* [gentoo-commits] repo/gentoo:master commit in: sci-libs/libmems/files/, sci-libs/libmems/
@ 2015-12-25 11:44 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2015-12-25 11:44 UTC (permalink / raw
To: gentoo-commits
commit: 319e280a8e026786b319d48de907e440049f490c
Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Thu Dec 24 23:32:17 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Dec 25 11:44:51 2015 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=319e280a
sci-libs/libmems: Version bump, fix bug 529770 and QA issues.
Package-Manager: portage-2.2.26
.../files/libmems-1.6_p1-broken-constness.patch | 24 +++++++++++++++
sci-libs/libmems/files/libmems-1.6_p1-build.patch | 10 ++++++
sci-libs/libmems/libmems-1.6_p1-r1.ebuild | 36 ++++++++++++++++++++++
3 files changed, 70 insertions(+)
diff --git a/sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch b/sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch
new file mode 100644
index 0000000..0bd922c
--- /dev/null
+++ b/sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch
@@ -0,0 +1,24 @@
+Fix bug 529770 caused by non-const copy constructor.
+
+--- libmems-1.6_p1/libMems/Aligner.cpp
++++ libmems-1.6_p1/libMems/Aligner.cpp
+@@ -939,7 +939,7 @@
+ MatchLeftEndComparator( unsigned seq = 0 ){
+ m_seq = seq;
+ }
+- MatchLeftEndComparator( MatchLeftEndComparator& msc ){
++ MatchLeftEndComparator( const MatchLeftEndComparator& msc ){
+ m_seq = msc.m_seq;
+ }
+ // TODO?? make this do a wraparound comparison if all is equal?
+--- libmems-1.6_p1/libMems/Aligner.h
++++ libmems-1.6_p1/libMems/Aligner.h
+@@ -49,7 +49,7 @@
+ LabeledMemComparator( uint seq ){
+ m_seq = seq;
+ }
+- LabeledMemComparator( LabeledMemComparator& lmc ){
++ LabeledMemComparator( const LabeledMemComparator& lmc ){
+ m_seq = lmc.m_seq;
+ }
+ boolean operator()(const LabeledMem& a, const LabeledMem& b) const{
diff --git a/sci-libs/libmems/files/libmems-1.6_p1-build.patch b/sci-libs/libmems/files/libmems-1.6_p1-build.patch
index 63e5f12..04d5dd9 100644
--- a/sci-libs/libmems/files/libmems-1.6_p1-build.patch
+++ b/sci-libs/libmems/files/libmems-1.6_p1-build.patch
@@ -17,3 +17,13 @@ index 6101f71..d66053d 100644
LIBMEMS_H = \
RepeatHash.h MatchHashEntry.h \
+--- a/libMems/dmSML/util.c
++++ b/libMems/dmSML/util.c
+@@ -2,6 +2,7 @@
+ #include "config.h"
+ #endif
+
++#include <stdlib.h>
+ #include <stdio.h>
+ #include "libMems/dmSML/util.h"
+
diff --git a/sci-libs/libmems/libmems-1.6_p1-r1.ebuild b/sci-libs/libmems/libmems-1.6_p1-r1.ebuild
new file mode 100644
index 0000000..2e094ab
--- /dev/null
+++ b/sci-libs/libmems/libmems-1.6_p1-r1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit autotools
+
+DESCRIPTION="Library for sci-biology/mauve"
+HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/"
+SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
+
+SLOT="0"
+LICENSE="GPL-2"
+IUSE="doc"
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="
+ dev-libs/boost
+ sci-libs/libgenome
+ sci-libs/libmuscle"
+DEPEND="${CDEPEND}
+ doc? ( app-doc/doxygen )"
+RDEPEND="${CDEPEND}"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-build.patch
+ "${FILESDIR}"/${P}-boost.patch
+ "${FILESDIR}"/${P}-gcc-4.7.patch
+ "${FILESDIR}"/${P}-broken-constness.patch
+ )
+
+src_prepare() {
+ default
+ eautoreconf
+}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-libs/libmems/files/, sci-libs/libmems/
@ 2015-12-25 11:44 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2015-12-25 11:44 UTC (permalink / raw
To: gentoo-commits
commit: 52486aed57b047d4c834cc10d4f70229e5e67891
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 25 11:01:28 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Dec 25 11:44:51 2015 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=52486aed
sci-libs/libmems: Fix for format-security
Package-Manager: portage-2.2.26
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
.../libmems/files/libmems-1.6_p1-format-security.patch | 16 ++++++++++++++++
sci-libs/libmems/libmems-1.6_p1-r1.ebuild | 1 +
2 files changed, 17 insertions(+)
diff --git a/sci-libs/libmems/files/libmems-1.6_p1-format-security.patch b/sci-libs/libmems/files/libmems-1.6_p1-format-security.patch
