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

2021-01-20 Thread Andrew Ammerlaan 
commit: 9103b70e66e9d368c3ef7105b432183c07f49da5
Author: Andrew Ammerlaan  riseup  net>
AuthorDate: Wed Jan 20 09:06:29 2021 +
Commit: Andrew Ammerlaan  riseup  net>
CommitDate: Wed Jan 20 09:06:29 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9103b70e

sci-biology/plinkseq: remove pack, upstream gone

Signed-off-by: Andrew Ammerlaan  riseup.net>

 sci-biology/plinkseq/metadata.xml | 12 --
 sci-biology/plinkseq/plinkseq-0.10.ebuild | 51 -
 sci-biology/plinkseq/plinkseq-.ebuild | 63 ---
 3 files changed, 126 deletions(-)

diff --git a/sci-biology/plinkseq/metadata.xml 
b/sci-biology/plinkseq/metadata.xml
deleted file mode 100644
index 138cb7705..0
--- a/sci-biology/plinkseq/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd";>
-
-   
-   mmokr...@fold.natur.cuni.cz
-   Martin Mokrejs
-   
-   
-   sci-biol...@gentoo.org
-   Gentoo Biology Project
-   
-

diff --git a/sci-biology/plinkseq/plinkseq-0.10.ebuild 
b/sci-biology/plinkseq/plinkseq-0.10.ebuild
deleted file mode 100644
index b1e4937d7..0
--- a/sci-biology/plinkseq/plinkseq-0.10.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit toolchain-funcs autotools-utils
-
-DESCRIPTION="C/C++ library for working with human genetic variation data"
-HOMEPAGE="http://atgu.mgh.harvard.edu/plinkseq";
-SRC_URI="http://psychgen.u.hpc.mssm.edu/plinkseq_downloads/plinkseq-src-latest.tgz
 -> ${P}.tgz"
-# https://bitbucket.org/statgen/plinkseq.git
-# http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="sys-libs/zlib
-   dev-libs/protobuf
-   !sci-biology/fsl" # file collision on /usr/bin/mm
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-   sed -e "s/gcc/$(tc-getCC)/g;s/g++/$(tc-getCXX)/g;s/-O3/${CFLAGS}/g" -i 
config_defs.Makefile || die
-   sed -e "s/= -static/=/g" -i config_defs.Makefile || die
-   rm -rf sources/ext/protobuf-* || die
-   rm sources/ext/protobuf sources/ext/sources/include/google || die
-   rm -rf sources/mongoose || die
-   sed -e 's@^all:.*@all: # skipping compilation of bundled 
dev-libs/protobuf@' -i sources/ext/Makefile || die
-   # TODO: fix also 
sources/ext/sources/include/DUMMY/include/google/protobuf/compiler/plugin.proto 
causing:
-   # plugin.proto: Import "google/protobuf/descriptor.proto" was not found 
or had errors.
-   # plugin.proto:74:12: "FileDescriptorProto" is not defined.
-   find . -name \*.proto | while read f; do \
-   d=`dirname $f`; \
-   pushd $d; \
-   protoc --cpp_out=. *.proto || exit 255; \
-   popd; \
-   done || die
-   autotools-utils_src_prepare
-}
-
-src_install(){
-   cd build/execs || die
-   # TODO: avoid file collision with sci-biology/fsl
-   # 
https://bitbucket.org/statgen/plinkseq/issue/9/rename-mm-filename-to-plinkseq_mm
-   # TODO: avoid file collision with www-servers/mongoose
-   dobin gcol browser pseq behead mm smp tab2vcf pdas
-}

diff --git a/sci-biology/plinkseq/plinkseq-.ebuild 
b/sci-biology/plinkseq/plinkseq-.ebuild
deleted file mode 100644
index cffdaff97..0
--- a/sci-biology/plinkseq/plinkseq-.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit toolchain-funcs git-r3
-
-DESCRIPTION="C/C++ library for working with human genetic variation data"
-HOMEPAGE="http://atgu.mgh.harvard.edu/plinkseq";
-EGIT_REPO_URI="https://bitbucket.org/statgen/plinkseq.git";
-# https://bitbucket.org/statgen/plinkseq/commits/all
-# http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="sys-libs/zlib
-   dev-libs/protobuf
-   !sci-biology/fsl" # file collision on /usr/bin/mm
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-   sed -e "s/gcc/$(tc-getCC)/g;s/g++/$(tc-getCXX)/g;s/-O3/${CFLAGS}/g" -i 
config_defs.Makefile || die
-   sed -e "s/= -static/=/g" -i config_defs.Makefile || die
-   rm -rf sources/ext/protobuf-* || die
-   rm sources/ext/protobuf sources/ext/sources/include/google || die
-   # we cannot zap calls to bundled mongoose because www-servers/mongoose 
does not build a library at all
-   # rm -rf sources/mongoose || die
-   # sed -e "s@$(MONGOOSE_LIB_DIR) @@;s@$(MONGOOSE_INC) 
@@;s@$(MONGOOSE_LIB_BASE_DIR) @@" - Makefile || die
-   sed -e 's@^all:.*@all: # skipping compilation of bundled 
dev-libs/protobuf@' -i sources/ext/Makefile || die
-   find . -name \*.proto | while read f; do \
-   d=

