[gentoo-commits] gentoo-x86 commit in sci-biology/emboss: emboss-6.6.0.ebuild metadata.xml ChangeLog

[Justin Lecher (jlec)]

jlec        15/03/28 17:03:16

  Modified:             metadata.xml ChangeLog
  Added:                emboss-6.6.0.ebuild
  Log:
  Import latest changes from science overlay, thanks Ted Tanberry for the work; fixes #504680
  
  (Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

Revision  Changes    Path
1.6                  sci-biology/emboss/metadata.xml

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/emboss/metadata.xml?rev=1.6&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/emboss/metadata.xml?rev=1.6&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/emboss/metadata.xml?r1=1.5&r2=1.6

Index: metadata.xml
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/emboss/metadata.xml,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- metadata.xml	11 Mar 2011 07:05:50 -0000	1.5
+++ metadata.xml	28 Mar 2015 17:03:16 -0000	1.6
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
-	<longdescription>
+  <herd>sci-biology</herd>
+  <longdescription>
 		EMBOSS is "The European Molecular Biology Open Software Suite".
 		EMBOSS is a free Open Source software analysis package specially
 		developed for the needs of the molecular biology (e.g. EMBnet) user



1.72                 sci-biology/emboss/ChangeLog

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/emboss/ChangeLog?rev=1.72&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/emboss/ChangeLog?rev=1.72&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/emboss/ChangeLog?r1=1.71&r2=1.72

Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v
retrieving revision 1.71
retrieving revision 1.72
diff -u -r1.71 -r1.72
--- ChangeLog	28 Dec 2014 16:46:09 -0000	1.71
+++ ChangeLog	28 Mar 2015 17:03:16 -0000	1.72
@@ -1,6 +1,16 @@
 # ChangeLog for sci-biology/emboss
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.71 2014/12/28 16:46:09 titanofold Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.72 2015/03/28 17:03:16 jlec Exp $
+
+*emboss-6.6.0 (28 Mar 2015)
+
+  28 Mar 2015; Justin Lecher <jlec@g.o> +emboss-6.6.0.ebuild,
+  +files/README.gentoo, +files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch,
+  +files/emboss-6.6.0_fix-build-system.patch,
+  +files/emboss-6.6.0_plplot-declarations.patch,
+  +files/emboss-6.6.0_qa-implicit-declarations.patch, metadata.xml:
+  Import latest changes from science overlay, thanks Ted Tanberry for the work;
+  fixes #504680
 
   28 Dec 2014; Aaron W. Swenson <titanofold@g.o> emboss-6.3.1_p4.ebuild,
   emboss-6.3.1_p4-r1.ebuild:



1.1                  sci-biology/emboss/emboss-6.6.0.ebuild

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/emboss/emboss-6.6.0.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/emboss/emboss-6.6.0.ebuild?rev=1.1&content-type=text/plain

Index: emboss-6.6.0.ebuild
===================================================================
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.6.0.ebuild,v 1.1 2015/03/28 17:03:16 jlec Exp $

EAPI=5

AUTOTOOLS_AUTORECONF=1
inherit autotools-utils emboss-r1 eutils readme.gentoo

DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"

KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
IUSE+=" minimal"

RDEPEND+=" !sys-devel/cons"
PDEPEND+="
	!minimal? (
		sci-biology/aaindex
		sci-biology/cutg
		sci-biology/prints
		sci-biology/prosite
		sci-biology/rebase
		)"

S="${WORKDIR}"/EMBOSS-${PV}

DOCS=( ChangeLog AUTHORS NEWS THANKS FAQ )

PATCHES=(
	"${FILESDIR}"/${P}_fix-build-system.patch
	"${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch
	"${FILESDIR}"/${P}_plplot-declarations.patch
	"${FILESDIR}"/${P}_qa-implicit-declarations.patch
)

src_install() {
	# Use autotools-utils_* to remove useless *.la files
	autotools-utils_src_install

	readme.gentoo_create_doc

	# Install env file for setting libplplot and acd files path.
	cat > 22emboss <<- EOF
		# ACD files location
		EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
		EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data"
	EOF
	doenvd 22emboss

	# Remove useless dummy files
	find "${ED}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files."

	# Move the provided codon files to a different directory. This will avoid
	# user confusion and file collisions on case-insensitive file systems (see
	# bug #115446). This change is documented in "README.gentoo".
	mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
			die "Failed to move CODON directory."
}