commit: 482233a91158648368385cc8dd54fb0a77059020 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Dec 24 11:53:03 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Dec 24 18:00:17 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=482233a9
sci-biology/mosaik: Fix building with GCC 7 Closes: https://bugs.gentoo.org/638362 Package-Manager: Portage-2.3.19, Repoman-2.3.6 sci-biology/mosaik/files/mosaik-2.2.30-gcc7.patch | 40 +++++++++++++++++++++++ sci-biology/mosaik/mosaik-2.2.30.ebuild | 13 +++----- 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() {
