Attachment #229245 for bug #259627




PORTNAME=		freebayes
DISTVERSIONPREFIX=	v
DISTVERSION=		1.3.5
PORTREVISION=		3
CATEGORIES=		biology

MAINTAINER=	jwb@FreeBSD.org

BROKEN_armv7=		fails to compile: invalid conversion between vector type and integer type
BROKEN_riscv64=		fails to compile: invalid conversion between vector type and integer type

LIB_DEPENDS=	libhts.so:biology/htslib \
		libtabix.so:biology/tabixpp

# Submodules use older versions than the ports, so we cannot safely unbundle
# No shared libs are built by the submodules so there will be no conflicts
USES=		compiler:c++14-lang localbase meson perl5 pkgconfig
USE_GITHUB=	yes
GH_ACCOUNT=	ekg
GH_TUPLE=	ekg:vcflib:d4073c3:vcflib/vcflib-temp \
		ekg:smithwaterman:2610e25:smithwaterman/vcflib/smithwaterman \
		ekg:multichoose:68733cd:multichoose/vcflib/multichoose \
		ekg:fastahack:bb33265:fastahack/vcflib/fastahack \
		ekg:intervaltree:17ddd57:intervaltree/vcflib/intervaltree \
		ekg:intervaltree:dbb4c51:interval1/intervaltree \
		vcflib:vcflib:5e3ce04:vcflib/vcflib-temp \
		ekg:fastahack:c68cebb:fastahack/vcflib/fastahack \
		ekg:filevercmp:1a9b779:filevercmp/vcflib/filevercmp \
		ekg:fsom:a6ef318:fsom/vcflib/fsom \
		ekg:filevercmp:1a9b779:filevercmp/vcflib/filevercmp \
		google:googletest:d225acc:googletest/vcflib/googletest \
		edawson:libVCFH:615a06b:libVCFH/vcflib/libVCFH \
		simd-everywhere:simde-no-tests:2931676:simd/vcflib/src/simde \
		ekg:intervaltree:b90527f:intervaltree2/intervaltree \
		ekg:tabixpp:b255df1:tabixpp/vcflib/tabixpp \
		ingydotnet:test-simple-bash:124673f:testsimplebash/test/test-simple-bash \
		illusori:bash-tap:c38fbfa:bashtap/test/bash-tap \
		samtools:htslib:b581944:htslib/contrib/htslib
USE_PERL5=	build

# GCC disables sse2 by default on i386, but it's required for vcflib
LDFLAGS+=		-lexecinfo
CFLAGS_i386=		-msse2
MAKE_JOBS_UNSAFE=	yes
PLIST_FILES=		bin/bamleftalign bin/freebayes

# GH_TUPLEs cannot seem to share a top-level subdirectory, so we work around
# by dumping the parent in a temp directory and then moving the contents
post-extract:
	${CP} -r ${WRKSRC}/vcflib-temp/* ${WRKSRC}/vcflib
	${MV} -n ${WRKSRC}/vcflib-temp/* ${WRKSRC}/vcflib

do-install:
	${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${STAGEDIR}${PREFIX}/bin

