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* [gentoo-commits] proj/sci:master commit in: sci-biology/abyss/files/, sci-biology/abyss/
@ 2016-04-13 10:47 Marius Brehler
  0 siblings, 0 replies; 3+ messages in thread
From: Marius Brehler @ 2016-04-13 10:47 UTC (permalink / raw
  To: gentoo-commits

commit:     9c102d9aebd555a1db337e89911a198ba8274b55
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Apr  3 18:04:28 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Sun Apr  3 18:04:28 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9c102d9a

sci-biology/abyss: moved to main tree

 sci-biology/abyss/abyss-1.3.3-r1.ebuild            | 42 ---------------
 sci-biology/abyss/abyss-1.3.4-r1.ebuild            | 47 -----------------
 sci-biology/abyss/abyss-1.3.6-r1.ebuild            | 59 ----------------------
 .../abyss/files/abyss-1.3.3-ac_prog_ar.patch       | 18 -------
 sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch  | 15 ------
 sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch | 40 ---------------
 sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch  | 15 ------
 sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch | 40 ---------------
 .../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 ---------------
 sci-biology/abyss/metadata.xml                     | 15 ------
 12 files changed, 364 deletions(-)

diff --git a/sci-biology/abyss/abyss-1.3.3-r1.ebuild b/sci-biology/abyss/abyss-1.3.3-r1.ebuild
deleted file mode 100644
index 76f15b4..0000000
--- a/sci-biology/abyss/abyss-1.3.3-r1.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-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/${P}.tar.gz"
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
-	dev-cpp/sparsehash
-	mpi? ( virtual/mpi )"
-RDEPEND="${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 \
-		"${FILESDIR}"/${P}-samtoafg.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-1.3.4-r1.ebuild b/sci-biology/abyss/abyss-1.3.4-r1.ebuild
deleted file mode 100644
index 762d49a..0000000
--- a/sci-biology/abyss/abyss-1.3.4-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 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
-	"${FILESDIR}"/${P}-samtoafg.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-r1.ebuild b/sci-biology/abyss/abyss-1.3.6-r1.ebuild
deleted file mode 100644
index a449c72..0000000
--- a/sci-biology/abyss/abyss-1.3.6-r1.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2015 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
-	"${FILESDIR}"/${P}-samtoafg.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=(
-		--docdir="${EPREFIX}/usr/share/doc/${PF}"
-		$(use_enable openmp)
-	)
-	autotools-utils_src_configure
-}

diff --git a/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch
deleted file mode 100644
index 300868f..0000000
--- a/sci-biology/abyss/files/abyss-1.3.3-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 5c6cb92..b99bedd 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
- 
- # Checks for header files.
- AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \

diff --git a/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch
deleted file mode 100644
index 42066f7..0000000
--- a/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- ParseAligns/abyss-fixmate.cc |    1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
-index 506ea0c..a0a403c 100644
---- a/ParseAligns/abyss-fixmate.cc
-+++ b/ParseAligns/abyss-fixmate.cc
-@@ -15,6 +15,7 @@
- #include <iterator>
- #include <sstream>
- #include <string>
-+#include <unistd.h>
- 
- using namespace std;
- 

diff --git a/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch
deleted file mode 100644
index cb7dfb0..0000000
--- a/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-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
- 

diff --git a/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch
deleted file mode 100644
index c2cc35c..0000000
--- a/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- ParseAligns/abyss-fixmate.cc |    1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
-index 1a169cf..36cc05b 100644
---- a/ParseAligns/abyss-fixmate.cc
-+++ b/ParseAligns/abyss-fixmate.cc
-@@ -16,6 +16,7 @@
- #include <iterator>
- #include <sstream>
- #include <string>
-+#include <unistd.h>
- 
- using namespace std;
- 

diff --git a/sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch
deleted file mode 100644
index cb7dfb0..0000000
--- a/sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-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
- 