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

2017-03-31 Thread Martin Mokrejs 
commit: ef3daf274a3921856131027f304698bad8b2d141
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Fri Mar 31 21:19:21 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Mar 31 21:19:21 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ef3daf27

sci-biology/plinkseq: we cannot zap bundled mongoose so easily

Package-Manager: Portage-2.3.5, Repoman-2.3.1

 sci-biology/plinkseq/plinkseq-.ebuild | 13 -
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/sci-biology/plinkseq/plinkseq-.ebuild 
b/sci-biology/plinkseq/plinkseq-.ebuild
index 461e62f84..cffdaff97 100644
--- a/sci-biology/plinkseq/plinkseq-.ebuild
+++ b/sci-biology/plinkseq/plinkseq-.ebuild
@@ -20,7 +20,6 @@ IUSE=""
 
 DEPEND="sys-libs/zlib
dev-libs/protobuf
-   www-servers/mongoose
!sci-biology/fsl" # file collision on /usr/bin/mm
 RDEPEND="${DEPEND}"
 
@@ -29,7 +28,9 @@ src_prepare(){
sed -e "s/= -static/=/g" -i config_defs.Makefile || die
rm -rf sources/ext/protobuf-* || die
rm sources/ext/protobuf sources/ext/sources/include/google || die
-   rm -rf sources/mongoose || die
+   # we cannot zap calls to bundled mongoose because www-servers/mongoose 
does not build a library at all
+   # rm -rf sources/mongoose || die
+   # sed -e "s@$(MONGOOSE_LIB_DIR) @@;s@$(MONGOOSE_INC) 
@@;s@$(MONGOOSE_LIB_BASE_DIR) @@" - Makefile || die
sed -e 's@^all:.*@all: # skipping compilation of bundled 
dev-libs/protobuf@' -i sources/ext/Makefile || die
find . -name \*.proto | while read f; do \
d=`dirname $f`; \
@@ -44,11 +45,13 @@ src_prepare(){
sed -e 
's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g'
 -i sources/plinkseq/sources/lib/matrix.pb.cpp || die
sed -e 
's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g'
 -i sources/plinkseq/sources/lib/variant.pb.cpp || die
local myinc=`pkg-config protobuf --variable=includedir`
-   sed -e "s@\$(PROTOBUF_LIB_BASE_DIR)/\$(INC_DIR)/@$myinc@" -i Makefile 
|| die
+   sed -e 's@$(PROTOBUF_LIB_BASE_DIR)/$(INC_DIR)/@'"${myinc}@" -i Makefile 
|| die
local mylib=`pkg-config protobuf --variable=libdir`
-   sed -e "s@$(PROTOBUF_LIB_BASE_DIR)/$(BLD_LIB_DIR)/@$mylib@" -i Makefile 
|| die
+   sed -e 's@$(PROTOBUF_LIB_BASE_DIR)/$(BLD_LIB_DIR)/@'"-L${mylib} @" -i 
Makefile || die # note the trailing space as it get prepended to PROTOBUF_LIBS
+   # anyway $(PROTOBUF_LIB_FULL_PATH) is a necessary build target, just 
drop it
+   sed -e 's@^PROTOBUF_LIB_FULL_PATH =.*/@PROTOBUF_LIB_FULL_PATH =@' -i 
Makefile || die
local mylibs=`pkg-config protobuf --libs`
-   sed -e "s@libprotobuf.a@$mylibs@" -i Makefile || die
+   sed -e "s@libprotobuf.a@ ${mylibs}@ " -i Makefile || die
 }
 
 src_install(){

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

2017-01-10 Thread Martin Mokrejs 
commit: 4ee5e3f90785b4a1571df2c0d6028a542557977e
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Tue Jan 10 12:16:12 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Jan 10 12:16:12 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4ee5e3f9

