gentoo resync : 29.06.2020

3 files changed, 78 insertions, 56 deletions

diff --git a/sci-biology/wgs-assembler/Manifest b/sci-biology/wgs-assembler/Manifest
index 1cb622926ec9..e45ac70e7741 100644
--- a/sci-biology/wgs-assembler/Manifest
+++ b/sci-biology/wgs-assembler/Manifest
@@ -1,5 +1,5 @@
-AUX wgs-assembler-7.0-build.patch 10279 BLAKE2B 9fd4a113d4ea3b07570c39e32892b535a0ed7d0e958602ca891c75fa3aa73a44d205fe43580e43d98cdafa1d431c12f68d5fe55e52aca82e451d5aae3ea2c551 SHA512 77e432319cb279d188ab74edda822f6b4dda127f1e5f1d75febb6fe0533b66d5bfd066781f1ff5d4d0d8f832c491d31ec470653b9c36b29d8280b5786783c5b9
+AUX wgs-assembler-7.0-build.patch 10479 BLAKE2B 906d057017be1b84b65812f5ee28b56a34c5a2a34e03d826270cf819e63363fbb72cef90884ce5df04db2758f662b76bbd46aab79fb53452fecd99a6be179c59 SHA512 524baaeaf66ab74ac4c0649e241c0d3f070b087b89a8b723c8886c280ea9ca8a78bdb83cdc32237965c9faf04faf97edb22587d9fdc6db345f3e8dfbf1a3e9b0
 AUX wgs-assembler-7.0-libtirpc.patch 516 BLAKE2B 1ee7876f767e559a008d86b8f6ccdbf70763646b782ea23d2bc9f74edab84ff633270ff15d0cd5b888674c5ee0d0bdcd3b73a48bf040f06f2a56bf4e366125cf SHA512 b2a29b2dc0578d4e8544dce258327a34ac4a5ca6bea3e901bee06d89618e9cba7f569fd54da6148372826d053829bc991db7c4cfd5a8564dd81545566698c947
 DIST wgs-7.0.tar.bz2 1952253 BLAKE2B 2dbff6ffb9f4310d3d1301405e74476b7b7bbed4359c1701b5100d9597db46cc9956ccbe467bb37f8976d176ab9f92bfabcd5d1210b1e10675cff9a87ff379b9 SHA512 e5ef1d4533e3dd17d13c6aca9631f5300768a258f8241f3f7f90de3785bf7a340b6896febe335682c282434c9983bc4a02fe2128a5b0e7ec415dd65e0fe400ba
-EBUILD wgs-assembler-7.0-r2.ebuild 1662 BLAKE2B 1c542685f8667e1901eb3950c084ad386e29a077d280e5c3ed24ae84fed71e4876a5c8bed80ea33c4b7b4c3b0c0720f0229d3efc1e2f1654548cdfeb32383e5b SHA512 ad0f1a44e14c9c714b7b6d00dda05bb9b16b9bdde29989d2fd4d785294053aae94d85d0b5ab92faeb2574e99f18a6c566c2c8cc01c5d920632a480aae6f88a4e
+EBUILD wgs-assembler-7.0-r2.ebuild 1492 BLAKE2B cea99ff2f1c8d6d6d2b08e23808480d6b2018d6741a8e18a0a09e90f8792139af499617fe9b70723257ef7b3d63a6f270acbf06d8a426eeda3f8b59485424237 SHA512 3eb63c55dc920cf70e3da4562c7e96cd14bd646f1d7cdf74cb58ee80fdffdbdd0fe6d0a0bce2d3e01450c1fd82ad6db3bee79e46b795e2c98357a314a13bd841
 MISC metadata.xml 354 BLAKE2B eaf844f74ea3b2a51cba2f00ebc0a3cc895312e04a995000e93426fa0e2f9d8601edb2011ff6c837f85b3a5755b819dc7ce517d3787c2e7bd37e097e144fb156 SHA512 b46f437eb224dbc7d7cec21941565ab48055f1d7b787fae7e66b135a8abeff0ea55dc191643d1e5f6212012001d98e4b7e8a7a655c9a66c9f3124bf7e700e193
diff --git a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch
index f7fb44743968..238541b512f2 100644
--- a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch
+++ b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch
@@ -1,33 +1,6 @@
