* [gentoo-commits] repo/gentoo:master commit in: sci-biology/cufflinks/files/, sci-biology/cufflinks/
@ 2016-04-03 16:14 David Seifert
0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2016-04-03 16:14 UTC (permalink / raw
To: gentoo-commits
commit: bed71574b0b2911b0e667931508bb5b069883b64
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Apr 3 16:14:04 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Apr 3 16:14:40 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bed71574
sci-biology/cufflinks: Depend only on sci-biology/samtools:0.1-legacy
Gentoo-Bug: 535716
* EAPI=6
* Updated boost in tree has fixed serialization for boost::shared_ptr
* Build system is now orthogonal to sci-biology/samtools:0 and does not
block updating to latest samtools
Package-Manager: portage-2.2.28
sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild | 39 +++++++++++++++++++
.../files/cufflinks-2.2.1-samtools-legacy.patch | 44 ++++++++++++++++++++++
2 files changed, 83 insertions(+)
diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
new file mode 100644
index 0000000..2ccac30
--- /dev/null
+++ b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit autotools flag-o-matic toolchain-funcs
+
+DESCRIPTION="Transcript assembly and differential expression/regulation for RNA-Seq"
+HOMEPAGE="http://cufflinks.cbcb.umd.edu/"
+SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="Artistic"
+IUSE="debug"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="sci-biology/samtools:0.1-legacy
+ >=dev-libs/boost-1.59.0:=
+ dev-cpp/eigen:3"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-samtools-legacy.patch
+ "${FILESDIR}"/${P}-flags.patch
+)
+
+src_prepare() {
+ default
+ eautoreconf
+ append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
+}
+
+src_configure() {
+ econf --disable-optim \
+ --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/" \
+ --with-bam="${EPREFIX}/usr/" \
+ $(use_enable debug)
+}
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch
new file mode 100644
index 0000000..374ce51
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch
@@ -0,0 +1,44 @@
+Modify the buildsystem to work with the legacy version of samtools,
+which can coexist with the most recent version of samtools.
+See also: https://bugs.gentoo.org/show_bug.cgi?id=577854
+
+--- cufflinks-2.2.1/ax_bam.m4
++++ cufflinks-2.2.1/ax_bam.m4
+@@ -102,7 +102,7 @@
+
+ AC_LANG_PUSH(C++)
+ AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
+- @%:@include <bam/bam.h>
++ @%:@include <bam-0.1-legacy/bam.h>
+ ]], [[
+ ]])],[
+ AC_MSG_RESULT(yes)
+@@ -171,7 +171,7 @@
+
+ AC_LANG_PUSH(C++)
+ AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
+- @%:@include <bam/version.hpp>
++ @%:@include <bam-0.1-legacy/version.hpp>
+ ]], [[
+ ]])],[
+ AC_MSG_RESULT(yes)
+@@ -189,7 +189,7 @@
+ AC_MSG_NOTICE([Your bam libraries seem too old (version $_version).])
+ fi
+ else
+- BAM_LIB="-lbam"
++ BAM_LIB="-lbam-0.1-legacy"
+ AC_SUBST(BAM_CPPFLAGS)
+ AC_SUBST(BAM_LDFLAGS)
+ AC_SUBST(BAM_LIB)
+--- cufflinks-2.2.1/src/hits.h
++++ cufflinks-2.2.1/src/hits.h
+@@ -18,7 +18,7 @@
+
+ #include <boost/shared_ptr.hpp>
+
+-#include <bam/sam.h>
++#include <bam-0.1-legacy/sam.h>
+
+ #include "common.h"
+ #include "multireads.h"
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/cufflinks/files/, sci-biology/cufflinks/
@ 2017-06-25 17:02 David Seifert
0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2017-06-25 17:02 UTC (permalink / raw
To: gentoo-commits
commit: 535d49953c74af2bb58478979d77d5588acaca20
Author: Peter Levine <plevine457 <AT> gmail <DOT> com>
AuthorDate: Thu Jun 22 05:25:12 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jun 25 16:59:09 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=535d4995
sci-biology/cufflinks: Fix building with GCC-6
Bug: https://bugs.gentoo.org/show_bug.cgi?id=594904
