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* [gentoo-commits] repo/gentoo:master commit in: sci-biology/emboss/
@ 2015-08-16 23:03 Mikle Kolyada
  0 siblings, 0 replies; 10+ messages in thread
From: Mikle Kolyada @ 2015-08-16 23:03 UTC (permalink / raw
  To: gentoo-commits

commit:     38d9d2230e883e0e48d7c21424f2baa7673fa4c3
Author:     Mikle Kolyada <zlogene <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 16 23:00:25 2015 +0000
Commit:     Mikle Kolyada <zlogene <AT> gentoo <DOT> org>
CommitDate: Sun Aug 16 23:00:25 2015 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=38d9d223

sci-biology/emboss: amd64 stable wrt bug #529038

Package-Manager: portage-2.2.20.1

 sci-biology/emboss/emboss-6.6.0.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild
index 22d650f..bea0a0d 100644
--- a/sci-biology/emboss/emboss-6.6.0.ebuild
+++ b/sci-biology/emboss/emboss-6.6.0.ebuild
@@ -10,7 +10,7 @@ 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"
+KEYWORDS="amd64 ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
 IUSE+=" minimal"
 LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
 


^ permalink raw reply related	[flat|nested] 10+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/emboss/
@ 2015-08-26 14:25 Mikle Kolyada
  0 siblings, 0 replies; 10+ messages in thread
From: Mikle Kolyada @ 2015-08-26 14:25 UTC (permalink / raw
  To: gentoo-commits

commit:     7b735875e325586d7418d4c7813658089652f227
Author:     Mikle Kolyada <zlogene <AT> gentoo <DOT> org>
AuthorDate: Wed Aug 26 14:22:31 2015 +0000
Commit:     Mikle Kolyada <zlogene <AT> gentoo <DOT> org>
CommitDate: Wed Aug 26 14:22:31 2015 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7b735875

sci-biology/emboss: x86 stable wrt bug #529038

Package-Manager: portage-2.2.20.1

 sci-biology/emboss/emboss-6.6.0.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild
index bea0a0d..a853743 100644
--- a/sci-biology/emboss/emboss-6.6.0.ebuild
+++ b/sci-biology/emboss/emboss-6.6.0.ebuild
@@ -10,7 +10,7 @@ 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"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos"
 IUSE+=" minimal"
 LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
 


^ permalink raw reply related	[flat|nested] 10+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/emboss/
@ 2015-08-26 14:26 Mikle Kolyada
  0 siblings, 0 replies; 10+ messages in thread
From: Mikle Kolyada @ 2015-08-26 14:26 UTC (permalink / raw
  To: gentoo-commits

commit:     0d040c84fbb38ead35451769d2b65a33af2fbf2a
Author:     Mikle Kolyada <zlogene <AT> gentoo <DOT> org>
AuthorDate: Wed Aug 26 14:23:48 2015 +0000
Commit:     Mikle Kolyada <zlogene <AT> gentoo <DOT> org>
CommitDate: Wed Aug 26 14:23:48 2015 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0d040c84

sci-biology/emboss: Drop old

Package-Manager: portage-2.2.20.1

 sci-biology/emboss/Manifest            |   1 -
 sci-biology/emboss/emboss-6.0.1.ebuild | 112 ---------------------------------
 2 files changed, 113 deletions(-)

diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
index c364f2c..6eae2dd 100644
--- a/sci-biology/emboss/Manifest
+++ b/sci-biology/emboss/Manifest
@@ -1,4 +1,3 @@
-DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
 DIST EMBOSS-6.3.1.tar.gz 23572243 SHA256 4f3290600a970c2a23a7e47f884d1fc8156ec40538f7191a6e83e23680d27a8d
 DIST EMBOSS-6.6.0.tar.gz 117962028 SHA256 7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a WHIRLPOOL 25241e865b1ad4e5459f84a2b0def7cd00a6e2904db714838dfe0533e01f8373cfdd4c78df225f9d2a77ead4cb9998791bd19f46b32e220810ad950fa288b9fe
 DIST emboss-6.3.1_p4.patch.gz 4070 SHA256 61d1b62e3148541d496103711db6526ba76488a0899af2c98264b03bf8d6e24c

