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freebayes: Remove obsolete pkg

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Mon Apr 15 09:13:47 2024 -0500
Changeset:	abe8496e8ac2612e95409fd04194719929b6c47c

Modified Files:
	Makefile
Removed Files:
	freebayes/DESCR
	freebayes/Makefile
	freebayes/PLIST
	freebayes/TODO
	freebayes/buildlink3.mk
	freebayes/distinfo
	freebayes/patches/patch-Makefile
	freebayes/patches/patch-SeqLib_bwa_Makefile
	freebayes/patches/patch-SeqLib_bwa_bwt__lite.c
	freebayes/patches/patch-SeqLib_bwa_bwtgap.h
	freebayes/patches/patch-SeqLib_bwa_kthread.c
	freebayes/patches/patch-SeqLib_fermi-lite_Makefile
	freebayes/patches/patch-SeqLib_htslib_Makefile
	freebayes/patches/patch-src_LargeFileSupport.h
	freebayes/patches/patch-src_Makefile
	freebayes/patches/patch-vcflib_Makefile
	freebayes/patches/patch-vcflib_tabixpp_Makefile

Log Message:
freebayes: Remove obsolete pkg

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=abe8496e8ac2612e95409fd04194719929b6c47c

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                                           |  1 -
 freebayes/DESCR                                    |  1 -
 freebayes/Makefile                                 | 43 -----------
 freebayes/PLIST                                    |  3 -
 freebayes/TODO                                     |  1 -
 freebayes/buildlink3.mk                            | 11 ---
 freebayes/distinfo                                 | 16 ----
 freebayes/patches/patch-Makefile                   | 23 ------
 freebayes/patches/patch-SeqLib_bwa_Makefile        | 31 --------
 freebayes/patches/patch-SeqLib_bwa_bwt__lite.c     | 13 ----
 freebayes/patches/patch-SeqLib_bwa_bwtgap.h        | 13 ----
 freebayes/patches/patch-SeqLib_bwa_kthread.c       | 13 ----
 freebayes/patches/patch-SeqLib_fermi-lite_Makefile | 25 ------
 freebayes/patches/patch-SeqLib_htslib_Makefile     | 32 --------
 freebayes/patches/patch-src_LargeFileSupport.h     | 14 ----
 freebayes/patches/patch-src_Makefile               | 90 ----------------------
 freebayes/patches/patch-vcflib_Makefile            | 16 ----
 freebayes/patches/patch-vcflib_tabixpp_Makefile    | 15 ----
 18 files changed, 361 deletions(-)

diffs:
diff --git a/Makefile b/Makefile
index a6c9582f08..30214eafc8 100644
--- a/Makefile
+++ b/Makefile
@@ -948,7 +948,6 @@ SUBDIR+=	fpc
 SUBDIR+=	fprobe
 SUBDIR+=	fractal
 SUBDIR+=	fragrouter
-SUBDIR+=	freebayes
 SUBDIR+=	freebsd-svn
 SUBDIR+=	freecad
 SUBDIR+=	freecell
diff --git a/freebayes/DESCR b/freebayes/DESCR
deleted file mode 100644
index 61c7a2badb..0000000000
--- a/freebayes/DESCR
+++ /dev/null
@@ -1 +0,0 @@
-yesian haplotype-based polymorphism discovery and genotyping.
