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* [gentoo-commits] proj/sci:master commit in: sci-biology/plink/
@ 2016-08-01 16:32 Martin Mokrejs
  0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2016-08-01 16:32 UTC (permalink / raw
  To: gentoo-commits

commit:     1bc9bf063980829008293505ed8468e6495b3113
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Aug  1 16:32:12 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Aug  1 16:32:12 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1bc9bf06

sci-biology/plink: version bump (non-maintainer)

Package-Manager: portage-2.3.0

 sci-biology/plink/metadata.xml                | 16 ++++++++
 sci-biology/plink/plink-1.90_pre160731.ebuild | 55 +++++++++++++++++++++++++++
 2 files changed, 71 insertions(+)

diff --git a/sci-biology/plink/metadata.xml b/sci-biology/plink/metadata.xml
new file mode 100644
index 0000000..c281934
--- /dev/null
+++ b/sci-biology/plink/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<use>
+		<flag name="webcheck">
+			add support for online update checking every time the program starts
+		</flag>
+		<flag name="R">
+			add support R language
+		</flag>
+	</use>
+</pkgmetadata>

diff --git a/sci-biology/plink/plink-1.90_pre160731.ebuild b/sci-biology/plink/plink-1.90_pre160731.ebuild
new file mode 100644
index 0000000..1048be0
--- /dev/null
+++ b/sci-biology/plink/plink-1.90_pre160731.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Whole genome association analysis toolset"
+HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/"
+SRC_URI="https://www.cog-genomics.org/static/bin/plink160731/plink_src.zip -> ${P}.zip"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="
+	app-arch/unzip
+	virtual/pkgconfig"
+RDEPEND="
+	sys-libs/zlib
+	virtual/cblas
+	virtual/lapack
+	"
+
+S="${WORKDIR}/"
+
+# Package collides with net-misc/putty. Renamed to p-link following discussion with Debian.
+# Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream.
+
+src_prepare() {
+	sed \
+		-e 's:zlib-1.2.8/zlib.h:zlib.h:g' \
+		-i *.{c,h} || die
+
+	sed \
+		-e 's:g++:$(CXX):g' \
+		-e 's:gcc:$(CC):g' \
+		-e 's:gfortran:$(FC):g' \
+		-i Makefile || die
+	tc-export PKG_CONFIG
+}
+
+src_compile() {
+	emake \
+		CXX=$(tc-getCXX) \
+		CFLAGS="${CFLAGS}" \
+		ZLIB="$($(tc-getPKG_CONFIG) --libs zlib)" \
+		BLASFLAGS="$($(tc-getPKG_CONFIG) --libs lapack cblas)"
+}
+
+src_install() {
+	newbin plink p-link
+}


^ permalink raw reply related	[flat|nested] 4+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/plink/
@ 2016-08-01 16:33 Martin Mokrejs
  0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2016-08-01 16:33 UTC (permalink / raw
  To: gentoo-commits

commit:     481f75c96110d35e8db04aca1f07a73c7efa993c
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Aug  1 16:33:19 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Aug  1 16:33:19 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=481f75c9

sci-biology/plink: actually add newer homepage (non-maintainer)

Package-Manager: portage-2.3.0

 sci-biology/plink/plink-1.90_pre160731.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sci-biology/plink/plink-1.90_pre160731.ebuild b/sci-biology/plink/plink-1.90_pre160731.ebuild
index 1048be0..d75584a 100644
--- a/sci-biology/plink/plink-1.90_pre160731.ebuild
+++ b/sci-biology/plink/plink-1.90_pre160731.ebuild
@@ -7,7 +7,8 @@ EAPI=5
 inherit eutils toolchain-funcs
 
 DESCRIPTION="Whole genome association analysis toolset"
-HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/"
+HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink
+	https://www.cog-genomics.org/plink2/"
 SRC_URI="https://www.cog-genomics.org/static/bin/plink160731/plink_src.zip -> ${P}.zip"
 
 LICENSE="GPL-3+"


^ permalink raw reply related	[flat|nested] 4+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/plink/
@ 2016-08-01 22:49 Martin Mokrejs
  0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2016-08-01 22:49 UTC (permalink / raw
  To: gentoo-commits

commit:     f24839e7208c79e59b719ca80d9c4fee81c4868f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Aug  1 22:49:13 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Aug  1 22:49:13 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f24839e7

sci-biology/plink: non-maintainer commit

Re-add USE=lapack logic adjusted to current sources which got lost in
 plink-1.90_pre140514 , could work around bug #589068

Package-Manager: portage-2.3.0

 sci-biology/plink/metadata.xml                |  8 --------
 sci-biology/plink/plink-1.90_pre160731.ebuild | 20 +++++++++++++++-----
 2 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/sci-biology/plink/metadata.xml b/sci-biology/plink/metadata.xml
index c281934..8417d15 100644
--- a/sci-biology/plink/metadata.xml
+++ b/sci-biology/plink/metadata.xml
@@ -5,12 +5,4 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
-	<use>
-		<flag name="webcheck">
-			add support for online update checking every time the program starts
-		</flag>
-		<flag name="R">
-			add support R language
-		</flag>
-	</use>
 </pkgmetadata>

diff --git a/sci-biology/plink/plink-1.90_pre160731.ebuild b/sci-biology/plink/plink-1.90_pre160731.ebuild
index d75584a..b57d6b1 100644
--- a/sci-biology/plink/plink-1.90_pre160731.ebuild
+++ b/sci-biology/plink/plink-1.90_pre160731.ebuild
@@ -14,16 +14,15 @@ SRC_URI="https://www.cog-genomics.org/static/bin/plink160731/plink_src.zip -> ${
 LICENSE="GPL-3+"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
+IUSE="lapack"
 