diff --git a/sci-biology/emboss/emboss-6.0.1.ebuild b/sci-biology/emboss/emboss-6.0.1.ebuild
deleted file mode 100644
index 0edfd7a..0000000
--- a/sci-biology/emboss/emboss-6.0.1.ebuild
+++ /dev/null
@@ -1,112 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=1
-
-inherit eutils
-
-DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
-HOMEPAGE="http://emboss.sourceforge.net/"
-SRC_URI="ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/EMBOSS-${PV}.tar.gz"
-LICENSE="GPL-2 LGPL-2"
-
-SLOT="0"
-KEYWORDS="amd64 ppc x86"
-IUSE="X png minimal"
-
-DEPEND="
-	X? ( x11-libs/libXt )
-	png? (
-		sys-libs/zlib
-		media-libs/libpng
-		media-libs/gd
-		)
-	!minimal? (
-		sci-biology/primer3
-		sci-biology/clustalw
-		)"
-
-RDEPEND="${DEPEND}
-	!sys-devel/cons"
-
-PDEPEND="
-	!minimal? (
-		sci-biology/aaindex
-		sci-biology/cutg
-		sci-biology/prints
-		sci-biology/prosite
-		sci-biology/rebase
-		sci-biology/transfac
-	)"
-
-S="${WORKDIR}/EMBOSS-${PV}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch
-
-	local link_string="$(pkg-config --libs x11)"
-	if use png; then
-		link_string="${link_string} -lgd $(pkg-config --libs libpng)"
-	fi
-	sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \
-		|| die "Failed to patch ajax Makefile"
-}
-
-src_compile() {
-	local myconf
-	myconf="--includedir=${D}/usr/include/emboss"
-	use X || myconf="${EXTRA_CONF} --without-x"
-	use png || myconf="${EXTRA_CONF} --without-pngdriver"
-
-	econf ${myconf}
-	# Do not install the JEMBOSS component (the --without-java configure option
-	# does not work). JEMBOSS will eventually be available as a separate package.
-	sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \
-			Makefile || die
-	emake || die
-}
-
-src_install() {
-	einstall || die "Failed to install program files."
-
-	dodoc AUTHORS ChangeLog FAQ NEWS README THANKS \
-			|| die "Failed to install documentation."
-	newdoc "${FILESDIR}"/${PN}-README.Gentoo-1 README.Gentoo \
-			|| die "Failed to install Gentoo readme file."
-
-	# Install env file for setting libplplot and acd files path.
-	cat <<- EOF > 22emboss
-		# plplot libs dir
-		PLPLOT_LIB="/usr/share/EMBOSS/"
-		# ACD files location
-		EMBOSS_ACDROOT="/usr/share/EMBOSS/acd"
-	EOF
-	doenvd 22emboss || die "Failed to install environment file."
-
-	# Symlink preinstalled docs to "/usr/share/doc".
-	dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals || die
-	dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs || die
-	dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die
-	dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html || die
-
-	# Clashes #330507
-	mv "${D}"/usr/bin/{digest,pepdigest} || die
-
-	# Remove useless dummy files from the image.
-	find emboss/data -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 "${D}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
-			die "Failed to move CODON directory."
-
-	# Move the provided restriction enzyme prototypes file to a different name.
-	# This avoids file collisions with versions of rebase that install their
-	# own enzyme prototypes file (see bug #118832).
-	mv "${D}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \
-			die "Failed to move enzyme equivalence file."
-}


^ permalink raw reply related	[flat|nested] 10+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/emboss/
@ 2015-08-26 17:22 Manuel Rüger
  0 siblings, 0 replies; 10+ messages in thread
From: Manuel Rüger @ 2015-08-26 17:22 UTC (permalink / raw
  To: gentoo-commits

commit:     0db67f06dd6358a4c5294cc79450616900e9160a
Author:     Manuel Rüger <mrueg <AT> gentoo <DOT> org>
AuthorDate: Wed Aug 26 17:21:50 2015 +0000
Commit:     Manuel Rüger <mrueg <AT> gentoo <DOT> org>
CommitDate: Wed Aug 26 17:21:50 2015 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0db67f06

sci-biology/emboss: Restore old version.