diff --git a/freebayes/Makefile b/freebayes/Makefile
deleted file mode 100644
index 87772cc6a9..0000000000
--- a/freebayes/Makefile
+++ /dev/null
@@ -1,43 +0,0 @@
-# $NetBSD$
-
-DISTNAME=	freebayes-2018.03.23
-CATEGORIES=	biology
-MASTER_SITES=	https://acadix.biz/Ports/distfiles/
-
-MAINTAINER=	weinertw%uwm.edu@localhost
-HOMEPAGE=	https://github.com/ekg/freebayes
-COMMENT=	Bayesian haplotype-based polymorphism discovery and genotyping
-LICENSE=	mit
-
-EXTRACT_SUFX=	.tar.xz
-
-USE_LANGUAGES=	c c++
-USE_LIBTOOL=	yes
-USE_TOOLS+=	gmake
-
-CFLAGS+=	-msse2
-CXXFLAGS+=	-std=c++11
-
-MAKE_JOBS_SAFE=	no
-
-.include "../../mk/bsd.prefs.mk"
-
-.if ${OPSYS} == Linux
-MAKE_FLAGS=	EXTRALIBS=${COMPILER_RPATH_FLAG}${PREFIX}/lib
-.else
-MAKE_FLAGS+=	EXTRALIBS=${COMPILER_RPATH_FLAG}${PREFIX}/lib
-.endif
-
-.if ${MACHINE_ARCH} == i386
-CFLAGS+=	-msse2
-.endif
-
-INSTALLATION_DIRS+=	bin
-
-do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${DESTDIR}${PREFIX}/bin
-
-.include "../../archivers/bzip2/buildlink3.mk"
-.include "../../archivers/xz/buildlink3.mk"
-.include "../../devel/zlib/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/freebayes/PLIST b/freebayes/PLIST
deleted file mode 100644
index e9b4294275..0000000000
--- a/freebayes/PLIST
+++ /dev/null
@@ -1,3 +0,0 @@
-@comment $NetBSD$
-bin/bamleftalign
-bin/freebayes
diff --git a/freebayes/TODO b/freebayes/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/freebayes/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/freebayes/buildlink3.mk b/freebayes/buildlink3.mk
deleted file mode 100644
index 0b6aff5038..0000000000
--- a/freebayes/buildlink3.mk
+++ /dev/null
@@ -1,11 +0,0 @@
-# $NetBSD$
-BUILDLINK_TREE+=	freebayes
-
-.if !defined(FREEBAYES_BUILDLINK3_MK)
-FREEBAYES_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.freebayes+=	freebayes>=2018.03.23
-BUILDLINK_PKGSRCDIR.freebayes?=		../../wip/freebayes
-.endif	# FREEBAYES_BUILDLINK3_MK
-
-BUILDLINK_TREE+=	-freebayes
diff --git a/freebayes/distinfo b/freebayes/distinfo
deleted file mode 100644
index fb74b05043..0000000000
--- a/freebayes/distinfo
+++ /dev/null
@@ -1,16 +0,0 @@
-$NetBSD$
-
-RMD160 (freebayes-2018.03.23.tar.xz) = bde7a441c76c2a16c89600d8b3fe0ce843146b37
-SHA512 (freebayes-2018.03.23.tar.xz) = 04f386b24d623e4b818a2b3ce12042c30db877b9ab08744466702573730ff8f853f7f2720d9a23f3c7b3abae8dc50fba3912e1695ad7d04dbddc3682754952e4
-Size (freebayes-2018.03.23.tar.xz) = 89782932 bytes
-SHA1 (patch-Makefile) = aace859fb9e85a132386d510771c34f0b9a0d47b
-SHA1 (patch-SeqLib_bwa_Makefile) = 3f8c8bd8720d5a4ceb7e29d1b83eba285d038323
-SHA1 (patch-SeqLib_bwa_bwt__lite.c) = de4f9efd1485a4b6c20837584e65406267833ccd
-SHA1 (patch-SeqLib_bwa_bwtgap.h) = a8abe98b7f0ad65104a763c19fd128bbb05f2ed8
-SHA1 (patch-SeqLib_bwa_kthread.c) = 5170b400af2f1f835cfcf5dda3875242f227bc89
-SHA1 (patch-SeqLib_fermi-lite_Makefile) = 55d999277d5d61dba7cae01b44a8f9ebff77142d
-SHA1 (patch-SeqLib_htslib_Makefile) = f7d332c3defd580a44feaa479e5c17509f73e02d
-SHA1 (patch-src_LargeFileSupport.h) = 2efb9a247582c85b080a1e1346e687c99686749d
-SHA1 (patch-src_Makefile) = afd89cc38dd7cd94d0d4a698a54a1c2a6be87f29
-SHA1 (patch-vcflib_Makefile) = ce29ade87027b7e638f0472653cec6e9aa809b15
-SHA1 (patch-vcflib_tabixpp_Makefile) = 433ddd3e4e643376fd0f7511032d6d20ab676459
diff --git a/freebayes/patches/patch-Makefile b/freebayes/patches/patch-Makefile
deleted file mode 100644
index 52e40e4f21..0000000000
--- a/freebayes/patches/patch-Makefile
+++ /dev/null
@@ -1,23 +0,0 @@
-$NetBSD$
-
-Use correct make binary & do not download an unused file.