Package-Manager: Portage-2.3.6, Repoman-2.3.2
Closes: https://github.com/gentoo/gentoo/pull/4969
sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild | 3 ++-
sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch | 14 ++++++++++++++
2 files changed, 16 insertions(+), 1 deletion(-)
diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
index 9ff0a2c7111..3e89f70a498 100644
--- a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
+++ b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -22,6 +22,7 @@ RDEPEND="${DEPEND}"
PATCHES=(
"${FILESDIR}"/${P}-samtools-legacy.patch
"${FILESDIR}"/${P}-flags.patch
+ "${FILESDIR}"/${P}-gcc6.patch
)
src_prepare() {
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch
new file mode 100644
index 00000000000..6ee9bcf456d
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch
@@ -0,0 +1,14 @@
+--- a/src/lemon/error.h
++++ b/src/lemon/error.h
+@@ -67,9 +67,9 @@
+ }
+
+ ExceptionMember& operator=(const ExceptionMember& copy) {
+- if (ptr.get() == 0) return;
++ if (ptr.get() == 0) return *this;
+ try {
+- if (!copy.valid()) return;
++ if (!copy.valid()) return *this;
+ *ptr = copy.get();
+ } catch (...) {}
+ }
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/cufflinks/files/, sci-biology/cufflinks/
@ 2017-09-16 10:58 David Seifert
0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2017-09-16 10:58 UTC (permalink / raw
To: gentoo-commits
commit: e8f6a4c4f1b147290aa62ef45d58084394ae56bd
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 16 10:54:51 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep 16 10:58:20 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e8f6a4c4
sci-biology/cufflinks: Fix boost TR1 header include
* Also fix missing python dependencies
Closes: https://bugs.gentoo.org/630654
Package-Manager: Portage-2.3.8, Repoman-2.3.3
sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild | 35 +++++++++++++++-------
.../cufflinks-2.2.1-boost-1.65-tr1-removal.patch | 14 +++++++++
2 files changed, 39 insertions(+), 10 deletions(-)
diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
index 3e89f70a498..89f8484fad6 100644
--- a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
+++ b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
@@ -3,37 +3,52 @@
EAPI=6
-inherit autotools flag-o-matic toolchain-funcs
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools flag-o-matic python-single-r1 toolchain-funcs
DESCRIPTION="Transcript assembly and differential expression/regulation for RNA-Seq"
HOMEPAGE="http://cufflinks.cbcb.umd.edu/"
SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz"
-SLOT="0"
LICENSE="Artistic"
-IUSE="debug"
+SLOT="0"
KEYWORDS="~amd64 ~x86"
+IUSE="debug"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-DEPEND="sci-biology/samtools:0.1-legacy
- >=dev-libs/boost-1.59.0:=
- dev-cpp/eigen:3"
-RDEPEND="${DEPEND}"
+RDEPEND="
+ sci-biology/samtools:0.1-legacy
+ >=dev-libs/boost-1.62.0:=
+ ${PYTHON_DEPS}"
+DEPEND="
+ ${RDEPEND}
+ dev-cpp/eigen:3
+ virtual/pkgconfig"
PATCHES=(
"${FILESDIR}"/${P}-samtools-legacy.patch
"${FILESDIR}"/${P}-flags.patch
"${FILESDIR}"/${P}-gcc6.patch
+ "${FILESDIR}"/${P}-boost-1.65-tr1-removal.patch
)
src_prepare() {
default
+ python_fix_shebang src/cuffmerge
+
eautoreconf
- append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
}
src_configure() {
- econf --disable-optim \
+ # keep in sync with Boost
+ append-cxxflags -std=c++14
+ append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
+
+ econf \
+ --disable-optim \
--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/" \
--with-bam="${EPREFIX}/usr/" \
- $(use_enable debug)
+ $(use_enable debug) \
+ PYTHON="${PYTHON}"
}
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch
new file mode 100644
index 00000000000..42a906e7a83
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch
@@ -0,0 +1,14 @@
+Boost 1.65 removed the TR1 headers.