.include <bsd.port.mk>




TIMESTAMP = 1635952798
SHA256 (ekg-freebayes-v1.3.5_GH0.tar.gz) = af195a8c54b742d01af5a7e1fd1781a89290d726b310216c83e78c650d7aee49
SIZE (ekg-freebayes-v1.3.5_GH0.tar.gz) = 2890213
SHA256 (ekg-vcflib-d4073c3_GH0.tar.gz) = 27ed96714eeaa871b8036bcb308db5256b8266cadd2689fbd1dbf3771611b879
SIZE (ekg-vcflib-d4073c3_GH0.tar.gz) = 19215364
SHA256 (ekg-smithwaterman-2610e25_GH0.tar.gz) = f907becb50945d0858d3bf7a64959905712244cbe8455b35ef1102ff893173ce
SIZE (ekg-smithwaterman-2610e25_GH0.tar.gz) = 39160
SHA256 (ekg-multichoose-68733cd_GH0.tar.gz) = 909baf2e462e43e71ba0d015fbe759c0ab95331c36d6c4ec65e4a92a7b9d3297
SIZE (ekg-multichoose-68733cd_GH0.tar.gz) = 6558
SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a
SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760
SHA256 (ekg-intervaltree-17ddd57_GH0.tar.gz) = c2274e2382f893241847f75940ad15bac9d1e122da4416b0d2fc61ebba527ee1
SIZE (ekg-intervaltree-17ddd57_GH0.tar.gz) = 72488
SHA256 (ekg-intervaltree-dbb4c51_GH0.tar.gz) = 1f3ba92a83cb782cf22dfb383b8c93c11c1c88e0b2e5fa434e24668260ecd1f8
SIZE (ekg-intervaltree-dbb4c51_GH0.tar.gz) = 3780
SHA256 (vcflib-vcflib-5e3ce04_GH0.tar.gz) = d084c1df7bb0004df18e013da3cbf896b642d853c855aea58ae029abe1d2097a
SIZE (vcflib-vcflib-5e3ce04_GH0.tar.gz) = 20119782
SHA256 (ekg-fastahack-c68cebb_GH0.tar.gz) = c6f7186bbe733ff78c25b2afd7e7ba79daa3ecd14a5876ea0b033a43744c876d
SIZE (ekg-fastahack-c68cebb_GH0.tar.gz) = 17312
SHA256 (ekg-filevercmp-1a9b779_GH0.tar.gz) = 34c21d1b58295bca72b92c1cd832a4171b07ec97c19ffc0d4d8ec67e266c6070
SIZE (ekg-filevercmp-1a9b779_GH0.tar.gz) = 3053
SHA256 (ekg-fsom-a6ef318_GH0.tar.gz) = 68351c16d5c4b96142409e38c6828b6199eae44eaa7579bde165734d4832565b
SIZE (ekg-fsom-a6ef318_GH0.tar.gz) = 9686
SHA256 (ekg-filevercmp-1a9b779_GH0.tar.gz) = 34c21d1b58295bca72b92c1cd832a4171b07ec97c19ffc0d4d8ec67e266c6070
SIZE (ekg-filevercmp-1a9b779_GH0.tar.gz) = 3053
SHA256 (google-googletest-d225acc_GH0.tar.gz) = 6880e0d51fa80a508ad5674ce483c1c468315faddac10d580b5505e8e7ef6bfa
SIZE (google-googletest-d225acc_GH0.tar.gz) = 1279815
SHA256 (edawson-libVCFH-615a06b_GH0.tar.gz) = 2774c26c55e1d155fe803b492a745a1d2a3659f4fdbe248d3187ce03edf87223
SIZE (edawson-libVCFH-615a06b_GH0.tar.gz) = 2295
SHA256 (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 3877e64f51a7368f768b40167e4cdff36a93d3047f722416581834f1eaf40f63
SIZE (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 203996
SHA256 (ekg-intervaltree-b90527f_GH0.tar.gz) = 4d9272046972e595e4ac771fe6958b4c166a35e2ac727fc977fc4e0b9f8e887c
SIZE (ekg-intervaltree-b90527f_GH0.tar.gz) = 72540
SHA256 (ekg-tabixpp-b255df1_GH0.tar.gz) = 96d9aa41f55f74498e267b582e93e986605913fbd830dca6bf4cac5d9f927bb9
SIZE (ekg-tabixpp-b255df1_GH0.tar.gz) = 3739
SHA256 (ingydotnet-test-simple-bash-124673f_GH0.tar.gz) = 19b5c27402d955909fcbf601ed02bcd7d9f2aa841e2158ecd93b9ff8f7ec1d98
SIZE (ingydotnet-test-simple-bash-124673f_GH0.tar.gz) = 6609
SHA256 (illusori-bash-tap-c38fbfa_GH0.tar.gz) = 5e658965f7c8730d7f29642ebb40b0e0beb701f992e391a1273af3b132ff66b8
SIZE (illusori-bash-tap-c38fbfa_GH0.tar.gz) = 5826
SHA256 (samtools-htslib-b581944_GH0.tar.gz) = 940f0acd7037af262e15388eff9a6d696d03966fef1bae19d663130926c365f4
SIZE (samtools-htslib-b581944_GH0.tar.gz) = 1501311




--- 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




--- SeqLib/bwa/Makefile.orig	2018-03-23 18:47:04 UTC
+++ 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 \