---- Makefile.orig	2018-03-23 14:01:01 UTC
-+++ Makefile
-@@ -5,7 +5,7 @@ wbamtools: vcflib/Makefile log
- 	cd src && $(MAKE) -f Makefile.bamtools
- 
- log: src/version_git.h
--	wget -q http://hypervolu.me/freebayes/build/$(shell cat src/version_git.h | grep v | cut -f 3 -d\  | sed s/\"//g) &
-+	# wget -q http://hypervolu.me/freebayes/build/$(shell cat src/version_git.h | grep v | cut -f 3 -d\  | sed s/\"//g) &
- 
- src/version_git.h:
- 	cd src && $(MAKE) autoversion
-@@ -27,7 +27,7 @@ uninstall:
- 	rm /usr/local/bin/freebayes /usr/local/bin/bamleftalign
- 
- test:
--	cd test && make test
-+	cd test && ${MAKE} test
- 
- clean:
- 	cd src && $(MAKE) clean
diff --git a/freebayes/patches/patch-SeqLib_bwa_Makefile b/freebayes/patches/patch-SeqLib_bwa_Makefile
deleted file mode 100644
index 21f989ed87..0000000000
--- a/freebayes/patches/patch-SeqLib_bwa_Makefile
+++ /dev/null
@@ -1,31 +0,0 @@
-$NetBSD$
-
-# Respect LDFLAGS from pkgsrc
-
---- SeqLib/bwa/Makefile.orig	2018-03-23 14:01:29.000000000 +0000
-+++ SeqLib/bwa/Makefile
-@@ -1,8 +1,8 @@
--CC=			gcc
-+CC ?=			gcc
- #CC=			clang --analyze
--CFLAGS=		-g -Wall -Wno-unused-function -O2
-+CFLAGS ?=		-g -Wall -Wno-unused-function -O2
- WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
--AR=			ar
-+AR ?=			ar
- DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
- ## moved is.o bwtiindex.o rope.o to LOBJS
- LOBJS=		utils.o kthread.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o \
-@@ -28,10 +28,10 @@ endif
- all:$(PROG)
- 
- bwa:libbwa.a $(AOBJS) main.o
--		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
-+	$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. $(LDFLAGS) -lbwa $(LIBS)
- 
- bwamem-lite:libbwa.a example.o
--		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
-+	$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. $(LDFLAGS) -lbwa $(LIBS)
- 
- libbwa.a:$(LOBJS)
- 		$(AR) -csru $@ $(LOBJS)
diff --git a/freebayes/patches/patch-SeqLib_bwa_bwt__lite.c b/freebayes/patches/patch-SeqLib_bwa_bwt__lite.c
deleted file mode 100644
index 53f5b7dc48..0000000000
--- a/freebayes/patches/patch-SeqLib_bwa_bwt__lite.c
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD$
-
-Add missing include.
---- SeqLib/bwa/bwt_lite.c.orig	2018-03-23 18:49:48 UTC
-+++ SeqLib/bwa/bwt_lite.c
-@@ -1,6 +1,7 @@
- #include <stdlib.h>
- #include <string.h>
- #include <stdio.h>
-+#include <sys/types.h>
- #include "bwt_lite.h"
- 
- #ifdef USE_MALLOC_WRAPPERS
diff --git a/freebayes/patches/patch-SeqLib_bwa_bwtgap.h b/freebayes/patches/patch-SeqLib_bwa_bwtgap.h
deleted file mode 100644
index e1cc56495e..0000000000
--- a/freebayes/patches/patch-SeqLib_bwa_bwtgap.h
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD$
-
-Add missing include.
