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
-
-
