*/*: sync with upstream

Taken from: FreeBSD

astro/py-ephem/Makefile

@@ -1,7 +1,7 @@
 # Created by: db
 
 PORTNAME=	ephem
-PORTVERSION=	4.1
+PORTVERSION=	4.1.1
 CATEGORIES=	astro math python
 MASTER_SITES=	CHEESESHOP
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}

astro/py-ephem/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1633030603
-SHA256 (ephem-4.1.tar.gz) = c076794a511a34b5b91871c1cf6374dbc323ec69fca3f50eb718f20b171259d6
-SIZE (ephem-4.1.tar.gz) = 1254139
+TIMESTAMP = 1638291557
+SHA256 (ephem-4.1.1.tar.gz) = dba9e05c78ce910ae75a06351a5592479191a8dc570ac0cd6d18a77e98138873
+SIZE (ephem-4.1.1.tar.gz) = 1254139

audio/plasma5-plasma-pa/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1636520680
-SHA256 (KDE/plasma/5.23.3/plasma-pa-5.23.3.tar.xz) = 13771e6d12d7033b96d5ae89fbbbb62d6e38a4b15e57226dc3c43a17c5daa355
-SIZE (KDE/plasma/5.23.3/plasma-pa-5.23.3.tar.xz) = 130804
+TIMESTAMP = 1638303613
+SHA256 (KDE/plasma/5.23.4/plasma-pa-5.23.4.tar.xz) = 4701dc362e615d321c1cc7b94240ab5b23898d7db8ec1a4ed49d84ac8907983c
+SIZE (KDE/plasma/5.23.4/plasma-pa-5.23.4.tar.xz) = 131064

benchmarks/flamegraph/Makefile

@@ -1,9 +1,7 @@
 # Created by: Johannes Dieterich <[email protected]>
 
 PORTNAME=	flamegraph
-DISTVERSIONPREFIX=	v
-DISTVERSION=	1.0-43
-DISTVERSIONSUFFIX=	-ga258e78
+PORTVERSION=	1.1
 CATEGORIES=	benchmarks
 
 MAINTAINER=	[email protected]
@@ -15,15 +13,16 @@ LICENSE_FILE=	${WRKSRC}/docs/cddl1.txt
 BUILD_DEPENDS=	bash>=0:shells/bash
 RUN_DEPENDS=	bash>=0:shells/bash
 
-USES=		shebangfix perl5
+USES=		shebangfix perl5 python
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	brendangregg
 GH_PROJECT=	FlameGraph
+GH_TAGNAME=	810687f
 
 NO_BUILD=	yes
 
-SHEBANG_FILES=	*.pl *.sh
+SHEBANG_FILES=	*.php *.pl *.py *.sh
 
 SOURCE_FILES=	aix-perf.pl \
 		difffolded.pl \
@@ -33,19 +32,23 @@ SOURCE_FILES=	aix-perf.pl \
 		range-perf.pl \
 		stackcollapse-aix.pl \
 		stackcollapse-bpftrace.pl \
+		stackcollapse-chrome-tracing.py \
 		stackcollapse-elfutils.pl \
 		stackcollapse-gdb.pl \
 		stackcollapse-go.pl \
 		stackcollapse-instruments.pl \
 		stackcollapse-java-exceptions.pl \
 		stackcollapse-jstack.pl \
 		stackcollapse-ljp.awk \
+		stackcollapse-perf-sched.awk \
 		stackcollapse-perf.pl \
 		stackcollapse-pmc.pl \
 		stackcollapse-recursive.pl \
+		stackcollapse-sample.awk \
 		stackcollapse-stap.pl \
 		stackcollapse-vsprof.pl \
 		stackcollapse-vtune.pl \
+		stackcollapse-xdebug.php \
 		stackcollapse.pl
 
 do-install:

benchmarks/flamegraph/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1606165740
-SHA256 (brendangregg-FlameGraph-v1.0-43-ga258e78_GH0.tar.gz) = e5bfaee2049e8d60c365fdaacb7ba3d424dd4a85018fdcd0d3c906a7578a14b7
-SIZE (brendangregg-FlameGraph-v1.0-43-ga258e78_GH0.tar.gz) = 1054300
+TIMESTAMP = 1638372585
+SHA256 (brendangregg-FlameGraph-1.1-810687f_GH0.tar.gz) = eee0efaaf522ecdf79757b8d3407fe5c6e0e34ccebd268bd9b9e1c2f01bb400a
+SIZE (brendangregg-FlameGraph-1.1-810687f_GH0.tar.gz) = 1056998

