[gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/, sci-biology/abyss/files/
commit: 159437c4bc58b8fcd12cc33bb11d8a4fef437f1b
Author: David Seifert gentoo org>
AuthorDate: Tue Dec 20 15:47:48 2016 +
Commit: David Seifert gentoo org>
CommitDate: Tue Dec 20 17:35:42 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=159437c4
sci-biology/abyss: Remove old
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/3183
sci-biology/abyss/Manifest | 3 --
sci-biology/abyss/abyss-1.3.3.ebuild | 42 -
sci-biology/abyss/abyss-1.3.6-r1.ebuild| 54 --
sci-biology/abyss/abyss-1.9.0-r1.ebuild| 53 -
.../abyss/files/abyss-1.3.3-ac_prog_ar.patch | 18
sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch | 15 --
.../abyss/files/abyss-1.3.6-ac_prog_ar.patch | 18
sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch | 15 --
sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch | 40
.../abyss/files/abyss-1.9.0-ac_prog_ar.patch | 18
sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch| 34 --
11 files changed, 310 deletions(-)
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
index f19563b..4c3779e 100644
--- a/sci-biology/abyss/Manifest
+++ b/sci-biology/abyss/Manifest
@@ -1,4 +1 @@
-DIST abyss-1.3.3.tar.gz 621480 SHA256
60396e2c8813952ceb1c66a3ad7c87eda984aa1e4952a14265217d9f639706a0 SHA512
4ec7fdd24bdb1e3d66e2bda50929122ff347107010701703e81ca1609fb1b4913c713991b3fe84a48ccfbc069e126f4f4120aafbab81e54e567a95a2f1099fb2
WHIRLPOOL
35f6fdfe60b70316e67bcbbb0a9c67e952302333e9ec71d893f2de7a94482dca1a604dc8cfef1ecee49e464244bb5df7469a8ad7bdc37bd54ff455b0f75b7914
-DIST abyss-1.3.6.tar.gz 678880 SHA256
4432a8b5046bdcb548b6f1b22069a6cade4dea26fc6f83ad5467548e4f3e7c95 SHA512
2c6d72e0227c4af2d5740a989168ad35a84b9236dc53b65a29a010c4e5f77e5c4bfaa38bfaa2f14fd530ae6df204294ff167bd40e79f61e8bad6a7489bf34ace
WHIRLPOOL
0677b1fd4090ba155fb876c0047a1ccd2ec2e220950e1e9940e1f3df05ef0abd3ba2e3dbabd500d6fab39a8f7d94e02e0a07410934733682a70fa605d2a8bc07
-DIST abyss-1.9.0.tar.gz 985480 SHA256
82e4050766a9c7fb87fd736f94724a02388efb1df847b40870a0fbf842917239 SHA512
d9da19f004bb97f9301f3be83ceb5361eb70f42139a1ef17129de99e03bda5de7680d718d76aed26d26f24c1d26c37e050801ff343acad007b76d2214955b83f
WHIRLPOOL
bd322afa9bf99a53aec177c79ca9618f39043cda606eb4e3d5dcfb46c26298d218fc154e2c46efadac59febb69dd625fe597101a1efbccc62ab8228b96cc
DIST abyss-2.0.2.tar.gz 1036135 SHA256
6482b81eb5439703c0dbf6cd7ac25cd0df7541d9e04ef7865343b241e21db460 SHA512
b19325b9d51e80378fc9818942c4005c94f470f0ad8ff6c1b8b593ad0216d35f9a99c0aa7c627082372690a6a7094ced8ca8efeb0bff6014ca46a67d7eb16a30
WHIRLPOOL
23447cb00b0bb9b5b8a724ba44f8d7193d9640ccd19956b42bbbd83b67557b66b7c68141d6f292c4ab11ab523286471d5ee1c938f22749a61162de056a0d903e
diff --git a/sci-biology/abyss/abyss-1.3.3.ebuild
b/sci-biology/abyss/abyss-1.3.3.ebuild
deleted file mode 100644
index 62b79f6..
