*/*: sync with upstream

Taken from: FreeBSD

audio/py-pyradio/Makefile

@@ -1,6 +1,6 @@
 PORTNAME=	pyradio
-DISTVERSION=	0.9.0
-PORTREVISION=	1
+DISTVERSION=	0.9.1
+PORTREVISION=	0
 CATEGORIES=	audio python
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
@@ -51,8 +51,6 @@ post-patch:
 	@${SED} -i.bak -e 's/\(distro =\) None/\1 ${OPSYS}/' \
 	 -e 's/\(enable_notifications =\) -1/\1 0/' \
 	 	${WRKSRC}/pyradio/config
-	@${SED} -i.bak -e "s,/usr/local/share/icons\(/pyradio.png\),${PREFIX}/share/pixmaps\1,1" \
-		${WRKSRC}/pyradio/log.py
 
 post-install:
 	${INSTALL_DATA} ${WRKSRC}/devel/${PORTNAME}.desktop \

audio/py-pyradio/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1674918558
-SHA256 (coderholic-pyradio-0.9.0_GH0.tar.gz) = 16f543df7c6f80fa4b8a5a08a75055b220c1df07d8e4306d091bb5bcc465e48f
-SIZE (coderholic-pyradio-0.9.0_GH0.tar.gz) = 664703
+TIMESTAMP = 1677253683
+SHA256 (coderholic-pyradio-0.9.1_GH0.tar.gz) = 0510eabdc5473b90821b38c142cf4dfa8229cb3c52d534fbfc625a0515f6f1e3
+SIZE (coderholic-pyradio-0.9.1_GH0.tar.gz) = 927676

audio/soundkonverter/Makefile

@@ -10,6 +10,9 @@ WWW=		https://github.com/dfaust/soundkonverter/
 
 LICENSE=	GPLv2
 
+DEPRECATED=	Unsupported upstream, consider using audio/cyanrip or audio/abcde (ripping CDs), audio/rsgain (ReplayGain scanning) and multimedia/ffmpeg (transcoding)
+EXPIRATION_DATE=2023-03-31
+
 LIB_DEPENDS=	libtag.so:audio/taglib \
 		libcdda_paranoia.so:audio/cdparanoia \
 		libphonon4qt5.so:multimedia/phonon

benchmarks/ddosify/Makefile

@@ -1,6 +1,6 @@
 PORTNAME=	ddosify
 DISTVERSIONPREFIX=	v
-DISTVERSION=	0.14.0
+DISTVERSION=	0.14.1
 CATEGORIES=	benchmarks
 
 MAINTAINER=	[email protected]
@@ -42,10 +42,16 @@ GH_TUPLE=	\
 
 PLIST_FILES=	bin/${PORTNAME}
 
-OPTIONS_DEFINE=	EMOJI
-OPTIONS_DEFAULT=EMOJI
+OPTIONS_DEFINE=	EMOJI ZSH
+OPTIONS_DEFAULT=EMOJI ZSH
 
 EMOJI_DESC=	Enable emojis in console output
 EMOJI_RUN_DEPENDS=	noto-emoji>0:x11-fonts/noto-emoji
 
+ZSH_PLIST_FILES=	share/zsh/site-functions/_${PORTNAME}
+
+post-install-ZSH-on:
+	@${MKDIR} ${STAGEDIR}${PREFIX}/share/zsh/site-functions
+	${INSTALL_DATA} ${WRKSRC}/completions/_${PORTNAME} ${STAGEDIR}${PREFIX}/share/zsh/site-functions/_${PORTNAME}
+
 .include <bsd.port.mk>

