* [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
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