---- SeqLib/bwa/bwtgap.h.orig	2018-03-23 18:49:18 UTC
-+++ SeqLib/bwa/bwtgap.h
-@@ -3,6 +3,7 @@
- 
- #include "bwt.h"
- #include "bwtaln.h"
-+#include <sys/types.h>
- 
- typedef struct { // recursion stack
- 	u_int32_t info; // score<<21 | i
diff --git a/freebayes/patches/patch-SeqLib_bwa_kthread.c b/freebayes/patches/patch-SeqLib_bwa_kthread.c
deleted file mode 100644
index 148fb653d8..0000000000
--- a/freebayes/patches/patch-SeqLib_bwa_kthread.c
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD$
-
-Add missing include.
---- SeqLib/bwa/kthread.c.orig	2018-03-23 18:48:35 UTC
-+++ SeqLib/bwa/kthread.c
-@@ -1,6 +1,7 @@
- #include <pthread.h>
- #include <stdlib.h>
- #include <limits.h>
-+#include <inttypes.h>
- 
- /************
-  * kt_for() *
diff --git a/freebayes/patches/patch-SeqLib_fermi-lite_Makefile b/freebayes/patches/patch-SeqLib_fermi-lite_Makefile
deleted file mode 100644
index 1a802a4aa3..0000000000
--- a/freebayes/patches/patch-SeqLib_fermi-lite_Makefile
+++ /dev/null
@@ -1,25 +0,0 @@
-$NetBSD$
-
-# Respect LDFLAGS from pkgsrc
-
---- SeqLib/fermi-lite/Makefile.orig	2018-03-23 14:01:29.000000000 +0000
-+++ SeqLib/fermi-lite/Makefile
-@@ -1,6 +1,6 @@
--CC=			gcc
--CFLAGS=		-g -Wall -O2 -Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once
--CPPFLAGS=
-+CC ?=			gcc
-+CFLAGS ?=		-g -Wall -O2 -Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once
-+CPPFLAGS ?=
- INCLUDES=	
- OBJS=		kthread.o misc.o \
- 			bseq.o htab.o bfc.o \
-@@ -17,7 +17,7 @@ LIBS=		-lm -lz -lpthread
- all:$(PROG)
- 
- fml-asm:libfml.a example.o
--		$(CC) $(CFLAGS) $^ -o $@ -L. -lfml $(LIBS)
-+		$(CC) $(CFLAGS) $^ -o $@ -L. $(LDFLAGS) -lfml $(LIBS)
- 
- libfml.a:$(OBJS)
- 		$(AR) -csru $@ $(OBJS)
diff --git a/freebayes/patches/patch-SeqLib_htslib_Makefile b/freebayes/patches/patch-SeqLib_htslib_Makefile
deleted file mode 100644
index cd46441e98..0000000000
--- a/freebayes/patches/patch-SeqLib_htslib_Makefile
+++ /dev/null
@@ -1,32 +0,0 @@
-$NetBSD$
-
-Allow makefile variable overrides
---- SeqLib/htslib/Makefile.orig	2018-03-23 18:41:02 UTC
-+++ SeqLib/htslib/Makefile
-@@ -22,20 +22,20 @@
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- # DEALINGS IN THE SOFTWARE.
- 
--CC     = gcc
--AR     = ar
--RANLIB = ranlib
-+CC     ?= gcc
-+AR     ?= ar
-+RANLIB ?= ranlib
- 
- # Default libraries to link if configure is not used
- htslib_default_libs = -lz -lm -lbz2 -llzma
- 
--CPPFLAGS =
-+CPPFLAGS ?=
- # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
- # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
- #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
--CFLAGS   = -g -Wall -O2
-+CFLAGS   ?= -g -Wall -O2
- EXTRA_CFLAGS_PIC = -fpic
--LDFLAGS  =
-+LDFLAGS  ?=
- LIBS     = $(htslib_default_libs)
- 
- prefix      = /usr/local
diff --git a/freebayes/patches/patch-src_LargeFileSupport.h b/freebayes/patches/patch-src_LargeFileSupport.h
deleted file mode 100644
index 039ceee11f..0000000000
--- a/freebayes/patches/patch-src_LargeFileSupport.h
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD$
-
-Add macro-ifdef check for FreeBSD.
