[gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/files/, sci-biology/SPAdes/
commit: dd4ee9b222cf98145af87c7ca36dc3d0e40cd8c0
Author: Horea Christian chymera eu>
AuthorDate: Mon Jan 22 17:59:43 2024 +
Commit: Horea Christian gmail com>
CommitDate: Mon Jan 22 17:59:43 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=dd4ee9b2
sci-biology/SPAdes: keyword 3.15.5 for ~amd64
Signed-off-by: Horea Christian chymera.eu>
sci-biology/SPAdes/SPAdes-3.15.5.ebuild| 8 ++--
sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch | 49 ++
2 files changed, 54 insertions(+), 3 deletions(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
index b6d344c37..4485619e3 100644
--- a/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
@@ -17,9 +17,7 @@ SRC_URI="
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS=""
-# Fails to build:
-# https://github.com/ablab/spades/issues/1238
+KEYWORDS="~amd64"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="
@@ -31,6 +29,10 @@ DEPEND="
RDEPEND="${DEPEND}"
BDEPEND="dev-build/cmake"
+PATCHES=(
+ "${FILESDIR}/${P}-gcc13.patch"
+)
+
src_install(){
einstalldocs
# WORKAROUND: This script does both compile and install in one go
diff --git a/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch
b/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch
new file mode 100644
index 0..3dd3f8c02
--- /dev/null
+++ b/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch
@@ -0,0 +1,49 @@
+From 3e802fa51d156fc958c36e25d607f20bf756f0bf Mon Sep 17 00:00:00 2001
+From: Bo YU
+Date: Wed, 19 Jul 2023 18:42:04 +0800
+Subject: [PATCH] fix build issues due to gcc-13
+
+Signed-off-by: Bo YU
+---
+ ext/include/llvm/Support/Signals.h | 1 +
+ src/common/pipeline/library_data.hpp | 1 +
+ src/common/sequence/nucl.hpp | 2 ++
+ 3 files changed, 4 insertions(+)
+
+diff --git a/assembler/ext/include/llvm/Support/Signals.h
b/assembler/ext/include/llvm/Support/Signals.h
+index e0a18e72f..148216b8f 100644
+--- a/ext/include/llvm/Support/Signals.h
b/ext/include/llvm/Support/Signals.h
+@@ -14,6 +14,7 @@
+ #ifndef LLVM_SUPPORT_SIGNALS_H
+ #define LLVM_SUPPORT_SIGNALS_H
+
++#include
+ #include
+
+ namespace llvm {
+diff --git a/assembler/src/common/pipeline/library_data.hpp
b/assembler/src/common/pipeline/library_data.hpp
+index 3cbaf0adb..1ffaa7b37 100644
+--- a/src/common/pipeline/library_data.hpp
b/src/common/pipeline/library_data.hpp
+@@ -8,6 +8,7 @@
+
+ #include
+ #include
++#include
+
+ // Forward decls for LLVM YAML API
+ namespace llvm { namespace yaml { class IO; template struct
MappingTraits; } }
+diff --git a/assembler/src/common/sequence/nucl.hpp
b/assembler/src/common/sequence/nucl.hpp
+index 9c7d6de13..e10e7f583 100755
+--- a/src/common/sequence/nucl.hpp
b/src/common/sequence/nucl.hpp
+@@ -8,6 +8,8 @@
+ #ifndef NUCL_HPP_
+ #define NUCL_HPP_
+
++#include
++
+ #include "utils/verify.hpp"
+
+ /**
[gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/files/, sci-biology/SPAdes/
commit: a5760c4470004861915035e9baf62ae5da7e8454
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sat May 13 21:47:11 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sat May 13 21:47:11 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a5760c44
sci-biology/SPAdes: fix compile issue but drop KEYWORDS because of QA issues
Use patch from https://github.com/Homebrew/homebrew-science/pull/5616
The package install its own *.py files outside of PYTHON's site-packages/.
The "make install" procedure is flakey shellscript and there is no setup.py so
we could
reuse common infrastructure for pythonic packages.
There are plenty of bundled 3rd-party apps, some of them compiling statically.
