commit: 5799b5f02fb7747823e3bba3e7fef06c5ce76469 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Sat Feb 13 11:24:07 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Sat Feb 13 11:24:28 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5799b5f0
sci-biology/canu: version bump, bump py targets Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> profiles/package.mask | 1 - .../canu/{canu-9999.ebuild => canu-2.1.1.ebuild} | 26 ++--- .../canu/files/canu-1.8_respect_CXXFLAGS.patch | 112 --------------------- 3 files changed, 10 insertions(+), 129 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 72e7e8c4b..07a777411 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -33,5 +33,4 @@ # Sam James <s...@gentoo.org> (2021-02-12) # These versions need Python 2.7 # Unspecified whether at build time (okay for now) or runtime (not) -=sci-biology/canu-9999 =sci-biology/Sibelia-9999 diff --git a/sci-biology/canu/canu-9999.ebuild b/sci-biology/canu/canu-2.1.1.ebuild similarity index 78% rename from sci-biology/canu/canu-9999.ebuild rename to sci-biology/canu/canu-2.1.1.ebuild index 2233e284a..1993440de 100644 --- a/sci-biology/canu/canu-9999.ebuild +++ b/sci-biology/canu/canu-2.1.1.ebuild @@ -1,29 +1,28 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -PYTHON_COMPAT=( python2_7 ) -PERL_EXPORT_PHASE_FUNCTIONS=no -inherit eutils java-pkg-2 perl-module multilib git-r3 +PYTHON_COMPAT=( python3_{7,8,9} ) + +inherit java-pkg-2 perl-module python-r1 multilib DESCRIPTION="Fork of a wgs-assembler for Oxfordnanopore and PacBio sequences" -HOMEPAGE="http://canu.readthedocs.io/en/latest" -EGIT_REPO_URI="https://github.com/marbl/canu.git" +HOMEPAGE="https://canu.readthedocs.io/en/latest" +SRC_URI="https://github.com/marbl/canu/releases/download/v${PV}/${P}.tar.xz" LICENSE="GPL-2" SLOT="0" -KEYWORDS="" -IUSE="" +KEYWORDS="~amd64" REQUIRED_USE="${PYTHON_REQUIRED_USE}" -RDEPEND=" +RDEPEND="${PYTHON_DEPS} >=virtual/jre-1.8:* dev-lang/perl virtual/perl-File-Path sci-visualization/gnuplot - " +" # =sci-biology/mhap-2.1.3 if we unbundle it DEPEND="${RDEPEND} >=virtual/jdk-1.8:* @@ -46,14 +45,9 @@ DEPEND="${RDEPEND} # Perl 5.12.0, or File::Path 2.08 # Java SE 8 # https://github.com/marbl/MHAP uses Apache maven -S="${WORKDIR}"/"${P}" # contains bundled mhap-2.1.3.jar, kmer, pbutgcns, FALCON -src_prepare(){ - epatch "${FILESDIR}"/canu-1.8_respect_CXXFLAGS.patch -} - src_compile(){ cd src || die emake diff --git a/sci-biology/canu/files/canu-1.8_respect_CXXFLAGS.patch b/sci-biology/canu/files/canu-1.8_respect_CXXFLAGS.patch deleted file mode 100644 index ac46e0ddd..000000000 --- a/sci-biology/canu/files/canu-1.8_respect_CXXFLAGS.patch +++ /dev/null @@ -1,112 +0,0 @@ -diff --git a/src/Makefile b/src/Makefile -index e2770f5a0..3cdb81a4c 100644 ---- a/src/Makefile -+++ b/src/Makefile -@@ -388,6 +388,22 @@ endif - # and remove -fomit-frame-pointer from CXXFLAGS. It added a bunch of complication and wasn't - # really used. - -+ifeq ($(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 - -