sci-biology/plinkseq: remove dangling symlinks

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/plinkseq/plinkseq-0.10.ebuild | 1 +
 sci-biology/plinkseq/plinkseq-.ebuild | 1 +
 2 files changed, 2 insertions(+)

diff --git a/sci-biology/plinkseq/plinkseq-0.10.ebuild 
b/sci-biology/plinkseq/plinkseq-0.10.ebuild
index 2934db5..b49f5b7 100644
--- a/sci-biology/plinkseq/plinkseq-0.10.ebuild
+++ b/sci-biology/plinkseq/plinkseq-0.10.ebuild
@@ -28,6 +28,7 @@ src_prepare(){
sed -e "s/gcc/$(tc-getCC)/g;s/g++/$(tc-getCXX)/g;s/-O3/${CFLAGS}/g" -i 
config_defs.Makefile || die
sed -e "s/= -static/=/g" -i config_defs.Makefile || die
rm -rf sources/ext/protobuf-* || die
+   rm sources/ext/protobuf sources/ext/sources/include/google || die
rm -rf sources/mongoose || die
sed -e 's@^all:.*@all: # skipping compilation of bundled 
dev-libs/protobuf@' -i sources/ext/Makefile || die
# TODO: fix also 
sources/ext/sources/include/DUMMY/include/google/protobuf/compiler/plugin.proto 
causing:

diff --git a/sci-biology/plinkseq/plinkseq-.ebuild 
b/sci-biology/plinkseq/plinkseq-.ebuild
index 939a2b8..c17fb39 100644
--- a/sci-biology/plinkseq/plinkseq-.ebuild
+++ b/sci-biology/plinkseq/plinkseq-.ebuild
@@ -29,6 +29,7 @@ src_prepare(){
sed -e "s/gcc/$(tc-getCC)/g;s/g++/$(tc-getCXX)/g;s/-O3/${CFLAGS}/g" -i 
config_defs.Makefile || die
sed -e "s/= -static/=/g" -i config_defs.Makefile || die
rm -rf sources/ext/protobuf-* || die
+   rm sources/ext/protobuf sources/ext/sources/include/google || die
rm -rf sources/mongoose || die
sed -e 's@^all:.*@all: # skipping compilation of bundled 
dev-libs/protobuf@' -i sources/ext/Makefile || die
find . -name \*.proto | while read f; do \

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

2017-01-09 Thread Martin Mokrejs 
commit: ced948b30611f98b4e88720d0d7f4654eb7ca953
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Tue Jan 10 01:05:47 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Jan 10 01:05:47 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ced948b3

sci-biology/plinkseq: note a file collision

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/plinkseq/plinkseq-0.10.ebuild | 3 ++-
 sci-biology/plinkseq/plinkseq-.ebuild | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/sci-biology/plinkseq/plinkseq-0.10.ebuild 
b/sci-biology/plinkseq/plinkseq-0.10.ebuild
index f39458b..2934db5 100644
--- a/sci-biology/plinkseq/plinkseq-0.10.ebuild
+++ b/sci-biology/plinkseq/plinkseq-0.10.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
 # $Id$
 
@@ -46,5 +46,6 @@ src_install(){
cd build/execs || die
# TODO: avoid file collision with sci-biology/fsl
# 
https://bitbucket.org/statgen/plinkseq/issue/9/rename-mm-filename-to-plinkseq_mm
+   # TODO: avoid file collision with www-servers/mongoose
dobin gcol browser pseq behead mm smp tab2vcf pdas
 }

diff --git a/sci-biology/plinkseq/plinkseq-.ebuild 
b/sci-biology/plinkseq/plinkseq-.ebuild
index 49c9a13..939a2b8 100644
--- a/sci-biology/plinkseq/plinkseq-.ebuild
+++ b/sci-biology/plinkseq/plinkseq-.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
 # $Id$
 
@@ -55,5 +55,6 @@ src_install(){
cd build/execs || die
# TODO: avoid file collision with sci-biology/fsl
# 
https://bitbucket.org/statgen/plinkseq/issue/9/rename-mm-filename-to-plinkseq_mm
+   # TODO: avoid file collision with www-servers/mongoose
dobin gcol browser pseq behead mm smp tab2vcf pdas
 }

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

2016-12-04 Thread Martin Mokrejs 
commit: 7fe9fb808188b046045fb31e3bf5a7d228511d09
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Sun Dec  4 18:41:07 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Dec  4 18:41:07 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7fe9fb80

sci-biology/plinkseq: fixing issues with bundled dev-libs/protobuf and 
www-servers/mongoose

The git repo received some commits this year so trying to create an ebuild
for that. It bailed out at more places than the latest release tarball
v0.10. The static Makefile needs more tweaks so that the values from
'pkg-config protobuf' calls get propagated properly. And not to look
for the removed protobuf and mongoose subdirs.