benchmarks/flamegraph/pkg-plist

@@ -6,17 +6,21 @@ bin/pkgsplit-perf.pl
 bin/range-perf.pl
 bin/stackcollapse-aix.pl
 bin/stackcollapse-bpftrace.pl
+bin/stackcollapse-chrome-tracing.py
 bin/stackcollapse-elfutils.pl
 bin/stackcollapse-gdb.pl
 bin/stackcollapse-go.pl
 bin/stackcollapse-instruments.pl
 bin/stackcollapse-java-exceptions.pl
 bin/stackcollapse-jstack.pl
 bin/stackcollapse-ljp.awk
+bin/stackcollapse-perf-sched.awk
 bin/stackcollapse-perf.pl
 bin/stackcollapse-pmc.pl
 bin/stackcollapse-recursive.pl
+bin/stackcollapse-sample.awk
 bin/stackcollapse-stap.pl
 bin/stackcollapse-vsprof.pl
 bin/stackcollapse-vtune.pl
+bin/stackcollapse-xdebug.php
 bin/stackcollapse.pl

biology/biostar-tools/Makefile

@@ -1,5 +1,5 @@
 PORTNAME=	biostar-tools
-PORTVERSION=	1.10.0
+PORTVERSION=	1.10.1
 CATEGORIES=	biology python
 
 MAINTAINER=	[email protected]
@@ -34,7 +34,6 @@ RUN_DEPENDS=	wget>0:ftp/wget \
 		seqtk>0:biology/seqtk \
 		datamash>0:textproc/datamash \
 		bcftools>0:biology/bcftools \
-		sra-tools>0:biology/sra-tools \
 		subread>0:biology/subread \
 		hisat2>0:biology/hisat2 \
 		trimmomatic>0:biology/trimmomatic \
@@ -68,11 +67,18 @@ RUN_DEPENDS=	wget>0:ftp/wget \
 
 USES=		metaport python
 
+.include <bsd.port.pre.mk>
+
+# Allow pkg build on non-amd64 systems until sra-tools supports them
+.if ${ARCH} == amd64
+RUN_DEPENDS+=	sra-tools>0:biology/sra-tools
+.endif
+
 SUB_FILES=	biostar-shell
 PLIST_FILES=	bin/biostar-shell
 
 do-install:
 	@${MKDIR} ${STAGEDIR}${PREFIX}/bin
 	${INSTALL_SCRIPT} ${WRKDIR}/biostar-shell ${STAGEDIR}${PREFIX}/bin
 
-.include <bsd.port.mk>
+.include <bsd.port.post.mk>

biology/biostar-tools/distinfo

@@ -1 +1 @@
-TIMESTAMP = 1636577480
+TIMESTAMP = 1638373720

biology/bwa/Makefile

@@ -1,6 +1,7 @@
 PORTNAME=	bwa
 PORTVERSION=	0.7.17
 DISTVERSIONPREFIX=v
+PORTREVISION=	1
 CATEGORIES=	biology
 
 PATCH_SITES=	https://github.com/lh3/bwa/commit/
@@ -11,16 +12,12 @@ COMMENT=	Burrows-Wheeler sequence aligner
 
 LICENSE=	GPLv3
 
-# From 0.7.9a: Recheck for 0.7.17.
-BROKEN_aarch64=		fails to compile: invalid conversion between vector type and integer type
-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_mips=		fails to compile: cc1: unrecognized command line option "-msse2"
 BROKEN_mips64=		fails to compile: cc1: unrecognized command line option "-msse2"
-BROKEN_powerpc64=	fails to compile: ksw.c: emmintrin.h: No such file or directory
-BROKEN_riscv64=		fails to compile: invalid conversion between vector type and integer type
 
-USES=		gmake perl5 shebangfix tar:bzip2
+BUILD_DEPENDS=	simde>0:devel/simde
+
+USES=		gmake localbase perl5 shebangfix tar:bzip2
 SHEBANG_FILES=	qualfa2fq.pl xa2multi.pl
 USE_PERL5=	run
 
@@ -34,9 +31,6 @@ PLIST_FILES=	bin/bwa bin/qualfa2fq.pl bin/xa2multi.pl man/man1/bwa.1.gz
 .if ${ARCH} == amd64 || ${ARCH} == i386
 # Avoid #error in emmintrin.h
 CFLAGS+=	-msse2
-.elif ${ARCH} == powerpc64le
-CFLAGS+=	-DNO_WARN_X86_INTRINSICS
-USES+=	compiler:gcc-c++11-lib
 .endif
 
 do-install:

biology/bwa/files/patch-ksw.c

@@ -0,0 +1,13 @@
+--- ksw.c.orig	2021-12-01 13:48:35 UTC
++++ ksw.c
+@@ -26,7 +26,9 @@
+ #include <stdlib.h>
+ #include <stdint.h>
+ #include <assert.h>
+-#include <emmintrin.h>
++// #include <emmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+ #include "ksw.h"
+
+ #ifdef USE_MALLOC_WRAPPERS

biology/minimap2/Makefile

@@ -1,24 +1,24 @@
-PORTNAME=	minimap2
+PORTNAME=		minimap2
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.22
-CATEGORIES=	biology
+DISTVERSION=		2.23
+CATEGORIES=		biology
 
