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
