commit: a93d11e69bfb168131822a534931dae912b5fbe2 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Feb 20 19:43:32 2019 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Feb 20 19:43:32 2019 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a93d11e6
sci-biology/canu: respect CXXFLAGS Package-Manager: Portage-2.3.61, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz> sci-biology/canu/canu-9999.ebuild | 35 ++++++- .../canu/files/canu-1.8_respect_CXXFLAGS.patch | 112 +++++++++++++++++++++ 2 files changed, 143 insertions(+), 4 deletions(-) diff --git a/sci-biology/canu/canu-9999.ebuild b/sci-biology/canu/canu-9999.ebuild index bef85d20f..2233e284a 100644 --- a/sci-biology/canu/canu-9999.ebuild +++ b/sci-biology/canu/canu-9999.ebuild @@ -1,9 +1,11 @@ # Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=5 -inherit java-pkg-2 git-r3 +PYTHON_COMPAT=( python2_7 ) +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit eutils java-pkg-2 perl-module multilib git-r3 DESCRIPTION="Fork of a wgs-assembler for Oxfordnanopore and PacBio sequences" HOMEPAGE="http://canu.readthedocs.io/en/latest"; @@ -14,6 +16,8 @@ SLOT="0" KEYWORDS="" IUSE="" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + RDEPEND=" >=virtual/jre-1.8:* dev-lang/perl @@ -24,8 +28,21 @@ RDEPEND=" DEPEND="${RDEPEND} >=virtual/jdk-1.8:* dev-java/ant-core + !sci-biology/wgs-assembler " +# Detected file collision(s): +# * sci-biology/wgs-assembler-8.3_rc2:0::science +# * /usr/bin/bogart +# * /usr/bin/bogus +# * /usr/bin/fastqAnalyze +# * /usr/bin/fastqSample +# * /usr/bin/fastqSimulate +# * /usr/bin/fastqSimulate-sort +# * /usr/bin/meryl +# * /usr/bin/overlapInCore +# * /usr/bin/utgcns + # Perl 5.12.0, or File::Path 2.08 # Java SE 8 # https://github.com/marbl/MHAP uses Apache maven @@ -33,6 +50,10 @@ S="${WORKDIR}"/"${P}" # contains bundled mhap-2.1.3.jar, kmer, pbutgcns, FALCON +src_prepare(){ + epatch "${FILESDIR}"/canu-1.8_respect_CXXFLAGS.patch +} + src_compile(){ cd src || die emake @@ -42,9 +63,15 @@ src_install(){ # installs # /usr/bin # /usr/lib/libcanu.a - # /usr/lib/site_perl/canu + # /usr/lib64/perl5/vendor_perl/5.28.0/lib/site_perl/canu # /usr/share/java/classes/mhap-2.1.3.jar rm -rf Linux-amd64/obj insinto /usr - doins -r Linux-amd64/{bin,lib,share} + doins -r Linux-amd64/{bin,share} + insinto /usr/$(get_libdir) + dolib Linux-amd64/lib/libcanu.a + rm Linux-amd64/lib/libcanu.a || die + perl_set_version + insinto ${VENDOR_LIB} + doins -r Linux-amd64/lib } diff --git a/sci-biology/canu/files/canu-1.8_respect_CXXFLAGS.patch b/sci-biology/canu/files/canu-1.8_respect_CXXFLAGS.patch new file mode 100644 index 000000000..ac46e0ddd --- /dev/null +++ b/sci-biology/canu/files/canu-1.8_respect_CXXFLAGS.patch @@ -0,0 +1,112 @@ +diff --git a/src/Makefile b/src/Makefile +index e2770f5a0..3cdb81a4c 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -388,6 +388,22 @@ endif + # and remove -fomit-frame-pointer from CXXFLAGS. It added a bunch of complication and wasn't + # really used. + ++ifeq ($(BUILDOPTIMIZED), 1) ++else ++ CXXFLAGS ?= -g3 ++endif ++ ++ifeq ($(BUILDDEBUG), 1) ++else ++ ifeq (${OSTYPE}, FreeBSD) ++ ifeq (${MACHINETYPE}, amd64) ++ CXXFLAGS ?= -O3 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer ++ else ++ CXXFLAGS ?= -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer ++ endif ++ endif ++endif ++ + ifeq (${OSTYPE}, Linux) + CC ?= gcc + CXX ?= g++ +@@ -398,16 +414,6 @@ ifeq (${OSTYPE}, Linux) + CXXFLAGS += -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat + + BUILDSTACKTRACE ?= 1 +- +- ifeq ($(BUILDOPTIMIZED), 1) +- else +- CXXFLAGS += -g3 +- endif +- +- ifeq ($(BUILDDEBUG), 1) +- else +- CXXFLAGS += -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +- endif + endif + + +@@ -479,16 +485,6 @@ ifeq (${OSTYPE}, Darwin) + + CXXFLAGS += -pthread -fPIC -m64 -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wno-format-truncation -Wformat + LDFLAGS += -pthread -lm +- +- ifeq ($(BUILDOPTIMIZED), 1) +- else +- CXXFLAGS += -g3 +- endif +- +- ifeq ($(BUILDDEBUG), 1) +- else +- CXXFLAGS += -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +- endif + endif + + +@@ -519,16 +515,6 @@ ifeq (${MACHINETYPE}, amd64) + + # callgrind + #CXXFLAGS += -g3 -Wa,--gstabs -save-temps +- +- ifeq ($(BUILDOPTIMIZED), 1) +- else +- CXXFLAGS += -g3 +- endif +- +- ifeq ($(BUILDDEBUG), 1) +- else +- CXXFLAGS += -O3 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +- endif + endif + endif + +@@ -544,16 +530,6 @@ ifeq (${MACHINETYPE}, arm) + CXXFLAGS += -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -Wno-parentheses + CXXFLAGS += -funroll-loops -fomit-frame-pointer + LDFLAGS += +- +- ifeq ($(BUILDOPTIMIZED), 1) +- else +- CXXFLAGS += -g3 +- endif +- +- ifeq ($(BUILDDEBUG), 1) +- else +- CXXFLAGS += -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +- endif + endif + endif + +@@ -566,16 +542,6 @@ ifneq (,$(findstring CYGWIN, ${OSTYPE})) + LDFLAGS := -fopenmp -pthread -lm + + CXXFLAGS += -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat +- +- ifeq ($(BUILDOPTIMIZED), 1) +- else +- CXXFLAGS += -g3 +- endif +- +- ifeq ($(BUILDDEBUG), 1) +- else +- CXXFLAGS += -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +- endif + endif + +
