commit: 646bf3998bdd7dce3da0f3ad2bd03e201361a391 Author: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> AuthorDate: Sat Sep 4 06:56:40 2021 +0000 Commit: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> CommitDate: Sat Sep 4 07:01:52 2021 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=646bf399
sci-biology/wgs-assembler: Remove last-rited package Closes: https://bugs.gentoo.org/610094 Closes: https://bugs.gentoo.org/715874 Closes: https://bugs.gentoo.org/731860 Closes: https://bugs.gentoo.org/739486 Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org> profiles/package.mask | 7 - sci-biology/wgs-assembler/Manifest | 1 - .../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 ------ 6 files changed, 358 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index b2e06f5ec90..1a4feb4b97b 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -175,13 +175,6 @@ dev-python/pydiff # as replacement. Bug #769017. app-i18n/man-pages-it -# David Seifert <[email protected]> (2021-08-05) -# Dead upstream, last release over 5 years ago, multiple -# build issues, fails to build with GCC 11. Use something like -# sci-biology/abyss or canu as a modern day replacement. -# Bug #610094, #715874, #731860, #739486, removal in 30 days. -sci-biology/wgs-assembler - # David Seifert <[email protected]> (2021-08-04) # Last release over 4 years ago, upstream pretty much dead, the # ecosystem has switched to dev-util/pkgconf, which is alive. Testing diff --git a/sci-biology/wgs-assembler/Manifest b/sci-biology/wgs-assembler/Manifest deleted file mode 100644 index 1139a2badf3..00000000000 --- a/sci-biology/wgs-assembler/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST wgs-7.0.tar.bz2 1952253 BLAKE2B 2dbff6ffb9f4310d3d1301405e74476b7b7bbed4359c1701b5100d9597db46cc9956ccbe467bb37f8976d176ab9f92bfabcd5d1210b1e10675cff9a87ff379b9 SHA512 e5ef1d4533e3dd17d13c6aca9631f5300768a258f8241f3f7f90de3785bf7a340b6896febe335682c282434c9983bc4a02fe2128a5b0e7ec415dd65e0fe400ba 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 238541b512f..00000000000 --- 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 7269b0b73c4..00000000000 --- 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 += $(ARCH_INC) - diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml deleted file mode 100644 index fa8a259ff76..00000000000 --- a/sci-biology/wgs-assembler/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">wgs-assembler</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild deleted file mode 100644 index a9193dfe180..00000000000 --- a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild +++ /dev/null @@ -1,66 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -DESCRIPTION="The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG" -HOMEPAGE="https://sourceforge.net/projects/wgs-assembler/"; -SRC_URI="mirror://sourceforge/${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 -}
