[gentoo-commits] gentoo-x86 commit in sci-biology/plink: metadata.xml ChangeLog plink-1.07-r1.ebuild plink-1.06.ebuild

[gentoo-commits] gentoo-x86 commit in sci-biology/plink: metadata.xml ChangeLog plink-1.07-r1.ebuild plink-1.06.ebuild

[Justin Lecher (jlec)]

jlec        10/11/26 13:57:26

  Modified:             metadata.xml ChangeLog
  Added:                plink-1.07-r1.ebuild
  Removed:              plink-1.06.ebuild
  Log:
  Fixes for #335975, respecting LDFLAGS/CXXFLAGS, supporting lapack, making R support optional
  
  (Portage version: 2.2.0_alpha5/cvs/Linux x86_64)

Revision  Changes    Path
1.2                  sci-biology/plink/metadata.xml

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/plink/metadata.xml?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/plink/metadata.xml?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/plink/metadata.xml?r1=1.1&r2=1.2

Index: metadata.xml
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/plink/metadata.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- metadata.xml	7 Mar 2009 04:37:27 -0000	1.1
+++ metadata.xml	26 Nov 2010 13:57:26 -0000	1.2
@@ -10,5 +10,8 @@
 		<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>



1.8                  sci-biology/plink/ChangeLog

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/plink/ChangeLog?rev=1.8&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/plink/ChangeLog?rev=1.8&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/plink/ChangeLog?r1=1.7&r2=1.8

Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/plink/ChangeLog,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- ChangeLog	5 Apr 2010 12:13:23 -0000	1.7
+++ ChangeLog	26 Nov 2010 13:57:26 -0000	1.8
@@ -1,33 +1,11 @@
 # ChangeLog for sci-biology/plink
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/ChangeLog,v 1.7 2010/04/05 12:13:23 phajdan.jr Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/ChangeLog,v 1.8 2010/11/26 13:57:26 jlec Exp $
 
-  05 Apr 2010; Pawel Hajdan jr <phajdan.jr@gentoo.org> plink-1.07.ebuild:
-  x86 stable wrt bug #311835
+*plink-1.07-r1 (26 Nov 2010)
 
-  29 Mar 2010; Pacho Ramos <pacho@gentoo.org> plink-1.07.ebuild:
-  amd64 stable, bug 311835
-
-*plink-1.07 (27 Jan 2010)
-
-  27 Jan 2010; Andrey Kislyuk <weaver@gentoo.org> +plink-1.07.ebuild:
-  Version bump
-
-  05 Aug 2009; Markus Meier <maekke@gentoo.org> plink-1.06.ebuild:
-  x86 stable, bug #279345
-
-  02 Aug 2009; <chainsaw@gentoo.org> plink-1.06.ebuild:
-  Marked stable on AMD64 as requested by Andrey "weaver" Kislyuk
-  <weaver@gentoo.org> in bug #279345. Arch-tested by Chad A. Simmons who
-  reports he has no test-suite; reporter confirmed and agreed compile-test
-  was sufficient.
-
-*plink-1.06 (21 Jun 2009)
-
-  21 Jun 2009; Andrey Kislyuk <weaver@gentoo.org>
-  -files/plink-1.05-gcc43.patch, -plink-1.05.ebuild, +plink-1.06.ebuild:
-  Version bump, change name to follow Debian, and drop old files
-
-  06 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
-  New package, ebuild written by Neil Shephard <nshephard@gmail.com> and me
+  26 Nov 2010; Justin Lecher <jlec@gentoo.org> +files/1.07-flags.patch,
+  -plink-1.06.ebuild, +plink-1.07-r1.ebuild, metadata.xml:
+  Fixes for #335975, respecting LDFLAGS/CXXFLAGS, supporting lapack, making R
+  support optional
 



1.1                  sci-biology/plink/plink-1.07-r1.ebuild

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/plink/plink-1.07-r1.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/plink/plink-1.07-r1.ebuild?rev=1.1&content-type=text/plain

Index: plink-1.07-r1.ebuild
===================================================================
# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/plink-1.07-r1.ebuild,v 1.1 2010/11/26 13:57:26 jlec Exp $

EAPI="2"

inherit eutils toolchain-funcs

DESCRIPTION="Whole genome association analysis toolset"
HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/"
SRC_URI="http://pngu.mgh.harvard.edu/~purcell/plink/dist/${P}-src.zip"

LICENSE="GPL-2"
SLOT="0"
IUSE="lapack -webcheck R"
KEYWORDS="~amd64 ~x86"

DEPEND="app-arch/unzip"
RDEPEND="lapack? ( virtual/lapack )"

S="${WORKDIR}/${P}-src"

# 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() {
	epatch "${FILESDIR}"/${PV}-flags.patch
	use webcheck || sed -i '/WITH_WEBCHECK =/ s/^/#/' "${S}/Makefile" || die
	use R || sed -i '/WITH_R_PLUGINS =/ s/^/#/' "${S}/Makefile" || die
	use lapack || sed -i '/WITH_LAPACK =/ s/^/#/' "${S}/Makefile" || die
}

src_compile() {
	emake \
		CXX_UNIX=$(tc-getCXX) \
		|| die
}

src_install() {
	newbin plink p-link || die
	dodoc README.txt || die
}