diff --git a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch
deleted file mode 100644
index 158e9b1..0000000
--- a/sci-biology/abyss/files/abyss-1.3.6-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-1.3.6-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch
deleted file mode 100644
index c2cc35c..0000000
--- a/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- ParseAligns/abyss-fixmate.cc |    1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
-index 1a169cf..36cc05b 100644
---- a/ParseAligns/abyss-fixmate.cc
-+++ b/ParseAligns/abyss-fixmate.cc
-@@ -16,6 +16,7 @@
- #include <iterator>
- #include <sstream>
- #include <string>
-+#include <unistd.h>
- 
- using namespace std;
- 

diff --git a/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch
deleted file mode 100644
index cb7dfb0..0000000
--- a/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-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
- 

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>


^ permalink raw reply related	[flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/abyss/files/, sci-biology/abyss/
@ 2016-10-12  6:30 Marius Brehler
  0 siblings, 0 replies; 3+ messages in thread
From: Marius Brehler @ 2016-10-12  6:30 UTC (permalink / raw
  To: gentoo-commits

commit:     b81e4c632efa6b2d53c8750b84deb2b315c86dd0
Author:     Sergei Trofimovich <slyfox <AT> inbox <DOT> ru>
AuthorDate: Fri Sep 23 13:16:56 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Fri Sep 23 13:16:56 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b81e4c63

sci-biology/abyss: tweak for gcc-6, bug #594254 (#681)

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<char>}’ 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 istream.

Reported-by: Toralf Förster
Bug: https://bugs.gentoo.org/594254

Package-Manager: portage-2.3.0

 sci-biology/abyss/abyss-1.9.0.ebuild            |  1 +
 sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch | 34 +++++++++++++++++++++++++
 2 files changed, 35 insertions(+)

diff --git a/sci-biology/abyss/abyss-1.9.0.ebuild b/sci-biology/abyss/abyss-1.9.0.ebuild
index b2de141..c32b477 100644
--- a/sci-biology/abyss/abyss-1.9.0.ebuild
+++ b/sci-biology/abyss/abyss-1.9.0.ebuild
@@ -33,6 +33,7 @@ DEPEND="${RDEPEND}
 
 PATCHES=(
 	"${FILESDIR}"/${P}-ac_prog_ar.patch
+	"${FILESDIR}"/${P}-gcc-6.patch
 )
 
 src_prepare() {

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
new file mode 100644
index 0000000..49a30f9
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch
@@ -0,0 +1,34 @@
+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.


^ permalink raw reply related	[flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/abyss/files/, sci-biology/abyss/
@ 2022-01-13 11:18 Andrew Ammerlaan
  0 siblings, 0 replies; 3+ messages in thread
From: Andrew Ammerlaan @ 2022-01-13 11:18 UTC (permalink / raw
  To: gentoo-commits

commit:     55988add1d9840ba07f1eea2067a77b6eba3a9e5
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 13 11:17:24 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Jan 13 11:18:40 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=55988add

sci-biology/abyss: move the new versions to ::gentoo

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/abyss/abyss-2.2.5-r1.ebuild            | 58 ----------------------
 sci-biology/abyss/abyss-2.3.0-r1.ebuild            | 58 ----------------------
 sci-biology/abyss/abyss-2.3.1.ebuild               | 58 ----------------------
 .../files/abyss-2.2.5-ContigProperties.h.patch     | 11 ----
 .../files/abyss-2.2.5-PathConsensus-assert.patch   | 11 ----
 sci-biology/abyss/metadata.xml                     | 18 -------
 6 files changed, 214 deletions(-)