This commit reverts 0d040c84fbb38ead35451769d2b65a33af2fbf2a.

Package-Manager: portage-2.2.20.1
RepoMan-Options: --force

 sci-biology/emboss/Manifest            |   1 +
 sci-biology/emboss/emboss-6.0.1.ebuild | 112 +++++++++++++++++++++++++++++++++
 2 files changed, 113 insertions(+)

diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
index 6eae2dd..c364f2c 100644
--- a/sci-biology/emboss/Manifest
+++ b/sci-biology/emboss/Manifest
@@ -1,3 +1,4 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
 DIST EMBOSS-6.3.1.tar.gz 23572243 SHA256 4f3290600a970c2a23a7e47f884d1fc8156ec40538f7191a6e83e23680d27a8d
 DIST EMBOSS-6.6.0.tar.gz 117962028 SHA256 7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a WHIRLPOOL 25241e865b1ad4e5459f84a2b0def7cd00a6e2904db714838dfe0533e01f8373cfdd4c78df225f9d2a77ead4cb9998791bd19f46b32e220810ad950fa288b9fe
 DIST emboss-6.3.1_p4.patch.gz 4070 SHA256 61d1b62e3148541d496103711db6526ba76488a0899af2c98264b03bf8d6e24c

diff --git a/sci-biology/emboss/emboss-6.0.1.ebuild b/sci-biology/emboss/emboss-6.0.1.ebuild
new file mode 100644
index 0000000..0edfd7a
--- /dev/null
+++ b/sci-biology/emboss/emboss-6.0.1.ebuild
@@ -0,0 +1,112 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=1
+
+inherit eutils
+
+DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
+HOMEPAGE="http://emboss.sourceforge.net/"
+SRC_URI="ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/EMBOSS-${PV}.tar.gz"
+LICENSE="GPL-2 LGPL-2"
+
+SLOT="0"
+KEYWORDS="amd64 ppc x86"
+IUSE="X png minimal"
+
+DEPEND="
+	X? ( x11-libs/libXt )
+	png? (
+		sys-libs/zlib
+		media-libs/libpng
+		media-libs/gd
+		)
+	!minimal? (
+		sci-biology/primer3
+		sci-biology/clustalw
+		)"
+
+RDEPEND="${DEPEND}
+	!sys-devel/cons"
+
+PDEPEND="
+	!minimal? (
+		sci-biology/aaindex
+		sci-biology/cutg
+		sci-biology/prints
+		sci-biology/prosite
+		sci-biology/rebase
+		sci-biology/transfac
+	)"
+
+S="${WORKDIR}/EMBOSS-${PV}"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch
+
+	local link_string="$(pkg-config --libs x11)"
+	if use png; then
+		link_string="${link_string} -lgd $(pkg-config --libs libpng)"
+	fi
+	sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \
+		|| die "Failed to patch ajax Makefile"
+}
+
+src_compile() {
+	local myconf
+	myconf="--includedir=${D}/usr/include/emboss"
+	use X || myconf="${EXTRA_CONF} --without-x"
+	use png || myconf="${EXTRA_CONF} --without-pngdriver"
+
+	econf ${myconf}
+	# Do not install the JEMBOSS component (the --without-java configure option
+	# does not work). JEMBOSS will eventually be available as a separate package.
+	sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \
+			Makefile || die
+	emake || die
+}
+
+src_install() {
+	einstall || die "Failed to install program files."
+
+	dodoc AUTHORS ChangeLog FAQ NEWS README THANKS \
+			|| die "Failed to install documentation."
+	newdoc "${FILESDIR}"/${PN}-README.Gentoo-1 README.Gentoo \
+			|| die "Failed to install Gentoo readme file."
+
+	# Install env file for setting libplplot and acd files path.
+	cat <<- EOF > 22emboss
+		# plplot libs dir
+		PLPLOT_LIB="/usr/share/EMBOSS/"
+		# ACD files location
+		EMBOSS_ACDROOT="/usr/share/EMBOSS/acd"
+	EOF
+	doenvd 22emboss || die "Failed to install environment file."
+
+	# Symlink preinstalled docs to "/usr/share/doc".
+	dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals || die
+	dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs || die
+	dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die
+	dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html || die
+
+	# Clashes #330507
+	mv "${D}"/usr/bin/{digest,pepdigest} || die
+
+	# Remove useless dummy files from the image.
+	find emboss/data -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 "${D}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
+			die "Failed to move CODON directory."
+
+	# Move the provided restriction enzyme prototypes file to a different name.
+	# This avoids file collisions with versions of rebase that install their
+	# own enzyme prototypes file (see bug #118832).
+	mv "${D}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \
+			die "Failed to move enzyme equivalence file."
+}


