pkgsrc-WIP-changes archive
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index][Old Index]
vcflib: Remove ancient, non-functional pkg
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Tue Nov 26 08:05:12 2024 -0600
Changeset: 138a6eceaec75a0e4590d98bdb853a29e0f8aee9
Modified Files:
Makefile
Removed Files:
vcflib/DESCR
vcflib/Makefile
vcflib/PLIST
vcflib/buildlink3.mk
vcflib/distinfo
vcflib/files/Makefile.external-libs
vcflib/patches/patch-src_cdflib.cpp
Log Message:
vcflib: Remove ancient, non-functional pkg
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=138a6eceaec75a0e4590d98bdb853a29e0f8aee9
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 1 -
vcflib/DESCR | 1 -
vcflib/Makefile | 56 ----------
vcflib/PLIST | 105 ------------------
vcflib/buildlink3.mk | 12 ---
vcflib/distinfo | 6 --
vcflib/files/Makefile.external-libs | 208 ------------------------------------
vcflib/patches/patch-src_cdflib.cpp | 14 ---
8 files changed, 403 deletions(-)
diffs:
diff --git a/Makefile b/Makefile
index 57ab9c7353..9d9b4243c7 100644
--- a/Makefile
+++ b/Makefile
@@ -5778,7 +5778,6 @@ SUBDIR+= vault
SUBDIR+= vaultwarden-web-vault
SUBDIR+= vcf-split
SUBDIR+= vcf2hap
-SUBDIR+= vcflib
SUBDIR+= vcftools
SUBDIR+= vcg
SUBDIR+= vcglib
diff --git a/vcflib/DESCR b/vcflib/DESCR
deleted file mode 100644
index 845dbab1b0..0000000000
--- a/vcflib/DESCR
+++ /dev/null
@@ -1 +0,0 @@
-[description of the port]
diff --git a/vcflib/Makefile b/vcflib/Makefile
deleted file mode 100644
index 5e4d960ee1..0000000000
--- a/vcflib/Makefile
+++ /dev/null
@@ -1,56 +0,0 @@
-# $NetBSD$
-
-DISTNAME= vcflib-${PORTVERSION}
-CATEGORIES= biology
-MASTER_SITES= ${MASTER_SITE_GITHUB:=vcflib/}
-GITHUB_TAG= 7e3d8066a6c6c0f22191a70d050ead23f9c453b3
-
-MAINTAINER= pkgsrc-users%NetBSD.org@localhost
-HOMEPAGE= https://github.com/vcflib/vcflib
-COMMENT= C++ library and CLI tools for parsing and manipulating VCF files
-LICENSE= mit
-
-USE_LANGUAGES= c c++
-USE_TOOLS+= gmake
-
-SUBST_CLASSES+= ldflags
-SUBST_FILES.ldflags= ${WRKSRC}/Makefile.external-libs
-SUBST_STAGE.ldflags= post-patch
-SUBST_SED.ldflags= -e "s|LDFLAGS =|LDFLAGS = ${COMPILER_RPATH_FLAG}${PREFIX}/lib|g"
-
-CXXFLAGS+= -I${PREFIX}/include/smithwaterman \
- -I${PREFIX}/include/multichoose \
- -I${PREFIX}/include/filevercmp \
- -I${PREFIX}/include/fastahack \
- -I${PREFIX}/include/intervaltree \
- -DVERSION='"${PORTVERSION}"'
-LDFLAGS+= ${COMPILER_RPATH_FLAG}${PREFIX}/lib
-MAKE_FLAGS= LIB_PATH+=${COMPILER_RPATH_FLAG}${PREFIX}/lib
-MAKE_FILE= Makefile.external-libs
-INSTALL_TARGET= install-strip
-
-PORTVERSION= 0.0.0.20180208
-
-.include "../../mk/bsd.prefs.mk"
-
-# GCC disables sse2 by default on i386, but it's required for vcflib
-.if ${MACHINE_ARCH} == i386
-CFLAGS+= -msse2
-.endif
-
-pre-configure:
- ${CP} ${FILESDIR}/Makefile.external-libs ${WRKSRC}
-
-post-install:
- cd ${DESTDIR}${PREFIX}/lib && ${LN} -s libvcflib.so.1 libvcflib.so
-
-.include "../../biology/htslib/buildlink3.mk"
-.include "../../wip/tabixpp/buildlink3.mk"
-.include "../../wip/smithwaterman/buildlink3.mk"
-.include "../../wip/fastahack/buildlink3.mk"
-.include "../../wip/filevercmp/buildlink3.mk"
-.include "../../wip/fsom/buildlink3.mk"
-.include "../../wip/multichoose/buildlink3.mk"
