Date: Wed, 3 Nov 2021 20:54:28 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: dc64b13129b8 - main - biology/freebayes: Update to 1.3.5 Message-ID: <202111032054.1A3KsSjf071381@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=dc64b13129b889531be2dae60218484f9444cf92 commit dc64b13129b889531be2dae60218484f9444cf92 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-11-03 20:49:05 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2021-11-03 20:49:05 +0000 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 --- biology/freebayes/Makefile | 53 +++++++++--------- biology/freebayes/distinfo | 60 ++++++++++----------- biology/freebayes/files/patch-Makefile | 20 ------- biology/freebayes/files/patch-SeqLib_bwa_Makefile | 14 ----- .../freebayes/files/patch-SeqLib_bwa_bwt__lite.c | 10 ---- biology/freebayes/files/patch-SeqLib_bwa_bwtgap.h | 10 ---- biology/freebayes/files/patch-SeqLib_bwa_kthread.c | 10 ---- biology/freebayes/files/patch-SeqLib_bwa_rle.h | 11 ---- .../files/patch-SeqLib_fermi-lite_Makefile | 12 ----- .../freebayes/files/patch-SeqLib_fermi-lite_rle.h | 11 ---- .../freebayes/files/patch-SeqLib_htslib_Makefile | 38 ------------- biology/freebayes/files/patch-src_Makefile | 62 ---------------------- biology/freebayes/files/patch-vcflib_Makefile | 13 ----- 13 files changed, 53 insertions(+), 271 deletions(-) diff --git a/biology/freebayes/Makefile b/biology/freebayes/Makefile index 225643cec02b..9ca877a4c665 100644 --- a/biology/freebayes/Makefile +++ b/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 @@ -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 - -# GCC disables sse2 by default on i386, but it's required for vcflib -CXXFLAGS+= --std=c++11 -CFLAGS_i386= -msse2 -MAKE_JOBS_UNSAFE= yes + 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 + +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> diff --git a/biology/freebayes/distinfo b/biology/freebayes/distinfo index 239c89905abb..1b22d3cb70ab 100644 --- a/biology/freebayes/distinfo +++ b/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 diff --git a/biology/freebayes/files/patch-Makefile b/biology/freebayes/files/patch-Makefile deleted file mode 100644 index 9c87b87ffbcb..000000000000 --- a/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 diff --git a/biology/freebayes/files/patch-SeqLib_bwa_Makefile b/biology/freebayes/files/patch-SeqLib_bwa_Makefile deleted file mode 100644 index 356ac3bd66ea..000000000000 --- a/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 \ diff --git a/biology/freebayes/files/patch-SeqLib_bwa_bwt__lite.c b/biology/freebayes/files/patch-SeqLib_bwa_bwt__lite.c deleted file mode 100644 index f664bd55c48a..000000000000 --- a/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 diff --git a/biology/freebayes/files/patch-SeqLib_bwa_bwtgap.h b/biology/freebayes/files/patch-SeqLib_bwa_bwtgap.h deleted file mode 100644 index 4b2e4322b70a..000000000000 --- a/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 diff --git a/biology/freebayes/files/patch-SeqLib_bwa_kthread.c b/biology/freebayes/files/patch-SeqLib_bwa_kthread.c deleted file mode 100644 index 5193e4a2a2ab..000000000000 --- a/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() * diff --git a/biology/freebayes/files/patch-SeqLib_bwa_rle.h b/biology/freebayes/files/patch-SeqLib_bwa_rle.h deleted file mode 100644 index 1e6b9580e7c0..000000000000 --- a/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)) diff --git a/biology/freebayes/files/patch-SeqLib_fermi-lite_Makefile b/biology/freebayes/files/patch-SeqLib_fermi-lite_Makefile deleted file mode 100644 index ba795955ec76..000000000000 --- a/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 \ diff --git a/biology/freebayes/files/patch-SeqLib_fermi-lite_rle.h b/biology/freebayes/files/patch-SeqLib_fermi-lite_rle.h deleted file mode 100644 index 6ad88b47fde5..000000000000 --- a/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)) diff --git a/biology/freebayes/files/patch-SeqLib_htslib_Makefile b/biology/freebayes/files/patch-SeqLib_htslib_Makefile deleted file mode 100644 index e533e6ca5f45..000000000000 --- a/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 diff --git a/biology/freebayes/files/patch-src_Makefile b/biology/freebayes/files/patch-src_Makefile deleted file mode 100644 index cfe34b3b4ead..000000000000 --- a/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 diff --git a/biology/freebayes/files/patch-vcflib_Makefile b/biology/freebayes/files/patch-vcflib_Makefile deleted file mode 100644 index c3df0fb79e6c..000000000000 --- a/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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