Removed Link Here

(-)biology/freebayes/files/patch-SeqLib_bwa_bwt__lite.c (-10 lines)
1	--- SeqLib/bwa/bwt_lite.c.orig 2018-03-23 18:49:48 UTC
2	+++ SeqLib/bwa/bwt_lite.c
3	@@ -1,6 +1,7 @@
4	#include <stdlib.h>
5	#include <string.h>
6	#include <stdio.h>
7	+#include <sys/types.h>
8	#include "bwt_lite.h"
9
10	#ifdef USE_MALLOC_WRAPPERS

Removed Link Here

(-)biology/freebayes/files/patch-SeqLib_bwa_bwtgap.h (-10 lines)
1	--- SeqLib/bwa/bwtgap.h.orig 2018-03-23 18:49:18 UTC
2	+++ SeqLib/bwa/bwtgap.h
3	@@ -3,6 +3,7 @@
4
5	#include "bwt.h"
6	#include "bwtaln.h"
7	+#include <sys/types.h>
8
9	typedef struct { // recursion stack
10	u_int32_t info; // score<<21 \| i

Removed Link Here

(-)biology/freebayes/files/patch-SeqLib_bwa_kthread.c (-10 lines)
1	--- SeqLib/bwa/kthread.c.orig 2018-03-23 18:48:35 UTC
2	+++ SeqLib/bwa/kthread.c
3	@@ -1,6 +1,7 @@
4	#include <pthread.h>
5	#include <stdlib.h>
6	#include <limits.h>
7	+#include <inttypes.h>
8
9	/************
10	* kt_for() *

Removed Link Here

(-)biology/freebayes/files/patch-SeqLib_bwa_rle.h (-11 lines)
1	--- SeqLib/bwa/rle.h.orig 2016-10-13 18:10:17 UTC
2	+++ SeqLib/bwa/rle.h
3	@@ -30,7 +30,7 @@ extern "C" {
4	* 43+3 codec *
5	******************/
6
7	-const uint8_t rle_auxtab[8];
8	+extern const uint8_t rle_auxtab[8];
9
10	#define RLE_MIN_SPACE 18
11	#define rle_nptr(block) ((uint16_t*)(block))




--- SeqLib/fermi-lite/Makefile.orig	2018-03-23 18:50:25 UTC
+++ 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 \

Removed Link Here

(-)biology/freebayes/files/patch-SeqLib_fermi-lite_rle.h (-11 lines)
1	--- SeqLib/fermi-lite/rle.h.orig 2016-09-01 20:47:53 UTC
2	+++ SeqLib/fermi-lite/rle.h
3	@@ -30,7 +30,7 @@ extern "C" {
4	* 43+3 codec *
5	******************/
6
7	-const uint8_t rle_auxtab[8];
8	+extern const uint8_t rle_auxtab[8];
9
10	#define RLE_MIN_SPACE 18
11	#define rle_nptr(block) ((uint16_t*)(block))




--- SeqLib/htslib/Makefile.orig	2017-06-20 12:40:28 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
@@ -86,7 +86,7 @@ BUILT_THRASH_PROGRAMS = \
 	test/thrash_threads5 \
 	test/thrash_threads6
 
-all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
+all: lib-static $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
 
 HTSPREFIX =
 include htslib_vars.mk




--- src/Makefile.orig	2018-03-23 14:01:01 UTC
+++ 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 \
@@ -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