-.include "../../wip/intervaltree/buildlink3.mk"
-.include "../../devel/zlib/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/vcflib/PLIST b/vcflib/PLIST
deleted file mode 100644
index 6b9b9749ac..0000000000
--- a/vcflib/PLIST
+++ /dev/null
@@ -1,105 +0,0 @@
-@comment $NetBSD$
-bin/LD
-bin/abba-baba
-bin/bFst
-bin/dumpContigsFromHeader
-bin/genotypeSummary
-bin/hapLrt
-bin/iHS
-bin/meltEHH
-bin/normalize-iHS
-bin/pFst
-bin/pVst
-bin/permuteGPAT++
-bin/permuteSmooth
-bin/plotHaps
-bin/popStats
-bin/segmentFst
-bin/segmentIhs
-bin/sequenceDiversity
-bin/smoother
-bin/vcf2dag
-bin/vcf2fasta
-bin/vcf2tsv
-bin/vcfaddinfo
-bin/vcfafpath
-bin/vcfallelicprimitives
-bin/vcfaltcount
-bin/vcfannotate
-bin/vcfannotategenotypes
-bin/vcfbreakmulti
-bin/vcfcat
-bin/vcfcheck
-bin/vcfclassify
-bin/vcfcleancomplex
-bin/vcfcombine
-bin/vcfcommonsamples
-bin/vcfcountalleles
-bin/vcfcreatemulti
-bin/vcfdistance
-bin/vcfecho
-bin/vcfentropy
-bin/vcfevenregions
-bin/vcffilter
-bin/vcffixup
-bin/vcfflatten
-bin/vcfgeno2alleles
-bin/vcfgeno2haplo
-bin/vcfgenosamplenames
-bin/vcfgenosummarize
-bin/vcfgenotypecompare
-bin/vcfgenotypes
-bin/vcfglbound
-bin/vcfglxgt
-bin/vcfhetcount
-bin/vcfhethomratio
-bin/vcfindex
-bin/vcfinfo2qual
-bin/vcfinfosummarize
-bin/vcfintersect
-bin/vcfkeepgeno
-bin/vcfkeepinfo
-bin/vcfkeepsamples
-bin/vcfleftalign
-bin/vcflength
-bin/vcfnormalizesvs
-bin/vcfnull2ref
-bin/vcfnumalt
-bin/vcfoverlay
-bin/vcfparsealts
-bin/vcfprimers
-bin/vcfqual2info
-bin/vcfrandom
-bin/vcfrandomsample
-bin/vcfremap
-bin/vcfremoveaberrantgenotypes
-bin/vcfremovesamples
-bin/vcfroc
-bin/vcfsample2info
-bin/vcfsamplediff
-bin/vcfsamplenames
-bin/vcfsitesummarize
-bin/vcfstats
-bin/vcfstreamsort
-bin/vcfuniq
-bin/vcfuniqalleles
-bin/vcfunphase
-bin/wcFst
-include/vcflib/BedReader.h
-include/vcflib/Variant.h
-include/vcflib/cdflib.hpp
-include/vcflib/convert.h
-include/vcflib/gpatInfo.hpp
-include/vcflib/join.h
-include/vcflib/mt19937ar.h
-include/vcflib/pdflib.hpp
-include/vcflib/rnglib.hpp
-include/vcflib/split.h
-include/vcflib/ssw.hpp
-include/vcflib/ssw_cpp.hpp
-include/vcflib/var.hpp
-include/vcflib/vec128int.h
-include/vcflib/veclib_types.h
-lib/libvcflib.a
-lib/libvcflib.so
-lib/libvcflib.so.1
diff --git a/vcflib/buildlink3.mk b/vcflib/buildlink3.mk
deleted file mode 100644
index dda36b41a0..0000000000
--- a/vcflib/buildlink3.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-# $NetBSD$
-
-BUILDLINK_TREE+= vcflib
-
-.if !defined(VCFLIB_BUILDLINK3_MK)
-VCFLIB_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.vcflib+= vcflib>=0.0.0.20180208
-BUILDLINK_PKGSRCDIR.vcflib?= ../../wip/vcflib
-.endif # VCFLIB_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -vcflib
diff --git a/vcflib/distinfo b/vcflib/distinfo
deleted file mode 100644
index e8e1282d41..0000000000
--- a/vcflib/distinfo
+++ /dev/null
@@ -1,6 +0,0 @@
-$NetBSD$
-
-RMD160 (vcflib-0.0.0.20180208-7e3d8066a6c6c0f22191a70d050ead23f9c453b3.tar.gz) = b82b051ab62173bee6145d3eded457bd7b2a31a0
-SHA512 (vcflib-0.0.0.20180208-7e3d8066a6c6c0f22191a70d050ead23f9c453b3.tar.gz) = 56a1b4fb49dfee966c131bfd81d9db970eb61967321a29769aae278c606193028f2d85a8ee943d9604938a7744b1e10207647f33456073036bc476c363bf4fc2