---- src/LargeFileSupport.h.orig	2018-03-23 21:15:04 UTC
-+++ src/LargeFileSupport.h
-@@ -8,7 +8,7 @@ typedef __int64 off_type;
- #define ftell64(a)     ftell(a)
- #define fseek64(a,b,c) fseek(a,b,c)
- typedef __int64_t off_type;
--#elif defined(__APPLE__)
-+#elif defined(__APPLE__) || defined(__FreeBSD__)
- #define ftell64(a)     ftello(a)
- #define fseek64(a,b,c) fseeko(a,b,c)
- typedef off_t off_type;
diff --git a/freebayes/patches/patch-src_Makefile b/freebayes/patches/patch-src_Makefile
deleted file mode 100644
index 3a44086e6c..0000000000
--- a/freebayes/patches/patch-src_Makefile
+++ /dev/null
@@ -1,90 +0,0 @@
-$NetBSD$
-
-Allow makefile variable overrides. Honor LDFLAGS. Honor make binary.
---- src/Makefile.orig	2018-03-30 18:35:02.370636951 +0000
-+++ src/Makefile
-@@ -5,8 +5,9 @@
- ################################################################################
- 
- # Compiler
--CXX=g++ ${CXXFLAGS}
--C=gcc
-+CXX ?= g++
-+# CXX += ${CXXFLAGS}
-+CC ?= gcc
- 
- export CXXFLAGS
- export C
-@@ -17,7 +18,7 @@ export LIBFLAGS
- 
- # Compiler flags
- 
--CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
-+CFLAGS += -D_FILE_OFFSET_BITS=64
- #CFLAGS=-O3 -static -D VERBOSE_DEBUG  # enables verbose debugging via --debug2
- 
- SEQLIB_ROOT=../SeqLib
-@@ -25,7 +26,7 @@ VCFLIB_ROOT=../vcflib
- TABIX_ROOT=$(VCFLIB_ROOT)/tabixpp
- HTSLIB_ROOT=$(SEQLIB_ROOT)/htslib
- 
--LIBS = -lz -llzma -lbz2 -lm -lpthread
-+LIBS = -lz -llzma -lbz2 -lm -lpthread #-lexecinfo
- INCLUDE = -I../src -I../ttmath -I$(VCFLIB_ROOT)/src/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) 
- #INCLUDE = -I../ttmath -I$(BAMTOOLS_ROOT)/src/ -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
- 
-@@ -46,10 +47,10 @@ gprof:
- .PHONY: all static debug profiling gprof
- 
- $(HTSLIB_ROOT)/libhts.a:
--	cd $(HTSLIB_ROOT) && make
-+	cd $(HTSLIB_ROOT) && ${MAKE}
- 
- $(SEQLIB_ROOT)/src/libseqlib.a:
--	cd $(SEQLIB_ROOT) && ./configure && make 
-+	cd $(SEQLIB_ROOT) && ./configure && ${MAKE} 
- 
- OBJECTS=BedReader.o \
- 		CNV.o \
-@@ -92,19 +93,19 @@ HEADERS=multichoose.h version_git.h
- # executables
- 
- freebayes ../bin/freebayes: freebayes.o $(OBJECTS) $(HEADERS) $(seqlib)
--	$(CXX) $(CXXFLAGS) $(INCLUDE) freebayes.o $(OBJECTS) -o ../bin/freebayes $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(INCLUDE) $(LDFLAGS) freebayes.o $(OBJECTS) -o ../bin/freebayes $(LIBS)
- 
- alleles ../bin/alleles: alleles.o $(OBJECTS) $(HEADERS) $(seqlib)
--	$(CXX) $(CXXFLAGS) $(INCLUDE) alleles.o $(OBJECTS) -o ../bin/alleles $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(INCLUDE) $(LDFLAGS) alleles.o $(OBJECTS) -o ../bin/alleles $(LIBS)
- 
- dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS) $(seqlib)
--	$(CXX) $(CXXFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(INCLUDE) $(LDFLAGS) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS)
