sci-biology/canu: respect CXXFLAGS

Package-Manager: Portage-2.3.61, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

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
+ 
+