--- a/sci-biology/abyss/abyss-1.3.3.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="4"
-
-inherit autotools eutils 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="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz;
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp"
-KEYWORDS="amd64 x86"
-
-DEPEND="
- dev-cpp/sparsehash
- dev-libs/boost
- mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-src_prepare() {
- tc-export AR
- epatch \
- "${FILESDIR}"/${P}-gcc-4.7.patch \
- "${FILESDIR}"/${P}-ac_prog_ar.patch
-
- sed -i -e "s/-Werror//" configure.ac || die #365195
- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
- eautoreconf
-}
-
-src_configure() {
- econf \
- --docdir="${EPREFIX}/usr/share/doc/${PF}" \
- $(use_enable openmp)
-}
diff --git a/sci-biology/abyss/abyss-1.3.6-r1.ebuild
b/sci-biology/abyss/abyss-1.3.6-r1.ebuild
deleted file mode 100644
index a4327b0..
--- a/sci-biology/abyss/abyss-1.3.6-r1.ebuild
+++ /dev/null
@@ -1,54 +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="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz;
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-cpp/sparsehash
-
[gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/, sci-biology/abyss/files/
commit: e5fd69e7be7b26a7b7481453553393865d823906
Author: Sergei Trofimovich gentoo org>
AuthorDate: Sun Sep 18 21:41:58 2016 +
Commit: Sergei Trofimovich gentoo org>
CommitDate: Sun Sep 18 21:42:08 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e5fd69e7
sci-biology/abyss: bump up to 1.9.0, tweak for gcc-6, bug #594254
On gcc-6 build failed as:
```
In file included from AssemblyAlgorithms.cpp:4:0:
../DataLayer/FastaReader.h: In member function ‘FastaReader::operator
void*() const’:
../DataLayer/FastaReader.h:49:35: error: cannot convert ‘std::istream {aka
std::basic_istream}’ to ‘void*’ ...
operator void*() const { return m_in; }
^~~~
```
In the following source:
```c++
static bool existFile(const char* f)
{
ifstream file(f);
return file;
}
```
c++98 provides file->operator void*()
c++11 provides file->explicit operator bool()
Hence the failure on c++11.
The change adds explicit casts around ifstream.
Reported-by: Toralf Förster
Bug: https://bugs.gentoo.org/594254
Package-Manager: portage-2.3.0
sci-biology/abyss/Manifest | 1 +
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 ++
4 files changed, 106 insertions(+)
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
index 9284afa..e995775 100644
--- a/sci-biology/abyss/Manifest
+++ b/sci-biology/abyss/Manifest
@@ -1,2 +1,3 @@
DIST abyss-1.3.3.tar.gz 621480 SHA256
60396e2c8813952ceb1c66a3ad7c87eda984aa1e4952a14265217d9f639706a0 SHA512
4ec7fdd24bdb1e3d66e2bda50929122ff347107010701703e81ca1609fb1b4913c713991b3fe84a48ccfbc069e126f4f4120aafbab81e54e567a95a2f1099fb2
WHIRLPOOL
35f6fdfe60b70316e67bcbbb0a9c67e952302333e9ec71d893f2de7a94482dca1a604dc8cfef1ecee49e464244bb5df7469a8ad7bdc37bd54ff455b0f75b7914
DIST abyss-1.3.6.tar.gz 678880 SHA256
4432a8b5046bdcb548b6f1b22069a6cade4dea26fc6f83ad5467548e4f3e7c95 SHA512
2c6d72e0227c4af2d5740a989168ad35a84b9236dc53b65a29a010c4e5f77e5c4bfaa38bfaa2f14fd530ae6df204294ff167bd40e79f61e8bad6a7489bf34ace
WHIRLPOOL
0677b1fd4090ba155fb876c0047a1ccd2ec2e220950e1e9940e1f3df05ef0abd3ba2e3dbabd500d6fab39a8f7d94e02e0a07410934733682a70fa605d2a8bc07
+DIST abyss-1.9.0.tar.gz 985480 SHA256