-Size (vcflib-0.0.0.20180208-7e3d8066a6c6c0f22191a70d050ead23f9c453b3.tar.gz) = 20139407 bytes
-SHA1 (patch-src_cdflib.cpp) = 1ad43c4f51e774d32891a50cba0c2ce233aa08f8
diff --git a/vcflib/files/Makefile.external-libs b/vcflib/files/Makefile.external-libs
deleted file mode 100644
index eb768d1cdd..0000000000
--- a/vcflib/files/Makefile.external-libs
+++ /dev/null
@@ -1,208 +0,0 @@
-#OBJ_DIR = ./
-HEADERS = src/Variant.h \
- src/split.h \
- src/pdflib.hpp \
- src/var.hpp \
- src/cdflib.hpp \
- src/rnglib.hpp \
- src/join.h
-SOURCES = src/Variant.cpp \
- src/rnglib.cpp \
- src/var.cpp \
- src/pdflib.cpp \
- src/cdflib.cpp \
- src/split.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-
-VCF_LIB_LOCAL:=$(shell pwd)
-BIN_DIR:=bin
-LIB_DIR:=lib
-SRC_DIR=src
-INC_DIR:=include
-OBJ_DIR:=obj
-
-LIB = libvcflib.a
-SOVERSION = 1
-SLIB = libvcflib.so.$(SOVERSION)
-
-# TODO
-#vcfstats.cpp
-
-BIN_SOURCES = src/vcfecho.cpp \
- src/vcfnormalizesvs.cpp \
- src/dumpContigsFromHeader.cpp \
- src/bFst.cpp \
- src/pVst.cpp \
- src/hapLrt.cpp \
- src/popStats.cpp \
- src/wcFst.cpp \
- src/iHS.cpp \
- src/segmentFst.cpp \
- src/segmentIhs.cpp \
- src/genotypeSummary.cpp \
- src/sequenceDiversity.cpp \
- src/pFst.cpp \
- src/smoother.cpp \
- src/LD.cpp \
- src/plotHaps.cpp \
- src/abba-baba.cpp \
- src/permuteGPAT++.cpp \
- src/permuteSmooth.cpp \
- src/normalize-iHS.cpp \
- src/meltEHH.cpp \
- src/vcfaltcount.cpp \
- src/vcfhetcount.cpp \
- src/vcfhethomratio.cpp \
- src/vcffilter.cpp \
- src/vcf2tsv.cpp \
- src/vcfgenotypes.cpp \
- src/vcfannotategenotypes.cpp \
- src/vcfcommonsamples.cpp \
- src/vcfremovesamples.cpp \
- src/vcfkeepsamples.cpp \
- src/vcfsamplenames.cpp \
- src/vcfgenotypecompare.cpp \
- src/vcffixup.cpp \
- src/vcfclassify.cpp \
- src/vcfsamplediff.cpp \
- src/vcfremoveaberrantgenotypes.cpp \
- src/vcfrandom.cpp \
- src/vcfparsealts.cpp \
- src/vcfstats.cpp \
- src/vcfflatten.cpp \
- src/vcfprimers.cpp \
- src/vcfnumalt.cpp \
- src/vcfcleancomplex.cpp \
- src/vcfintersect.cpp \
- src/vcfannotate.cpp \
- src/vcfallelicprimitives.cpp \
- src/vcfoverlay.cpp \
- src/vcfaddinfo.cpp \
- src/vcfkeepinfo.cpp \
- src/vcfkeepgeno.cpp \
- src/vcfafpath.cpp \
- src/vcfcountalleles.cpp \
- src/vcflength.cpp \
- src/vcfdistance.cpp \
- src/vcfrandomsample.cpp \
- src/vcfentropy.cpp \
- src/vcfglxgt.cpp \
- src/vcfroc.cpp \
- src/vcfcheck.cpp \
- src/vcfstreamsort.cpp \
- src/vcfuniq.cpp \
- src/vcfuniqalleles.cpp \
- src/vcfremap.cpp \
- src/vcf2fasta.cpp \
- src/vcfsitesummarize.cpp \
- src/vcfbreakmulti.cpp \
- src/vcfcreatemulti.cpp \
- src/vcfevenregions.cpp \
- src/vcfcat.cpp \
- src/vcfgenosummarize.cpp \
- src/vcfgenosamplenames.cpp \
- src/vcfgeno2haplo.cpp \
- src/vcfleftalign.cpp \
- src/vcfcombine.cpp \
- src/vcfgeno2alleles.cpp \
- src/vcfindex.cpp \
- src/vcf2dag.cpp \
- src/vcfsample2info.cpp \
- src/vcfqual2info.cpp \
- src/vcfinfo2qual.cpp \
- src/vcfglbound.cpp \
- src/vcfunphase.cpp \
- src/vcfnull2ref.cpp \
- src/vcfinfosummarize.cpp
-
-# when we can figure out how to build on mac
-# src/vcfsom.cpp
-
-#BINS = $(BIN_SOURCES:.cpp=)
-BINS = $(addprefix bin/,$(notdir $(BIN_SOURCES:.cpp=)))
-SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
-# Use ?= to allow overriding from the env or command-line.