--- 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
 

Return to bug 259627

Lines 1-7 Link Here

(-)biology/freebayes/Makefile (-26 / +22 lines)
1	PORTNAME= freebayes	1	PORTNAME= freebayes
2	DISTVERSIONPREFIX= v	2	DISTVERSIONPREFIX= v
3	DISTVERSION= 1.2.0	3	DISTVERSION= 1.3.5
4	PORTREVISION= 3
5	CATEGORIES= biology	4	CATEGORIES= biology
6		5
7	MAINTAINER= jwb@FreeBSD.org	6	MAINTAINER= jwb@FreeBSD.org
Lines 14-54 BROKEN_armv6= fails to compile: invalid conversion be Link Here
14	BROKEN_armv7= fails to compile: invalid conversion between vector type and integer type	13	BROKEN_armv7= fails to compile: invalid conversion between vector type and integer type
15	BROKEN_riscv64= fails to compile: invalid conversion between vector type and integer type	14	BROKEN_riscv64= fails to compile: invalid conversion between vector type and integer type
16		15
		16	LIB_DEPENDS= libhts.so:biology/htslib \
		17	libtabix.so:biology/tabixpp
		18
17	# Submodules use older versions than the ports, so we cannot safely unbundle	19	# Submodules use older versions than the ports, so we cannot safely unbundle
18	# No shared libs are built by the submodules so there will be no conflicts	20	# No shared libs are built by the submodules so there will be no conflicts
19	USES= compiler:c++11-lang gmake tar:xz	21	USES= compiler:c++14-lang localbase meson perl5 pkgconfig
20	USE_GITHUB= yes	22	USE_GITHUB= yes
21	GH_ACCOUNT= ekg	23	GH_ACCOUNT= ekg
22	GH_TUPLE= walaj:SeqLib:5941c68:SeqLib/SeqLib-temp \	24	GH_TUPLE= ekg:vcflib:d4073c3:vcflib/vcflib-temp \
23	jwalabroad:bwa:c02766e:bwa/SeqLib/bwa \	25	ekg:smithwaterman:2610e25:smithwaterman/vcflib/smithwaterman \
24	jwalabroad:fermi-lite:5bc90f8:fermi/SeqLib/fermi-lite \	26	ekg:multichoose:68733cd:multichoose/vcflib/multichoose \
25	samtools:htslib:49fdfbd:htslib/SeqLib/htslib \	27	ekg:fastahack:bb33265:fastahack/vcflib/fastahack \
26	ekg:bamtools:e77a43f:bamtools/bamtools \	28	ekg:intervaltree:17ddd57:intervaltree/vcflib/intervaltree \
27	ekg:intervaltree:dbb4c51:interval1/intervaltree \
28	vcflib:vcflib:5e3ce04:vcflib/vcflib-temp \
29	ekg:fastahack:c68cebb:fastahack/vcflib/fastahack \
30	ekg:filevercmp:1a9b779:filevercmp/vcflib/filevercmp \
31	ekg:fsom:a6ef318:fsom/vcflib/fsom \	29	ekg:fsom:a6ef318:fsom/vcflib/fsom \
32	google:googletest:d225acc:google/vcflib/googletest \	30	ekg:filevercmp:1a9b779:filevercmp/vcflib/filevercmp \
33	ekg:intervaltree:b704f19:interval2/vcflib/intervaltree \	31	google:googletest:d225acc:googletest/vcflib/googletest \
34	ekg:multichoose:73d35da:multichoose/vcflib/multichoose \	32	edawson:libVCFH:615a06b:libVCFH/vcflib/libVCFH \
35	ekg:smithwaterman:84c08d7:smithwaterman/vcflib/smithwaterman \	33	simd-everywhere:simde-no-tests:2931676:simd/vcflib/src/simde \
36	ekg:tabixpp:80012f8:tabixpp/vcflib/tabixpp \	34	ekg:intervaltree:b90527f:intervaltree2/intervaltree \
37	samtools:htslib:0f298ce:hts2/vcflib/tabixpp/htslib	35	ekg:tabixpp:b255df1:tabixpp/vcflib/tabixpp \
		36	ingydotnet:test-simple-bash:124673f:testsimplebash/test/test-simple-bash \
		37	illusori:bash-tap:c38fbfa:bashtap/test/bash-tap \
		38	samtools:htslib:b581944:htslib/contrib/htslib
		39	USE_PERL5= build
38		40
39	# GCC disables sse2 by default on i386, but it's required for vcflib	41	# GCC disables sse2 by default on i386, but it's required for vcflib
40	CXXFLAGS+= --std=c++11	42	LDFLAGS+= -lexecinfo
41	CFLAGS_i386= -msse2
42	MAKE_JOBS_UNSAFE= yes
43	PLIST_FILES= bin/bamleftalign bin/freebayes	43	PLIST_FILES= bin/bamleftalign bin/freebayes
44		44
45	# GH_TUPLEs cannot seem to share a top-level subdirectory, so we work around	45	# GH_TUPLEs cannot seem to share a top-level subdirectory, so we work around
46	# by dumping the parent in a temp directory and then moving the contents	46	# by dumping the parent in a temp directory and then moving the contents
47	post-extract:	47	post-extract:
48	${MV} -n ${WRKSRC}/SeqLib-temp/* ${WRKSRC}/SeqLib	48	${CP} -r ${WRKSRC}/vcflib-temp/* ${WRKSRC}/vcflib
49	${MV} -n ${WRKSRC}/vcflib-temp/* ${WRKSRC}/vcflib
50		49
51	do-install:
52	${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${STAGEDIR}${PREFIX}/bin
53
54	.include <bsd.port.mk>	50	.include <bsd.port.mk>