Package-Manager: portage-2.3.2

 sci-biology/plinkseq/plinkseq-0.10.ebuild |  8 +++--
 sci-biology/plinkseq/plinkseq-.ebuild | 59 +++
 2 files changed, 64 insertions(+), 3 deletions(-)

diff --git a/sci-biology/plinkseq/plinkseq-0.10.ebuild 
b/sci-biology/plinkseq/plinkseq-0.10.ebuild
index 71871e8..f39458b 100644
--- a/sci-biology/plinkseq/plinkseq-0.10.ebuild
+++ b/sci-biology/plinkseq/plinkseq-0.10.ebuild
@@ -20,14 +20,16 @@ KEYWORDS=""
 IUSE=""
 
 DEPEND="sys-libs/zlib
-   dev-libs/protobuf"
+   dev-libs/protobuf
+   !sci-biology/fsl" # file collision on /usr/bin/mm
 RDEPEND="${DEPEND}"
 
 src_prepare(){
sed -e "s/gcc/$(tc-getCC)/g;s/g++/$(tc-getCXX)/g;s/-O3/${CFLAGS}/g" -i 
config_defs.Makefile || die
sed -e "s/= -static/=/g" -i config_defs.Makefile || die
rm -rf sources/ext/protobuf-* || die
-   sed -e 's#^all:.*#all: echo "skipping compilation of bundled 
dev-libs/protobuf"#' -i sources/ext/Makefile || die
+   rm -rf sources/mongoose || die
+   sed -e 's@^all:.*@all: # skipping compilation of bundled 
dev-libs/protobuf@' -i sources/ext/Makefile || die
# TODO: fix also 
sources/ext/sources/include/DUMMY/include/google/protobuf/compiler/plugin.proto 
causing:
# plugin.proto: Import "google/protobuf/descriptor.proto" was not found 
or had errors.
# plugin.proto:74:12: "FileDescriptorProto" is not defined.
@@ -44,5 +46,5 @@ src_install(){
cd build/execs || die
# TODO: avoid file collision with sci-biology/fsl
# 
https://bitbucket.org/statgen/plinkseq/issue/9/rename-mm-filename-to-plinkseq_mm
-   dobin gcol browser pseq behead mm smp tab2vcf mongoose pdas
+   dobin gcol browser pseq behead mm smp tab2vcf pdas
 }

diff --git a/sci-biology/plinkseq/plinkseq-.ebuild 
b/sci-biology/plinkseq/plinkseq-.ebuild
new file mode 100644
index 000..49c9a13
--- /dev/null
+++ b/sci-biology/plinkseq/plinkseq-.ebuild
@@ -0,0 +1,59 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+
+inherit toolchain-funcs git-r3
+
+DESCRIPTION="C/C++ library for working with human genetic variation data"
+HOMEPAGE="http://atgu.mgh.harvard.edu/plinkseq";
+EGIT_REPO_URI="https://bitbucket.org/statgen/plinkseq.git";
+# https://bitbucket.org/statgen/plinkseq/commits/all
+# http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sys-libs/zlib
+   dev-libs/protobuf
+   www-servers/mongoose
+   !sci-biology/fsl" # file collision on /usr/bin/mm
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+   sed -e "s/gcc/$(tc-getCC)/g;s/g++/$(tc-getCXX)/g;s/-O3/${CFLAGS}/g" -i 
config_defs.Makefile || die
+   sed -e "s/= -static/=/g" -i config_defs.Makefile || die
+   rm -rf sources/ext/protobuf-* || die
+   rm -rf sources/mongoose || die
+   sed -e 's@^all:.*@all: # skipping compilation of bundled 
dev-libs/protobuf@' -i sources/ext/Makefile || die
+   find . -name \*.proto | while read f; do \
+   d=`dirname $f`; \
+   pushd $d; \
+   protoc --cpp_out=. *.proto || exit 255; \
+   popd; \
+   done || die
+   #
+   # recopy the updated files
+   cp -p sources/plinkseq/sources/lib/matrix.pb.h 
sources/plinkseq/sources/include/plinkseq/matrix.pb.h || die
+   cp -p sources/plinkseq/sources/lib/variant.pb.h 
sources/plinkseq/sources/include/plinkseq/variant.pb.h || die
+   sed -e 
's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g'
 -i sources/plinkseq/sources/lib/matrix.pb.cpp || die
+   sed -e 
's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g'
 -i sources/plinkseq/sources/lib/variant.pb.cpp || die
+   local myinc=`pkg-config protobuf --variable=includedir`
+   sed -e "s@\$(PROTOBUF_LIB_BASE_DIR)/\$(INC_DIR)/@$myinc@" -i Makefile 
|| die
+   local mylib=`pkg-config protobuf --variable=libdir`
+   sed -e "s@$(PROTOBUF_LIB_BASE_DIR)/$(BLD_LIB_DIR)/@$mylib@" -i Makefile 
|| die
+   local mylibs