^ permalink raw reply related	[flat|nested] 10+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/emboss/
@ 2015-08-27 13:47 Justin Lecher
  0 siblings, 0 replies; 10+ messages in thread
From: Justin Lecher @ 2015-08-27 13:47 UTC (permalink / raw
  To: gentoo-commits

commit:     08fae0a30263fd06fe51ac5b75301d574be9e1be
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Aug 27 13:47:31 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Aug 27 13:47:54 2015 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=08fae0a3

sci-biology/emboss: Drop old

obsolets multiple bugs

Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=542274
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=534418
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=521604
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=514014
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=493724
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=406279
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=393311
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=382321
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=378443

Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/emboss/Manifest                  |   3 -
 sci-biology/emboss/emboss-6.0.1.ebuild       | 112 -------------------------
 sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild | 117 ---------------------------
 3 files changed, 232 deletions(-)

diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
index c364f2c..42ec060 100644
--- a/sci-biology/emboss/Manifest
+++ b/sci-biology/emboss/Manifest
@@ -1,4 +1 @@
-DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
-DIST EMBOSS-6.3.1.tar.gz 23572243 SHA256 4f3290600a970c2a23a7e47f884d1fc8156ec40538f7191a6e83e23680d27a8d
 DIST EMBOSS-6.6.0.tar.gz 117962028 SHA256 7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a WHIRLPOOL 25241e865b1ad4e5459f84a2b0def7cd00a6e2904db714838dfe0533e01f8373cfdd4c78df225f9d2a77ead4cb9998791bd19f46b32e220810ad950fa288b9fe
-DIST emboss-6.3.1_p4.patch.gz 4070 SHA256 61d1b62e3148541d496103711db6526ba76488a0899af2c98264b03bf8d6e24c