Lines 1-35 Link Here

(-)biology/freebayes/distinfo (-31 / +29 lines)
1	TIMESTAMP = 1523932688	1	TIMESTAMP = 1635952798
2	SHA256 (ekg-freebayes-v1.2.0_GH0.tar.gz) = a5626636112966cac87095365986722d1c871759f03c5a143646da65c416ba8a	2	SHA256 (ekg-freebayes-v1.3.5_GH0.tar.gz) = af195a8c54b742d01af5a7e1fd1781a89290d726b310216c83e78c650d7aee49
3	SIZE (ekg-freebayes-v1.2.0_GH0.tar.gz) = 2639725	3	SIZE (ekg-freebayes-v1.3.5_GH0.tar.gz) = 2890213
4	SHA256 (walaj-SeqLib-5941c68_GH0.tar.gz) = 0ac2b63f5fd7b1cec20a18ebb6799bf1f9b88d6c7cd95f7dd7410b1b82c8703f	4	SHA256 (ekg-vcflib-d4073c3_GH0.tar.gz) = 27ed96714eeaa871b8036bcb308db5256b8266cadd2689fbd1dbf3771611b879
5	SIZE (walaj-SeqLib-5941c68_GH0.tar.gz) = 314968	5	SIZE (ekg-vcflib-d4073c3_GH0.tar.gz) = 19215364
6	SHA256 (jwalabroad-bwa-c02766e_GH0.tar.gz) = cce547db0efef8572d63b47d2065f07e36f770fc8a6f15f5cd03d6fa9ab9b1f7	6	SHA256 (ekg-smithwaterman-2610e25_GH0.tar.gz) = f907becb50945d0858d3bf7a64959905712244cbe8455b35ef1102ff893173ce
7	SIZE (jwalabroad-bwa-c02766e_GH0.tar.gz) = 205546	7	SIZE (ekg-smithwaterman-2610e25_GH0.tar.gz) = 39160
8	SHA256 (jwalabroad-fermi-lite-5bc90f8_GH0.tar.gz) = 2b3b9b637f48dc3239618efd6b55183eef6b6232013c217eb1c319f1dd3da224	8	SHA256 (ekg-multichoose-68733cd_GH0.tar.gz) = 909baf2e462e43e71ba0d015fbe759c0ab95331c36d6c4ec65e4a92a7b9d3297
9	SIZE (jwalabroad-fermi-lite-5bc90f8_GH0.tar.gz) = 248454	9	SIZE (ekg-multichoose-68733cd_GH0.tar.gz) = 6558
10	SHA256 (samtools-htslib-49fdfbd_GH0.tar.gz) = 0bc9c7d48e2a439badf5990113ae3e4de9acd05e4c090938236ee40588d115b9	10	SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a
11	SIZE (samtools-htslib-49fdfbd_GH0.tar.gz) = 1145082	11	SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760
12	SHA256 (ekg-bamtools-e77a43f_GH0.tar.gz) = d3a143636ccedcc54417a2d6d88dd726c7d2c046318620b88c7ba2fb30b01419	12	SHA256 (ekg-intervaltree-17ddd57_GH0.tar.gz) = c2274e2382f893241847f75940ad15bac9d1e122da4416b0d2fc61ebba527ee1
13	SIZE (ekg-bamtools-e77a43f_GH0.tar.gz) = 540118	13	SIZE (ekg-intervaltree-17ddd57_GH0.tar.gz) = 72488
14	SHA256 (ekg-intervaltree-dbb4c51_GH0.tar.gz) = 1f3ba92a83cb782cf22dfb383b8c93c11c1c88e0b2e5fa434e24668260ecd1f8
15	SIZE (ekg-intervaltree-dbb4c51_GH0.tar.gz) = 3780
16	SHA256 (vcflib-vcflib-5e3ce04_GH0.tar.gz) = d084c1df7bb0004df18e013da3cbf896b642d853c855aea58ae029abe1d2097a
17	SIZE (vcflib-vcflib-5e3ce04_GH0.tar.gz) = 20119782
18	SHA256 (ekg-fastahack-c68cebb_GH0.tar.gz) = c6f7186bbe733ff78c25b2afd7e7ba79daa3ecd14a5876ea0b033a43744c876d
19	SIZE (ekg-fastahack-c68cebb_GH0.tar.gz) = 17312
20	SHA256 (ekg-filevercmp-1a9b779_GH0.tar.gz) = 34c21d1b58295bca72b92c1cd832a4171b07ec97c19ffc0d4d8ec67e266c6070
21	SIZE (ekg-filevercmp-1a9b779_GH0.tar.gz) = 3053
