[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/, sci-biology/abyss/files/

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     1ee6452972e294f0825ef450ec0f53cda42cb65f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 10 00:20:33 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 10 00:20:33 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1ee64529

sci-biology/abyss: removing old, 2.0.2 in main repo already

 sci-biology/abyss/abyss-1.9.0.ebuild               | 53 ----------------------
 .../abyss/files/abyss-1.9.0-ac_prog_ar.patch       | 18 --------
 sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch    | 34 --------------
 sci-biology/abyss/metadata.xml                     | 15 ------
 4 files changed, 120 deletions(-)

diff --git a/sci-biology/abyss/abyss-1.9.0.ebuild b/sci-biology/abyss/abyss-1.9.0.ebuild
deleted file mode 100644
index c32b477..0000000
--- a/sci-biology/abyss/abyss-1.9.0.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=6
-
-inherit autotools toolchain-funcs
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
-SRC_URI="https://github.com/bcgsc/abyss/archive/1.9.0.tar.gz -> ${P}.tar.gz"
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	dev-cpp/sparsehash
-	dev-libs/boost
-	misc-haskell? ( dev-libs/gmp:0=
-			virtual/libffi:0=
-	)
-	mpi? ( virtual/mpi )
-"
-DEPEND="${RDEPEND}
-	misc-haskell? ( dev-lang/ghc
-			dev-haskell/mmap )
-"
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-PATCHES=(
-	"${FILESDIR}"/${P}-ac_prog_ar.patch
-	"${FILESDIR}"/${P}-gcc-6.patch
-)
-
-src_prepare() {
-	default
-	tc-export AR
-	sed -i -e "s/-Werror//" configure.ac || die #365195
-	sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
-	eautoreconf
-}
-
-src_configure() {
-	# disable building haskell tool Misc/samtobreak
-	# unless request by user: bug #534412
-	use misc-haskell || export ac_cv_prog_ac_ct_GHC=
-
-	econf $(use_enable openmp)
-}

diff --git a/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch
deleted file mode 100644
index 158e9b1..0000000
--- a/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch
+++ /dev/null
@@ -1,18 +0,0 @@
- configure.ac | 4 ++++
- 1 file changed, 4 insertions(+)
-
-diff --git a/configure.ac b/configure.ac
-index 9d4bb66..aa94364 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -12,6 +12,10 @@ AC_PROG_CPP
- AC_PROG_CXX
- AC_PROG_INSTALL
- AC_PROG_RANLIB
-+AN_MAKEVAR([AR], [AC_PROG_AR])
-+AN_PROGRAM([ar], [AC_PROG_AR])
-+AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
-+AC_PROG_AR
- AC_CHECK_TOOL(GHC, ghc)
- AM_CONDITIONAL([HAVE_GHC], [test "$GHC"])
- 

diff --git a/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch b/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch
deleted file mode 100644
index 49a30f9..0000000
--- a/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-diff --git a/DataBase/db-csv.cc b/DataBase/db-csv.cc
-index 05cac19..48e3b44 100644
---- a/DataBase/db-csv.cc
-+++ b/DataBase/db-csv.cc
-@@ -18,11 +18,11 @@ static const char TABLE_LIST[] =
- typedef vector<string> vs;
- 
- static bool existFile(const char* f)
- {
- 	ifstream file(f);
--	return file;
-+	return bool(file);
- }
- 
- template <typename D>
- static bool existTable(
- 		D& db, const string& t)
-diff --git a/SimpleGraph/SimpleGraph.cpp b/SimpleGraph/SimpleGraph.cpp
-index 373ec70..0a9ebd3 100644
---- a/SimpleGraph/SimpleGraph.cpp
-+++ b/SimpleGraph/SimpleGraph.cpp
-@@ -645,11 +645,11 @@ static void* worker(void* pArg)
- 	for (;;) {
- 		/** Lock the input stream. */
- 		static pthread_mutex_t inMutex = PTHREAD_MUTEX_INITIALIZER;
- 		pthread_mutex_lock(&inMutex);
- 		EstimateRecord er;
--		bool good = (*arg.in) >> er;
-+		bool good = bool((*arg.in) >> er);
- 		pthread_mutex_unlock(&inMutex);
- 		if (!good)
- 			break;
- 
- 		// Flip the anterior distance estimates.

diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml
deleted file mode 100644
index c0c84f0..0000000
--- a/sci-biology/abyss/metadata.xml
+++ /dev/null
@@ -1,15 +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>
-  <maintainer type="project">
-    <email>haskell@gentoo.org</email>
-    <name>Gentoo Haskell</name>
-  </maintainer>
-  <use>
-    <flag name='misc-haskell'>build abyss-samtobreak tool, pull in haskell toolchain</flag>
-  </use>
-</pkgmetadata>