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

2016-07-31 Thread Martin Mokrejs 
commit: 0bcd2e23d38e6dcf01c69ff75da32c5f419881c5
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Sun Jul 31 22:40:36 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Jul 31 22:40:36 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0bcd2e23

sci-biology/plinkseq: plugin.proto:74:12: FileDescriptorProto is not defined

Package-Manager: portage-2.3.0

 sci-biology/plinkseq/plinkseq-0.10.ebuild | 12 ++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/sci-biology/plinkseq/plinkseq-0.10.ebuild 
b/sci-biology/plinkseq/plinkseq-0.10.ebuild
index e8665ce..71871e8 100644
--- a/sci-biology/plinkseq/plinkseq-0.10.ebuild
+++ b/sci-biology/plinkseq/plinkseq-0.10.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -28,7 +28,15 @@ src_prepare(){
sed -e "s/= -static/=/g" -i config_defs.Makefile || die
rm -rf sources/ext/protobuf-* || die
sed -e 's#^all:.*#all: echo "skipping compilation of bundled 
dev-libs/protobuf"#' -i sources/ext/Makefile || die
-   find . -name \*.proto | while read f; do d=`dirname $f`; pushd $d; 
protoc --cpp_out=. *.proto || exit 255; popd; done || die
+   # TODO: fix also 
sources/ext/sources/include/DUMMY/include/google/protobuf/compiler/plugin.proto 
causing:
+   # plugin.proto: Import "google/protobuf/descriptor.proto" was not found 
or had errors.
+   # plugin.proto:74:12: "FileDescriptorProto" is not defined.
+   find . -name \*.proto | while read f; do \
+   d=`dirname $f`; \
+   pushd $d; \
+   protoc --cpp_out=. *.proto || exit 255; \
+   popd; \
+   done || die
autotools-utils_src_prepare
 }

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

2016-07-18 Thread Martin Mokrejs 
commit: 27fe4b6568a7d820178adf8f7b963bfeb79f966e
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Mon Jul 18 11:03:20 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Jul 18 11:03:20 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=27fe4b65

sci-biology/plinkseq: zap bundled dev-libs/protobuf; needs more fixes

Package-Manager: portage-2.2.28

 sci-biology/plinkseq/plinkseq-0.10.ebuild | 13 ++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/sci-biology/plinkseq/plinkseq-0.10.ebuild 
b/sci-biology/plinkseq/plinkseq-0.10.ebuild
index 1c94b80..e8665ce 100644
--- a/sci-biology/plinkseq/plinkseq-0.10.ebuild
+++ b/sci-biology/plinkseq/plinkseq-0.10.ebuild
@@ -4,7 +4,9 @@
 
 EAPI=5
 
-inherit toolchain-funcs
+AUTOTOOLS_AUTORECONF=yes
+
+inherit toolchain-funcs autotools-utils
 
 DESCRIPTION="C/C++ library for working with human genetic variation data"
 HOMEPAGE="http://atgu.mgh.harvard.edu/plinkseq";
@@ -14,15 +16,20 @@ 
SRC_URI="http://psychgen.u.hpc.mssm.edu/plinkseq_downloads/plinkseq-src-latest.t
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
 IUSE=""
 
