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authorDavid Seifert <soap@gentoo.org>2017-12-24 12:53:03 +0100
committerDavid Seifert <soap@gentoo.org>2017-12-24 19:00:17 +0100
commit482233a91158648368385cc8dd54fb0a77059020 (patch)
tree5b99c0ba33730a2a2244f763ccdde5b688a77944 /sci-biology
parentdev-python/PythonQt: version bump to 3.2. (diff)
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sci-biology/mosaik: Fix building with GCC 7
Closes: https://bugs.gentoo.org/638362 Package-Manager: Portage-2.3.19, Repoman-2.3.6
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/mosaik/files/mosaik-2.2.30-gcc7.patch40
-rw-r--r--sci-biology/mosaik/mosaik-2.2.30.ebuild13
2 files changed, 45 insertions, 8 deletions
diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-gcc7.patch b/sci-biology/mosaik/files/mosaik-2.2.30-gcc7.patch
new file mode 100644
index 00000000000..ebf925a0cbb
--- /dev/null
+++ b/sci-biology/mosaik/files/mosaik-2.2.30-gcc7.patch
@@ -0,0 +1,40 @@
+--- a/CommonSource/ExternalReadFormats/BamWriter.cpp
++++ b/CommonSource/ExternalReadFormats/BamWriter.cpp
+@@ -496,7 +496,7 @@
+ buffer[6] = 0xffffffff; // mate_pos
+ buffer[7] = 0; // ins_size
+
+- const char* startChar = '\0';
++ const char* startChar = NULL;
+
+ // write the block size
+ const unsigned int dataBlockSize = nameLen + packedCigarLen + encodedQueryLen + queryLen;
+@@ -652,7 +652,7 @@
+ unsigned int zaTagLen = 0;
+ string zaTag;
+ char* pZaTag;
+- if ((zaString != 0) && (zaString != (char)0)) {
++ if ((zaString != 0) && (zaString[0] != '\0')) {
+ zaTagLen = 3 + strlen( zaString ) + 1;
+ zaTag.resize( zaTagLen );
+ pZaTag = (char*)zaTag.data();
+@@ -776,7 +776,7 @@
+ BgzfWrite(mdTag.data(), mdTagLen);
+
+ // write the ZA tag
+- if ( zaString != 0 && (zaString != (char)0))
++ if ( zaString != 0 && (zaString[0] != '\0'))
+ BgzfWrite(zaTag.data(), zaTagLen);
+
+ // write the ZN tag
+--- a/MosaikAligner/AlignmentThread.cpp
++++ b/MosaikAligner/AlignmentThread.cpp
+@@ -591,7 +591,7 @@
+ buffer.al = al;
+ buffer.noCigarMdNm = noCigarMdNm;
+ buffer.notShowRnamePos = notShowRnamePos;
+- if ( zaString == (char)0 )
++ if ( zaString == NULL )
+ buffer.zaString.clear();
+ else
+ buffer.zaString = zaString;
diff --git a/sci-biology/mosaik/mosaik-2.2.30.ebuild b/sci-biology/mosaik/mosaik-2.2.30.ebuild
index 45633c47dab..874edba4504 100644
--- a/sci-biology/mosaik/mosaik-2.2.30.ebuild
+++ b/sci-biology/mosaik/mosaik-2.2.30.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
@@ -11,18 +11,15 @@ SRC_URI="https://github.com/wanpinglee/MOSAIK/archive/5c25216d3522d6a33e53875cd7
LICENSE="GPL-2"
SLOT="0"
-IUSE=""
KEYWORDS="~amd64 ~x86"
-DEPEND=""
-RDEPEND=""
-
S="${WORKDIR}/${P}/src"
PATCHES=(
- "${FILESDIR}/${P}-remove-platform-code.patch"
- "${FILESDIR}/${P}-fix-build-system.patch"
- "${FILESDIR}/${P}-Wformat-security.patch"
+ "${FILESDIR}"/${P}-remove-platform-code.patch
+ "${FILESDIR}"/${P}-fix-build-system.patch
+ "${FILESDIR}"/${P}-Wformat-security.patch
+ "${FILESDIR}"/${P}-gcc7.patch
)
src_configure() {