git: dc64b13129b8 - main - biology/freebayes: Update to 1.3.5
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Date: Wed, 03 Nov 2021 20:54:28 UTC
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
-