[gentoo-commits] proj/sci:master commit in: sci-biology/plink/

[Martin Mokrejs]

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-biol...@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"
+}