-DEPEND="sys-libs/zlib"
+DEPEND="sys-libs/zlib
+   dev-libs/protobuf"
 RDEPEND="${DEPEND}"
 
 src_prepare(){
sed -e "s/gcc/$(tc-getCC)/g;s/g++/$(tc-getCXX)/g;s/-O3/${CFLAGS}/g" -i 
config_defs.Makefile || die
sed -e "s/= -static/=/g" -i config_defs.Makefile || die
+   rm -rf sources/ext/protobuf-* || die
+   sed -e 's#^all:.*#all: echo "skipping compilation of bundled 
dev-libs/protobuf"#' -i sources/ext/Makefile || die
+   find . -name \*.proto | while read f; do d=`dirname $f`; pushd $d; 
protoc --cpp_out=. *.proto || exit 255; popd; done || die
+   autotools-utils_src_prepare
 }
 
 src_install(){

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

2015-05-25 Thread Martin Mokrejs 
commit: 8127edeb1ec2ed6da587a58df3dc146a1a83712f
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Mon May 25 22:39:40 2015 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon May 25 22:39:40 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=8127edeb

reported a file collision to upstream

Package-Manager: portage-2.2.18

 sci-biology/plinkseq/ChangeLog| 4 
 sci-biology/plinkseq/plinkseq-0.10.ebuild | 2 ++
 2 files changed, 6 insertions(+)

diff --git a/sci-biology/plinkseq/ChangeLog b/sci-biology/plinkseq/ChangeLog
index ade0615..10c843e 100644
--- a/sci-biology/plinkseq/ChangeLog
+++ b/sci-biology/plinkseq/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  25 May 2015; Martin Mokrejs 
+  plinkseq-0.10.ebuild:
+  reported a file collision to upstream
+
 *plinkseq-0.10 (10 May 2015)
 
   10 May 2015; Martin Mokrejs  +metadata.xml,

diff --git a/sci-biology/plinkseq/plinkseq-0.10.ebuild 
b/sci-biology/plinkseq/plinkseq-0.10.ebuild
index 153c161..22f917b 100644
--- a/sci-biology/plinkseq/plinkseq-0.10.ebuild
+++ b/sci-biology/plinkseq/plinkseq-0.10.ebuild
@@ -27,5 +27,7 @@ src_prepare(){
 
 src_install(){
cd build/execs || die
+   # TODO: avoid file collision with sci-biology/fsl
+   # 
https://bitbucket.org/statgen/plinkseq/issue/9/rename-mm-filename-to-plinkseq_mm
dobin gcol browser pseq behead mm smp tab2vcf mongoose pdas
 }

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

2015-05-10 Thread Martin Mokrejs 
commit: 1b4bf42026e44bf3a934c852e0f4cb4db84036c8
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Sun May 10 19:20:25 2015 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun May 10 19:20:25 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1b4bf420

sci-biology/plinkseq: new package

Package-Manager: portage-2.2.18

 sci-biology/plinkseq/ChangeLog|  9 +
 sci-biology/plinkseq/metadata.xml |  9 +
 sci-biology/plinkseq/plinkseq-0.10.ebuild | 31 +++
 3 files changed, 49 insertions(+)

diff --git a/sci-biology/plinkseq/ChangeLog b/sci-biology/plinkseq/ChangeLog
new file mode 100644
index 000..ade0615
--- /dev/null
+++ b/sci-biology/plinkseq/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/plinkseq
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*plinkseq-0.10 (10 May 2015)
+
+  10 May 2015; Martin Mokrejs  +metadata.xml,
+  +plinkseq-0.10.ebuild:
+  sci-biology/plinkseq: new package

diff --git a/sci-biology/plinkseq/metadata.xml 
b/sci-biology/plinkseq/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/plinkseq/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+  sci-biology
+  
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+  
+

diff --git a/sci-biology/plinkseq/plinkseq-0.10.ebuild 
b/sci-biology/plinkseq/plinkseq-0.10.ebuild
new file mode 100644
index 000..153c161
--- /dev/null
+++ b/sci-biology/plinkseq/plinkseq-0.10.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION="C/C++ library for working with human genetic variation data"
+HOMEPAGE="http://atgu.mgh.harvard.edu/plinkseq";
+SRC_URI="http://psychgen.u.hpc.mssm.edu/plinkseq_downloads/plinkseq-src-latest.tgz
 -> ${P}.tgz"
+# https://bitbucket.org/statgen/plinkseq.git
+# http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="sys-libs/zlib"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+   sed -e "s/gcc/$(tc-getCC)/g;s/g++/$(tc-getCXX)/g;s/-O3/${CFLAGS}/g" -i 
config_defs.Makefile || die
+   sed -e "s/= -static/=/g" -i config_defs.Makefile || die
+}
+
+src_install(){
+   cd build/execs || die
+   dobin gcol browser pseq behead mm smp tab2vcf mongoose pdas
+}