benchmarks/ddosify/distinfo

@@ -1,6 +1,6 @@
-TIMESTAMP = 1676594619
-SHA256 (ddosify-ddosify-v0.14.0_GH0.tar.gz) = d5965607cc908581ad29f4b8734095a0a0a9f1ddb6d6b21ca01f1beeb31e4501
-SIZE (ddosify-ddosify-v0.14.0_GH0.tar.gz) = 1191821
+TIMESTAMP = 1677211717
+SHA256 (ddosify-ddosify-v0.14.1_GH0.tar.gz) = f6cf425377677122920b69f04bdb217ba894bfea2211aced6860b7087c744b88
+SIZE (ddosify-ddosify-v0.14.1_GH0.tar.gz) = 1193951
 SHA256 (antchfx-xmlquery-v1.3.13_GH0.tar.gz) = e882143ac161874fc3d9a91f1e19ab78271b5aa37a7d8541e728b566c405e36c
 SIZE (antchfx-xmlquery-v1.3.13_GH0.tar.gz) = 21490
 SHA256 (antchfx-xpath-v1.2.1_GH0.tar.gz) = cd9962512d4b3611b500621c1aeaf12780648845f7c976050c2bcba5c5d222c4

biology/Makefile

@@ -11,6 +11,7 @@
     SUBDIR += bamutil
     SUBDIR += barrnap
     SUBDIR += bbmap
+    SUBDIR += bcf-score
     SUBDIR += bcftools
     SUBDIR += bedtools
     SUBDIR += bfc

biology/bcf-score/Makefile

@@ -0,0 +1,51 @@
+PORTNAME=	bcf-score
+DISTVERSION=	1.16
+CATEGORIES=	biology
+MASTER_SITES=	https://software.broadinstitute.org/software/score/
+DISTFILES+=	score_${DISTVERSION}-20221221.tar.gz
+
+MAINTAINER=	[email protected]
+COMMENT=	Bcftools plugins for GWAS-VCF summary statistics files
+WWW=		https://software.broadinstitute.org/software/score/
+
+LICENSE=	MIT
+
+LIB_DEPENDS=	libhts.so:biology/htslib
+BUILD_DEPENDS=	bash:shells/bash
+RUN_DEPENDS=	bcftools>=${PORTVERSION}:biology/bcftools
+
+USES=		autoreconf gmake localbase perl5 python:env shebangfix
+USE_GITHUB=	yes
+USE_PERL5=	test
+
+GH_ACCOUNT=	samtools
+GH_PROJECT=	bcftools
+GH_TAGNAME=	1.17
+GNU_CONFIGURE=	yes
+SHEBANG_FILES=	misc/* test/test.pl
+
+post-extract:
+	@${CP} ${WRKDIR}/*.c ${WRKDIR}/*.h ${WRKSRC}/plugins
+	@${MKDIR} ${WRKSRC}/bcf-score
+	@${CP} ${WRKDIR}/*.R ${WRKSRC}/bcf-score
+
+pre-configure:
+	@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' \
+		${WRKSRC}/configure.ac
+
+# One .so for each .c in the score distfile
+do-install:
+	${MKDIR} ${STAGEDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/blupx.so \
+		${STAGEDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/liftover.so \
+		${STAGEDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/metal.so \
+		${STAGEDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/munge.so \
+		${STAGEDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/score.so \
+		${STAGEDIR}${PREFIX}/libexec/bcftools
+	(cd ${WRKSRC}/bcf-score && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR})
+
+.include <bsd.port.mk>

biology/bcf-score/distinfo

@@ -0,0 +1,5 @@
+TIMESTAMP = 1677335027
+SHA256 (score_1.16-20221221.tar.gz) = f5f7331f2f670ea26cbc48a924e1467ac13c69aaf3b2a56599e3decda9375c0b
+SIZE (score_1.16-20221221.tar.gz) = 61927
+SHA256 (samtools-bcftools-1.16-1.17_GH0.tar.gz) = e6fdb4c94b531671ea8a0b00cb9245aa2602f6c4480621e45dac76338f590b9e
+SIZE (samtools-bcftools-1.16-1.17_GH0.tar.gz) = 3481344

