*/*: sync with upstream

Taken from: FreeBSD

archivers/engrampa/Makefile

@@ -1,7 +1,7 @@
 # Created by: Anders Nordby <[email protected]>
 
 PORTNAME=	engrampa
-PORTVERSION=	1.24.2
+PORTVERSION=	1.26.0
 CATEGORIES=	archivers mate
 MASTER_SITES=	MATE
 DIST_SUBDIR=	mate

archivers/engrampa/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1623458443
-SHA256 (mate/engrampa-1.24.2.tar.xz) = ee280d288c974732ec7bc2d1c3e18fa563b33a30f3e4cb3e976ebc71be6c4674
-SIZE (mate/engrampa-1.24.2.tar.xz) = 1687432
+TIMESTAMP = 1633995542
+SHA256 (mate/engrampa-1.26.0.tar.xz) = 97cdb2c22c32315a38803d4147dfad9de7309e30ce8f37ac9f600709ad075ee3
+SIZE (mate/engrampa-1.26.0.tar.xz) = 1761596

archivers/engrampa/pkg-plist

@@ -6,7 +6,6 @@ man/man1/engrampa.1.gz
 share/applications/engrampa.desktop
 share/caja/extensions/libcaja-engrampa.caja-extension
 share/dbus-1/services/org.mate.Engrampa.service
-%%DATADIR%%/packages.match
 share/help/C/engrampa/figures/engrampa_home.png
 share/help/C/engrampa/figures/engrampa_leftarrow.png
 share/help/C/engrampa/figures/engrampa_main_window.png

archivers/rar/Makefile

@@ -19,13 +19,14 @@ LICENSE_PERMS=	auto-accept dist-mirror pkg-mirror
 ONLY_FOR_ARCHS=	amd64 i386
 
 USES=		cpe
-CPE_VENDOR=	rarlab
 
 NO_BUILD=	yes
 WRKSRC=		${WRKDIR}/rar
 
 PLIST_FILES=	bin/rar etc/rarfiles.lst lib/default.sfx man/cat1/rar.1.gz
 
+CPE_VENDOR=	rarlab
+
 do-install:
 	${INSTALL_PROGRAM} ${WRKSRC}/rar ${STAGEDIR}${PREFIX}/bin
 	${INSTALL_DATA} ${WRKSRC}/rarfiles.lst ${STAGEDIR}${PREFIX}/etc

archivers/unrar/Makefile

@@ -18,8 +18,6 @@ LICENSE_PERMS=	auto-accept dist-mirror pkg-mirror
 
 USES+=		compiler:c++11-lang cpe
 
-CPE_VENDOR=	rarlab
-
 LDFLAGS+=	-lpthread
 MAKE_ARGS=	CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" STRIP="${STRIP_CMD}"
 MAKEFILE=	makefile
@@ -31,6 +29,8 @@ SLAVEDIRS=	archivers/unrar-iconv
 
 CONFLICTS_INSTALL?=	unrar-iconv
 
+CPE_VENDOR=	rarlab
+
 OPTIONS_DEFINE=	OPENSSL_AES
 OPTIONS_DEFAULT=OPENSSL_AES
 OPENSSL_AES_DESC=	Use OpenSSL implementation of AES

archivers/unshield/Makefile

@@ -12,11 +12,11 @@ LICENSE_FILE=	${WRKSRC}/LICENSE
 
 USES=		cmake cpe pathfix ssl
 
-CPE_VENDOR=	unshield_project
-
 CFLAGS+=	-fPIC
 USE_LDCONFIG=	yes
 
+CPE_VENDOR=	unshield_project
+
 GH_ACCOUNT=	twogood
 USE_GITHUB=	yes
 

astro/p5-Astro-Catalog/Makefile

@@ -1,7 +1,7 @@
 # Created by: ijliao
 
 PORTNAME=	Astro-Catalog
-PORTVERSION=	4.35
+PORTVERSION=	4.36
 CATEGORIES=	astro perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-
@@ -11,7 +11,6 @@ COMMENT=	Generic stellar catalogue object
 