- 
- bamleftalign ../bin/bamleftalign: $(SEQLIB_ROOT)/src/libseqlib.a $(HTSLIB_ROOT)/libhts.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
--	$(CXX) $(CXXFLAGS) $(INCLUDE) bamleftalign.o $(OBJECTS) -o ../bin/bamleftalign $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(INCLUDE) $(LDFLAGS) bamleftalign.o $(OBJECTS) -o ../bin/bamleftalign $(LIBS)
- 
- bamfiltertech ../bin/bamfiltertech: $(SEQLIB_ROOT)/src/libseqlib.a $(HTSLIB_ROOT)/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS)
--	$(CXX) $(CXXFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(INCLUDE) $(LDFLAGS) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)
- 
- 
- # objects
-@@ -122,7 +123,7 @@ freebayes.o: freebayes.cpp TryCatch.h $(
- 	$(CXX) $(CXXFLAGS) $(INCLUDE) -c freebayes.cpp
- 
- fastlz.o: fastlz.c fastlz.h
--	$(C) $(CFLAGS) $(INCLUDE) -c fastlz.c	
-+	$(CC) $(CFLAGS) $(INCLUDE) -c fastlz.c	
- 
- Parameters.o: Parameters.cpp Parameters.h Version.h
- 	$(CXX) $(CXXFLAGS) $(INCLUDE) -c Parameters.cpp
-@@ -277,5 +278,5 @@ autoversion:
- 
- clean:
- 	rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} tabix.hpp
--	if [ -d $(BAMTOOLS_ROOT)/build ]; then make -C $(BAMTOOLS_ROOT)/build clean; fi
--	make -C $(VCFLIB_ROOT)/smithwaterman clean
-+	if [ -d $(BAMTOOLS_ROOT)/build ]; then ${MAKE} -C $(BAMTOOLS_ROOT)/build clean; fi
-+	${MAKE} -C $(VCFLIB_ROOT)/smithwaterman clean
diff --git a/freebayes/patches/patch-vcflib_Makefile b/freebayes/patches/patch-vcflib_Makefile
deleted file mode 100644
index cf0b91dbc8..0000000000
--- a/freebayes/patches/patch-vcflib_Makefile
+++ /dev/null
@@ -1,16 +0,0 @@
-$NetBSD$
-
-Allow makefile variable overrides.
---- vcflib/Makefile.orig	2018-03-23 18:36:07 UTC
-+++ vcflib/Makefile
-@@ -136,8 +136,8 @@ all: $(OBJECTS) $(BINS)
- 
- GIT_VERSION := $(shell git describe --abbrev=4 --dirty --always)
- 
--CXX = g++
--CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x 
-+CXX ?= g++
-+CXXFLAGS += -D_FILE_OFFSET_BITS=64 -std=c++0x 
- #CXXFLAGS = -O2
- #CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
- 
diff --git a/freebayes/patches/patch-vcflib_tabixpp_Makefile b/freebayes/patches/patch-vcflib_tabixpp_Makefile
deleted file mode 100644
index ee18552345..0000000000
--- a/freebayes/patches/patch-vcflib_tabixpp_Makefile
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD$
-
-# Respect LDFLAGS from pkgsrc
-
---- vcflib/tabixpp/Makefile.orig	2018-03-31 13:42:56.711911472 +0000
-+++ vcflib/tabixpp/Makefile
-@@ -39,7 +39,7 @@ htslib/libhts.a:
- 
- tabix++: tabix.o main.cpp $(HTS_LIB)
- 	$(CXX) $(CXXFLAGS) -o $@ main.cpp tabix.o $(INCLUDES) $(LIBPATH) \
--		-lhts -lpthread -lm -lz
-+		$(LDFLAGS) -lhts -lpthread -lm -lz
- 
- cleanlocal:
- 	rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a tabix.aux tabix.log \
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