diff --git a/sci-biology/abyss/abyss-2.2.5-r1.ebuild b/sci-biology/abyss/abyss-2.2.5-r1.ebuild
deleted file mode 100644
index d9134813b..000000000
--- a/sci-biology/abyss/abyss-2.2.5-r1.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-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/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	dev-cpp/sparsehash
-	dev-libs/boost:=
-	misc-haskell? (
-		dev-libs/gmp:0=
-		dev-libs/libffi:0=
-	)
-	mpi? ( sys-cluster/openmpi )"
-DEPEND="${RDEPEND}
-	misc-haskell? (
-		dev-lang/ghc
-	)"
-
-PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch
-		"${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch
-	)
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-src_prepare() {
-	default
-	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) --enable-maxk=256
-}

diff --git a/sci-biology/abyss/abyss-2.3.0-r1.ebuild b/sci-biology/abyss/abyss-2.3.0-r1.ebuild
deleted file mode 100644
index d9134813b..000000000
--- a/sci-biology/abyss/abyss-2.3.0-r1.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-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/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	dev-cpp/sparsehash
-	dev-libs/boost:=
-	misc-haskell? (
-		dev-libs/gmp:0=
-		dev-libs/libffi:0=
-	)
-	mpi? ( sys-cluster/openmpi )"
-DEPEND="${RDEPEND}
-	misc-haskell? (
-		dev-lang/ghc
-	)"
-
-PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch
-		"${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch
-	)
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-src_prepare() {
-	default
-	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) --enable-maxk=256
-}

diff --git a/sci-biology/abyss/abyss-2.3.1.ebuild b/sci-biology/abyss/abyss-2.3.1.ebuild
deleted file mode 100644
index d9134813b..000000000
--- a/sci-biology/abyss/abyss-2.3.1.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-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/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	dev-cpp/sparsehash
-	dev-libs/boost:=
-	misc-haskell? (
-		dev-libs/gmp:0=
-		dev-libs/libffi:0=
-	)
-	mpi? ( sys-cluster/openmpi )"
-DEPEND="${RDEPEND}
-	misc-haskell? (
-		dev-lang/ghc
-	)"
-
-PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch
-		"${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch
-	)
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-src_prepare() {
-	default
-	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) --enable-maxk=256
-}

diff --git a/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch b/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch
deleted file mode 100644
index 95181f082..000000000
--- a/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- abyss-2.2.5/Common/ContigProperties.h.ori	2020-09-18 20:42:12.000000000 +0200
-+++ abyss-2.2.5/Common/ContigProperties.h	2021-04-14 12:31:23.682158000 +0200
-@@ -171,7 +171,7 @@
- template <typename T>
- ContigProperties& operator+=(ContigProperties& a, const T& b)
- {
--	assert((int)a.length + (int)b.distance > 0);
-+	assert((int)a.length + (int)b.distance >= 0);
- 	a.length += b.distance;
- 	return a;
- }

diff --git a/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch b/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch
deleted file mode 100644
index 754e25acc..000000000
--- a/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- abyss-2.2.5/MergePaths/PathConsensus.cpp	2020-09-18 20:42:12.000000000 +0200
-+++ abyss-2.2.5/MergePaths/PathConsensus.cpp	2021-04-12 22:26:28.780547000 +0200
-@@ -379,7 +379,7 @@
- 		unsigned overlap, Sequence& seq,
- 		const Sequence& s, const ContigNode& node, const Path& path)
- {
--	assert(s.length() > overlap);
-+	assert(s.length() >= overlap);
- 	Sequence ao;
- 	Sequence bo(s, 0, overlap);
- 	Sequence o;

diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml
deleted file mode 100644
index 47116e507..000000000
--- a/sci-biology/abyss/metadata.xml
+++ /dev/null
@@ -1,18 +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>
-  <upstream>
-    <remote-id type="github">bcgsc/abyss</remote-id>
-  </upstream>
-</pkgmetadata>


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Thread overview: 3+ messages (download: mbox.gz follow: Atom feed
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2016-04-13 10:47 [gentoo-commits] proj/sci:master commit in: sci-biology/abyss/files/, sci-biology/abyss/ Marius Brehler
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2016-10-12  6:30 Marius Brehler
2022-01-13 11:18 Andrew Ammerlaan

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