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

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* [gentoo-commits] proj/sci:master commit in: sci-biology/plinkseq/
@ 2015-05-10 19:21 Martin Mokrejs
  0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2015-05-10 19:21 UTC (permalink / raw
  To: gentoo-commits

commit:     1b4bf42026e44bf3a934c852e0f4cb4db84036c8
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun May 10 19:20:25 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun May 10 19:20:25 2015 +0000
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 0000000..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 <mmokrejs@fold.natur.cuni.cz> +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 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/plinkseq/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>

diff --git a/sci-biology/plinkseq/plinkseq-0.10.ebuild b/sci-biology/plinkseq/plinkseq-0.10.ebuild
new file mode 100644
index 0000000..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
+}


^ permalink raw reply related	[flat|nested] 9+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/plinkseq/
@ 2015-05-25 22:40 Martin Mokrejs
  0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2015-05-25 22:40 UTC (permalink / raw
  To: gentoo-commits

commit:     8127edeb1ec2ed6da587a58df3dc146a1a83712f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 25 22:39:40 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 25 22:39:40 2015 +0000
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 <mmokrejs@fold.natur.cuni.cz>
+  plinkseq-0.10.ebuild:
+  reported a file collision to upstream
+
 *plinkseq-0.10 (10 May 2015)
 
   10 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +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
 }


^ permalink raw reply related	[flat|nested] 9+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/plinkseq/
@ 2016-07-18 11:03 Martin Mokrejs
  0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2016-07-18 11:03 UTC (permalink / raw
  To: gentoo-commits

commit:     27fe4b6568a7d820178adf8f7b963bfeb79f966e
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jul 18 11:03:20 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jul 18 11:03:20 2016 +0000
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(){


^ permalink raw reply related	[flat|nested] 9+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/plinkseq/
@ 2016-07-31 22:40 Martin Mokrejs
  0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2016-07-31 22:40 UTC (permalink / raw
  To: gentoo-commits

commit:     0bcd2e23d38e6dcf01c69ff75da32c5f419881c5
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jul 31 22:40:36 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jul 31 22:40:36 2016 +0000
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
 }
 


^ permalink raw reply related	[flat|nested] 9+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/plinkseq/
@ 2016-12-04 18:41 Martin Mokrejs
  0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2016-12-04 18:41 UTC (permalink / raw
  To: gentoo-commits

commit:     7fe9fb808188b046045fb31e3bf5a7d228511d09
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Dec  4 18:41:07 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Dec  4 18:41:07 2016 +0000
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-9999.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-9999.ebuild b/sci-biology/plinkseq/plinkseq-9999.ebuild
new file mode 100644
index 0000000..49c9a13
--- /dev/null
+++ b/sci-biology/plinkseq/plinkseq-9999.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)/@$mylib@" -i Makefile || die
+	local mylibs=`pkg-config protobuf --libs`
+	sed -e "s@libprotobuf.a@$mylibs@" -i Makefile || die
+}
+
+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 pdas
+}


^ permalink raw reply related	[flat|nested] 9+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/plinkseq/
@ 2017-01-10  1:05 Martin Mokrejs
  0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2017-01-10  1:05 UTC (permalink / raw
  To: gentoo-commits

commit:     ced948b30611f98b4e88720d0d7f4654eb7ca953
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 10 01:05:47 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 10 01:05:47 2017 +0000
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-9999.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-9999.ebuild b/sci-biology/plinkseq/plinkseq-9999.ebuild
index 49c9a13..939a2b8 100644
--- a/sci-biology/plinkseq/plinkseq-9999.ebuild
+++ b/sci-biology/plinkseq/plinkseq-9999.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
 }


^ permalink raw reply related	[flat|nested] 9+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/plinkseq/
@ 2017-01-10 12:16 Martin Mokrejs
  0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2017-01-10 12:16 UTC (permalink / raw
  To: gentoo-commits

commit:     4ee5e3f90785b4a1571df2c0d6028a542557977e
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 10 12:16:12 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 10 12:16:12 2017 +0000
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-9999.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-9999.ebuild b/sci-biology/plinkseq/plinkseq-9999.ebuild
index 939a2b8..c17fb39 100644
--- a/sci-biology/plinkseq/plinkseq-9999.ebuild
+++ b/sci-biology/plinkseq/plinkseq-9999.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 \


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* [gentoo-commits] proj/sci:master commit in: sci-biology/plinkseq/
@ 2017-03-31 21:20 Martin Mokrejs
  0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2017-03-31 21:20 UTC (permalink / raw
  To: gentoo-commits

commit:     ef3daf274a3921856131027f304698bad8b2d141
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 31 21:19:21 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 31 21:19:21 2017 +0000
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-9999.ebuild | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/sci-biology/plinkseq/plinkseq-9999.ebuild b/sci-biology/plinkseq/plinkseq-9999.ebuild
index 461e62f84..cffdaff97 100644
--- a/sci-biology/plinkseq/plinkseq-9999.ebuild
+++ b/sci-biology/plinkseq/plinkseq-9999.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(){


^ permalink raw reply related	[flat|nested] 9+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/plinkseq/
@ 2021-01-20  9:06 Andrew Ammerlaan
  0 siblings, 0 replies; 9+ messages in thread
From: Andrew Ammerlaan @ 2021-01-20  9:06 UTC (permalink / raw
  To: gentoo-commits

commit:     9103b70e66e9d368c3ef7105b432183c07f49da5
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Jan 20 09:06:29 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Jan 20 09:06:29 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9103b70e

sci-biology/plinkseq: remove pack, upstream gone

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/plinkseq/metadata.xml         | 12 ------
 sci-biology/plinkseq/plinkseq-0.10.ebuild | 51 -------------------------
 sci-biology/plinkseq/plinkseq-9999.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..000000000
--- a/sci-biology/plinkseq/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>

diff --git a/sci-biology/plinkseq/plinkseq-0.10.ebuild b/sci-biology/plinkseq/plinkseq-0.10.ebuild
deleted file mode 100644
index b1e4937d7..000000000
--- 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-9999.ebuild b/sci-biology/plinkseq/plinkseq-9999.ebuild
deleted file mode 100644
index cffdaff97..000000000
--- a/sci-biology/plinkseq/plinkseq-9999.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=`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)/@'"-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
-}
-
-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
-}


^ permalink raw reply related	[flat|nested] 9+ messages in thread

end of thread, other threads:[~2021-01-20  9:06 UTC | newest]

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2015-05-10 19:21 [gentoo-commits] proj/sci:master commit in: sci-biology/plinkseq/ Martin Mokrejs
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2015-05-25 22:40 Martin Mokrejs
2016-07-18 11:03 Martin Mokrejs
2016-07-31 22:40 Martin Mokrejs
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2017-01-10  1:05 Martin Mokrejs
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