 DEPEND="
 	app-arch/unzip
 	virtual/pkgconfig"
 RDEPEND="
 	sys-libs/zlib
-	virtual/cblas
-	virtual/lapack
-	"
+	lapack? ( virtual/lapack
+		virtual/cblas )"
 
 S="${WORKDIR}/"
 
@@ -31,6 +30,7 @@ S="${WORKDIR}/"
 # Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream.
 
 src_prepare() {
+	rm -rf zlib-1.2.8 || die
 	sed \
 		-e 's:zlib-1.2.8/zlib.h:zlib.h:g' \
 		-i *.{c,h} || die
@@ -40,17 +40,27 @@ src_prepare() {
 		-e 's:gcc:$(CC):g' \
 		-e 's:gfortran:$(FC):g' \
 		-i Makefile || die
+	if ! use lapack; then
+		sed -e 's/^NO_LAPACK =/NO_LAPACK = 1/' -i Makefile || die
+		sed -e 's@^// #define NOLAPACK@#define NOLAPACK@' -i plink_common.h || die
+	fi
 	tc-export PKG_CONFIG
 }
 
 src_compile() {
+	local blasflags
+	use lapack && blasflags="$($(tc-getPKG_CONFIG) --libs lapack cblas)"
 	emake \
 		CXX=$(tc-getCXX) \
 		CFLAGS="${CFLAGS}" \
 		ZLIB="$($(tc-getPKG_CONFIG) --libs zlib)" \
-		BLASFLAGS="$($(tc-getPKG_CONFIG) --libs lapack cblas)"
+		BLASFLAGS="$blasflags"
 }
 
 src_install() {
 	newbin plink p-link
 }
+
+pkg_postinst(){
+	einfo "plink binary is now renamed to p-link to avoid file collision"
+}


^ permalink raw reply related	[flat|nested] 4+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/plink/
@ 2020-09-22 11:12 Aisha Tammy
  0 siblings, 0 replies; 4+ messages in thread
From: Aisha Tammy @ 2020-09-22 11:12 UTC (permalink / raw
  To: gentoo-commits

commit:     18aa9950c2cb926a31bce5ae82792ec5115a1941
Author:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Tue Sep 22 11:08:45 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Tue Sep 22 11:08:45 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=18aa9950

sci-biology/plink: drop package

present in ::gentoo

Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 sci-biology/plink/metadata.xml                |  8 ----
 sci-biology/plink/plink-1.90_pre160731.ebuild | 65 ---------------------------
 2 files changed, 73 deletions(-)

diff --git a/sci-biology/plink/metadata.xml b/sci-biology/plink/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/plink/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>

diff --git a/sci-biology/plink/plink-1.90_pre160731.ebuild b/sci-biology/plink/plink-1.90_pre160731.ebuild
deleted file mode 100644
index 525cfbcbb..000000000
--- a/sci-biology/plink/plink-1.90_pre160731.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Whole genome association analysis toolset"
-HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink
-	https://www.cog-genomics.org/plink2/"
-SRC_URI="https://www.cog-genomics.org/static/bin/plink160731/plink_src.zip -> ${P}.zip"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="lapack"
-
-DEPEND="
-	app-arch/unzip
-	virtual/pkgconfig"
-RDEPEND="
-	sys-libs/zlib
-	lapack? ( virtual/lapack
-		virtual/cblas )"
-
-S="${WORKDIR}/"
-
-# Package collides with net-misc/putty. Renamed to p-link following discussion with Debian.
-# Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream.
-
-src_prepare() {
-	rm -rf zlib-1.2.8 || die
-	sed \
-		-e 's:zlib-1.2.8/zlib.h:zlib.h:g' \
-		-i *.{c,h} || die
-
-	sed \
-		-e 's:g++:$(CXX):g' \
-		-e 's:gcc:$(CC):g' \
-		-e 's:gfortran:$(FC):g' \
-		-i Makefile || die
-	if ! use lapack; then
-		sed -e 's/^NO_LAPACK =/NO_LAPACK = 1/' -i Makefile || die
-		sed -e 's@^// #define NOLAPACK@#define NOLAPACK@' -i plink_common.h || die
-	fi
-	tc-export PKG_CONFIG
-}
-
-src_compile() {
-	local blasflags
-	use lapack && blasflags="$($(tc-getPKG_CONFIG) --libs lapack cblas)"
-	emake \
-		CXX=$(tc-getCXX) \
-		CFLAGS="${CFLAGS}" \
-		ZLIB="$($(tc-getPKG_CONFIG) --libs zlib)" \
-		BLASFLAGS="$blasflags"
-}
-
-src_install() {
-	newbin plink p-link
-}
-
-pkg_postinst(){
-	einfo "plink binary is now renamed to p-link to avoid file collision"
-}


^ permalink raw reply related	[flat|nested] 4+ messages in thread

end of thread, other threads:[~2020-09-22 11:12 UTC | newest]

Thread overview: 4+ messages (download: mbox.gz follow: Atom feed
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2016-08-01 16:33 [gentoo-commits] proj/sci:master commit in: sci-biology/plink/ Martin Mokrejs
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2016-08-01 22:49 Martin Mokrejs
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