[gentoo-commits] proj/sci:master commit in: sci-biology/embassy-meme/, sci-biology/embassy-cbstools/, sci-biology/emboss/, ...

[Justin Lecher]

commit:     e9842579c0fcb075170d823068ec4bfa4fbf8cda
Author:     Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Sat Mar 28 16:06:49 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Mar 28 16:06:49 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e9842579

Updated emboss-r1.eclass and all embassy/emboss packages to confirm to QA standards.

 eclass/emboss-r1.eclass                              | 20 +++++---------------
 .../embassy-cbstools-1.0.0.650.ebuild                |  2 ++
 .../embassy-clustalomega-1.1.0.ebuild                |  2 ++
 .../embassy-domainatrix-0.1.650.ebuild               |  2 ++
 .../embassy-domalign/embassy-domalign-0.1.650.ebuild |  2 ++
 .../embassy-domsearch-0.1.650.ebuild                 |  2 ++
 .../embassy-emnu/embassy-emnu-1.05.650.ebuild        |  2 ++
 .../embassy-esim4/embassy-esim4-1.0.0.650.ebuild     |  2 ++
 .../embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild     |  2 ++
 .../embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild |  2 ++
 sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild |  2 ++
 sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild |  2 ++
 .../embassy-phylipnew-3.69.650.ebuild                |  2 ++
 .../embassy-signature-0.1.650.ebuild                 |  2 ++
 .../embassy-structure-0.1.650.ebuild                 |  2 ++
 sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild |  2 ++
 .../embassy-vienna/embassy-vienna-1.7.2.650.ebuild   |  2 ++
 sci-biology/emboss/emboss-6.6.0.ebuild               |  2 ++
 18 files changed, 39 insertions(+), 15 deletions(-)

diff --git a/eclass/emboss-r1.eclass b/eclass/emboss-r1.eclass
index e82b413..00d00f7 100644
--- a/eclass/emboss-r1.eclass
+++ b/eclass/emboss-r1.eclass
@@ -38,17 +38,14 @@
 # @ECLASS-VARIABLE: EBO_EXTRA_ECONF
 # @DEFAULT_UNSET
 # @DESCRIPTION:
-# Extra config options passed to econf, similar to EXTRA_ECONF.
+# Extra config options passed to econf, similar to EXTRA_ECONF
+# but can be set by the ebuild.
 
 case ${EAPI:-0} in
 	5) ;;
 	*) die "this eclass doesn't support < EAPI 5" ;;
 esac
 
-if [[ -f "${FILESDIR}"/${P}_fix-build-system.patch ]]; then
-	AUTOTOOLS_AUTORECONF=1
-fi
-
 inherit autotools-utils eutils flag-o-matic
 
 HOMEPAGE="http://emboss.sourceforge.net/"
@@ -88,20 +85,15 @@ fi
 # @DESCRIPTION:
 # Does the following things
 #
-#  1. Patches with "${FILESDIR}"/${P}_fix-build-system.patch, if present,
-#     and eventually runs eautoreconf in autotools-utils
-#  2. Patches with "${FILESDIR}"/${PF}.patch, if present
-#  3. Applies ${PATCHES[@]} via autotools-utils.eclass
+#  1. Renames configure.in to configure.ac, if possible
+#  2. Applies ${PATCHES[@]} and runs autotools via autotools-utils.eclass
 #
 
 emboss-r1_src_prepare() {
-	if [[ -f "${FILESDIR}"/${P}_fix-build-system.patch ]]; then
+	if [[ -e configure.in ]]; then
 		mv configure.{in,ac} || die
-		epatch "${FILESDIR}"/${P}_fix-build-system.patch
 	fi
 
-	[[ -f "${FILESDIR}"/${PF}.patch ]] && epatch "${FILESDIR}"/${PF}.patch
-
 	autotools-utils_src_prepare
 }
 
@@ -118,7 +110,6 @@ emboss-r1_src_prepare() {
 #  --enable-large
 #  --without-java
 #  --enable-systemlibs
-#  --docdir="${EPREFIX}/usr/share/doc/${PF}"
 #  ${EBO_EXTRA_ECONF}
 
 emboss-r1_src_configure() {
@@ -131,7 +122,6 @@ emboss-r1_src_configure() {
 		--enable-large
 		--without-java
 		--enable-systemlibs
-		--docdir="${EPREFIX}/usr/share/doc/${PF}"
 		${EBO_EXTRA_ECONF}
 	)
 

diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild
index dd78911..a903ba3 100644
--- a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild
+++ b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild
@@ -6,6 +6,8 @@ EAPI=5
 
 EBO_DESCRIPTION="applications from the CBS group"
 