biology/bcf-score/files/patch-Makefile

@@ -0,0 +1,33 @@
+--- Makefile.orig	2021-03-17 09:16:18 UTC
++++ Makefile
+@@ -58,13 +58,14 @@ pluginpath  = $(plugindir)
+ # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
+ misc_bindir = $(bindir)
+
+-MKDIR_P = mkdir -p
+-INSTALL = install -p
+-INSTALL_DATA    = $(INSTALL) -m 644
+-INSTALL_DIR     = $(MKDIR_P) -m 755
+-INSTALL_MAN     = $(INSTALL_DATA)
+-INSTALL_PROGRAM = $(INSTALL)
+-INSTALL_SCRIPT  = $(INSTALL_PROGRAM)
++# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set
++MKDIR_P 	= mkdir -p
++INSTALL 	= install -p
++INSTALL_DATA    = ${BSD_INSTALL_DATA}
++INSTALL_DIR     = $(MKDIR_P)
++INSTALL_MAN     = ${BSD_INSTALL_MAN}
++INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
++INSTALL_SCRIPT  = ${BSD_INSTALL_SCRIPT}
+
+ PROGRAMS = bcftools
+ MISC_SCRIPTS = \
+@@ -142,7 +143,7 @@ print-version:
+ ifdef USE_GPL
+     main.o : EXTRA_CPPFLAGS += -DUSE_GPL
+     OBJS += polysomy.o peakfit.o
+-    GSL_LIBS ?= -lgsl -lcblas
++    GSL_LIBS ?= -lgslcblas
+ endif
+
+ print-%:

biology/bcf-score/files/patch-configure.ac

@@ -0,0 +1,11 @@
+--- configure.ac.orig	2018-07-18 08:34:29 UTC
++++ configure.ac
+@@ -23,7 +23,7 @@
+ # DEALINGS IN THE SOFTWARE.
+
+ dnl Process this file with autoconf to produce a configure script
+-AC_INIT([BCFtools], m4_esyscmd_s([./version.sh 2>/dev/null]),
++AC_INIT([BCFtools], [@PORTVERSION@],
+         [[email protected]], [], [http://www.htslib.org/])
+ AC_PREREQ([2.63])  dnl This version introduced 4-argument AC_CHECK_HEADER
+ AC_CONFIG_SRCDIR([main.c])

biology/bcf-score/pkg-descr

@@ -0,0 +1,3 @@
+Score is a set of tools in the form of a bcftools plugin, for handling
+and converting summary statistics files following the GWAS-VCF
+specification.

biology/bcf-score/pkg-plist

@@ -0,0 +1,6 @@
+libexec/bcftools/blupx.so
+libexec/bcftools/liftover.so
+libexec/bcftools/metal.so
+libexec/bcftools/munge.so
+libexec/bcftools/score.so
+%%DATADIR%%/assoc_plot.R

biology/bcftools/Makefile

@@ -1,5 +1,5 @@
 PORTNAME=	bcftools
-PORTVERSION=	1.16
+PORTVERSION=	1.17
 CATEGORIES=	biology
 
 MAINTAINER=	[email protected]

biology/bcftools/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1672094717
-SHA256 (samtools-bcftools-1.16_GH0.tar.gz) = c44c85a04e058e1f1eceeb712106031100bbd700b8ff3f623f7ff872469a4ba3
-SIZE (samtools-bcftools-1.16_GH0.tar.gz) = 3432435
+TIMESTAMP = 1677246068
+SHA256 (samtools-bcftools-1.17_GH0.tar.gz) = e6fdb4c94b531671ea8a0b00cb9245aa2602f6c4480621e45dac76338f590b9e
+SIZE (samtools-bcftools-1.17_GH0.tar.gz) = 3481344

biology/bcftools/pkg-plist

@@ -30,6 +30,7 @@ libexec/bcftools/impute-info.so
 libexec/bcftools/indel-stats.so
 libexec/bcftools/isecGT.so
 libexec/bcftools/mendelian.so
+libexec/bcftools/mendelian2.so
 libexec/bcftools/missing2ref.so
 libexec/bcftools/parental-origin.so
 libexec/bcftools/prune.so

