petsc-3.2_p7-disable-env-warnings.patch
diff --git a/sci-mathematics/petsc/files/petsc-3.2_p6-disable-rpath.patch b/sci-mathematics/petsc/files/petsc-3.2_p7-disable-rpath.patch
index 3c443b29f..3c443b29f 100644
--- a/sci-mathematics/petsc/files/petsc-3.2_p6-disable-rpath.patch
+++ b/sci-mathematics/petsc/files/petsc-3.2_p7-disable-rpath.patch
diff --git a/sci-mathematics/petsc/files/petsc-3.3-disable-env-warnings.patch b/sci-mathematics/petsc/files/petsc-3.3-disable-env-warnings.patch
deleted file mode 100644
index d2ee44e1d..000000000
--- a/sci-mathematics/petsc/files/petsc-3.3-disable-env-warnings.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Index: petsc-3.2-p6/config/BuildSystem/config/setCompilers.py
-===================================================================
---- petsc-3.2-p6.orig/config/BuildSystem/config/setCompilers.py
-+++ petsc-3.2-p6/config/BuildSystem/config/setCompilers.py
-@@ -1463,7 +1463,7 @@ This way - mpi compilers from '''+self.a
-                  'LDFLAGS','LIBS','MPI_DIR']
-     for envVal in ignoreEnv:
-       if envVal in os.environ:
--        self.logPrintBox('***** WARNING: '+envVal+' found in enviornment variables - ignoring ******')
-+        #self.logPrintBox('***** WARNING: '+envVal+' found in enviornment variables - ignoring ******')
-         del os.environ[envVal]
-     return
- 
diff --git a/sci-mathematics/petsc/petsc-3.2_p6.ebuild b/sci-mathematics/petsc/petsc-3.2_p7.ebuild
index a0b84e0ac..5c8f5b531 100644
--- a/sci-mathematics/petsc/petsc-3.2_p6.ebuild
+++ b/sci-mathematics/petsc/petsc-3.2_p7.ebuild
@@ -59,8 +59,6 @@ PATCHES=(
 	"${FILESDIR}"/${P}-configure-pic.patch
 	"${FILESDIR}"/${P}-disable-env-warnings.patch
 	"${FILESDIR}"/${P}-disable-rpath.patch
-	"${FILESDIR}"/${P}-fix-xops.patch
-	"${FILESDIR}"/${P}-fix-afterimage.patch
 )
 
 src_configure() {
diff --git a/sci-mathematics/petsc/petsc-3.3_p1.ebuild b/sci-mathematics/petsc/petsc-3.3_p5.ebuild
index 0490a56ef..de5dd8fcd 100644
--- a/sci-mathematics/petsc/petsc-3.3_p1.ebuild
+++ b/sci-mathematics/petsc/petsc-3.3_p5.ebuild
@@ -57,7 +57,6 @@ S="${WORKDIR}/${MY_P}"
 
 PATCHES=(
 	"${FILESDIR}"/${P%_*}-configure-pic.patch
-	"${FILESDIR}"/${P%_*}-disable-env-warnings.patch
 	"${FILESDIR}"/${P%_*}-disable-rpath.patch
 )