- kmer/Make.rules   |  4 ++--
- kmer/configure.sh | 20 +++++++++----------
- src/c_make.as     | 58 +++++++++++++++++++++++++++----------------------------
- src/c_make.gen    |  4 ++--
- 4 files changed, 43 insertions(+), 43 deletions(-)
-
-diff --git a/kmer/Make.rules b/kmer/Make.rules
-index f904b13..5c2d477 100644
---- a/kmer/Make.rules
-+++ b/kmer/Make.rules
-@@ -139,12 +139,12 @@ ${ALL_CXX_DEPS}:%.d:%
- ## EXE targets
- ALL_C_EXES   :=$(strip $(foreach x,${//},${${x:.=.C_EXES}}))
- ${ALL_C_EXES}:
--	${-CC} ${CLD} ${CLDFLAGS} -o $@ $+ ${CLIBS}
-+	${-CC} ${CLD} ${CLDFLAGS} ${LDFLAGS} -o $@ $+ ${CLIBS}
- __SUBGOALS__+=$${${1:.=.C_EXES}}
- 
- ALL_CXX_EXES :=$(strip $(foreach x,${//},${${x:.=.CXX_EXES}}))
- ${ALL_CXX_EXES}:
--	${-CXX} ${CXXLD} ${CXXLDFLAGS} -o $@ $+ ${CXXLIBS}
-+	${-CXX} ${CXXLD} ${CXXLDFLAGS} ${LDFLAGS} -o $@ $+ ${CXXLIBS}
- __SUBGOALS__+=$${${1:.=.CXX_EXES}}
- 
- define .RULE-install-copy-C-CXX-EXES
-diff --git a/kmer/configure.sh b/kmer/configure.sh
-index 2f0d5ea..9daf89f 100755
 --- a/kmer/configure.sh
 +++ b/kmer/configure.sh
-@@ -254,13 +254,13 @@ EOF
+@@ -254,13 +254,13 @@
  # -*- makefile -*-
  #  Linux, optimized
  CC                := $CC
@@ -46,7 +19,7 @@ index 2f0d5ea..9daf89f 100755
  CXXLIBS           := -pthread -ldl
  ARFLAGS           := ruvs
  INSTALL/          := $target/
-@@ -272,13 +272,13 @@ EOF
+@@ -272,13 +272,13 @@
  # -*- makefile -*-
  #  Linux64, optimized
  CC                := $CC
@@ -65,11 +38,37 @@ index 2f0d5ea..9daf89f 100755
  CXXLIBS           := -pthread -ldl
  ARFLAGS           := ruvs
  INSTALL/          := $target/
-diff --git a/src/c_make.as b/src/c_make.as
-index 0172807..4304589 100644
+@@ -401,8 +401,8 @@
+ .O                := .o
+ CLD               := \${CC}
+ CXXLD             := \${CXX}
+-CCDEP		  := gcc -MM -MG
+-CXXDEP	          := g++ -MM -MG
++CCDEP             := \$(CC) -MM -MG
++CXXDEP            := \$(CXX) -MM -MG
+ CLIBS             += -lm -lbz2
+ CXXLIBS           += -lm -lbz2
+ PYTHON            := $PYTHON
+--- a/kmer/Make.rules
++++ b/kmer/Make.rules
+@@ -139,12 +139,12 @@
+ ## EXE targets
+ ALL_C_EXES   :=$(strip $(foreach x,${//},${${x:.=.C_EXES}}))
+ ${ALL_C_EXES}:
+-	${-CC} ${CLD} ${CLDFLAGS} -o $@ $+ ${CLIBS}
++	${-CC} ${CLD} ${CLDFLAGS} ${LDFLAGS} -o $@ $+ ${CLIBS}
+ __SUBGOALS__+=$${${1:.=.C_EXES}}
+ 
+ ALL_CXX_EXES :=$(strip $(foreach x,${//},${${x:.=.CXX_EXES}}))
+ ${ALL_CXX_EXES}:
+-	${-CXX} ${CXXLD} ${CXXLDFLAGS} -o $@ $+ ${CXXLIBS}
++	${-CXX} ${CXXLD} ${CXXLDFLAGS} ${LDFLAGS} -o $@ $+ ${CXXLIBS}
+ __SUBGOALS__+=$${${1:.=.CXX_EXES}}
+ 
+ define .RULE-install-copy-C-CXX-EXES
 --- a/src/c_make.as
 +++ b/src/c_make.as
-@@ -64,27 +64,27 @@ include $(LOCAL_WORK)/src/c_make.gen
+@@ -64,27 +64,27 @@
  