 MAINTAINER=	[email protected]
 COMMENT=	Pairwise aligner for genomic and spliced nucleotide sequences
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
-ONLY_FOR_ARCHS=	amd64 i386
-ONLY_FOR_ARCHS_REASON=	uses hard-coded SSE instructions
+BUILD_DEPENDS=	simde>0:devel/simde
 
-USES=		gmake
+USES=		gmake localbase
 USE_GITHUB=	yes
 
 GH_ACCOUNT=	lh3
 
-MAKE_ARGS+=	CFLAGS+=-Wextra
 ALL_TARGET=	extra
 INSTALL_TARGET=	install-strip
 
+MAKEFILE=	Makefile.simde
+
 .include <bsd.port.mk>

biology/minimap2/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1629640993
-SHA256 (lh3-minimap2-v2.22_GH0.tar.gz) = b625a7580d9b5996f2553ee90ffcec84870bd9b88c009c9d71e8c1c648c53ed6
-SIZE (lh3-minimap2-v2.22_GH0.tar.gz) = 251821
+TIMESTAMP = 1638198281
+SHA256 (lh3-minimap2-v2.23_GH0.tar.gz) = 1837465234bfec0fc8acaa3bdd371dfc57cf56137f7e6b8c723dcbed2f03f144
+SIZE (lh3-minimap2-v2.23_GH0.tar.gz) = 252484

biology/minimap2/files/patch-Makefile.simde

@@ -0,0 +1,82 @@
+--- Makefile.simde.orig	2021-11-18 22:11:48 UTC
++++ Makefile.simde
+@@ -1,13 +1,26 @@
+-CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
+-CPPFLAGS=	-DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
+-INCLUDES=	-Ilib/simde
+-OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o map.o format.o pe.o seed.o esterr.o splitidx.o \
+-			ksw2_extz2_simde.o ksw2_extd2_simde.o ksw2_exts2_simde.o ksw2_ll_simde.o
++
++# Makefile patches rejected by upstream
++
++CFLAGS?=	-g -Wall -O2
++CFLAGS+=	-Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__
++CPPFLAGS?=	-DHAVE_KALLOC
++OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o \
++		index.o lchain.o align.o hit.o map.o format.o pe.o seed.o \
++		esterr.o splitidx.o ksw2_extz2_simde.o ksw2_extd2_simde.o \
++		ksw2_exts2_simde.o ksw2_ll_simde.o
+ PROG=		minimap2
+ PROG_EXTRA=	sdust minimap2-lite
+ LIBS=		-lm -lz -lpthread
+
++PREFIX?=	/usr/local
++MAN1DIR?=	${PREFIX}/man/man1
++DATADIR?=	${PREFIX}/share/minimap2
+
++MKDIR?=		mkdir
++CP?=		cp	
++INSTALL?=	install
++STRIP?=		strip
++
+ ifneq ($(arm_neon),) # if arm_neon is defined
+ ifeq ($(aarch64),)   #if aarch64 is not defined
+ 	CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
+@@ -26,7 +39,7 @@ ifneq ($(tsan),)
+ 	LIBS+=-fsanitize=thread
+ endif
+
+-.PHONY:all extra clean depend
++.PHONY:all extra install install-strip clean depend
+ .SUFFIXES:.c .o
+
+ .c.o:
+@@ -49,18 +62,34 @@ sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ke
+ 		$(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz
+
+ ksw2_ll_simde.o:ksw2_ll_sse.c ksw2.h kalloc.h
+-		$(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@
++		$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
+
+ ksw2_extz2_simde.o:ksw2_extz2_sse.c ksw2.h kalloc.h
+-		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
++		$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
+
+ ksw2_extd2_simde.o:ksw2_extd2_sse.c ksw2.h kalloc.h
+-		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
++		$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
+
+ ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h
+-		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
++		$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
+
+ # other non-file targets
++
++
++install: all
++	${MKDIR} -p ${DESTDIR}${PREFIX}/bin
++	${MKDIR} -p ${DESTDIR}${MAN1DIR}
++	${MKDIR} -p ${DESTDIR}${DATADIR}
++	${INSTALL} -c minimap2 ${DESTDIR}${PREFIX}/bin
++	${INSTALL} -c minimap2-lite ${DESTDIR}${PREFIX}/bin
++	${INSTALL} -c sdust ${DESTDIR}${PREFIX}/bin
++	${INSTALL} -c minimap2.1 ${DESTDIR}${MAN1DIR}
++	${CP} -R test ${DESTDIR}${DATADIR}
++
++install-strip: install
++	${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2
++	${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2-lite
++	${STRIP} ${DESTDIR}${PREFIX}/bin/sdust
+
+ clean:
+ 		rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg*