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@gentoo.org>

5 files changed, 0 insertions, 351 deletions

diff --git a/sci-biology/wgs-assembler/Manifest b/sci-biology/wgs-assembler/Manifest
deleted file mode 100644
index 1139a2badf36..000000000000
--- 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 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 += $(ARCH_INC)
- 
diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml
deleted file mode 100644
index fa8a259ff764..000000000000
--- a/sci-biology/wgs-assembler/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">wgs-assembler</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild
deleted file mode 100644
index a9193dfe1807..000000000000
--- a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG"
-HOMEPAGE="https://sourceforge.net/projects/wgs-assembler/"
-SRC_URI="mirror://sourceforge/${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
-}