commit: d5262133d2c941fbbf3995e7512d6d98df6fb250
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar 6 14:55:12 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar 6 14:55:12 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d5262133
sci-biology/stringtie: cleanup old
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/stringtie/files/Makefile.patch | 112 --------------------------
sci-biology/stringtie/stringtie-1.3.4d.ebuild | 33 --------
2 files changed, 145 deletions(-)
diff --git a/sci-biology/stringtie/files/Makefile.patch
b/sci-biology/stringtie/files/Makefile.patch
deleted file mode 100644
index b7efa605c..000000000
--- a/sci-biology/stringtie/files/Makefile.patch
+++ /dev/null
@@ -1,112 +0,0 @@
---- stringtie-1.3.4d/Makefile 2018-06-26 00:36:17.119583211 +0200
-+++ stringtie-1.3.4d/Makefile 2018-06-26 00:46:43.406712302 +0200
-@@ -1,28 +1,32 @@
--BAM := ./samtools-0.1.18
--#path to the directory where the samtools package was built (in place)
--#so libbam.a and *.h files MUST be in here
-+#-- for now these MUST point to the included samtools-0.x.x and gclib
subdirectories
-+BAM := ./samtools-0.1.18
-+GDIR := ./gclib
-+#--
-
--GDIR :=./gclib
-+INCDIRS := -I. -I${GDIR} -I${BAM}
-
--INCDIRS := -I. -I${GDIR} -I${BAM}
--
--CC := g++
-+#CXX ?= g++
-+CXX := $(if $(CXX),$(CXX),g++)
-
- BASEFLAGS := -Wall -Wextra ${INCDIRS} -fsigned-char -D_FILE_OFFSET_BITS=64 \
- -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti
-+#for gcc 8+ add: -Wno-class-memaccess
-+
-+
-+LINKER := $(if $(LINKER),$(LINKER),g++)
-
--LINKER := g++
-+LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g)
-
--LDFLAGS := -g -L${BAM} $(LDFLAGS)
-+LDFLAGS += -L${BAM}
-
--LIBS := -lbam -lz
-+LIBS := -lbam -lz
-
- ifneq (,$(findstring nothreads,$(MAKECMDGOALS)))
- NOTHREADS=1
- endif
-
- #detect MinGW (Windows environment)
--ifneq (,$(findstring mingw,$(shell ${CC} -dumpmachine)))
-+ifneq (,$(findstring mingw,$(shell ${CXX} -dumpmachine)))
- WINDOWS=1
- endif
-
-@@ -63,7 +67,8 @@ endif
- ifneq (,$(filter %release %static, $(MAKECMDGOALS)))
- # -- release build
- RELEASE_BUILD=1
-- CFLAGS := -DNDEBUG -g $(BASEFLAGS) $(CFLAGS) -O3
-+ CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O3)
-+ CXXFLAGS += -DNDEBUG $(BASEFLAGS)
- else
- ifneq (,$(filter %memcheck %memdebug, $(MAKECMDGOALS)))
- #use sanitizer in gcc 4.9+
-@@ -72,21 +77,21 @@ else
- ifeq "$(GCCVER49)" "0"
- $(error gcc version 4.9 or greater is required for this build target)
- endif
-- CFLAGS := -fno-omit-frame-pointer -fsanitize=undefined
-fsanitize=address $(BASEFLAGS)
-+ CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O0)
-+ CXXFLAGS += -fno-omit-frame-pointer -fsanitize=undefined
-fsanitize=address $(BASEFLAGS)
- GCCVER5 := $(shell expr `g++ -dumpversion | cut -f1 -d.` \>= 5)
- ifeq "$(GCCVER5)" "1"
-- CFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero
-fsanitize=vptr
-- CFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
-- #CFLAGS += -fcheck-pointer-bounds -mmpx
-+ CXXFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero
-fsanitize=vptr
-+ CXXFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
-+ #CXXFLAGS += -fcheck-pointer-bounds -mmpx
- endif
-- CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector
$(CFLAGS)
-+ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector
- LIBS := -lasan -lubsan -ldl $(LIBS)
- else
-- ifeq (,$(findstring clean,$(MAKECMDGOALS)))
- #just plain debug build
- DEBUG_BUILD=1
-- CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
-- endif
-+ CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O0)
-+ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
- endif
- endif
-
-@@ -106,23 +111,20 @@ ifdef DEBUG_BUILD
- DBG_WARN+='WARNING: built DEBUG version [much slower], use "make clean
release" for a faster, optimized version of the program.'
- endif
-
--
- OBJS := ${GDIR}/GBase.o ${GDIR}/GArgs.o ${GDIR}/GStr.o ${GDIR}/GBam.o \
- ${GDIR}/gdna.o ${GDIR}/codons.o ${GDIR}/GFaSeqGet.o ${GDIR}/gff.o
-
--
- ifneq (,$(filter %memtrace %memusage %memuse, $(MAKECMDGOALS)))
-- CFLAGS += -DGMEMTRACE
-+ CXXFLAGS += -DGMEMTRACE
- OBJS += ${GDIR}/proc_mem.o
- endif
-
- ifndef NOTHREADS
- OBJS += ${GDIR}/GThreads.o
- endif
-
--
- %.o : %.cpp
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- OBJS += rlink.o tablemaker.o tmerge.o
-
diff --git a/sci-biology/stringtie/stringtie-1.3.4d.ebuild
b/sci-biology/stringtie/stringtie-1.3.4d.ebuild
deleted file mode 100644
index 953999e87..000000000
--- a/sci-biology/stringtie/stringtie-1.3.4d.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Transcriptome assembler and RNA-Seq analysis on BAM files aka
cufflinks"
-HOMEPAGE="https://ccb.jhu.edu/software/stringtie
- https://github.com/gpertea/stringtie";
-SRC_URI="http://ccb.jhu.edu/software/stringtie/dl/${P}.tar.gz";
-
-LICENSE="Artistic-2 MIT" # MIT from bundled samtools-0.1.18
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-# contains bundled and modified samtools-0.1.18
-# https://github.com/gpertea/stringtie/issues/185#issuecomment-400128090
-#
-# contains bundled gclib (0.9.8?), a modified version?
-# https://github.com/gpertea/stringtie/issues/186#issuecomment-400131844
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-PATCHES=( "${FILESDIR}"/Makefile.patch )
-
-src_compile(){
- emake release
-}
-
-src_install(){
- dobin stringtie
- dodoc README
-}
