1
0
mirror of https://git.FreeBSD.org/ports.git synced 2025-01-26 09:46:09 +00:00

biology/freebayes: Update to 1.3.5

Fixes build on powerpc64 and aarch64, possibly others.

Changes:        https://github.com/freebayes/freebayes/tags

PR:             259627
Reported by:    pkubaj
This commit is contained in:
Jason W. Bacon 2021-11-03 15:49:05 -05:00
parent 6893887275
commit dc64b13129
13 changed files with 52 additions and 270 deletions

View File

@ -1,7 +1,6 @@
PORTNAME= freebayes
DISTVERSIONPREFIX= v
DISTVERSION= 1.2.0
PORTREVISION= 3
DISTVERSION= 1.3.5
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
@ -9,46 +8,42 @@ COMMENT= Bayesian haplotype-based polymorphism discovery and genotyping
LICENSE= MIT
BROKEN_aarch64= fails to compile: invalid conversion between vector type and integer type
# These should be rechecked: Same error resolved on aarch64 in 1.3.5 update.
BROKEN_armv6= fails to compile: invalid conversion between vector type and integer type
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
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${STAGEDIR}${PREFIX}/bin
${CP} -r ${WRKSRC}/vcflib-temp/* ${WRKSRC}/vcflib
.include <bsd.port.mk>

View File

@ -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

View File

@ -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

View File

@ -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 \

View File

@ -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

View File

@ -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

View File

@ -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() *

View File

@ -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))

View File

@ -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 \

View File

@ -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))

View File

@ -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

View File

@ -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

View File

@ -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