diff --git a/sci-biology/emboss/emboss-6.0.1.ebuild b/sci-biology/emboss/emboss-6.0.1.ebuild
deleted file mode 100644
index 0edfd7a..0000000
--- a/sci-biology/emboss/emboss-6.0.1.ebuild
+++ /dev/null
@@ -1,112 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=1
-
-inherit eutils
-
-DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
-HOMEPAGE="http://emboss.sourceforge.net/"
-SRC_URI="ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/EMBOSS-${PV}.tar.gz"
-LICENSE="GPL-2 LGPL-2"
-
-SLOT="0"
-KEYWORDS="amd64 ppc x86"
-IUSE="X png minimal"
-
-DEPEND="
-	X? ( x11-libs/libXt )
-	png? (
-		sys-libs/zlib
-		media-libs/libpng
-		media-libs/gd
-		)
-	!minimal? (
-		sci-biology/primer3
-		sci-biology/clustalw
-		)"
-
-RDEPEND="${DEPEND}
-	!sys-devel/cons"
-
-PDEPEND="
-	!minimal? (
-		sci-biology/aaindex
-		sci-biology/cutg
-		sci-biology/prints
-		sci-biology/prosite
-		sci-biology/rebase
-		sci-biology/transfac
-	)"
-
-S="${WORKDIR}/EMBOSS-${PV}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch
-
-	local link_string="$(pkg-config --libs x11)"
-	if use png; then
-		link_string="${link_string} -lgd $(pkg-config --libs libpng)"
-	fi
-	sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \
-		|| die "Failed to patch ajax Makefile"
-}
-
-src_compile() {
-	local myconf
-	myconf="--includedir=${D}/usr/include/emboss"
-	use X || myconf="${EXTRA_CONF} --without-x"
-	use png || myconf="${EXTRA_CONF} --without-pngdriver"
-
-	econf ${myconf}
-	# Do not install the JEMBOSS component (the --without-java configure option
-	# does not work). JEMBOSS will eventually be available as a separate package.
-	sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \
-			Makefile || die
-	emake || die
-}
-
-src_install() {
-	einstall || die "Failed to install program files."
-
-	dodoc AUTHORS ChangeLog FAQ NEWS README THANKS \
-			|| die "Failed to install documentation."
-	newdoc "${FILESDIR}"/${PN}-README.Gentoo-1 README.Gentoo \
-			|| die "Failed to install Gentoo readme file."
-
-	# Install env file for setting libplplot and acd files path.
-	cat <<- EOF > 22emboss
-		# plplot libs dir
-		PLPLOT_LIB="/usr/share/EMBOSS/"
-		# ACD files location
-		EMBOSS_ACDROOT="/usr/share/EMBOSS/acd"
-	EOF
-	doenvd 22emboss || die "Failed to install environment file."
-
-	# Symlink preinstalled docs to "/usr/share/doc".
-	dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals || die
-	dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs || die
-	dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die
-	dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html || die
-
-	# Clashes #330507
-	mv "${D}"/usr/bin/{digest,pepdigest} || die
-
-	# Remove useless dummy files from the image.
-	find emboss/data -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 "${D}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
-			die "Failed to move CODON directory."
-
-	# Move the provided restriction enzyme prototypes file to a different name.
-	# This avoids file collisions with versions of rebase that install their
-	# own enzyme prototypes file (see bug #118832).
-	mv "${D}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \
-			die "Failed to move enzyme equivalence file."
-}

diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
deleted file mode 100644
index e8baba4..0000000
--- a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
+++ /dev/null
@@ -1,117 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="4"
-
-inherit autotools eutils
-
-MY_PATCH="4"
-
-DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
-HOMEPAGE="http://emboss.sourceforge.net/"
-SRC_URI="
-	ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/EMBOSS-${PV/_p${MY_PATCH}}.tar.gz
-	ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/fixes/patches/patch-1-${MY_PATCH}.gz -> ${P}.patch.gz"
-
-LICENSE="GPL-2 LGPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
-IUSE="doc minimal mysql pdf png postgres static-libs X"
-
-DEPEND="
-	dev-libs/expat
-	dev-libs/libpcre:3
-	sci-libs/plplot
-	sys-libs/zlib
-	mysql? ( virtual/mysql )
-	pdf? ( media-libs/libharu )
-	png? (
-		sys-libs/zlib
-		media-libs/libpng
-		media-libs/gd
-		)
-	postgres? ( dev-db/postgresql )
-	!minimal? (
-		sci-biology/primer3
-		sci-biology/clustalw
-		)
-	X? ( x11-libs/libXt )"
-RDEPEND="${DEPEND}
-	!sys-devel/cons"
-PDEPEND="
-	!minimal? (
-		sci-biology/aaindex
-		sci-biology/cutg
-		sci-biology/prints
-		sci-biology/prosite
-		sci-biology/rebase
-		sci-biology/transfac
-		)"
-
-S="${WORKDIR}/EMBOSS-${PV/_p${MY_PATCH}}"
-
-src_prepare() {
-	epatch "${WORKDIR}"/${P}.patch
-	epatch \
-		"${FILESDIR}"/${PV}-unbundle-libs.patch \
-		"${FILESDIR}/${PF}_plcol.patch"
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		$(use_with X x) \
-		$(use_with png pngdriver "${EPREFIX}/usr") \
-		$(use_with doc docroot "${EPREFIX}/usr") \
-		$(use_with pdf hpdf "${EPREFIX}/usr") \
-		$(use_with mysql mysql "${EPREFIX}/usr/bin/mysql_config") \
-		$(use_with postgres postgresql "${EPREFIX}/usr/bin/pg_config") \
-		$(use_enable amd64 64) \
-		$(use_enable static-libs static) \
-		--without-java \
-		--enable-large \
-		--enable-systemlibs \
-		--includedir="${ED}/usr/include/emboss"
-}
-
-src_install() {
-	einstall || die "Failed to install program files."
-
-	dodoc AUTHORS ChangeLog FAQ NEWS README THANKS
-	sed "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \
-	dodoc README.Gentoo
-
-	# Install env file for setting libplplot and acd files path.
-	cat <<- EOF > 22emboss
-		# plplot libs dir
-		PLPLOT_LIB="${EPREFIX}/usr/share/EMBOSS/"
-		# ACD files location
-		EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
-	EOF
-	doenvd 22emboss
-
-	# Symlink preinstalled docs to "/usr/share/doc".
-	dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals
-	dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs
-	dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials
-	dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html
-
-	# Clashes #330507
-	mv "${ED}"/usr/bin/{digest,pepdigest} || die
-
-	# Remove useless dummy files from the image.
-	find emboss/data -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 "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
-			die "Failed to move CODON directory."
-
-	# Move the provided restriction enzyme prototypes file to a different name.
-	# This avoids file collisions with versions of rebase that install their
-	# own enzyme prototypes file (see bug #118832).
-	mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \
-			die "Failed to move enzyme equivalence file."
-}


^ permalink raw reply related	[flat|nested] 10+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/emboss/
@ 2016-07-28 21:36 Austin English
  0 siblings, 0 replies; 10+ messages in thread
From: Austin English @ 2016-07-28 21:36 UTC (permalink / raw
  To: gentoo-commits

commit:     38ae04afecd43fd2a719b34977d8cf660cf409c2
Author:     Austin English <wizardedit <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 28 21:35:04 2016 +0000
Commit:     Austin English <wizardedit <AT> gentoo <DOT> org>
CommitDate: Thu Jul 28 21:36:48 2016 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=38ae04af

sci-biology/emboss: add a blocker for games-action/xbomber #589918

Gentoo-Bug: https://bugs.gentoo.org/589918

Package-Manager: portage-2.3.0

 sci-biology/emboss/emboss-6.6.0.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild
index 5c4c77d..53f101f 100644
--- a/sci-biology/emboss/emboss-6.6.0.ebuild
+++ b/sci-biology/emboss/emboss-6.6.0.ebuild
@@ -15,7 +15,8 @@ KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos"
 IUSE+=" minimal"
 LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
 
-RDEPEND+=" !sys-devel/cons"
+RDEPEND+="!games-action/xbomber
+		!sys-devel/cons"
 PDEPEND+="
 	!minimal? (
 		sci-biology/aaindex


^ permalink raw reply related	[flat|nested] 10+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/emboss/
@ 2017-02-06 21:27 David Seifert
  0 siblings, 0 replies; 10+ messages in thread
From: David Seifert @ 2017-02-06 21:27 UTC (permalink / raw
  To: gentoo-commits

commit:     06033e6b1c4f28f88b1135fa26de456bb7ddf22f
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Feb  6 20:48:01 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Feb  6 21:25:46 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=06033e6b

sci-biology/emboss: Remove ppc from KEYWORDS

Package-Manager: Portage-2.3.3, Repoman-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/3856

 sci-biology/emboss/emboss-6.6.0.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild
index 53f101f..8b1d211 100644
--- a/sci-biology/emboss/emboss-6.6.0.ebuild
+++ b/sci-biology/emboss/emboss-6.6.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -11,7 +11,7 @@ inherit autotools-utils emboss-r1 eutils readme.gentoo-r1
 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"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos"
 IUSE+=" minimal"
 LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
 


