[gentoo-commits] repo/gentoo:master commit in: sci-biology/vaal/files/, sci-biology/vaal/
commit: cb6d535b3916484987d9c531cd30c043149d797b
Author: Mikle Kolyada gentoo org>
AuthorDate: Mon Jul 22 10:06:54 2019 +
Commit: Mikle Kolyada gentoo org>
CommitDate: Mon Jul 22 10:06:54 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=cb6d535b
sci-biology/vaal: remove last rited package
Signed-off-by: Mikle Kolyada gentoo.org>
sci-biology/vaal/Manifest | 3 --
sci-biology/vaal/files/vaal-46233-libieee.patch | 12 --
sci-biology/vaal/metadata.xml | 8
sci-biology/vaal/vaal-46233-r2.ebuild | 49 -
4 files changed, 72 deletions(-)
diff --git a/sci-biology/vaal/Manifest b/sci-biology/vaal/Manifest
deleted file mode 100644
index 59235379245..000
--- a/sci-biology/vaal/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST VAAL_manual.doc 48128 BLAKE2B
cc31bcdfd4d6faa8c247a9d23a6254ac8a8f8f5de20f8d188c7ed57b9f8231920b4fc7e246394b1bb48ebf457a777d82e704b51b91feb6191e5da331e5765aa9
SHA512
4da21b6559659764e108c118773bd8ed365b67e3a22de52c7c13429979bb765e7f5d05955ce746a7a55e8d3a6baa752ad575289e71dfd7fb5b8b7207f5cff171
-DIST vaal-46233.tar.gz 1148052 BLAKE2B
c3fa8ebd722e41bfa1e821d988316900a07d502b6a6b2be394b7227f269ae60a47645b45b6616a782189dcef8a1ea341265e40f257d2ee3f005e8d023273e0b6
SHA512
7a6927d06e1788411063d38e446b7e3c93192e4322a33ea652855f72e550f35debcdb970b895f1fb8504411a54d9096f3dcf506faebd33d50eb033937e15a321
-DIST vaal-46233_remove-namespace-std.patch.bz2 5879 BLAKE2B
eb10f5cec8c65c12461346b151dc2c6d60a6f980cdfda78bd97bf0cc33451f808481763e5766b76a78d3d8ef6d5f2f8798bf7b8a7b605e0d32867fdaa9073e3a
SHA512
4141094b68b4f9c643abf15d2c5e1486525a69b9d8762cd8034abd3e6f85726ed50d7f25edfcf88fc429ab90db288a583f14b2b5d8e6605cdbfab515f295979c
diff --git a/sci-biology/vaal/files/vaal-46233-libieee.patch
b/sci-biology/vaal/files/vaal-46233-libieee.patch
deleted file mode 100644
index 9f5760c0cb1..000
--- a/sci-biology/vaal/files/vaal-46233-libieee.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -ruN vaal-46233.orig/configure.ac vaal-46233/configure.ac
vaal-46233.orig/configure.ac 2018-09-29 21:58:06.059065798 +0200
-+++ vaal-46233/configure.ac2018-09-29 22:22:35.947845554 +0200
-@@ -12,7 +12,7 @@
- AX_PTHREAD
- AC_OPENMP
-
--CXXFLAGS="$CXXFLAGS -std=c++11 -Wextra -Wall -Wsign-promo
-Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long
-Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote .
-DNDEBUG"
-+CXXFLAGS="$CXXFLAGS -std=c++11 -Wextra -Wall -Wsign-promo
-Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long
-Wno-parentheses -fno-nonansi-builtins -fno-strict-aliasing -iquote . -DNDEBUG"
-
- OS_RELEASE="`uname -r`"
- AC_SUBST(CXXFLAGS)
diff --git a/sci-biology/vaal/metadata.xml b/sci-biology/vaal/metadata.xml
deleted file mode 100644
index 959160fe46b..000
--- a/sci-biology/vaal/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
-sci-biol...@gentoo.org
-Gentoo Biology Project
-
-
diff --git a/sci-biology/vaal/vaal-46233-r2.ebuild
b/sci-biology/vaal/vaal-46233-r2.ebuild
deleted file mode 100644
index 0ac15e6ff63..000
--- a/sci-biology/vaal/vaal-46233-r2.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools
-
-DESCRIPTION="Algorithm for detecting SNPs, indels, and other polymorphisms"
-HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd/;
-SRC_URI="
- ftp://ftp.broad.mit.edu/pub/crd/VAAL/latest_source_code/${P}.tar.gz
- ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc
- https://dev.gentoo.org/~mgorny/dist/${P}_remove-namespace-std.patch.bz2;
-
-LICENSE="Whitehead-MIT"
-SLOT="0"
-KEYWORDS="amd64"
-IUSE="openmp"
-
-RDEPEND="
