From 677b7ba5c317778df2ad7e70df94b9b7eec4adbc Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Fri, 10 Sep 2021 04:21:55 +0100 Subject: gentoo resync : 10.09.2021 --- sci-biology/wgs-assembler/Manifest | 5 - .../files/wgs-assembler-7.0-build.patch | 257 --------------------- .../files/wgs-assembler-7.0-libtirpc.patch | 16 -- sci-biology/wgs-assembler/metadata.xml | 11 - .../wgs-assembler/wgs-assembler-7.0-r2.ebuild | 66 ------ 5 files changed, 355 deletions(-) delete mode 100644 sci-biology/wgs-assembler/Manifest delete mode 100644 sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch delete mode 100644 sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch delete mode 100644 sci-biology/wgs-assembler/metadata.xml delete mode 100644 sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild (limited to 'sci-biology/wgs-assembler') diff --git a/sci-biology/wgs-assembler/Manifest b/sci-biology/wgs-assembler/Manifest deleted file mode 100644 index e45ac70e7741..000000000000 --- a/sci-biology/wgs-assembler/Manifest +++ /dev/null @@ -1,5 +0,0 @@ -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 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 deleted file mode 100644 index 238541b512f2..000000000000 --- a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch +++ /dev/null @@ -1,257 +0,0 @@ ---- a/kmer/configure.sh -+++ b/kmer/configure.sh -@@ -254,13 +254,13 @@ - # -*- makefile -*- - # Linux, optimized - CC := $CC --SHLIB_FLAGS := -shared --CFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer --CLDFLAGS := -L/usr/local/lib -+SHLIB_FLAGS := -shared ${LDFLAGS} -+CFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -+CLDFLAGS := - CLIBS := -pthread -ldl - CXX := $CXX --CXXFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer --CXXLDFLAGS := -L/usr/local/lib -+CXXFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -+CXXLDFLAGS := - CXXLIBS := -pthread -ldl - ARFLAGS := ruvs - INSTALL/ := $target/ -@@ -272,13 +272,13 @@ - # -*- makefile -*- - # Linux64, optimized - CC := $CC --SHLIB_FLAGS := -shared --CFLAGS_COMPILE := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer --CLDFLAGS := -L/usr/local/lib -+SHLIB_FLAGS := -shared ${LDFLAGS} -+CFLAGS_COMPILE := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -+CLDFLAGS := - CLIBS := -pthread -ldl - CXX := $CXX --CXXFLAGS_COMPILE := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer --CXXLDFLAGS := -L/usr/local/lib -+CXXFLAGS_COMPILE := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -+CXXLDFLAGS := - CXXLIBS := -pthread -ldl - ARFLAGS := ruvs - INSTALL/ := $target/ -@@ -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__+=$${${1:.=.C_EXES}} - - ALL_CXX_EXES :=$(strip $(foreach x,${//},${${x:.=.CXX_EXES}})) - ${ALL_CXX_EXES}: -- ${-CXX} ${CXXLD} ${CXXLDFLAGS} -o $@ $+ ${CXXLIBS} -+ ${-CXX} ${CXXLD} ${CXXLDFLAGS} ${LDFLAGS} -o $@ $+ ${CXXLIBS} - __SUBGOALS__+=$${${1:.=.CXX_EXES}} - - define .RULE-install-copy-C-CXX-EXES ---- a/src/c_make.as -+++ b/src/c_make.as -@@ -64,27 +64,27 @@ - - ifeq ($(OSTYPE), Linux) - ifeq ($(MACHINETYPE), i686) -- ARCH_LDFLAGS += -pthread -lm -- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX -+ LINK_LIBS += -pthread -lm -+ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX - ARCH_LIB = /usr/X11R6/lib - endif - ifeq ($(MACHINETYPE), amd64) -- ARCH_LDFLAGS += -pthread -lm -- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX -+ LINK_LIBS += -pthread -lm -+ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX - ARCH_LIB = /usr/lib64 /usr/X11R6/lib64 - endif - ifeq ($(MACHINETYPE), ia64) -- ARCH_LDFLAGS += -pthread -lm -- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -+ LINK_LIBS += -pthread -lm -+ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 - ARCH_LIB = /usr/X11R6/lib - endif - - ifeq ($(BUILDDEBUG), 1) -- ARCH_CFLAGS += -g -- ARCH_LDFLAGS += -+ ARCH_CFLAGS += -+ LINK_LIBS += - else -- ARCH_CFLAGS += -O2 -- ARCH_LDFLAGS += -Wl,-O1 -+ ARCH_CFLAGS += -+ LINK_LIBS += - endif - endif - -@@ -94,19 +94,19 @@ - - ifeq ($(OSTYPE), FreeBSD) - ifeq ($(MACHINETYPE), i386) -- ARCH_LDFLAGS += -pthread -lthr -lm -- ARCH_CFLAGS = -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -- ARCH_CFLAGS = -pthread -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -+ LINK_LIBS += -pthread -lthr -lm -+ ARCH_CFLAGS = -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -+ ARCH_CFLAGS = -pthread -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare - endif - ifeq ($(MACHINETYPE), amd64) -- ARCH_LDFLAGS += -pthread -lthr -lm -- ARCH_CFLAGS = -pthread -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -- ARCH_CFLAGS = -pthread -Wall -Wextra -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -+ LINK_LIBS += -pthread -lthr -lm -+ ARCH_CFLAGS = -pthread -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -+ ARCH_CFLAGS = -pthread -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat - endif - - ifeq ($(BUILDCOVERAGE), 1) - ARCH_CFLAGS += -g -fprofile-arcs -ftest-coverage -- ARCH_LDFLAGS += -lgcov -+ LINK_LIBS += -lgcov - else - ifeq ($(BUILDDEBUG), 1) - ARCH_CFLAGS += -g -@@ -126,8 +126,6 @@ - - - ifeq ($(OSTYPE), Darwin) -- CC = gcc -- CXX = g++ - ARCH_CFLAGS = -D_THREAD_SAFE - - ifeq ($(MACHINETYPE), ppc) -@@ -140,14 +138,14 @@ - - ifeq ($(MACHINETYPE), i386) - ifeq ($(BUILDDEBUG), 1) -- ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g -- ARCH_LDFLAGS += -m64 -lm -+ ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g -+ LINK_LIBS += -m64 -lm - else - # Wow, -Wshorten-64-to-32 is tough -- ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast -+ ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast - # ARCH_CFLAGS += -Wextra - # ARCH_CFLAGS += -pedantic (see above about pedantic) -- ARCH_LDFLAGS += -m64 -lm -+ LINK_LIBS += -m64 -lm - endif - endif - -@@ -161,23 +159,23 @@ - ifeq ($(OSTYPE), SunOS) - ifeq ($(MACHINETYPE), i86pc) - ARCH_CFLAGS = -DBYTE_ORDER=LITTLE_ENDIAN -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads -- ARCH_LDFLAGS += -lm -+ LINK_LIBS += -lm - endif - - ifeq ($(MACHINETYPE), sparc32) - ARCH_CFLAGS = -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads -- ARCH_LDFLAGS += -lm -lnsl -lsocket -+ LINK_LIBS += -lm -lnsl -lsocket - endif - - ifeq ($(MACHINETYPE), sparc64) - ARCH_CFLAGS = -m64 -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads -- ARCH_LDFLAGS += -m64 -lm -lnsl -lsocket -+ LINK_LIBS += -lm -lnsl -lsocket - endif - - ifeq ($(BUILDDEBUG), 1) -- ARCH_CFLAGS += -g -+ ARCH_CFLAGS += - else -- ARCH_CFLAGS += -O -+ ARCH_CFLAGS += - endif - endif - -@@ -186,14 +184,14 @@ - - ifeq ($(BUILDPROFILE), 1) - ARCH_CFLAGS += -pg -- ARCH_LDFLAGS += -pg -+ LINK_LIBS += -pg - endif - - # One can argue that CXXFLAGS should be separate. For now, we only - # add to the flags. - - CFLAGS += $(ARCH_CFLAGS) --CXXFLAGS += $(ARCH_CFLAGS) $(ARCH_CXXFLAGS) -+CXXFLAGS += $(ARCH_CXXFLAGS) - LDFLAGS += $(ARCH_LDFLAGS) - - INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS))) -@@ -205,7 +203,7 @@ - OBJ_SEARCH_PATH = $(LOCAL_OBJ) - - ifeq ($(SITE_NAME), JCVI) -- LDFLAGS += -lcurl -+ LINK_LIBS += -lcurl - endif - - # The order of compilation here is very carefully chosen to be the ---- a/src/c_make.gen -+++ b/src/c_make.gen -@@ -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); \ -- $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS) -+ $(CC) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS) - - $(CXX_PROGS): - @ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++"; - cd $(LOCAL_OBJ); \ -- $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS) -+ $(CXX) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS) - - $(SCRIPT_PROGS): %.sh: - @echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++"; diff --git a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch deleted file mode 100644 index 7269b0b73c48..000000000000 --- a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch +++ /dev/null @@ -1,16 +0,0 @@ -diff -ruN wgs-7.0.orig/src/c_make.as wgs-7.0/src/c_make.as ---- wgs-7.0.orig/src/c_make.as 2018-04-29 23:00:02.200181987 +0200 -+++ wgs-7.0/src/c_make.as 2018-04-29 23:17:33.612700507 +0200 -@@ -196,6 +196,12 @@ - CXXFLAGS += $(ARCH_CXXFLAGS) - LDFLAGS += $(ARCH_LDFLAGS) - -+# libtirpc -+ -+CFLAGS += -I/usr/include/tirpc -+CXXFLAGS += -I/usr/include/tirpc -+LINK_LIBS += -ltirpc -+ - INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS))) - INC_IMPORT_DIRS += $(ARCH_INC) - diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml deleted file mode 100644 index fa8a259ff764..000000000000 --- a/sci-biology/wgs-assembler/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - - wgs-assembler - - diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild deleted file mode 100644 index a9193dfe1807..000000000000 --- a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild +++ /dev/null @@ -1,66 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -DESCRIPTION="The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG" -HOMEPAGE="https://sourceforge.net/projects/wgs-assembler/" -SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 x86" - -DEPEND=" - net-libs/libtirpc - x11-libs/libXt - !x11-terms/terminator" -RDEPEND="${DEPEND} - app-shells/tcsh - dev-perl/Log-Log4perl" - -S="${WORKDIR}/wgs-${PV}" - -PATCHES=( - "${FILESDIR}"/${P}-build.patch - "${FILESDIR}"/${P}-libtirpc.patch -) - -src_configure() { - tc-export AR CC CXX - - cd kmer || die - ./configure.sh || die -} - -src_compile() { - # not really an install target - emake -C kmer -j1 install - emake -C src -j1 SITE_NAME=LOCAL -} - -src_install() { - OSTYPE=$(uname) - MACHTYPE=$(uname -m) - MACHTYPE=${MACHTYPE/x86_64/amd64} - MY_S="${OSTYPE}-${MACHTYPE}" - sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die - - sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die - sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die - sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die - - dobin kmer/${MY_S}/bin/* - - insinto /usr/include/${PN} - doins -r kmer/${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/* - - dodoc README -} -- cgit v1.2.3