 LICENSE=	GPLv3
 
-# p5-Astro-FITS-CFITSIO is a recommended dependency
 BUILD_DEPENDS=	${RUN_DEPENDS}
 RUN_DEPENDS=	p5-Astro-Coords>=0.12:astro/p5-Astro-Coords \
 		p5-Astro-FITS-CFITSIO>=1.03:astro/p5-Astro-FITS-CFITSIO \

astro/p5-Astro-Catalog/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1588450874
-SHA256 (Astro-Catalog-4.35.tar.gz) = 7110588444f9f14f5ffc256dd7242ca1a8b2ea6ee9a4f95096cb7028081e0347
-SIZE (Astro-Catalog-4.35.tar.gz) = 266376
+TIMESTAMP = 1634041740
+SHA256 (Astro-Catalog-4.36.tar.gz) = 5f7a710ec3b3ec9f3a4fbfb6e25d232127b8e0e40b99235f8eec8e8fad82065f
+SIZE (Astro-Catalog-4.36.tar.gz) = 271375

astro/p5-Astro-Catalog/pkg-plist

@@ -1,3 +1,4 @@
+bin/catalog_convert
 etc/skycat.cfg.sample
 etc/sss.cfg.sample
 %%SITE_PERL%%/Astro/Catalog.pm
@@ -9,7 +10,9 @@ etc/sss.cfg.sample
 %%SITE_PERL%%/Astro/Catalog/IO/FINDOFF.pm
 %%SITE_PERL%%/Astro/Catalog/IO/FITSTable.pm
 %%SITE_PERL%%/Astro/Catalog/IO/GaiaPick.pm
+%%SITE_PERL%%/Astro/Catalog/IO/Hedwig.pm
 %%SITE_PERL%%/Astro/Catalog/IO/JCMT.pm
+%%SITE_PERL%%/Astro/Catalog/IO/JCMT_OT_SC.pm
 %%SITE_PERL%%/Astro/Catalog/IO/LCOGTFITSTable.pm
 %%SITE_PERL%%/Astro/Catalog/IO/Northstar.pm
 %%SITE_PERL%%/Astro/Catalog/IO/RITMatch.pm
@@ -18,6 +21,7 @@ etc/sss.cfg.sample
 %%SITE_PERL%%/Astro/Catalog/IO/Simple.pm
 %%SITE_PERL%%/Astro/Catalog/IO/TST.pm
 %%SITE_PERL%%/Astro/Catalog/IO/UKIRTBS.pm
+%%SITE_PERL%%/Astro/Catalog/IO/VEX.pm
 %%SITE_PERL%%/Astro/Catalog/IO/VOTable.pm
 %%SITE_PERL%%/Astro/Catalog/IO/XY.pm
 %%SITE_PERL%%/Astro/Catalog/Item.pm
@@ -38,6 +42,7 @@ etc/sss.cfg.sample
 %%SITE_PERL%%/Astro/Catalog/Transport/REST.pm
 %%SITE_PERL%%/Astro/Catalog/Transport/WebService.pm
 %%SITE_PERL%%/Tk/AstroCatalog.pm
+%%PERL5_MAN1%%/catalog_convert.1.gz
 %%PERL5_MAN3%%/Astro::Catalog.3.gz
 %%PERL5_MAN3%%/Astro::Catalog::IO::ASCII.3.gz
 %%PERL5_MAN3%%/Astro::Catalog::IO::ASSM.3.gz
@@ -47,7 +52,9 @@ etc/sss.cfg.sample
 %%PERL5_MAN3%%/Astro::Catalog::IO::FINDOFF.3.gz
 %%PERL5_MAN3%%/Astro::Catalog::IO::FITSTable.3.gz
 %%PERL5_MAN3%%/Astro::Catalog::IO::GaiaPick.3.gz
+%%PERL5_MAN3%%/Astro::Catalog::IO::Hedwig.3.gz
 %%PERL5_MAN3%%/Astro::Catalog::IO::JCMT.3.gz
+%%PERL5_MAN3%%/Astro::Catalog::IO::JCMT_OT_SC.3.gz
 %%PERL5_MAN3%%/Astro::Catalog::IO::LCOGTFITSTable.3.gz
 %%PERL5_MAN3%%/Astro::Catalog::IO::Northstar.3.gz
 %%PERL5_MAN3%%/Astro::Catalog::IO::RITMatch.3.gz
@@ -56,6 +63,7 @@ etc/sss.cfg.sample
 %%PERL5_MAN3%%/Astro::Catalog::IO::Simple.3.gz
 %%PERL5_MAN3%%/Astro::Catalog::IO::TST.3.gz
 %%PERL5_MAN3%%/Astro::Catalog::IO::UKIRTBS.3.gz
+%%PERL5_MAN3%%/Astro::Catalog::IO::VEX.3.gz
 %%PERL5_MAN3%%/Astro::Catalog::IO::VOTable.3.gz
 %%PERL5_MAN3%%/Astro::Catalog::IO::XY.3.gz
 %%PERL5_MAN3%%/Astro::Catalog::Item.3.gz