new file mode 100644
index 0000000..3ad3da2
--- /dev/null
+++ b/sci-libs/libmems/files/libmems-1.6_p1-format-security.patch
@@ -0,0 +1,16 @@
+ libMems/dmSML/dmsort.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/libMems/dmSML/dmsort.c b/libMems/dmSML/dmsort.c
+index 4c99215..2cbfa7e 100644
+--- a/libMems/dmSML/dmsort.c
++++ b/libMems/dmSML/dmsort.c
+@@ -825,7 +825,7 @@ int InitdmSML( long working_mb, long buffer_size, const char* input_filename, co
+ if ( fgets(buf, sizeof(buf), fp) )
+ {
+ sscanf(buf, "MemTotal: %ld kB", &memTotal);
+- fprintf( stderr, buf );
++ fprintf( stderr, "%s", buf );
+ }
+ fclose(fp);
+ // allocate about 6/10 of physical memory
diff --git a/sci-libs/libmems/libmems-1.6_p1-r1.ebuild b/sci-libs/libmems/libmems-1.6_p1-r1.ebuild
index 2e094ab..ac61e54 100644
--- a/sci-libs/libmems/libmems-1.6_p1-r1.ebuild
+++ b/sci-libs/libmems/libmems-1.6_p1-r1.ebuild
@@ -28,6 +28,7 @@ PATCHES=(
"${FILESDIR}"/${P}-boost.patch
"${FILESDIR}"/${P}-gcc-4.7.patch
"${FILESDIR}"/${P}-broken-constness.patch
+ "${FILESDIR}"/${P}-format-security.patch
)
src_prepare() {
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-libs/libmems/files/, sci-libs/libmems/
@ 2016-09-24 19:02 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2016-09-24 19:02 UTC (permalink / raw
To: gentoo-commits
commit: 8ee85fd0668f17101b4dd8ad1b35ee0194521184
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 24 15:03:46 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep 24 19:02:07 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8ee85fd0
sci-libs/libmems: Allow for compiling with GCC 6
Gentoo-bug: 594814
* Patch taken from Debian
* Add sub-slot operator for dev-libs/boost
* Delete .la files
Package-Manager: portage-2.3.1
.../libmems/files/libmems-1.6_p1-fix-c++14.patch | 18 +++++++++++++++
...s-1.6_p1-r1.ebuild => libmems-1.6_p1-r2.ebuild} | 27 ++++++++++++++++------
2 files changed, 38 insertions(+), 7 deletions(-)
diff --git a/sci-libs/libmems/files/libmems-1.6_p1-fix-c++14.patch b/sci-libs/libmems/files/libmems-1.6_p1-fix-c++14.patch
new file mode 100644
index 00000000..bde8efe
--- /dev/null
+++ b/sci-libs/libmems/files/libmems-1.6_p1-fix-c++14.patch
@@ -0,0 +1,18 @@
+Description: Correct compilation with g++-6
+Author: Gert Wollny <gw.fossdev@gmail.com>
+Bug-Debian: https://bugs.debian.org/811870
+Forwarded: yes
+Bug: https://sourceforge.net/p/mauve/bugs/46/
+Last-Update: 2016-06-30
+
+--- a/libMems/ProgressiveAligner.cpp
++++ b/libMems/ProgressiveAligner.cpp
+@@ -1599,7 +1599,7 @@
+ c.SetLeftEnd(child_1, ancestral_matches[mI]->LeftEnd(1));
+ c.SetOrientation(child_1, ancestral_matches[mI]->Orientation(1));
+ c.SetLength(ancestral_matches[mI]->Length(1), child_1);
+- cga_list.push_back(make_tuple(c.Copy(), &bs[mI], ancestral_matches[mI]));
++ cga_list.push_back(boost::tuples::make_tuple(c.Copy(), &bs[mI], ancestral_matches[mI]));
+ }
+
+ stack<node_id_t> node_stack;
diff --git a/sci-libs/libmems/libmems-1.6_p1-r1.ebuild b/sci-libs/libmems/libmems-1.6_p1-r2.ebuild
similarity index 64%
rename from sci-libs/libmems/libmems-1.6_p1-r1.ebuild
rename to sci-libs/libmems/libmems-1.6_p1-r2.ebuild
index ac61e54..c00e615 100644
--- a/sci-libs/libmems/libmems-1.6_p1-r1.ebuild
+++ b/sci-libs/libmems/libmems-1.6_p1-r2.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
# $Id$
@@ -12,16 +12,15 @@ SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
SLOT="0"
LICENSE="GPL-2"
-IUSE="doc"
+IUSE="doc static-libs"
KEYWORDS="~amd64 ~x86"
-CDEPEND="
- dev-libs/boost
+RDEPEND="
+ dev-libs/boost:=
sci-libs/libgenome
sci-libs/libmuscle"
-DEPEND="${CDEPEND}
+DEPEND="${RDEPEND}
doc? ( app-doc/doxygen )"
-RDEPEND="${CDEPEND}"
PATCHES=(
"${FILESDIR}"/${P}-build.patch
@@ -29,9 +28,23 @@ PATCHES=(
"${FILESDIR}"/${P}-gcc-4.7.patch
"${FILESDIR}"/${P}-broken-constness.patch
"${FILESDIR}"/${P}-format-security.patch
- )
+ "${FILESDIR}"/${P}-fix-c++14.patch
+)
src_prepare() {
default
eautoreconf
}
+
+src_configure() {
+ econf \
+ --enable-shared \
+ $(use_enable static-libs static)
+}
+
+src_install() {
+ default
+
+ # package provides .pc files
+ find "${D}" -name '*.la' -delete || die
+}
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