- !sci-biology/allpaths
- !sci-biology/allpathslg"
-DEPEND="
- ${RDEPEND}
- dev-libs/boost"
-
-DOCS=( "${DISTDIR}/VAAL_manual.doc" )
-PATCHES=(
- "${FILESDIR}/${P}-libieee.patch"
- "${WORKDIR}/${P}_remove-namespace-std.patch"
-)
-
-src_prepare() {
- sed \
- -e '/COPYING/d' \
- -i src/Makefile.am || die
-
- sed \
- -e 's:-ggdb::g' \
- -e '/AC_OPENMP_CEHCK/d' \
- -i configure.ac || die
- default
- eautoreconf
-}
-
-src_configure() {
- econf \
- $(use_enable openmp)
-}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/vaal/files/, sci-biology/vaal/
commit: c24d4349f4e48f2a8aeda81be28d40e91d979f40
Author: Andreas K. Hüttel gentoo org>
AuthorDate: Sat Sep 29 20:33:49 2018 +
Commit: Andreas Hüttel gentoo org>
CommitDate: Sat Sep 29 20:34:30 2018 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c24d4349
sci-biology/vaal: Add build fix for glibc 2.27
Closes: https://bugs.gentoo.org/647878
Signed-off-by: Andreas K. Hüttel gentoo.org>
Package-Manager: Portage-2.3.49, Repoman-2.3.10
sci-biology/vaal/files/vaal-46233-libieee.patch | 12
sci-biology/vaal/vaal-46233-r2.ebuild | 3 ++-
2 files changed, 14 insertions(+), 1 deletion(-)
diff --git a/sci-biology/vaal/files/vaal-46233-libieee.patch
b/sci-biology/vaal/files/vaal-46233-libieee.patch
new file mode 100644
index 000..9f5760c0cb1
--- /dev/null
+++ b/sci-biology/vaal/files/vaal-46233-libieee.patch
@@ -0,0 +1,12 @@
+diff -ruN vaal-46233.orig/configure.ac vaal-46233/configure.ac
+--- vaal-46233.orig/configure.ac 2018-09-29 21:58:06.059065798 +0200
vaal-46233/configure.ac2018-09-29 22:22:35.947845554 +0200
+@@ -12,7 +12,7 @@
+ AX_PTHREAD
+ AC_OPENMP
+
+-CXXFLAGS="$CXXFLAGS -std=c++11 -Wextra -Wall -Wsign-promo
-Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long
-Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote .
-DNDEBUG"
++CXXFLAGS="$CXXFLAGS -std=c++11 -Wextra -Wall -Wsign-promo
-Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long
-Wno-parentheses -fno-nonansi-builtins -fno-strict-aliasing -iquote . -DNDEBUG"
+
+ OS_RELEASE="`uname -r`"
+ AC_SUBST(CXXFLAGS)
diff --git a/sci-biology/vaal/vaal-46233-r2.ebuild
b/sci-biology/vaal/vaal-46233-r2.ebuild
index 85076f33057..0ac15e6ff63 100644
--- a/sci-biology/vaal/vaal-46233-r2.ebuild
+++ b/sci-biology/vaal/vaal-46233-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -26,6 +26,7 @@ DEPEND="
DOCS=( "${DISTDIR}/VAAL_manual.doc" )
PATCHES=(
+ "${FILESDIR}/${P}-libieee.patch"
"${WORKDIR}/${P}_remove-namespace-std.patch"
)
[gentoo-commits] repo/gentoo:master commit in: sci-biology/vaal/files/, sci-biology/vaal/
commit: dd0d369425cbd225ec9c58a76456c4f539bda386
Author: Michał Górny gentoo org>
AuthorDate: Sat Dec 9 23:24:48 2017 +
Commit: Michał Górny gentoo org>
CommitDate: Sun Dec 10 00:05:29 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=dd0d3694
sci-biology/vaal: [QA] Move the patch to a distfile
Closes: https://bugs.gentoo.org/620620
sci-biology/vaal/Manifest | 5 +-
.../files/vaal-46233_remove-namespace-std.patch| 911 -
sci-biology/vaal/vaal-46233-r2.ebuild | 5 +-
3 files changed, 6 insertions(+), 915 deletions(-)
diff --git a/sci-biology/vaal/Manifest b/sci-biology/vaal/Manifest
index 8276750cfdc..59235379245 100644
--- a/sci-biology/vaal/Manifest
+++ b/sci-biology/vaal/Manifest
@@ -1,2 +1,3 @@
-DIST VAAL_manual.doc 48128 SHA256
08b662105e8db41b33ea5d6626b58d5a5d793b1dd40fdc663a7068d9abacdc83 SHA512
4da21b6559659764e108c118773bd8ed365b67e3a22de52c7c13429979bb765e7f5d05955ce746a7a55e8d3a6baa752ad575289e71dfd7fb5b8b7207f5cff171
WHIRLPOOL
3a7432974921946e28cd037e47b79fd31631f7a7915a96589a8485b84a3296e1e7d8768e84f4f9086b2648e270f9f84f1e73261bb0b492b3fa7a6cc6fe36f175
