*/*: sync with upstream

Taken from: FreeBSD

accessibility/feedbackd/Makefile

@@ -1,5 +1,5 @@
 PORTNAME=	feedbackd
-PORTVERSION=	s20210809
+PORTVERSION=	s20211019
 CATEGORIES=	accessibility
 
 MAINTAINER=	[email protected]
@@ -16,7 +16,7 @@ USE_GNOME=	glib20
 USE_LDCONFIG=	yes
 GL_SITE=	https://source.puri.sm
 GL_ACCOUNT=	Librem5
-GL_COMMIT=	587cbf31889f1e26d818e36915cfe0577dc0272f
+GL_COMMIT=	8e9bbd9d4ccc092a1f8b37551b7cdf2c32b5f8b8
 SHEBANG_FILES=	build-aux/post_install.py
 GLIB_SCHEMAS=	org.sigxcpu.feedbackd.gschema.xml
 

accessibility/feedbackd/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1631148275
-SHA256 (Librem5-feedbackd-587cbf31889f1e26d818e36915cfe0577dc0272f_GL0.tar.gz) = 066dfa01d7fec7b6ff4eb7e5084fc813748511c8ab3d68251c86575e7c906352
-SIZE (Librem5-feedbackd-587cbf31889f1e26d818e36915cfe0577dc0272f_GL0.tar.gz) = 81091
+TIMESTAMP = 1634653444
+SHA256 (Librem5-feedbackd-8e9bbd9d4ccc092a1f8b37551b7cdf2c32b5f8b8_GL0.tar.gz) = 40cb77294faffec6523f760fe7a885f2cc1b9019127f0d342fbeb9b368f7b6e7
+SIZE (Librem5-feedbackd-8e9bbd9d4ccc092a1f8b37551b7cdf2c32b5f8b8_GL0.tar.gz) = 81788

archivers/ark/Makefile

@@ -1,5 +1,6 @@
 PORTNAME=	ark
 DISTVERSION=	${KDE_APPLICATIONS_VERSION}
+PORTREVISION=	1
 CATEGORIES=	archivers kde kde-applications
 
 MAINTAINER=	[email protected]
@@ -9,7 +10,7 @@ LICENSE=	GPLv2+
 LICENSE_FILE=	${WRKSRC}/COPYING
 
 USES=		cmake compiler:c++11-lang desktop-file-utils gettext libarchive kde:5 \
-		cpe qt:5 shared-mime-info tar:xz
+		cpe qt:5 tar:xz
 USE_KDE=	archive auth bookmarks codecs completion config configwidgets \
 		coreaddons crash dbusaddons doctools i18n iconthemes \
 		itemmodels itemviews jobwidgets khtml kio parts pty service \

audio/musicpd/Makefile

@@ -1,7 +1,7 @@
 PORTNAME=	musicpd
-PORTVERSION=	0.23
+PORTVERSION=	0.23.1
 CATEGORIES=	audio
-MASTER_SITES=	https://www.musicpd.org/download/mpd/${PORTVERSION}/
+MASTER_SITES=	https://www.musicpd.org/download/mpd/${PORTVERSION:R}/
 DISTNAME=	mpd-${PORTVERSION}
 
 MAINTAINER=	[email protected]

audio/musicpd/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1634384255
-SHA256 (mpd-0.23.tar.xz) = 73562c7e6d5815e84de9485c9947c98fa5b9c2d761c3fb23df7004b9b8beb85a
-SIZE (mpd-0.23.tar.xz) = 764184
+TIMESTAMP = 1634768410
+SHA256 (mpd-0.23.1.tar.xz) = 93990f026886cee3b8707b38cef575b1904f4a6e5fc6d92b2a82ba2a3a6302bd
+SIZE (mpd-0.23.1.tar.xz) = 764920

biology/bamutil/Makefile

@@ -1,6 +1,6 @@
 PORTNAME=	bamutil
 DISTVERSIONPREFIX=	v
-DISTVERSION=	1.0.14
+DISTVERSION=	1.0.15
 CATEGORIES=	biology
 