+Bug: https://bugs.gentoo.org/show_bug.cgi?id=630654
+
+--- a/src/biascorrection.h
++++ b/src/biascorrection.h
+@@ -15,7 +15,7 @@
+ #include <vector>
+ #include <list>
+ #include <string>
+-#include <boost/tr1/unordered_map.hpp>
++#include <boost/unordered_map.hpp>
+ #include <boost/thread.hpp>
+ #include "common.h"
+
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/cufflinks/files/, sci-biology/cufflinks/
@ 2017-12-24 11:30 David Seifert
0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2017-12-24 11:30 UTC (permalink / raw
To: gentoo-commits
commit: ccbd59a1a246014bf441e44a9f2bd8632a70c20e
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 24 11:30:20 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Dec 24 11:30:38 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ccbd59a1
sci-biology/cufflinks: Fix building with GCC 7
Closes: https://bugs.gentoo.org/641580
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild | 2 +
.../files/cufflinks-2.2.1-format-security.patch | 16 +++
.../cufflinks/files/cufflinks-2.2.1-gcc7.patch | 121 +++++++++++++++++++++
3 files changed, 139 insertions(+)
diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
index 89f8484fad6..745baffad99 100644
--- a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
+++ b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
@@ -31,6 +31,8 @@ PATCHES=(
"${FILESDIR}"/${P}-flags.patch
"${FILESDIR}"/${P}-gcc6.patch
"${FILESDIR}"/${P}-boost-1.65-tr1-removal.patch
+ "${FILESDIR}"/${P}-gcc7.patch
+ "${FILESDIR}"/${P}-format-security.patch
)
src_prepare() {
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch
new file mode 100644
index 00000000000..fa13f78d8b5
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch
@@ -0,0 +1,16 @@
+Author: Andreas Tille <tille@debian.org>
+Date: Wed, 22 May 2013 13:27:40 +0200
+Description: When building with --format-security (Debhelper 9 hardening)
+ this patch is needed to build successfully
+
+--- a/src/locfit/makecmd.c
++++ b/src/locfit/makecmd.c
+@@ -200,7 +200,7 @@ char *cmdline;
+ /* vs is used to store the command line string. */
+ sprintf(vn,"=clstr%d",clcount);
+ vs = createvar(vn,STSYSTEM,1+strlen(cmdline),VCHAR);
+- sprintf((char *)vdptr(vs),cmdline);
++ sprintf((char *)vdptr(vs),"%s",cmdline);
+
+ /* va is used to store pointers to the command line fields. */
+ sprintf(vn,"=cline%d",clcount);
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch
new file mode 100644
index 00000000000..48fe6e10ac9
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch
@@ -0,0 +1,121 @@
+Author: Alex Mestiashvili <mailatgoogl@gmail.com>
+Origin: https://lists.debian.org/debian-med/2017/09/msg00021.html
+Bug-Debian: https://bugs.debian.org/871234
+Description: Fix gcc-7 build issue, thanks to Jeff Epler <jepler@unpythonic.net>
+--- a/src/GHash.hh
++++ b/src/GHash.hh
+@@ -88,7 +88,7 @@
+ //nextkey is SET to the corresponding key
+ GHashEntry* NextEntry() { //returns a pointer to a GHashEntry
+ register int pos=fCurrentEntry;
+- while (pos<fCapacity && hash[pos].hash<0) pos++;
++ while (pos<fCapacity && (hash[pos].hash)<0) pos++;
+ if (pos==fCapacity) {
+ fCurrentEntry=fCapacity;
+ return NULL;
+@@ -186,7 +186,7 @@
+ x=HASH2(h,n);
+ GASSERT(1<=x && x<n);
+ while(k[p].hash!=-1) p=(p+x)%n;
+- GASSERT(k[p].hash<0);
++ GASSERT((k[p].hash)<0);
+ k[p]=hash[i];
+ }
+ }
+@@ -225,7 +225,7 @@
+ GTRACE(("GHash::insert: key=\"%s\"\n",ky));
+ //GMessage("GHash::insert: key=\"%s\"\n",ky);
+ GASSERT(0<=i && i<fCapacity);
+- GASSERT(hash[i].hash<0);
++ GASSERT((hash[i].hash)<0);
+ hash[i].hash=h;
+ hash[i].mark=mrk;
+ hash[i].key=Gstrdup(ky);
+@@ -266,7 +266,7 @@
+ GTRACE(("GHash::insert: key=\"%s\"\n",ky));
+ //GMessage("GHash::insert: key=\"%s\"\n",ky);
+ GASSERT(0<=i && i<fCapacity);
+- GASSERT(hash[i].hash<0);
++ GASSERT((hash[i].hash)<0);
+ hash[i].hash=h;
+ hash[i].mark=mrk;
+ hash[i].key=(char *)ky;
+@@ -310,7 +310,7 @@
+ if(i==-1) i=p;
+ GTRACE(("GHash::replace: %08x: inserting: \"%s\"\n",this,ky));
+ GASSERT(0<=i && i<fCapacity);
+- GASSERT(hash[i].hash<0);
++ GASSERT((hash[i].hash)<0);
+ hash[i].hash=h;
+ hash[i].mark=mrk;
+ hash[i].key=Gstrdup(ky);
+@@ -412,7 +412,7 @@
+
+ template <class OBJ> char* GHash<OBJ>::NextKey() {
+ register int pos=fCurrentEntry;
+- while (pos<fCapacity && hash[pos].hash<0) pos++;
