* [gentoo-commits] repo/gentoo:master commit in: sci-biology/mosaik/files/, sci-biology/mosaik/
@ 2017-12-24 18:00 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2017-12-24 18:00 UTC (permalink / raw
To: gentoo-commits
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() {
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/mosaik/files/, sci-biology/mosaik/
@ 2021-07-25 23:06 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2021-07-25 23:06 UTC (permalink / raw
To: gentoo-commits
commit: 60b0fd58e2765499b9d2a83c3293b7021b05908c
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Jul 25 23:06:31 2021 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jul 25 23:06:31 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=60b0fd58
sci-biology/mosaik: Fix GCC 11 build
Closes: https://bugs.gentoo.org/788331
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/mosaik/files/mosaik-2.2.30-gcc11.patch | 60 ++++++++++++++++++++++
sci-biology/mosaik/mosaik-2.2.30.ebuild | 8 +--
2 files changed, 64 insertions(+), 4 deletions(-)
diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-gcc11.patch b/sci-biology/mosaik/files/mosaik-2.2.30-gcc11.patch
new file mode 100644
index 00000000000..918d882983a
--- /dev/null
+++ b/sci-biology/mosaik/files/mosaik-2.2.30-gcc11.patch
@@ -0,0 +1,60 @@
+--- a/CommonSource/DataStructures/UnorderedMap.h
++++ b/CommonSource/DataStructures/UnorderedMap.h
+@@ -42,13 +42,9 @@
+
+ #else // all decent C++ compilers
+
+-#ifdef WIN32
+ #include <unordered_map>
+-#else // Linux
+-#include <tr1/unordered_map>
+-#endif
+
+-using namespace std::tr1;
++using namespace std;
+
+ #endif
+
+--- a/CommonSource/DataStructures/UnorderedSet.h
++++ b/CommonSource/DataStructures/UnorderedSet.h
+@@ -42,13 +42,9 @@
+
+ #else // all decent C++ compilers
+
+-#ifdef WIN32
+ #include <unordered_set>
+-#else // Linux
+-#include <tr1/unordered_set>
+-#endif
+
+-using namespace std::tr1;
++using namespace std;
+
+ #endif
+
+--- a/CommonSource/Utilities/RegexUtilities.h
++++ b/CommonSource/Utilities/RegexUtilities.h
+@@ -12,10 +12,7 @@
+ #define REGEXUTILITIES_H_
+
+ #include <iostream>
+-#ifdef WIN32
+ #include <regex>
+-using namespace std::tr1;
+-#endif
+ #include <string>
+ #include <vector>
+ #include <cstdlib>
+--- a/MosaikBuild/MosaikBuild.h
++++ b/MosaikBuild/MosaikBuild.h
+@@ -15,10 +15,7 @@
+ #include <iostream>
+ #include <fstream>
+ #include <map>
+-#ifdef WIN32
+ #include <regex>
+-using namespace std::tr1;
+-#endif
+ #include <set>
+ #include <sstream>
+ #include "ColorspaceUtilities.h"
diff --git a/sci-biology/mosaik/mosaik-2.2.30.ebuild b/sci-biology/mosaik/mosaik-2.2.30.ebuild
index 874edba4504..633738b8f4c 100644
--- a/sci-biology/mosaik/mosaik-2.2.30.ebuild
+++ b/sci-biology/mosaik/mosaik-2.2.30.ebuild
@@ -1,25 +1,25 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
inherit flag-o-matic toolchain-funcs vcs-snapshot
DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies"
HOMEPAGE="https://github.com/wanpinglee/MOSAIK"
SRC_URI="https://github.com/wanpinglee/MOSAIK/archive/5c25216d3522d6a33e53875cd76a6d65001e4e67.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${P}/src"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-S="${WORKDIR}/${P}/src"
-
PATCHES=(
"${FILESDIR}"/${P}-remove-platform-code.patch
"${FILESDIR}"/${P}-fix-build-system.patch
"${FILESDIR}"/${P}-Wformat-security.patch
"${FILESDIR}"/${P}-gcc7.patch
+ "${FILESDIR}"/${P}-gcc11.patch
)
src_configure() {
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/mosaik/files/, sci-biology/mosaik/
@ 2022-06-13 12:10 Sam James
0 siblings, 0 replies; 3+ messages in thread
From: Sam James @ 2022-06-13 12:10 UTC (permalink / raw
To: gentoo-commits
commit: 3a8ddd083f460ba38a0950f1da70ff0ac2108bff
Author: Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 13 12:09:55 2022 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Mon Jun 13 12:10:16 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3a8ddd08
sci-biology/mosaik: fix build with GCC 12
Closes: https://bugs.gentoo.org/851669
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-biology/mosaik/files/mosaik-2.2.30-gcc12-time.patch | 11 +++++++++++
sci-biology/mosaik/mosaik-2.2.30.ebuild | 1 +
2 files changed, 12 insertions(+)
diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-gcc12-time.patch b/sci-biology/mosaik/files/mosaik-2.2.30-gcc12-time.patch
new file mode 100644
index 000000000000..1bc63bfd4776
--- /dev/null
+++ b/sci-biology/mosaik/files/mosaik-2.2.30-gcc12-time.patch
@@ -0,0 +1,11 @@
+https://bugs.gentoo.org/851669
+--- a/CommonSource/Utilities/SafeFunctions.h
++++ b/CommonSource/Utilities/SafeFunctions.h
+@@ -17,6 +17,7 @@
+ #include <cstdio>
+ #include <cstdarg>
+ #include <cstring>
++#include <ctime>
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <errno.h>
diff --git a/sci-biology/mosaik/mosaik-2.2.30.ebuild b/sci-biology/mosaik/mosaik-2.2.30.ebuild
index 0aee0a2cfbd9..a929f1160f67 100644
--- a/sci-biology/mosaik/mosaik-2.2.30.ebuild
+++ b/sci-biology/mosaik/mosaik-2.2.30.ebuild
@@ -20,6 +20,7 @@ PATCHES=(
"${FILESDIR}"/${P}-Wformat-security.patch
"${FILESDIR}"/${P}-gcc7.patch
"${FILESDIR}"/${P}-gcc11.patch
+ "${FILESDIR}"/${P}-gcc12-time.patch
)
src_configure() {
^ permalink raw reply related [flat|nested] 3+ messages in thread
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