22	SHA256 (ekg-fsom-a6ef318_GH0.tar.gz) = 68351c16d5c4b96142409e38c6828b6199eae44eaa7579bde165734d4832565b	14	SHA256 (ekg-fsom-a6ef318_GH0.tar.gz) = 68351c16d5c4b96142409e38c6828b6199eae44eaa7579bde165734d4832565b
23	SIZE (ekg-fsom-a6ef318_GH0.tar.gz) = 9686	15	SIZE (ekg-fsom-a6ef318_GH0.tar.gz) = 9686
		16	SHA256 (ekg-filevercmp-1a9b779_GH0.tar.gz) = 34c21d1b58295bca72b92c1cd832a4171b07ec97c19ffc0d4d8ec67e266c6070
		17	SIZE (ekg-filevercmp-1a9b779_GH0.tar.gz) = 3053
24	SHA256 (google-googletest-d225acc_GH0.tar.gz) = 6880e0d51fa80a508ad5674ce483c1c468315faddac10d580b5505e8e7ef6bfa	18	SHA256 (google-googletest-d225acc_GH0.tar.gz) = 6880e0d51fa80a508ad5674ce483c1c468315faddac10d580b5505e8e7ef6bfa
25	SIZE (google-googletest-d225acc_GH0.tar.gz) = 1279815	19	SIZE (google-googletest-d225acc_GH0.tar.gz) = 1279815
26	SHA256 (ekg-intervaltree-b704f19_GH0.tar.gz) = 7e38b5f5873790afbcfdf6adbb621cdf4a1d9f22e28934a8edfe62cd65918f0d	20	SHA256 (edawson-libVCFH-615a06b_GH0.tar.gz) = 2774c26c55e1d155fe803b492a745a1d2a3659f4fdbe248d3187ce03edf87223
27	SIZE (ekg-intervaltree-b704f19_GH0.tar.gz) = 3768	21	SIZE (edawson-libVCFH-615a06b_GH0.tar.gz) = 2295
28	SHA256 (ekg-multichoose-73d35da_GH0.tar.gz) = af52475d7568863ad8173aebfb6b8b87690118bad8945876b629a2b3c05577cf	22	SHA256 (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 3877e64f51a7368f768b40167e4cdff36a93d3047f722416581834f1eaf40f63
29	SIZE (ekg-multichoose-73d35da_GH0.tar.gz) = 4697	23	SIZE (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 203996
30	SHA256 (ekg-smithwaterman-84c08d7_GH0.tar.gz) = 299c9e28e50977642d1538f8940852976b6db3241619eb1f40b78484b1cde58e	24	SHA256 (ekg-intervaltree-b90527f_GH0.tar.gz) = 4d9272046972e595e4ac771fe6958b4c166a35e2ac727fc977fc4e0b9f8e887c
31	SIZE (ekg-smithwaterman-84c08d7_GH0.tar.gz) = 38382	25	SIZE (ekg-intervaltree-b90527f_GH0.tar.gz) = 72540
32	SHA256 (ekg-tabixpp-80012f8_GH0.tar.gz) = 6aecc865673776bec4e2ddb14e629a4798ad36bf8f7639968812a6262675fb3f	26	SHA256 (ekg-tabixpp-b255df1_GH0.tar.gz) = 96d9aa41f55f74498e267b582e93e986605913fbd830dca6bf4cac5d9f927bb9
33	SIZE (ekg-tabixpp-80012f8_GH0.tar.gz) = 3530	27	SIZE (ekg-tabixpp-b255df1_GH0.tar.gz) = 3739
34	SHA256 (samtools-htslib-0f298ce_GH0.tar.gz) = 829bb54383745fb923ed5d8dabbb6aa8b5d9501601c7a4163276d86aca1196ee	28	SHA256 (ingydotnet-test-simple-bash-124673f_GH0.tar.gz) = 19b5c27402d955909fcbf601ed02bcd7d9f2aa841e2158ecd93b9ff8f7ec1d98
35	SIZE (samtools-htslib-0f298ce_GH0.tar.gz) = 1065854	29	SIZE (ingydotnet-test-simple-bash-124673f_GH0.tar.gz) = 6609
		30	SHA256 (illusori-bash-tap-c38fbfa_GH0.tar.gz) = 5e658965f7c8730d7f29642ebb40b0e0beb701f992e391a1273af3b132ff66b8
		31	SIZE (illusori-bash-tap-c38fbfa_GH0.tar.gz) = 5826
		32	SHA256 (samtools-htslib-b581944_GH0.tar.gz) = 940f0acd7037af262e15388eff9a6d696d03966fef1bae19d663130926c365f4
		33	SIZE (samtools-htslib-b581944_GH0.tar.gz) = 1501311

Removed Link Here

(-)biology/freebayes/files/patch-Makefile (-20 lines)
1	--- Makefile.orig 2018-03-23 14:01:01 UTC
2	+++ Makefile
3	@@ -5,7 +5,7 @@ wbamtools: vcflib/Makefile log
4	cd src && $(MAKE) -f Makefile.bamtools
5
6	log: src/version_git.h
7	- wget -q http://hypervolu.me/freebayes/build/$(shell cat src/version_git.h \| grep v \| cut -f 3 -d\ \| sed s/\"//g) &
8	+ # wget -q http://hypervolu.me/freebayes/build/$(shell cat src/version_git.h \| grep v \| cut -f 3 -d\ \| sed s/\"//g) &
9
10	src/version_git.h:
11	cd src && $(MAKE) autoversion
12	@@ -27,7 +27,7 @@ uninstall:
13	rm /usr/local/bin/freebayes /usr/local/bin/bamleftalign
14
15	test:
16	- cd test && make test
17	+ cd test && ${MAKE} test
18
19	clean:
20	cd src && $(MAKE) clean

Removed Link Here

(-)biology/freebayes/files/patch-SeqLib_bwa_Makefile (-14 lines)
1	--- SeqLib/bwa/Makefile.orig 2018-03-23 18:47:04 UTC
2	+++ SeqLib/bwa/Makefile
3	@@ -1,8 +1,8 @@
4	-CC= gcc
5	+CC ?= gcc
6	#CC= clang --analyze
7	-CFLAGS= -g -Wall -Wno-unused-function -O2
8	+CFLAGS ?= -g -Wall -Wno-unused-function -O2
9	WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
10	-AR= ar
11	+AR ?= ar
12	DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC)
13	## moved is.o bwtiindex.o rope.o to LOBJS
14	LOBJS= utils.o kthread.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o \

Removed Link Here

(-)biology/freebayes/files/patch-SeqLib_fermi-lite_Makefile (-12 lines)
1	--- SeqLib/fermi-lite/Makefile.orig 2018-03-23 18:50:25 UTC
2	+++ SeqLib/fermi-lite/Makefile
3	@@ -1,6 +1,6 @@
4	-CC= gcc
5	-CFLAGS= -g -Wall -O2 -Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once
6	-CPPFLAGS=
7	+CC ?= gcc
8	+CFLAGS ?= -g -Wall -O2 -Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once
9	+CPPFLAGS ?=
10	INCLUDES=
11	OBJS= kthread.o misc.o \
12	bseq.o htab.o bfc.o \

Removed Link Here

(-)biology/freebayes/files/patch-SeqLib_htslib_Makefile (-38 lines)
1	--- SeqLib/htslib/Makefile.orig 2017-06-20 12:40:28 UTC
2	+++ SeqLib/htslib/Makefile
3	@@ -22,20 +22,20 @@
4	# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
5	# DEALINGS IN THE SOFTWARE.
6
7	-CC = gcc
8	-AR = ar
9	-RANLIB = ranlib
10	+CC ?= gcc
11	+AR ?= ar
12	+RANLIB ?= ranlib
13
14	# Default libraries to link if configure is not used
15	htslib_default_libs = -lz -lm -lbz2 -llzma
16
17	-CPPFLAGS =
18	+CPPFLAGS ?=
19	# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
20	# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
21	#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
22	-CFLAGS = -g -Wall -O2
23	+CFLAGS ?= -g -Wall -O2
24	EXTRA_CFLAGS_PIC = -fpic
25	-LDFLAGS =
26	+LDFLAGS ?=
27	LIBS = $(htslib_default_libs)
28
29	prefix = /usr/local
30	@@ -86,7 +86,7 @@ BUILT_THRASH_PROGRAMS = \
31	test/thrash_threads5 \
32	test/thrash_threads6
33
34	-all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
35	+all: lib-static $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
36
37	HTSPREFIX =
38	include htslib_vars.mk

Removed Link Here

(-)biology/freebayes/files/patch-src_Makefile (-62 lines)
1	--- src/Makefile.orig 2018-03-23 14:01:01 UTC
2	+++ src/Makefile
3	@@ -5,8 +5,9 @@
4	################################################################################
5
6	# Compiler
7	-CXX=g++ ${CXXFLAGS}
8	-C=gcc
9	+CXX ?= g++
10	+# CXX += ${CXXFLAGS}
11	+CC ?= gcc
12
13	export CXXFLAGS
14	export C
15	@@ -17,7 +18,7 @@ export LIBFLAGS
16
17	# Compiler flags
18
19	-CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
20	+CFLAGS += -D_FILE_OFFSET_BITS=64
21	#CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
22
23	SEQLIB_ROOT=../SeqLib
24	@@ -25,7 +26,7 @@ VCFLIB_ROOT=../vcflib
25	TABIX_ROOT=$(VCFLIB_ROOT)/tabixpp
26	HTSLIB_ROOT=$(SEQLIB_ROOT)/htslib
27
28	-LIBS = -lz -llzma -lbz2 -lm -lpthread
29	+LIBS = -lz -llzma -lbz2 -lm -lpthread -lexecinfo
30	INCLUDE = -I../src -I../ttmath -I$(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)
31	#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
32
33	@@ -46,10 +47,10 @@ gprof:
34	.PHONY: all static debug profiling gprof
35
36	$(HTSLIB_ROOT)/libhts.a:
37	- cd $(HTSLIB_ROOT) && make
38	+ cd $(HTSLIB_ROOT) && ${MAKE}
39
40	$(SEQLIB_ROOT)/src/libseqlib.a:
41	- cd $(SEQLIB_ROOT) && ./configure && make
42	+ cd $(SEQLIB_ROOT) && ./configure && ${MAKE}
43
44	OBJECTS=BedReader.o \
45	CNV.o \
46	@@ -122,7 +123,7 @@ freebayes.o: freebayes.cpp TryCatch.h $(
47	$(CXX) $(CXXFLAGS) $(INCLUDE) -c freebayes.cpp
48
49	fastlz.o: fastlz.c fastlz.h
50	- $(C) $(CFLAGS) $(INCLUDE) -c fastlz.c
51	+ $(CC) $(CFLAGS) $(INCLUDE) -c fastlz.c
52
53	Parameters.o: Parameters.cpp Parameters.h Version.h
54	$(CXX) $(CXXFLAGS) $(INCLUDE) -c Parameters.cpp
55	@@ -277,5 +278,5 @@ autoversion:
56
57	clean:
58	rm -rf .o .cgh ~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/.o ../vcflib/tabixpp/*.{o,a} tabix.hpp
59	- if [ -d $(BAMTOOLS_ROOT)/build ]; then make -C $(BAMTOOLS_ROOT)/build clean; fi
60	- make -C $(VCFLIB_ROOT)/smithwaterman clean
61	+ if [ -d $(BAMTOOLS_ROOT)/build ]; then ${MAKE} -C $(BAMTOOLS_ROOT)/build clean; fi
62	+ ${MAKE} -C $(VCFLIB_ROOT)/smithwaterman clean

Removed Link Here

(-)biology/freebayes/files/patch-vcflib_Makefile (-13 lines)
1	--- vcflib/Makefile.orig 2018-03-23 18:36:07 UTC
2	+++ vcflib/Makefile
3	@@ -136,8 +136,8 @@ all: $(OBJECTS) $(BINS)
4
5	GIT_VERSION := $(shell git describe --abbrev=4 --dirty --always)
6
7	-CXX = g++
8	-CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x
9	+CXX ?= g++
10	+CXXFLAGS += -D_FILE_OFFSET_BITS=64 -std=c++0x
11	#CXXFLAGS = -O2
12	#CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
13