 MAINTAINER=	[email protected]

biology/bamutil/distinfo

@@ -1,5 +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
+TIMESTAMP = 1634754069
+SHA256 (statgen-bamUtil-v1.0.15_GH0.tar.gz) = 24ac4bdb81eded6e33f60dba85ec3d32ebdb06d42f75df775c2632bbfbd8cce9
+SIZE (statgen-bamUtil-v1.0.15_GH0.tar.gz) = 1929150
+SHA256 (statgen-libStatGen-v1.0.15_GH0.tar.gz) = 075dcd891409c48d76c0c66186c0cc479bc3cd50bba093e7f318e1d1d19961ff
+SIZE (statgen-libStatGen-v1.0.15_GH0.tar.gz) = 560782

biology/fastp/Makefile

@@ -1,6 +1,6 @@
 PORTNAME=		fastp
 DISTVERSIONPREFIX=	v
-DISTVERSION=		0.22.0
+DISTVERSION=		0.23.1
 CATEGORIES=		biology
 
 MAINTAINER=	[email protected]
@@ -9,7 +9,10 @@ COMMENT=	Ultra-fast all-in-one FASTQ preprocessor
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-USES=		compiler:c++11-lang gmake
+LIB_DEPENDS=	libdeflate.so:archivers/libdeflate \
+		libisal.so:devel/isa-l
+
+USES=		compiler:c++11-lang gmake localbase:ldflags
 USE_GITHUB=	yes
 
 GH_ACCOUNT=	OpenGene

biology/fastp/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1630006835
-SHA256 (OpenGene-fastp-v0.22.0_GH0.tar.gz) = a7ef81cc39daed7ac6bfc254697345c448095539e1b5b45f3a8ab286098be456
-SIZE (OpenGene-fastp-v0.22.0_GH0.tar.gz) = 141257
+TIMESTAMP = 1634739193
+SHA256 (OpenGene-fastp-v0.23.1_GH0.tar.gz) = 32cb16ea1199a5f722d3c5caa24d1aaace4b24f6efa0fd774f227d8a80ebb8f3
+SIZE (OpenGene-fastp-v0.23.1_GH0.tar.gz) = 163190

biology/fastp/files/patch-Makefile

@@ -1,42 +1,57 @@
---- Makefile.orig	2020-04-08 07:26:52 UTC
+--- Makefile.orig	2021-10-19 02:19:29 UTC
 +++ Makefile
-@@ -3,9 +3,11 @@ DIR_SRC := ./src
+@@ -2,11 +2,13 @@ DIR_INC := ./inc
+ DIR_SRC := ./src
  DIR_OBJ := ./obj
 
- PREFIX ?= /usr/local
-+DESTDIR ?=
- BINDIR ?= $(PREFIX)/bin
- INCLUDE_DIRS ?=
- LIBRARY_DIRS ?=
-+STRIP_CMD ?= strip
+-PREFIX ?= /usr/local
+-BINDIR ?= $(PREFIX)/bin
+-INCLUDE_DIRS ?=
+-LIBRARY_DIRS ?=
++PREFIX	?= /usr/local
++BINDIR	?= $(PREFIX)/bin
++INCLUDE_DIRS	?=
++LIBRARY_DIRS	?=
 
++STRIP	?= strip
++
  SRC := $(wildcard ${DIR_SRC}/*.cpp)
  OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC}))
-@@ -15,13 +17,14 @@ TARGET := fastp
+
+@@ -15,15 +17,19 @@ TARGET := fastp
  BIN_TARGET := ${TARGET}
 
  CXX ?= g++
--CXXFLAGS := -std=c++11 -g -O3 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS}
+-CXXFLAGS := -std=c++11 -pthread -g -O3 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS}
++# Optional flags that the user can override by setting CXXFLAGS in the
++# env or make argument
 +CXXFLAGS ?= -g -O3
++# Required flags
 +CXXFLAGS += -std=c++11 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir))
- LIBS := -lz -lpthread
+ LIBS := -lisal -ldeflate -lpthread
+ STATIC_FLAGS := -static -Wl,--no-as-needed -pthread
 -LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) $(LD_FLAGS)
++# Append required flags to standard LDFLAGS from env
 +LDFLAGS += $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS)
+ STATIC_LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(STATIC_FLAGS) $(LIBS) $(STATIC_LD_FLAGS)
 