-
-MAKE ?= make
-LOCALBASE ?= /usr/local
-LIB_PATH ?= ${LOCALBASE}/lib
-
-CC ?= cc
-CXX ?= c++
-CXXFLAGS ?= -O3
-CFLAGS += -D_FILE_OFFSET_BITS=64 -fPIC
-CXXFLAGS += $(CFLAGS) --std=c++11
-#CXXFLAGS += -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
-
-DESTDIR ?= stage
-PREFIX ?= /usr/local
-STRIP ?= strip
-INSTALL ?= install -c
-MKDIR ?= mkdir -p
-AR ?= ar
-
-SSW = src/ssw.o src/ssw_cpp.o
-
-INCLUDES = -I${LOCALBASE}/include \
- -I${LOCALBASE}/include/smithwaterman \
- -I${LOCALBASE}/include/multichoose \
- -I${LOCALBASE}/include/fastahack \
- -I${LOCALBASE}/include/intervaltree
-LDFLAGS += -L. -lvcflib \
- -L$(LIB_PATH) -lsw -ltabix -lhts -lfastahack -lfilevercmp \
- -lpthread -lz -lm
-
-all: $(OBJECTS) $(BINS) $(LIB) $(SLIB)
-
-ssw.o: src/ssw.h
-ssw_cpp.o: src/ssw_cpp.h
-
-openmp:
- $(MAKE) CXXFLAGS="$(CXXFLAGS) -fopenmp -D HAS_OPENMP"
-
-profiling:
- $(MAKE) CXXFLAGS="$(CXXFLAGS) -g" all
-
-gprof:
- $(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
-
-$(OBJECTS): $(SOURCES) $(HEADERS)
- $(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(CXXFLAGS)
-
-$(SHORTBINS):
- $(MAKE) $(BIN_DIR)/$@
-
-$(BINS): $(BIN_SOURCES) $(LIB) $(OBJECTS) $(SSW) pre
- $(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(CXXFLAGS) $(LDFLAGS)
-
-$(LIB): $(OBJECTS) $(SSW)
- ar rs $(LIB) $(OBJECTS) $(SSW)
-
-$(SLIB): $(OBJECTS) $(SSW)
- $(CXX) -shared -Wl,-soname,$(SLIB) -o $(SLIB) $(OBJECTS) $(SSW)
-
-install: all
- $(MKDIR) $(DESTDIR)$(PREFIX)/bin
- $(MKDIR) $(DESTDIR)$(PREFIX)/include/vcflib
- $(MKDIR) $(DESTDIR)$(PREFIX)/lib
- $(INSTALL) bin/* $(DESTDIR)$(PREFIX)/bin
- $(INSTALL) -m644 src/*.h src/*.hpp $(DESTDIR)$(PREFIX)/include/vcflib
- $(INSTALL) -m644 $(LIB) $(DESTDIR)$(PREFIX)/lib
- $(INSTALL) $(SLIB) $(DESTDIR)$(PREFIX)/lib
-
-install-strip: install
- $(STRIP) $(DESTDIR)$(PREFIX)/bin/* $(DESTDIR)$(PREFIX)/lib/$(SLIB)
-
-test: $(BINS)
- @prove -Itests/lib -w tests/*.t
-
-clean:
- rm -f $(BINS) $(OBJECTS)
- rm -f ssw_cpp.o ssw.o
- rm -f $(LIB)
- rm -rf $(BIN_DIR)
-
-pre:
- mkdir -p $(BIN_DIR)
-
-.PHONY: clean all test pre
diff --git a/vcflib/patches/patch-src_cdflib.cpp b/vcflib/patches/patch-src_cdflib.cpp
deleted file mode 100644
index 466198c82a..0000000000
--- a/vcflib/patches/patch-src_cdflib.cpp
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD$
-
-Fix missing pointer dereference
---- src/cdflib.cpp.orig 2018-03-09 20:31:19 UTC
-+++ src/cdflib.cpp
-@@ -10040,7 +10040,7 @@ void negative_binomial_cdf_values ( int
- 1, 2, 3,
- 0, 1, 2 };
-
-- if ( n_data < 0 )
-+ if ( *n_data < 0 )
- {
- *n_data = 0;
- }
Home |
Main Index |
Thread Index |
Old Index