audio/zrythm/Makefile

@@ -56,11 +56,16 @@ SHEBANG_FILES=	scripts/collect_translatables.sh
 
 GLIB_SCHEMAS=	org.zrythm.Zrythm.gschema.xml
 
-
 LDFLAGS+=	${LOCALBASE}/lib/libfftw3_threads.so ${LOCALBASE}/lib/libfftw3f_threads.so # these libs are required but aren't returned by pkg-config for fftw3
 
 BINARY_ALIAS=	git=false python3=${PYTHON_CMD}
 
+.include <bsd.port.options.mk>
+
+.if ${ARCH} == powerpc64
+MESON_ARGS=	-Db_lto=false
+.endif
+
 post-patch: # https://git.zrythm.org/zrythm/zrythm/issues/299
 	@${REINPLACE_CMD} 's|<malloc.h>|<stdlib.h>|' ${WRKSRC}/ext/midilib/src/*.c
 

audio/zrythm/files/patch-ext_qm-dsp_meson.build

@@ -0,0 +1,12 @@
+--- ext/qm-dsp/meson.build.orig	2021-10-13 01:44:29 UTC
++++ ext/qm-dsp/meson.build
+@@ -39,9 +39,6 @@ qm_dsp_lib = static_library (
+     '-Wall',
+     '-Wextra',
+     '-O3',
+-    '-msse',
+-    '-msse2',
+-    '-mfpmath=sse',
+     '-ftree-vectorize',
+     '-DUSE_PTHREADS',
+     ],

biology/Makefile

@@ -6,6 +6,7 @@
     SUBDIR += avida
     SUBDIR += babel
     SUBDIR += bamtools
+    SUBDIR += bamutil
     SUBDIR += bbmap
     SUBDIR += bcftools
     SUBDIR += bedtools

biology/bamutil/Makefile

@@ -0,0 +1,26 @@
+PORTNAME=	bamutil
+DISTVERSIONPREFIX=	v
+DISTVERSION=	1.0.14
+CATEGORIES=	biology
+
+MAINTAINER=	[email protected]
+COMMENT=	Utilities for working with SAM/BAM files
+
+LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/copyrights/COPYING
+
+USES=		gmake
+USE_GITHUB=	yes
+
+GH_ACCOUNT=	statgen
+GH_PROJECT=	bamUtil
+
+# Build needs access to libStatGen Makefiles, so can't install separately
+GH_TUPLE=	statgen:libStatGen:v${DISTVERSION}:statgen/libStatGen
+
+MAKE_ENV=	LIB_PATH_GENERAL=${WRKSRC}/libStatGen
+MAKE_ENV+=	INSTALLDIR=${STAGEDIR}${PREFIX}/bin
+
+PLIST_FILES=	bin/bam
+
+.include <bsd.port.mk>