- 
+-
  ${BIN_TARGET}:${OBJ}
 -	$(CXX) $(OBJ) -o $@ $(LD_FLAGS)
 +	$(CXX) $(OBJ) -o $@ $(LDFLAGS)
 
- ${DIR_OBJ}/%.o:${DIR_SRC}/%.cpp make_obj_dir
- 	$(CXX) -c $< -o $@ $(CXXFLAGS)
-@@ -38,5 +41,8 @@ make_obj_dir:
+ static:${OBJ}
+ 	$(CXX) $(OBJ) -o ${BIN_TARGET} $(STATIC_LD_FLAGS)
+@@ -49,6 +55,11 @@ make_obj_dir:
+ 		mkdir $(DIR_OBJ) ; \
  	fi
 
++# Respect DESTDIR for staged installs (used by most package managers)
  install:
 -	install $(TARGET) $(BINDIR)/$(TARGET)
 +	install $(TARGET) $(DESTDIR)$(BINDIR)/$(TARGET)
  	@echo "Installed."
 +
++# Many package managers use install-strip target if debugging is not enabled
 +install-strip: install
-+	$(STRIP_CMD) $(DESTDIR)$(BINDIR)/$(TARGET)
++	$(STRIP) $(DESTDIR)$(BINDIR)/$(TARGET)

biology/fastp/files/patch-src_main.cpp

@@ -0,0 +1,17 @@
+--- src/main.cpp.orig	2021-10-19 02:19:29 UTC
++++ src/main.cpp
+@@ -1,4 +1,5 @@
+ #include <stdio.h>
++#include <sysexits.h>
+ #include "fastqreader.h"
+ #include "unittest.h"
+ #include <time.h>
+@@ -18,7 +19,7 @@ int main(int argc, char* argv[]){
+     if(argc == 1) {
+         cerr << "fastp: an ultra-fast all-in-one FASTQ preprocessor" << endl << "version " << FASTP_VER << endl;
+         //cerr << "fastp --help to see the help"<<endl;
+-        //return 0;
++        return EX_USAGE;
+     }
+     if (argc == 2 && strcmp(argv[1], "test")==0){
+         UnitTest tester;

cad/verilator/Makefile

@@ -1,7 +1,6 @@
 PORTNAME=	verilator
 DISTVERSIONPREFIX=	v
-DISTVERSION=	4.212
-PORTREVISION=	1
+DISTVERSION=	4.214
 CATEGORIES=	cad
 
 MAINTAINER=	[email protected]
@@ -21,7 +20,7 @@ RUN_DEPENDS=	gmake:devel/gmake # verilator runs gmake for the --hierarchical opt
 USES=		bison compiler:c++14-lang gmake localbase:ldflags pathfix perl5 python:build,run,test shebangfix tar:tgz
 USE_GITHUB=	yes
 
-SHEBANG_FILES=	bin/verilator_ccache_report
+SHEBANG_FILES=	bin/verilator_ccache_report bin/verilator_profcfunc bin/verilator_gantt
 
 GNU_CONFIGURE=	yes
 CONFIGURE_ENV=	INSTALL_PROGRAM="${INSTALL_SCRIPT}"

cad/verilator/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1631566759
-SHA256 (verilator-verilator-v4.212_GH0.tar.gz) = 7b655859e4e75c9673141aede8f5a20f47e4c380055d1a588d5be60cbbc73619
-SIZE (verilator-verilator-v4.212_GH0.tar.gz) = 2430634
+TIMESTAMP = 1634760933
+SHA256 (verilator-verilator-v4.214_GH0.tar.gz) = e14c7f6ffb00a6746ae2a8ea0424e90a1a30067e8ae4c96b8c42689ca1ca0b1f
+SIZE (verilator-verilator-v4.214_GH0.tar.gz) = 2438281