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
 inherit emboss-r1
 
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"

diff --git a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild
index e6636ac..62621f3 100644
--- a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild
+++ b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild
@@ -6,6 +6,8 @@ EAPI=5
 
 EBO_DESCRIPTION="Clustal Omega - Scalable multiple protein sequences alignment"
 
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
 inherit emboss-r1
 
 KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"

diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild
index 2380532..276f646 100644
--- a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild
+++ b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild
@@ -6,6 +6,8 @@ EAPI=5
 
 EBO_DESCRIPTION="Protein domain analysis add-on package"
 
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
 inherit emboss-r1
 
 KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"

diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild
index 157e1af..140ab99 100644
--- a/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild
+++ b/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild
@@ -6,6 +6,8 @@ EAPI=5
 
 EBO_DESCRIPTION="Protein domain alignment add-on package"
 
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
 inherit emboss-r1
 
 KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"

diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild
index f0d1265..1e1c29c 100644
--- a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild
+++ b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild
@@ -6,6 +6,8 @@ EAPI=5
 
 EBO_DESCRIPTION="Protein domain search add-on package"
 
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
 inherit emboss-r1
 
 KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"

diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild
index fe88b98..0291af7 100644
--- a/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild
+++ b/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild
@@ -7,6 +7,8 @@ EAPI=5
 EBO_DESCRIPTION="Simple menu of EMBOSS applications"
 EBO_EXTRA_ECONF="$(use_enable ncurses curses)"
 
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
 inherit emboss-r1
 
 KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"

diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild
index 3085960..c6fc9de 100644
--- a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild
+++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild
@@ -6,6 +6,8 @@ EAPI=5
 
 EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA"
 
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
 inherit emboss-r1
 
 KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"

diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild
index 8f2a68a..918e9fd 100644
--- a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild
+++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild
@@ -6,6 +6,8 @@ EAPI=5
 
 EBO_DESCRIPTION="wrappers for HMMER - Biological sequence analysis with profile HMMs"
 
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
 inherit emboss-r1
 
 KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"

diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild
index 11c44d8..a30e837 100644
--- a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild
+++ b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild
@@ -6,6 +6,8 @@ EAPI=5
 
 EBO_DESCRIPTION="InterProScan motif detection add-on package"
 
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
 inherit emboss-r1
 
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"

diff --git a/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild b/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild
index ffc88d1..473b7c5 100644
--- a/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild
+++ b/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild
@@ -6,6 +6,8 @@ EAPI=5
 
 EBO_DESCRIPTION="wrappers for MEME - Multiple Em for Motif Elicitation"
 
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
 inherit emboss-r1
 
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"

diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild
index f692c91..d77af20 100644
--- a/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild
+++ b/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild
@@ -7,6 +7,8 @@ EAPI=5
 EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor"
 EBO_EXTRA_ECONF="$(use_enable ncurses curses)"
 
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
 inherit emboss-r1
 
 KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"

diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild
index 602bec9..4b92ca0 100644
--- a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild
+++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild
@@ -6,6 +6,8 @@ EAPI=5
 
 EBO_DESCRIPTION="the Phylogeny Inference Package"
 
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
 inherit emboss-r1
 
 LICENSE+=" freedist"

diff --git a/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild b/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild
index 693de26..1cfd5aa 100644
--- a/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild
+++ b/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild
@@ -6,6 +6,8 @@ EAPI=5
 
 EBO_DESCRIPTION="Protein signature add-on package"
 
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
 inherit emboss-r1
 
 KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"

diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild
index 896612d..377bb48 100644
--- a/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild
+++ b/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild
@@ -6,6 +6,8 @@ EAPI=5
 
 EBO_DESCRIPTION="Protein structure add-on package"
 
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
 inherit emboss-r1
 
 KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"

diff --git a/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild b/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild
index 0a77dfb..8e8eb56 100644
--- a/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild
+++ b/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild
@@ -6,6 +6,8 @@ EAPI=5
 
 EBO_DESCRIPTION="Transmembrane protein display"
 
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
 inherit emboss-r1
 
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"

diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild
index e6af9a5..87c5576 100644
--- a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild
+++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild
@@ -6,6 +6,8 @@ EAPI=5
 
 EBO_DESCRIPTION="Vienna RNA package - RNA folding"
 
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
 inherit emboss-r1
 
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"

diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild
index 59285d7..82f17af 100644
--- a/sci-biology/emboss/emboss-6.6.0.ebuild
+++ b/sci-biology/emboss/emboss-6.6.0.ebuild
@@ -4,6 +4,7 @@
 
 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"
@@ -27,6 +28,7 @@ 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