^ permalink raw reply related	[flat|nested] 10+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/emboss/
@ 2021-03-12 15:31 Andreas Sturmlechner
  0 siblings, 0 replies; 10+ messages in thread
From: Andreas Sturmlechner @ 2021-03-12 15:31 UTC (permalink / raw
  To: gentoo-commits

commit:     c4919007b325c1ab3852e60f64926ff98984d16f
Author:     Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 12 10:06:50 2021 +0000
Commit:     Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
CommitDate: Fri Mar 12 15:31:15 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c4919007

sci-biology/emboss: EAPI-7 bump, minor style

Bug: https://bugs.gentoo.org/770262
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org>

 sci-biology/emboss/emboss-6.6.0-r1.ebuild | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/sci-biology/emboss/emboss-6.6.0-r1.ebuild b/sci-biology/emboss/emboss-6.6.0-r1.ebuild
index 2aa5aa9bc5c..1c74ded5e22 100644
--- a/sci-biology/emboss/emboss-6.6.0-r1.ebuild
+++ b/sci-biology/emboss/emboss-6.6.0-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 EBO_EAUTORECONF=1
 
@@ -9,10 +9,11 @@ inherit emboss-r2 readme.gentoo-r1
 
 DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
 SRC_URI="ftp://emboss.open-bio.org/pub/${PN^^}/${P^^}.tar.gz"
+S="${WORKDIR}/${P^^}"
 
+LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="minimal"
-LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
 
 RDEPEND="
 	!games-action/xbomber
@@ -27,8 +28,6 @@ PDEPEND="
 		sci-biology/rebase
 	)"
 
-S="${WORKDIR}/${P^^}"
-
 PATCHES=(
 	"${FILESDIR}"/${P}_fix-build-system.patch
 	"${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch
@@ -42,20 +41,20 @@ src_install() {
 	readme.gentoo_create_doc
 
 	# Install env file for setting libplplot and acd files path.
-	cat > 22emboss <<- EOF || die
+	newenvd - 22emboss <<- EOF || die
 		# 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 "${ED%/}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files"
+	find "${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 "${ED%/}"/usr/share/EMBOSS/data/CODONS{,.orig} \
+	mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} \
 		|| die "Failed to move CODON directory"
 }
 


^ permalink raw reply related	[flat|nested] 10+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/emboss/
@ 2022-02-13 23:28 David Seifert
  0 siblings, 0 replies; 10+ messages in thread
From: David Seifert @ 2022-02-13 23:28 UTC (permalink / raw
  To: gentoo-commits

commit:     d4378caa9f3a31d8baf594d0b7452ccc98dd5bd2
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 13 23:28:30 2022 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Feb 13 23:28:30 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d4378caa

sci-biology/emboss: update EAPI 7 -> 8

Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/emboss/Manifest                           |  2 +-
 ...{emboss-6.6.0-r1.ebuild => emboss-6.6.0-r2.ebuild} | 19 +++++++++++--------
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
index f97d826f09b6..fa61d72a1db4 100644
--- a/sci-biology/emboss/Manifest
+++ b/sci-biology/emboss/Manifest
@@ -1,2 +1,2 @@
 DIST EMBOSS-6.6.0.tar.gz 117962028 BLAKE2B 91bf3c680290bd975d2ddb5251089d7f75f8a44a26e1247e93d2c9cf2f23e6b89c4218022ba1af0c940136ff56782f40d2c4604dc756b400ae23f223da7f3cca SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a
-DIST emboss-6.6.0-patches.tar.xz 5408 BLAKE2B ec1c55c90a64b1c27645804411b44e413ae881b1637ad2b8dfcff172e15b841cc3d2807039761f8307b0b5a29ab5b1a2c840e189f326091aa9ce25317ec9cda6 SHA512 942681df428f6254c1711902f667c6e8c71babf3e9b0c73b8b7d2fbfa5e8856ce5817560280948e588f6037011ad7055a3af5b88a58fc2b14349869927c889eb
+DIST emboss-6.6.0-patches-r1.tar.xz 5384 BLAKE2B 7899141862880d000e1624e9df914b1918cd02645c0d14128bcffd41d76e3669404a718f25471795268e4a00d610377186b7cb73a126e30f74df80d04d22faf9 SHA512 95825a3bcaa6340d26fde65f3b77574e42fd424440ee48f2fad94b6e696346fe4f6e4ab48c7dcfe1e9c3311a8a7750defc004c2db40cc36f42e980a19e6bd0bd