  ifeq ($(OSTYPE), Linux)
    ifeq ($(MACHINETYPE), i686)
@@ -107,7 +106,7 @@ index 0172807..4304589 100644
    endif
  endif
  
-@@ -94,19 +94,19 @@ endif
+@@ -94,19 +94,19 @@
  
  ifeq ($(OSTYPE), FreeBSD)
    ifeq ($(MACHINETYPE), i386)
@@ -134,7 +133,16 @@ index 0172807..4304589 100644
    else
      ifeq ($(BUILDDEBUG), 1)
        ARCH_CFLAGS   += -g
-@@ -140,14 +140,14 @@ ifeq ($(OSTYPE), Darwin)
+@@ -126,8 +126,6 @@
+ 
+ 
+ ifeq ($(OSTYPE), Darwin)
+-  CC               = gcc
+-  CXX              = g++
+   ARCH_CFLAGS      = -D_THREAD_SAFE
+ 
+   ifeq ($(MACHINETYPE), ppc)
+@@ -140,14 +138,14 @@
  
    ifeq ($(MACHINETYPE), i386)
      ifeq ($(BUILDDEBUG), 1)
@@ -153,7 +161,7 @@ index 0172807..4304589 100644
      endif
    endif
  
-@@ -161,23 +161,23 @@ endif
+@@ -161,23 +159,23 @@
  ifeq ($(OSTYPE), SunOS)
    ifeq ($(MACHINETYPE), i86pc)
      ARCH_CFLAGS    = -DBYTE_ORDER=LITTLE_ENDIAN -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads
@@ -182,7 +190,7 @@ index 0172807..4304589 100644
    endif
  endif
  
-@@ -186,14 +186,14 @@ endif
+@@ -186,14 +184,14 @@
  
  ifeq ($(BUILDPROFILE), 1)
    ARCH_CFLAGS  += -pg
@@ -199,7 +207,7 @@ index 0172807..4304589 100644
  LDFLAGS         += $(ARCH_LDFLAGS)
  
  INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS)))
-@@ -205,7 +205,7 @@ LIB_IMPORT_DIRS += $(ARCH_LIB)
+@@ -205,7 +203,7 @@
  OBJ_SEARCH_PATH  = $(LOCAL_OBJ)
  
  ifeq ($(SITE_NAME), JCVI)
@@ -208,11 +216,31 @@ index 0172807..4304589 100644
  endif
  
  #  The order of compilation here is very carefully chosen to be the
-diff --git a/src/c_make.gen b/src/c_make.gen
-index 7b5227c..c27b777 100644
 --- a/src/c_make.gen
 +++ b/src/c_make.gen
-@@ -396,12 +396,12 @@ $(LIBRARIES):
+@@ -248,10 +248,6 @@
+ #### Do not redefine if (a) passed in on command line, or (b)
+ #### defined in an environment variable.
+ 
+-ifneq "$(origin CC)" "environment"
+-CC=gcc
+-endif
+-
+ ifneq "$(origin CPPFLAGS)" "environment"
+ CPPFLAGS=
+ endif
+@@ -264,10 +260,6 @@
+ CDEFS=
+ endif
+ 
+-ifneq "$(origin CXX)" "environment"
+-CXX=g++
+-endif
+-
+ ifneq "$(origin CXXFLAGS)" "environment"
+ CXXFLAGS=
+ endif
+@@ -396,12 +388,12 @@
  $(C_PROGS):
  	@ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++";
  	cd $(LOCAL_OBJ); \
diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild
index fc5869667f02..a9193dfe1807 100644
--- a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild
+++ b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG"
 HOMEPAGE="https://sourceforge.net/projects/wgs-assembler/"
@@ -12,7 +12,6 @@ SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="amd64 x86"
-IUSE="static-libs"
 
 DEPEND="
 	net-libs/libtirpc
@@ -29,13 +28,10 @@ PATCHES=(
 	"${FILESDIR}"/${P}-libtirpc.patch
 )
 
-src_prepare() {
-	default
-	tc-export CC CXX
-}
-
 src_configure() {
-	cd "${S}/kmer"
+	tc-export AR CC CXX
+
+	cd kmer || die
 	./configure.sh || die
 }
 
@@ -57,16 +53,14 @@ src_install() {
 	sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die
 
 	dobin kmer/${MY_S}/bin/*
-	insinto /usr/$(get_libdir)/${PN}
-	use static-libs && doins kmer/${MY_S}/lib/*
 
 	insinto /usr/include/${PN}
-	doins kmer/${MY_S}/include/*
+	doins -r kmer/${MY_S}/include/.
 
 	insinto /usr/share/${PN}/lib
 	doins -r ${MY_S}/bin/TIGR
 	rm -rf ${MY_S}/bin/TIGR || die
 	dobin ${MY_S}/bin/*
-	use static-libs && dolib.a ${MY_S}/lib/*
+
 	dodoc README
 }