biology/bamutil/distinfo

@@ -0,0 +1,5 @@
+TIMESTAMP = 1634051641
+SHA256 (statgen-bamUtil-v1.0.14_GH0.tar.gz) = f5ec8d5e98a3797742106c3413a4ab1622d8787e38b29b3df4cddb59d77efda5
+SIZE (statgen-bamUtil-v1.0.14_GH0.tar.gz) = 1916953
+SHA256 (statgen-libStatGen-v1.0.14_GH0.tar.gz) = 70a504c5cc4838c6ac96cdd010644454615cc907df4e3794c999baf958fa734b
+SIZE (statgen-libStatGen-v1.0.14_GH0.tar.gz) = 558924

biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.lib

@@ -0,0 +1,17 @@
+--- libStatGen/Makefiles/Makefile.lib.orig	2021-10-12 15:28:34 UTC
++++ libStatGen/Makefiles/Makefile.lib
+@@ -34,11 +34,11 @@ profile: $(STAT_GEN_LIB_PROFILE)
+ # To build the library, build the objects
+ # Then add them to the library
+ $(STAT_GEN_LIB_OPT): $(OBJECTS_OPT)
+-	ar -cru $@ $(OBJECTS_OPT)
++	ar -cr $@ $(OBJECTS_OPT)
+ $(STAT_GEN_LIB_DEBUG): $(OBJECTS_DEBUG)
+-	ar -cru $@ $(OBJECTS_DEBUG)
++	ar -cr $@ $(OBJECTS_DEBUG)
+ $(STAT_GEN_LIB_PROFILE): $(OBJECTS_PROFILE)
+-	ar -cru $@ $(OBJECTS_PROFILE)
++	ar -cr $@ $(OBJECTS_PROFILE)
+
+ UNAME=$(shell uname)
+

biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.toolchain

@@ -0,0 +1,13 @@
+--- libStatGen/Makefiles/Makefile.toolchain.orig	2021-10-12 15:09:29 UTC
++++ libStatGen/Makefiles/Makefile.toolchain
+@@ -51,8 +51,8 @@ endif
+
+ # CPP0X=-std=c++0x
+
+-CXX     = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)g++ $(CPP0X)
+-CC      = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)gcc
++CXX     = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)c++ $(CPP0X)
++CC      = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)cc
+ LD      = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)ld
+ AR      = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)ar
+ RANLIB  = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)ranlib

biology/bamutil/files/patch-libStatGen_vcf_VcfRecordGenotype.cpp

@@ -0,0 +1,11 @@
+--- libStatGen/vcf/VcfRecordGenotype.cpp.orig	2021-10-12 15:13:03 UTC
++++ libStatGen/vcf/VcfRecordGenotype.cpp
+@@ -176,7 +176,7 @@ bool VcfRecordGenotype::setString(const std::string& k
+     if(sampleNum >= mySamples.size())
+     {
+         // Out of range sample index.
+-        return(NULL);
++        return(false);
+     }
+     // Set the field in the sample.
+     return(mySamples.get(sampleNum).setString(key, value));

biology/bamutil/pkg-descr

@@ -0,0 +1,6 @@
+Utilities for working on SAM/BAM files from The Center for Statistical
+Genetics at the University of Michigan School of Public Health.  It
+includes numerous functions such as splitting, merging, trimming reads,
+filtering, validation, diff, etc.
+
+WWW: https://github.com/statgen/bamUtil

biology/biostar-tools/Makefile

@@ -1,5 +1,5 @@
 PORTNAME=	biostar-tools
-PORTVERSION=	1.7.0
+PORTVERSION=	1.8.0
 CATEGORIES=	biology python
 