82e4050766a9c7fb87fd736f94724a02388efb1df847b40870a0fbf842917239 SHA512
d9da19f004bb97f9301f3be83ceb5361eb70f42139a1ef17129de99e03bda5de7680d718d76aed26d26f24c1d26c37e050801ff343acad007b76d2214955b83f
WHIRLPOOL
bd322afa9bf99a53aec177c79ca9618f39043cda606eb4e3d5dcfb46c26298d218fc154e2c46efadac59febb69dd625fe597101a1efbccc62ab8228b96cc
diff --git a/sci-biology/abyss/abyss-1.9.0.ebuild
b/sci-biology/abyss/abyss-1.9.0.ebuild
new file mode 100644
index ..c32b477
--- /dev/null
+++ b/sci-biology/abyss/abyss-1.9.0.ebuild
@@ -0,0 +1,53 @@
+# 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
new file mode 100644
index ..158e9b1
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch
@@ -0,0 +1,18 @@
+ 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],
[gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/, sci-biology/abyss/files/
commit: f462f85a318159798956f27b851268e7fd0c2a16
Author: David Seifert gentoo org>
AuthorDate: Sun Apr 3 17:57:05 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sun Apr 3 17:57:05 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f462f85a
sci-biology/abyss: Latest ebuild from science-overlay
* EAPI=6
Package-Manager: portage-2.2.28
sci-biology/abyss/abyss-1.3.6-r1.ebuild| 54 ++
sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch | 40
2 files changed, 94 insertions(+)
diff --git a/sci-biology/abyss/abyss-1.3.6-r1.ebuild
b/sci-biology/abyss/abyss-1.3.6-r1.ebuild
new file mode 100644
index 000..a4327b0
--- /dev/null
+++ b/sci-biology/abyss/abyss-1.3.6-r1.ebuild
@@ -0,0 +1,54 @@
+# 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="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz;
+
+LICENSE="abyss"
+SLOT="0"
+IUSE="+mpi openmp misc-haskell"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-cpp/sparsehash
+ dev-libs/boost
+ misc-haskell? ( dev-libs/gmp:0=
+ virtual/libffi:0=
+ )
+ mpi? ( virtual/mpi )
+"
+DEPEND="${RDEPEND}
+ misc-haskell? ( dev-lang/ghc
+ dev-haskell/mmap )
+"
+
+# todo: --enable-maxk=N configure option
+# todo: fix automagic mpi toggling
+
+PATCHES=(
+ "${FILESDIR}"/${P}-gcc-4.7.patch
+ "${FILESDIR}"/${P}-ac_prog_ar.patch
+ "${FILESDIR}"/${P}-samtoafg.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-1.3.6-samtoafg.patch
b/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch
new file mode 100644
index 000..cb7dfb0
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch
@@ -0,0 +1,40 @@
+Hello,
+
+I see Shaun Jackmans' (abyss-)sam2afg script is available within the
+Amos source repository. I find this very useful for coercing output from
+assemblers which which don't track read location into amos by remapping
+reads against the assembly and converting to afg - not ideal but better
+than nothing when you don't have the 'real' read locations to work with.
+
+This fails, however when reads are aligned with 'bwa mem', which can
+output multi-part alignments. sam2afg checks for reuse of the same read
+id (presumably to prevent the generation of non-unique eid values),
+consequently encountering multiple alignments for a read causes it to die.
+
+The following one-line patch allows sam2afg to skip these secondary
+alignments present in 'bwa mem' output, provided bwa mem has been run
+with the '-M' argument which sets the SAM 'secondary alignment' flag on
+the alignments in question.
+
+Hopefully this will also be of use to others...
+
+Best Regards,
+James
+
+--
+Dr. James Abbott
+Lead Bioinformatician
+Bioinformatics Support Service
+Imperial College, London
+
+
+--- abyss-1.3.6/bin/abyss-samtoafg.ori 2015-05-23 23:43:46.797747928 +0200
abyss-1.3.6/bin/abyss-samtoafg 2015-05-23 23:44:09.227747743 +0200
+@@ -105,6 +105,7 @@
+ die unless defined $qqual;
+
+ $tstart--; # convert to zero-based coordinate
++next if $flag & 0x100; # secondary alignment
+ $qid .= "/1" if $flag & 0x40; #FREAD1
+ $qid .= "/2" if $flag & 0x80; #FREAD2
+
[gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/, sci-biology/abyss/files/
commit: 61b63e5e683cf45cb9f52dca6b4f5462a472dc84
Author: David Seifert gentoo org>
AuthorDate: Sun Apr 3 18:00:32 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sun Apr 3 18:00:32 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=61b63e5e
sci-biology/abyss: Remove old
Package-Manager: portage-2.2.28
sci-biology/abyss/Manifest| 1 -
sci-biology/abyss/abyss-1.3.4.ebuild | 46 --
sci-biology/abyss/abyss-1.3.6.ebuild | 58 ---
sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch | 15 --
4 files changed, 120 deletions(-)
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
index 77dfde1..9284afa 100644
--- a/sci-biology/abyss/Manifest
+++ b/sci-biology/abyss/Manifest
@@ -1,3 +1,2 @@
DIST abyss-1.3.3.tar.gz 621480 SHA256
60396e2c8813952ceb1c66a3ad7c87eda984aa1e4952a14265217d9f639706a0 SHA512
4ec7fdd24bdb1e3d66e2bda50929122ff347107010701703e81ca1609fb1b4913c713991b3fe84a48ccfbc069e126f4f4120aafbab81e54e567a95a2f1099fb2
WHIRLPOOL
35f6fdfe60b70316e67bcbbb0a9c67e952302333e9ec71d893f2de7a94482dca1a604dc8cfef1ecee49e464244bb5df7469a8ad7bdc37bd54ff455b0f75b7914
-DIST abyss-1.3.4.tar.gz 640545 SHA256
6b6ccb04baaa9d244dd67d95e1512a934d2e54fd28a539149b6845ed5c496baf SHA512
0fa4c14117699945e007412deaeeccca27124a210669accbc1444baf5a4de1a17e1f9b48e6ee43fefed63f0d56b933c847363e59a0fc2bad60ae6d603cd8c09e
WHIRLPOOL
42b16f22bc47c8f29b07c256d504d6f58119c64fdcf0e198fd8b836ceb45139fd5cadc7feec72adf958800e55eb1065a449ce7dd288339887dcea4ab13623c01
DIST abyss-1.3.6.tar.gz 678880 SHA256
4432a8b5046bdcb548b6f1b22069a6cade4dea26fc6f83ad5467548e4f3e7c95 SHA512
2c6d72e0227c4af2d5740a989168ad35a84b9236dc53b65a29a010c4e5f77e5c4bfaa38bfaa2f14fd530ae6df204294ff167bd40e79f61e8bad6a7489bf34ace
WHIRLPOOL
0677b1fd4090ba155fb876c0047a1ccd2ec2e220950e1e9940e1f3df05ef0abd3ba2e3dbabd500d6fab39a8f7d94e02e0a07410934733682a70fa605d2a8bc07
diff --git a/sci-biology/abyss/abyss-1.3.4.ebuild
b/sci-biology/abyss/abyss-1.3.4.ebuild
deleted file mode 100644
index e230da8..000
--- a/sci-biology/abyss/abyss-1.3.4.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end
sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/;
-SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz;
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- dev-cpp/sparsehash
- mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-PATCHES=(
- "${FILESDIR}"/${P}-gcc-4.7.patch
- "${FILESDIR}"/${PN}-1.3.3-ac_prog_ar.patch
- )
-
-src_prepare() {
- tc-export AR
- sed -i -e "s/-Werror//" configure.ac || die #365195
- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
- autotools-utils_src_prepare
-}
-
-src_configure() {
- local myeconfargs=(
- --docdir="${EPREFIX}/usr/share/doc/${PF}"
- $(use_enable openmp)
- )
- autotools-utils_src_configure
-}
diff --git a/sci-biology/abyss/abyss-1.3.6.ebuild
b/sci-biology/abyss/abyss-1.3.6.ebuild
deleted file mode 100644
index 904b3e1..000
--- a/sci-biology/abyss/abyss-1.3.6.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end
sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/;
-SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz;
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-cpp/sparsehash
- dev-libs/boost
- misc-haskell? ( dev-libs/gmp:0=
- virtual/libffi:0=
- )
- mpi? ( virtual/mpi )
-"
-DEPEND="${RDEPEND}
- misc-haskell? ( dev-lang/ghc
- dev-haskell/mmap )
-"
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-PATCHES=(
- "${FILESDIR}"/${P}-gcc-4.7.patch
- "${FILESDIR}"/${P}-ac_prog_ar.patch
- )
-
-src_prepare() {
- tc-export AR
- sed -i -e "s/-Werror//" configure.ac || die #365195
- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
- autotools-utils_src_prepare
-}
-
-src_configure() {
- # disable building haskell tool Misc/samtobreak
- # unless request by user: bug #534412
- use misc-haskell || export ac_cv_prog_ac_ct_GHC=
-
- local myeconfargs=(
-