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/SPAdes/SPAdes-3.10.1.ebuild| 47 +-
.../files/SPAdes-3.10.1-fix-missing-include.patch | 10 +
2 files changed, 48 insertions(+), 9 deletions(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
index 36f724d83..73050c1e4 100644
--- a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
@@ -12,13 +12,13 @@ HOMEPAGE="http://bioinf.spbau.ru/en/spades;
SRC_URI="
http://spades.bioinf.spbau.ru/release${PV}/SPAdes-${PV}.tar.gz
http://spades.bioinf.spbau.ru/release${PV}/manual.html ->
${P}_manual.html
- http://spades.bioinf.spbau.ru/release3.9.1/dipspades_manual.html ->
${P}_dipspades_manual.html
- http://spades.bioinf.spbau.ru/release3.9.1/rnaspades_manual.html ->
${P}_rnaspades_manual.html
- http://spades.bioinf.spbau.ru/release3.9.1/truspades_manual.html ->
${P}_truspades_manual.html"
+ http://spades.bioinf.spbau.ru/release${PV}/dipspades_manual.html ->
${P}_dipspades_manual.html
+ http://spades.bioinf.spbau.ru/release${PV}/rnaspades_manual.html ->
${P}_rnaspades_manual.html
+ http://spades.bioinf.spbau.ru/release${PV}/truspades_manual.html ->
${P}_truspades_manual.html"
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
IUSE=""
DEPEND="
@@ -28,6 +28,26 @@ DEPEND="
dev-libs/boost"
RDEPEND="${DEPEND}"
+# BUG: "${S}"/ext/src/ contains plenty of bundled 3rd-party tools. Drop them
all and properly DEPEND on their
+# existing packages
+# nlopt
+# llvm
+# python_libs
+# bamtools
+# ConsensusCore
+# ssw
+# jemalloc
+# htrie
+# getopt_pp
+# cppformat
+# cityhash
+# samtools
+# bwa
+
+# BUG: "${S}"/ext/tools/ contains even two version of bwa
+# bwa-0.7.12
+# bwa-0.6.2
+
pkg_pretend() {
if [[ ${MERGE_TYPE} != binary ]]; then
if [[ $(tc-getCXX) == *g++ ]] ; then
@@ -39,13 +59,22 @@ pkg_pretend() {
fi
}
-#src_compile(){
-# # grr, it actually also installs the files into $DESTDIR but that is
purged before pkg_qmerge starts
-# PREFIX="${D}"/usr ./spades_compile.sh || die
-#}
+src_prepare(){
+ # https://github.com/Homebrew/homebrew-science/pull/5616
+ epatch "${FILESDIR}"/"${P}"-fix-missing-include.patch
+ cp -p spades_compile.sh spades_install.sh || die
+ sed -e 's/make install/#make install/;s/cd $PREFIX/#cd $PREFIX/' -i
spades_compile.sh || die
+ default
+}
+
+src_compile(){
+ # grr, it actually also installs the files into $DESTDIR but that is
purged before pkg_qmerge starts
+ PREFIX="${D}"/usr ./spades_compile.sh || die
+}
src_install(){
- PREFIX="${ED}"/usr ./spades_compile.sh || die
+ PREFIX="${ED}"/usr sh ./spades_install.sh || die
+ # BUG: move *.py files to standard site-packages/ subdirectories
insinto /usr/share/"${PN}"
dodoc "${DISTDIR}"/${P}_*manual.html
}
diff --git a/sci-biology/SPAdes/files/SPAdes-3.10.1-fix-missing-include.patch
b/sci-biology/SPAdes/files/SPAdes-3.10.1-fix-missing-include.patch
new file mode 100644
index 0..bb6d75797
--- /dev/null
+++ b/sci-biology/SPAdes/files/SPAdes-3.10.1-fix-missing-include.patch
@@ -0,0 +1,10 @@
+--- SPAdes-3.10.1/src/common/utils/segfault_handler.hpp.ori2017-05-13
22:43:01.296207276 +0200
SPAdes-3.10.1/src/common/utils/segfault_handler.hpp2017-05-13
22:43:41.437310225 +0200
+@@ -12,6 +12,7 @@
+ #include "boost/noncopyable.hpp"
+
+ #include
++#include
+
+ struct segfault_handler : boost::noncopyable {
+ typedef std::function callback_t;