++ while (pos<fCapacity && (hash[pos].hash)<0) pos++;
+ if (pos==fCapacity) {
+ fCurrentEntry=fCapacity;
+ return NULL;
+@@ -425,7 +425,7 @@
+
+ template <class OBJ> OBJ* GHash<OBJ>::NextData() {
+ register int pos=fCurrentEntry;
+- while (pos<fCapacity && hash[pos].hash<0) pos++;
++ while (pos<fCapacity && (hash[pos].hash)<0) pos++;
+ if (pos==fCapacity) {
+ fCurrentEntry=fCapacity;
+ return NULL;
+@@ -439,7 +439,7 @@
+
+ template <class OBJ> OBJ* GHash<OBJ>::NextData(char* &nextkey) {
+ register int pos=fCurrentEntry;
+- while (pos<fCapacity && hash[pos].hash<0) pos++;
++ while (pos<fCapacity && (hash[pos].hash)<0) pos++;
+ if (pos==fCapacity) {
+ fCurrentEntry=fCapacity;
+ nextkey=NULL;
+@@ -457,16 +457,16 @@
+ // Get first non-empty entry
+ template <class OBJ> int GHash<OBJ>::First() const {
+ register int pos=0;
+- while(pos<fCapacity){ if(0<=hash[pos].hash) break; pos++; }
+- GASSERT(fCapacity<=pos || 0<=hash[pos].hash);
++ while(pos<fCapacity){ if(0<=(hash[pos].hash)) break; pos++; }
++ GASSERT(fCapacity<=pos || 0<=(hash[pos].hash));
+ return pos;
+ }
+
+ // Get last non-empty entry
+ template <class OBJ> int GHash<OBJ>::Last() const {
+ register int pos=fCapacity-1;
+- while(0<=pos){ if(0<=hash[pos].hash) break; pos--; }
+- GASSERT(pos<0 || 0<=hash[pos].hash);
++ while(0<=pos){ if(0<=(hash[pos].hash)) break; pos--; }
++ GASSERT(pos<0 || 0<=(hash[pos].hash));
+ return pos;
+ }
+
+@@ -474,8 +474,8 @@
+ // Find next valid entry
+ template <class OBJ> int GHash<OBJ>::Next(int pos) const {
+ GASSERT(0<=pos && pos<fCapacity);
+- while(++pos <= fCapacity-1){ if(0<=hash[pos].hash) break; }
+- GASSERT(fCapacity<=pos || 0<=hash[pos].hash);
++ while(++pos <= fCapacity-1){ if(0<=(hash[pos].hash)) break; }
++ GASSERT(fCapacity<=pos || 0<=(hash[pos].hash));
+ return pos;
+ }
+
+@@ -483,8 +483,8 @@
+ // Find previous valid entry
+ template <class OBJ> int GHash<OBJ>::Prev(int pos) const {
+ GASSERT(0<=pos && pos<fCapacity);
+- while(--pos >= 0){ if(0<=hash[pos].hash) break; }
+- GASSERT(pos<0 || 0<=hash[pos].hash);
++ while(--pos >= 0){ if(0<=(hash[pos].hash)) break; }
++ GASSERT(pos<0 || 0<=(hash[pos].hash));
+ return pos;
+ }
+
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/cufflinks/files/, sci-biology/cufflinks/
@ 2018-06-30 14:59 David Seifert
0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2018-06-30 14:59 UTC (permalink / raw
To: gentoo-commits
commit: e035eabc7b791b9854e53cf596b65e8330ef6e83
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 30 14:58:58 2018 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Jun 30 14:59:32 2018 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e035eabc
sci-biology/cufflinks: Fix implicit conversion in make_pair call
Closes: https://bugs.gentoo.org/650416
Package-Manager: Portage-2.3.41, Repoman-2.3.9
sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild | 3 ++-
.../cufflinks/files/cufflinks-2.2.1-gcc5-make_shared.patch | 11 +++++++++++
2 files changed, 13 insertions(+), 1 deletion(-)
diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
index 745baffad99..3892e03e23b 100644
--- a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
+++ b/sci-biology/cufflinks/cufflinks-2.2.1-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
@@ -33,6 +33,7 @@ PATCHES=(
"${FILESDIR}"/${P}-boost-1.65-tr1-removal.patch
"${FILESDIR}"/${P}-gcc7.patch
"${FILESDIR}"/${P}-format-security.patch
+ "${FILESDIR}"/${P}-gcc5-make_shared.patch
)
src_prepare() {
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc5-make_shared.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc5-make_shared.patch
new file mode 100644
index 00000000000..67a28df1024
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc5-make_shared.patch
@@ -0,0 +1,11 @@
+--- a/src/differential.cpp
++++ b/src/differential.cpp
+@@ -575,7 +575,7 @@
+ boost::mutex::scoped_lock lock(meta_data_lock);
+ #endif
+ pair<SampleDiffMetaDataTable::iterator, bool> p;
+- p = meta_data_table.insert(make_pair(description, new SampleDifferenceMetaData()));
++ p = meta_data_table.insert(make_pair(description, boost::make_shared<SampleDifferenceMetaData>()));
+ return p.first->second;
+ }
+
^ permalink raw reply related [flat|nested] 5+ messages in thread
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