-DIST vaal-46233.tar.gz 1148052 SHA256
a1c27ae25583c1333c5169bb33a37cf461bc93b1c18c7e49f585c1cdc9e5a131 SHA512
7a6927d06e1788411063d38e446b7e3c93192e4322a33ea652855f72e550f35debcdb970b895f1fb8504411a54d9096f3dcf506faebd33d50eb033937e15a321
WHIRLPOOL
e848bcd6b2dd0c0c52142a3d55acef6a98b816e37355d22386bf3a2fac21e1318a821a394ebd5851cd530aa9afb0d178debc3f74638ee0d0820209a0f432f59f
+DIST VAAL_manual.doc 48128 BLAKE2B
cc31bcdfd4d6faa8c247a9d23a6254ac8a8f8f5de20f8d188c7ed57b9f8231920b4fc7e246394b1bb48ebf457a777d82e704b51b91feb6191e5da331e5765aa9
SHA512
4da21b6559659764e108c118773bd8ed365b67e3a22de52c7c13429979bb765e7f5d05955ce746a7a55e8d3a6baa752ad575289e71dfd7fb5b8b7207f5cff171
+DIST vaal-46233.tar.gz 1148052 BLAKE2B
c3fa8ebd722e41bfa1e821d988316900a07d502b6a6b2be394b7227f269ae60a47645b45b6616a782189dcef8a1ea341265e40f257d2ee3f005e8d023273e0b6
SHA512
7a6927d06e1788411063d38e446b7e3c93192e4322a33ea652855f72e550f35debcdb970b895f1fb8504411a54d9096f3dcf506faebd33d50eb033937e15a321
+DIST vaal-46233_remove-namespace-std.patch.bz2 5879 BLAKE2B
eb10f5cec8c65c12461346b151dc2c6d60a6f980cdfda78bd97bf0cc33451f808481763e5766b76a78d3d8ef6d5f2f8798bf7b8a7b605e0d32867fdaa9073e3a
SHA512
4141094b68b4f9c643abf15d2c5e1486525a69b9d8762cd8034abd3e6f85726ed50d7f25edfcf88fc429ab90db288a583f14b2b5d8e6605cdbfab515f295979c
diff --git a/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch
b/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch
deleted file mode 100644
index c3c3ec03248..000
--- a/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch
+++ /dev/null
@@ -1,911 +0,0 @@
-Remove 'using namespace std' causing massive havoc with newly
-introduced std::align in GCC-5. Fix bug
-https://bugs.gentoo.org/show_bug.cgi?id=568438
-
vaal-46233/src/efasta/EfastaTools.cc
-+++ vaal-46233/src/efasta/EfastaTools.cc
-@@ -18,6 +18,8 @@
- #include "math/Functions.h"
- #include "math/Array.h"
-
-+using std::set;
-+
- #define Err(message) \
- {cout << message << endl << "\nInvalid.\n" << endl; \
- TracebackThisProcess( );}
vaal-46233/src/Equiv.cc
-+++ vaal-46233/src/Equiv.cc
-@@ -9,6 +9,8 @@
- #include "Equiv.h"
- #include "Vec.h"
-
-+using std::swap;
-+
- bool equivalence_relation::equiv(int a, int b) const
- {if ( a == b ) return true;
- int c = a;
vaal-46233/src/FastaFilestream.cc
-+++ vaal-46233/src/FastaFilestream.cc
-@@ -13,6 +13,8 @@
-
- #include
-
-+using std::string;
-+
- template
- FastaFilestream::FastaFilestream( const String&
filename,
- FastaNameParser*
name_parser )
vaal-46233/src/FastaFilestreamPreview.cc
-+++ vaal-46233/src/FastaFilestreamPreview.cc
-@@ -11,6 +11,8 @@
-
- #include
-
-+using std::streamoff;
-+
- FastaFilestreamPreview::FastaFilestreamPreview(istream& filestream)
- : max_sequence_size_(0), start_offset_(0)
- {
vaal-46233/src/FastaFilestreamPreview.h
-+++ vaal-46233/src/FastaFilestreamPreview.h
-@@ -12,6 +12,8 @@
-
- #include "Vec.h"
-
-+using std::streampos;
-+
- // FastaFilestreamPreview understands just enough about the fasta
- // format to be able to count the number of sequences in the specified
- // filestream and to know where each sequence starts in that filestream.
vaal-46233/src/Fastavector.cc
-+++ vaal-46233/src/Fastavector.cc
-@@ -14,6 +14,8 @@
- #include
- #include
-
-+using std::max;
-+
- // Split this into chunks, separated by gaps ('n'), and return each chunk as a
- // gapless fastavector.
- // TODO: generalize this into a templatized STL algorithm.
vaal-46233/src/Fastavector.h
-+++ vaal-46233/src/Fastavector.h
-@@ -24,6 +24,9 @@
- #include
- #include
-
-+using std::string;
-+using