diff --git a/sci-biology/emboss/emboss-6.6.0-r1.ebuild b/sci-biology/emboss/emboss-6.6.0-r2.ebuild
similarity index 86%
rename from sci-biology/emboss/emboss-6.6.0-r1.ebuild
rename to sci-biology/emboss/emboss-6.6.0-r2.ebuild
index 766dd6a61b0c..01af5e2fa977 100644
--- a/sci-biology/emboss/emboss-6.6.0-r1.ebuild
+++ b/sci-biology/emboss/emboss-6.6.0-r2.ebuild
@@ -1,16 +1,14 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
-EBO_EAUTORECONF=1
-
-inherit emboss-r2 readme.gentoo-r1
+inherit autotools emboss-r3 readme.gentoo-r1
 
 DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
 SRC_URI="
 	ftp://emboss.open-bio.org/pub/${PN^^}/${P^^}.tar.gz
-	https://dev.gentoo.org/~soap/distfiles/${P}-patches.tar.xz"
+	https://dev.gentoo.org/~soap/distfiles/${P}-patches-r1.tar.xz"
 S="${WORKDIR}/${P^^}"
 
 LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
@@ -39,13 +37,18 @@ PATCHES=(
 	"${WORKDIR}"/patches/${P}-Wimplicit-function-declaration.patch
 )
 
+src_prepare() {
+	default
+	eautoreconf
+}
+
 src_install() {
-	emboss-r2_src_install
+	emboss-r3_src_install
 
 	readme.gentoo_create_doc
 
 	# Install env file for setting libplplot and acd files path.
-	newenvd - 22emboss <<- EOF || die
+	newenvd - 22emboss <<- EOF
 		# ACD files location
 		EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
 		EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data"


^ permalink raw reply related	[flat|nested] 10+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/emboss/
@ 2024-03-30 19:36 David Seifert
  0 siblings, 0 replies; 10+ messages in thread
From: David Seifert @ 2024-03-30 19:36 UTC (permalink / raw
  To: gentoo-commits

commit:     92cb387a0aa19b2cf594e25dcfa91a60f85c57e9
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 30 19:36:42 2024 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Mar 30 19:36:42 2024 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=92cb387a

sci-biology/emboss: avoid file collision with dev-texlive/texlive-latexextra

Closes: https://bugs.gentoo.org/927976
Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/emboss/{emboss-6.6.0-r2.ebuild => emboss-6.6.0-r3.ebuild} | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/sci-biology/emboss/emboss-6.6.0-r2.ebuild b/sci-biology/emboss/emboss-6.6.0-r3.ebuild
similarity index 94%
rename from sci-biology/emboss/emboss-6.6.0-r2.ebuild
rename to sci-biology/emboss/emboss-6.6.0-r3.ebuild
index 79d3034a0985..5a43c0ff89ef 100644
--- a/sci-biology/emboss/emboss-6.6.0-r2.ebuild
+++ b/sci-biology/emboss/emboss-6.6.0-r3.ebuild
@@ -64,6 +64,9 @@ src_install() {
 	# bug #115446). This change is documented in "README.gentoo".
 	mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} \
 		|| die "Failed to move CODON directory"
+
+	# collision with dev-texlive/texlive-latexextra, bug #927976
+	mv "${ED}"/usr/bin/{,emboss-}wordcount || die
 }
 
 pkg_postinst() {


^ permalink raw reply related	[flat|nested] 10+ messages in thread
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