 MAINTAINER=	[email protected]
@@ -60,7 +60,8 @@ RUN_DEPENDS=	wget>0:ftp/wget \
 		clustal-omega>0:biology/clustal-omega \
 		${PYTHON_PKGNAMEPREFIX}pywgsim>0:biology/py-pywgsim@${PY_FLAVOR} \
 		sam2pairwise>0:biology/sam2pairwise \
-		kallisto>0:biology/kallisto
+		kallisto>0:biology/kallisto \
+		bamutil>0:biology/bamutil
 
 USES=		metaport python
 

biology/biostar-tools/distinfo

@@ -1 +1 @@
-TIMESTAMP = 1632744796
+TIMESTAMP = 1634056949

biology/diamond/Makefile

@@ -1,7 +1,6 @@
 PORTNAME=	diamond
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.0.11-1
-DISTVERSIONSUFFIX=	-g810a3904
+DISTVERSION=	2.0.12
 CATEGORIES=	biology
 
 MAINTAINER=	[email protected]

biology/diamond/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1625576969
-SHA256 (bbuchfink-diamond-v2.0.11-1-g810a3904_GH0.tar.gz) = 4876be5c8dc0b070ca5208e7833af5d492e0e8928347f8fe63feed9044eec303
-SIZE (bbuchfink-diamond-v2.0.11-1-g810a3904_GH0.tar.gz) = 1473340
+TIMESTAMP = 1634050594
+SHA256 (bbuchfink-diamond-v2.0.12_GH0.tar.gz) = d0468959ea677cc8e90a6fbd9506f3fb1fbd1b415d30bf398ac2524bb5b6f20c
+SIZE (bbuchfink-diamond-v2.0.12_GH0.tar.gz) = 1489676

biology/jellyfish/Makefile

@@ -12,7 +12,7 @@ COMMENT=	Fast, memory-efficient counting of k-mers in DNA
 LICENSE=	BSD3CLAUSE GPLv3+
 LICENSE_COMB=	dual
 LICENSE_FILE_BSD3CLAUSE=	${WRKSRC}/LICENSE-BSD-3-Clause
-LICENSE_FILE_GPLv3=		${WRKSRC}/LICENSE-GPL-3.0
+LICENSE_FILE_GPLv3+ =		${WRKSRC}/LICENSE-GPL-3.0
 
 LIB_DEPENDS=	libhts.so:biology/htslib
 

cad/kicad-library-packages3d-devel/Makefile

@@ -2,7 +2,7 @@
 
 PORTNAME=	kicad
 DISTVERSION=	r${GIT_P3D_DATE}
-#PORTREVISION=	1
+PORTREVISION=	0
 CATEGORIES=	cad
 MASTER_SITES=	https://gitlab.com/kicad/libraries/${PORTNAME}-packages3D/-/archive/${GL_COMMIT}/
 PKGNAMESUFFIX=	-library-packages3d-devel

comms/qtel/Makefile

@@ -2,7 +2,6 @@
 
 PORTNAME=	qtel
 
-MAINTAINER=	[email protected]
 COMMENT=	Qtel Echolink client
 
 LICENSE=	GPLv2

comms/svxlink/Makefile

@@ -8,7 +8,7 @@ CATEGORIES=	comms hamradio
 MAINTAINER=	[email protected]
 COMMENT?=	General purpose ham radio voice services
 
-LICENSE=	GPLv2
+LICENSE?=	GPLv2
 
 LIB_DEPENDS?=	libgsm.so:audio/gsm \
 		libspeex.so:audio/speex \

converters/pdf2djvu/Makefile

@@ -1,6 +1,6 @@
 PORTNAME=	pdf2djvu
 DISTVERSION=	0.9.17.1
-PORTREVISION=	14
+PORTREVISION=	15
 CATEGORIES=	converters
 MASTER_SITES=	https://github.com/jwilk/${PORTNAME}/releases/download/${PORTVERSION}/