Attachment 229245 Details for Bug 259627 – v2

[patch] v2

freebayes.patch (text/plain), 16.58 KB, created by Piotr Kubaj on 2021-11-03 15:22:42 UTC

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Creator: Piotr Kubaj

Created: 2021-11-03 15:22:42 UTC

Size: 16.58 KB

patch

obsolete

>diff f3f7446a00538cc58e3342c0def011efd48593d8 /usr/ports
>blob - 225643cec02b8ea0ef9d6552b0dea7204c9ee9cc
>file + biology/freebayes/Makefile
>--- biology/freebayes/Makefile
>+++ biology/freebayes/Makefile
>@@ -1,7 +1,6 @@
> PORTNAME=		freebayes
> DISTVERSIONPREFIX=	v
>-DISTVERSION=		1.2.0
>-PORTREVISION=		3
>+DISTVERSION=		1.3.5
> CATEGORIES=		biology
> 
> MAINTAINER=	jwb@FreeBSD.org
>@@ -14,41 +13,38 @@ BROKEN_armv6=		fails to compile: invalid conversion be
> 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++11-lang gmake tar:xz
>+USES=		compiler:c++14-lang localbase meson perl5 pkgconfig
> USE_GITHUB=	yes
> GH_ACCOUNT=	ekg
>-GH_TUPLE=	walaj:SeqLib:5941c68:SeqLib/SeqLib-temp \
>-		jwalabroad:bwa:c02766e:bwa/SeqLib/bwa \
>-		jwalabroad:fermi-lite:5bc90f8:fermi/SeqLib/fermi-lite \
>-		samtools:htslib:49fdfbd:htslib/SeqLib/htslib \
>-		ekg:bamtools:e77a43f:bamtools/bamtools \
>-		ekg:intervaltree:dbb4c51:interval1/intervaltree \
>-		vcflib:vcflib:5e3ce04:vcflib/vcflib-temp \
>-		ekg:fastahack:c68cebb:fastahack/vcflib/fastahack \
>-		ekg:filevercmp:1a9b779:filevercmp/vcflib/filevercmp \
>+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:fsom:a6ef318:fsom/vcflib/fsom \
>-		google:googletest:d225acc:google/vcflib/googletest \
>-		ekg:intervaltree:b704f19:interval2/vcflib/intervaltree \
>-		ekg:multichoose:73d35da:multichoose/vcflib/multichoose \
>-		ekg:smithwaterman:84c08d7:smithwaterman/vcflib/smithwaterman \
>-		ekg:tabixpp:80012f8:tabixpp/vcflib/tabixpp \
>-		samtools:htslib:0f298ce:hts2/vcflib/tabixpp/htslib
>+		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
>-CXXFLAGS+=		--std=c++11
>-CFLAGS_i386=		-msse2
>-MAKE_JOBS_UNSAFE=	yes
>+LDFLAGS+=		-lexecinfo
> 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:
>-	${MV} -n ${WRKSRC}/SeqLib-temp/* ${WRKSRC}/SeqLib
>-	${MV} -n ${WRKSRC}/vcflib-temp/* ${WRKSRC}/vcflib
>+	${CP} -r ${WRKSRC}/vcflib-temp/* ${WRKSRC}/vcflib
> 
>-do-install:
>-	${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${STAGEDIR}${PREFIX}/bin
>-
> .include <bsd.port.mk>
>blob - 239c89905abb36a657e3d11a2f4703cd2143f854
>file + biology/freebayes/distinfo
>--- biology/freebayes/distinfo
>+++ biology/freebayes/distinfo
>@@ -1,35 +1,33 @@
>-TIMESTAMP = 1523932688
>-SHA256 (ekg-freebayes-v1.2.0_GH0.tar.gz) = a5626636112966cac87095365986722d1c871759f03c5a143646da65c416ba8a
>-SIZE (ekg-freebayes-v1.2.0_GH0.tar.gz) = 2639725
>-SHA256 (walaj-SeqLib-5941c68_GH0.tar.gz) = 0ac2b63f5fd7b1cec20a18ebb6799bf1f9b88d6c7cd95f7dd7410b1b82c8703f
>-SIZE (walaj-SeqLib-5941c68_GH0.tar.gz) = 314968
>-SHA256 (jwalabroad-bwa-c02766e_GH0.tar.gz) = cce547db0efef8572d63b47d2065f07e36f770fc8a6f15f5cd03d6fa9ab9b1f7
>-SIZE (jwalabroad-bwa-c02766e_GH0.tar.gz) = 205546
>-SHA256 (jwalabroad-fermi-lite-5bc90f8_GH0.tar.gz) = 2b3b9b637f48dc3239618efd6b55183eef6b6232013c217eb1c319f1dd3da224
>-SIZE (jwalabroad-fermi-lite-5bc90f8_GH0.tar.gz) = 248454
>-SHA256 (samtools-htslib-49fdfbd_GH0.tar.gz) = 0bc9c7d48e2a439badf5990113ae3e4de9acd05e4c090938236ee40588d115b9
>-SIZE (samtools-htslib-49fdfbd_GH0.tar.gz) = 1145082
>-SHA256 (ekg-bamtools-e77a43f_GH0.tar.gz) = d3a143636ccedcc54417a2d6d88dd726c7d2c046318620b88c7ba2fb30b01419
>-SIZE (ekg-bamtools-e77a43f_GH0.tar.gz) = 540118
>-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
>+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-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 (ekg-intervaltree-b704f19_GH0.tar.gz) = 7e38b5f5873790afbcfdf6adbb621cdf4a1d9f22e28934a8edfe62cd65918f0d
>-SIZE (ekg-intervaltree-b704f19_GH0.tar.gz) = 3768
>-SHA256 (ekg-multichoose-73d35da_GH0.tar.gz) = af52475d7568863ad8173aebfb6b8b87690118bad8945876b629a2b3c05577cf
>-SIZE (ekg-multichoose-73d35da_GH0.tar.gz) = 4697
>-SHA256 (ekg-smithwaterman-84c08d7_GH0.tar.gz) = 299c9e28e50977642d1538f8940852976b6db3241619eb1f40b78484b1cde58e
>-SIZE (ekg-smithwaterman-84c08d7_GH0.tar.gz) = 38382
>-SHA256 (ekg-tabixpp-80012f8_GH0.tar.gz) = 6aecc865673776bec4e2ddb14e629a4798ad36bf8f7639968812a6262675fb3f
>-SIZE (ekg-tabixpp-80012f8_GH0.tar.gz) = 3530
>-SHA256 (samtools-htslib-0f298ce_GH0.tar.gz) = 829bb54383745fb923ed5d8dabbb6aa8b5d9501601c7a4163276d86aca1196ee
>-SIZE (samtools-htslib-0f298ce_GH0.tar.gz) = 1065854
>+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
>blob - 9c87b87ffbcb0ef62f567efb5bbb35fc89fe7035
>file + /dev/null
>--- biology/freebayes/files/patch-Makefile
>+++ /dev/null
>@@ -1,20 +0,0 @@
>---- 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
>blob - 356ac3bd66ea5b8a51cebfedcfcd4233cf5b4bf7
>file + /dev/null
>--- biology/freebayes/files/patch-SeqLib_bwa_Makefile
>+++ /dev/null
>@@ -1,14 +0,0 @@
>---- 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 \
>blob - f664bd55c48a0c9d7ae1e2164bfe1ae280168f63
>file + /dev/null
>--- biology/freebayes/files/patch-SeqLib_bwa_bwt__lite.c
>+++ /dev/null
>@@ -1,10 +0,0 @@
>---- 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
>blob - 4b2e4322b70a828669ce60f0edaf3496c938a192
>file + /dev/null
>--- biology/freebayes/files/patch-SeqLib_bwa_bwtgap.h
>+++ /dev/null
>@@ -1,10 +0,0 @@
>---- 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
>blob - 5193e4a2a2abf32157f1241d0468952935be2543
>file + /dev/null
>--- biology/freebayes/files/patch-SeqLib_bwa_kthread.c
>+++ /dev/null
>@@ -1,10 +0,0 @@
>---- 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() *
>blob - 1e6b9580e7c0ae9115c1a0977327533f9ebeaded
>file + /dev/null
>--- biology/freebayes/files/patch-SeqLib_bwa_rle.h
>+++ /dev/null
>@@ -1,11 +0,0 @@
>---- SeqLib/bwa/rle.h.orig	2016-10-13 18:10:17 UTC
>-+++ SeqLib/bwa/rle.h
>-@@ -30,7 +30,7 @@ extern "C" {
>-  *** 43+3 codec ***
>-  ******************/
>- 
>--const uint8_t rle_auxtab[8];
>-+extern const uint8_t rle_auxtab[8];
>- 
>- #define RLE_MIN_SPACE 18
>- #define rle_nptr(block) ((uint16_t*)(block))
>blob - ba795955ec7661a559a4c2d378160bad8d251691
>file + /dev/null
>--- biology/freebayes/files/patch-SeqLib_fermi-lite_Makefile
>+++ /dev/null
>@@ -1,12 +0,0 @@
>---- 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 \
>blob - 6ad88b47fde5f067ceac182bf728b58f5bcde38c
>file + /dev/null
>--- biology/freebayes/files/patch-SeqLib_fermi-lite_rle.h
>+++ /dev/null
>@@ -1,11 +0,0 @@
>---- SeqLib/fermi-lite/rle.h.orig	2016-09-01 20:47:53 UTC
>-+++ SeqLib/fermi-lite/rle.h
>-@@ -30,7 +30,7 @@ extern "C" {
>-  *** 43+3 codec ***
>-  ******************/
>- 
>--const uint8_t rle_auxtab[8];
>-+extern const uint8_t rle_auxtab[8];
>- 
>- #define RLE_MIN_SPACE 18
>- #define rle_nptr(block) ((uint16_t*)(block))
>blob - e533e6ca5f45d5fdcb7b8af59252e1f5ed430bd0
>file + /dev/null
>--- biology/freebayes/files/patch-SeqLib_htslib_Makefile
>+++ /dev/null
>@@ -1,38 +0,0 @@
>---- 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
>blob - cfe34b3b4eadc99e565c7b35da537377304e1a77
>file + /dev/null
>--- biology/freebayes/files/patch-src_Makefile
>+++ /dev/null
>@@ -1,62 +0,0 @@
>---- 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
>blob - c3df0fb79e6c8fe9edb95466c0c0119a3b345ba9
>file + /dev/null
>--- biology/freebayes/files/patch-vcflib_Makefile
>+++ /dev/null
>@@ -1,13 +0,0 @@
>---- 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
>-

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Attachments on bug 259627: 229241 | 229245 | 229250 | 229251