cad/verilator/pkg-plist

@@ -8,8 +8,6 @@ bin/verilator_profcfunc
 libdata/pkgconfig/verilator.pc
 man/man1/verilator.1.gz
 man/man1/verilator_coverage.1.gz
-man/man1/verilator_gantt.1.gz
-man/man1/verilator_profcfunc.1.gz
 %%DATADIR%%/bin/verilator_ccache_report
 %%DATADIR%%/bin/verilator_includer
 %%DATADIR%%/examples/cmake_hello_c/CMakeLists.txt
@@ -47,6 +45,8 @@ man/man1/verilator_profcfunc.1.gz
 %%DATADIR%%/examples/xml_py/Makefile
 %%DATADIR%%/examples/xml_py/sub.v
 %%DATADIR%%/examples/xml_py/top.v
+%%DATADIR%%/examples/xml_py/vl_file_copy
+%%DATADIR%%/examples/xml_py/vl_hier_graph
 %%DATADIR%%/include/gtkwave/fastlz.c
 %%DATADIR%%/include/gtkwave/fastlz.h
 %%DATADIR%%/include/gtkwave/fst_config.h
@@ -75,6 +75,7 @@ man/man1/verilator_profcfunc.1.gz
 %%DATADIR%%/include/verilated_heavy.h
 %%DATADIR%%/include/verilated_imp.h
 %%DATADIR%%/include/verilated_intrinsics.h
+%%DATADIR%%/include/verilated_profiler.h
 %%DATADIR%%/include/verilated_save.cpp
 %%DATADIR%%/include/verilated_save.h
 %%DATADIR%%/include/verilated_sc.h

databases/grass7/Makefile

@@ -1,8 +1,7 @@
 # Created by: Mikael URANKAR and Loïc BARTOLETTI
 
 PORTNAME=	grass
-PORTVERSION=	7.8.5
-PORTREVISION=	4
+PORTVERSION=	7.8.6
 CATEGORIES=	databases geography
 MASTER_SITES=	https://grass.osgeo.org/%SUBDIR%/ \
 		http://grass.cict.fr/%SUBDIR%/ \
@@ -148,18 +147,6 @@ GRASS_INST_DIR=	${PORTNAME}${VER}
 MANDIRS=	${PREFIX}/grass${VER}/docs/man/man1
 
 post-patch:
-	${REINPLACE_CMD} -e \
-		's|make -C|$$(MAKE) -C| ; \
-		 /^BINDIR/s|=.*|=	$${DESTDIR}$${UNIX_BIN}| ; \
-		 /test /s| $$(INST_DIR)| $${DESTDIR}$${INST_DIR}|g ; \
-		 /tar /s| $$(INST_DIR)| $${DESTDIR}$${INST_DIR}|g ; \
-		 /chmod /s| $$(INST_DIR)| $${DESTDIR}$${INST_DIR}|g ; \
-		 /tar /s| $$(INST_DIR)| $${DESTDIR}$${INST_DIR}|g ; \
-		 /rm /s| $$(INST_DIR)| $${DESTDIR}$${INST_DIR}|g ; \
-		 /$$(MAKE) /s| $$(INST_DIR)| $${DESTDIR}$${INST_DIR}|g ; \
-		 /^$$(INST_DIR)\//s|$$(INST_DIR)|$${DESTDIR}$${INST_DIR}|g ; \
-		 s|> $$(INST_DIR)|> $${DESTDIR}$${INST_DIR}|' \
-		${WRKSRC}/include/Make/Install.make
 	${REINPLACE_CMD} \
 		's|= python3|= ${PYTHON_CMD:T}|' ${WRKSRC}/include/Make/Platform.make.in
 	${REINPLACE_CMD} -e \

databases/grass7/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1610555224
-SHA256 (grass-7.8.5.tar.gz) = a359bb665524ecccb643335d70f5436b1c84ffb6a0e428b78dffebacd983ff37
-SIZE (grass-7.8.5.tar.gz) = 61801712
+TIMESTAMP = 1634368600
+SHA256 (grass-7.8.6.tar.gz) = d85e17b0a717e344cdda8f6c5bdeb86763e48d1ee74a62ab471dc8e1293993be
+SIZE (grass-7.8.6.tar.gz) = 66331264