biology/htslib/Makefile

@@ -1,5 +1,5 @@
 PORTNAME=	htslib
-DISTVERSION=	1.16
+DISTVERSION=	1.17
 CATEGORIES=	biology devel
 # Github generated distfiles are incomplete, so use custom tarball
 MASTER_SITES=	https://github.com/samtools/htslib/releases/download/${DISTVERSION}/

biology/htslib/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1672094487
-SHA256 (htslib-1.16.tar.bz2) = 606b7c7aff73734cf033ecd156f40529fa5792f54524952a28938ca0890d7924
-SIZE (htslib-1.16.tar.bz2) = 4466776
+TIMESTAMP = 1677245487
+SHA256 (htslib-1.17.tar.bz2) = 763779288c40f07646ec7ad98b96c378c739171d162ad98398868783b721839f
+SIZE (htslib-1.17.tar.bz2) = 4619884

biology/htslib/files/patch-Makefile

@@ -1,33 +1,14 @@
---- Makefile.orig	2021-03-20 15:53:14 UTC
+--- Makefile.orig	2023-02-24 13:35:28 UTC
 +++ Makefile
-@@ -53,13 +53,14 @@ man5dir     = $(mandir)/man5
- man7dir     = $(mandir)/man7
- pkgconfigdir= $(prefix)/libdata/pkgconfig
-
--MKDIR_P = mkdir -p
--INSTALL = install -p
--INSTALL_DATA    = $(INSTALL) -m 644
--INSTALL_DIR     = $(MKDIR_P) -m 755
--INSTALL_LIB     = $(INSTALL_DATA)
--INSTALL_MAN     = $(INSTALL_DATA)
+@@ -60,9 +60,9 @@ INSTALL = install -p
+ INSTALL_DATA    = $(INSTALL) -m 644
+ INSTALL_DIR     = $(MKDIR_P) -m 755
+ LIB_PERM        = 644
+-INSTALL_LIB     = $(INSTALL) -m $(LIB_PERM)
++INSTALL_LIB     = $(BSD_INSTALL_LIB)
+ INSTALL_MAN     = $(INSTALL_DATA)
 -INSTALL_PROGRAM = $(INSTALL)
-+# Use ports BSD_INSTALL_PROGRAM to strip if WITH_DEBUG is not set
-+MKDIR_P         = mkdir -p
-+INSTALL 	= install -p
-+INSTALL_DATA    = ${BSD_INSTALL_DATA}
-+INSTALL_DIR     = $(MKDIR_P)
-+INSTALL_LIB     = ${BSD_INSTALL_LIB}
-+INSTALL_MAN     = ${BSD_INSTALL_MAN}
-+INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
++INSTALL_PROGRAM = $(BSD_INSTALL_PROGRAM)
 
  # Set by config.mk if plugins are enabled
  plugindir =
-@@ -102,7 +103,7 @@ BUILT_THRASH_PROGRAMS = \
- 	test/thrash_threads6 \
- 	test/thrash_threads7
-
--all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) \
-+all: lib-static lib-shared $(BUILT_PROGRAMS) plugins \
-      htslib_static.mk htslib-uninstalled.pc
-
- ALL_CPPFLAGS = -I. $(CPPFLAGS)

biology/samtools/Makefile

@@ -1,5 +1,5 @@
 PORTNAME=	samtools
-DISTVERSION=	1.16.1
+DISTVERSION=	1.17
 CATEGORIES=	biology
 
 MAINTAINER=	[email protected]

biology/samtools/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1672094602
-SHA256 (samtools-samtools-1.16.1_GH0.tar.gz) = 70a7f358088929272d8c22d6063290ac8420f5351fba237a99fe17851a45d8be
-SIZE (samtools-samtools-1.16.1_GH0.tar.gz) = 4992787
+TIMESTAMP = 1677245969
+SHA256 (samtools-samtools-1.17_GH0.tar.gz) = f76ec1880468ecaa5341a7256ae896f2cfb191193dbb683046776fb81e18af49
+SIZE (samtools-samtools-1.17_GH0.tar.gz) = 5459752

biology/samtools/pkg-plist

@@ -29,6 +29,7 @@ man/man1/samtools-cat.1.gz
 man/man1/samtools-collate.1.gz
 man/man1/samtools-consensus.1.gz
 man/man1/samtools-coverage.1.gz
+man/man1/samtools-cram-size.1.gz
 man/man1/samtools-depad.1.gz
 man/man1/samtools-depth.1.gz
 man/man1/samtools-dict.1.gz
@@ -50,6 +51,7 @@ man/man1/samtools-phase.1.gz
 man/man1/samtools-quickcheck.1.gz
 man/man1/samtools-reference.1.gz
 man/man1/samtools-reheader.1.gz
+man/man1/samtools-reset.1.gz
 man/man1/samtools-rmdup.1.gz
 man/man1/samtools-samples.1.gz
 man/man1/samtools-sort.1.gz

cad/geda/Makefile

@@ -12,12 +12,6 @@ WWW=		http://www.gpleda.org/
 
 LICENSE=	GPLv2+
 
-.if ${/usr/bin/ld:L:tA} == /usr/bin/ld.lld
-BROKEN=		ld: error: ../src/.libs/libgeda.so: undefined reference to g_input_stream_get_type
-.endif
-DEPRECATED=	Broken with lld
-EXPIRATION_DATE=	2023-03-20
-
 LIB_DEPENDS=	libstroke.so:devel/libstroke \
 		libguile.so:lang/guile1
 RUN_DEPENDS=	gawk:lang/gawk\
@@ -35,8 +29,6 @@ GNU_CONFIGURE=	yes
 CONFIGURE_ARGS=	--with-libstroke=${LOCALBASE}
 INSTALL_TARGET=	install-strip
 USE_LDCONFIG=	yes
-CPPFLAGS+=	-I${LOCALBASE}/include
-LDFLAGS+=	-L${LOCALBASE}/lib
 DOCSDIR=	${PREFIX}/share/doc/${PORTNAME}-gaf
 DATADIR=	${PREFIX}/share/gEDA
 INFO=		geda-scheme

cad/geda/files/patch-configure

@@ -9,3 +9,12 @@
    case "$host" in
      *-*-linux*)
        OS_LINUX=yes
+@@ -20127,7 +20127,7 @@ fi
+
+     # If a prefix to search was specified, then add the appropriate
+     # flags.
+-    if test "X$libstroke_use" = "X"; then
++    if test -n "$libstroke_prefix"; then
+       LIBSTROKE_LDFLAGS="-L$libstroke_prefix/lib"
+       LIBSTROKE_CFLAGS="-I$libstroke_prefix/include"
+     fi

cad/geda/files/patch-gnetlist_src_Makefile.in

@@ -0,0 +1,11 @@
+--- gnetlist/src/Makefile.in.orig	2013-09-25 21:55:31 UTC
++++ gnetlist/src/Makefile.in
+@@ -439,7 +439,7 @@ gnetlist_CPPFLAGS = -I$(top_srcdir)/libgeda/include -I
+ gnetlist_CFLAGS = $(GCC_CFLAGS) $(MINGW_CFLIGS) $(GLIB_CFLAGS) \
+ 	$(GUILE_CFLAGS) $(GDK_PIXBUF_CFLAGS)
+
+-gnetlist_LDFLAGS = $(GLIB_LIBS) $(GUILE_LIBS) $(GDK_PIXBUF_LIBS)
++gnetlist_LDFLAGS = $(GLIB_LIBS) -lgio-2.0 $(GUILE_LIBS) $(GDK_PIXBUF_LIBS)
+ gnetlist_LDADD = $(top_builddir)/libgeda/src/libgeda.la
+ MOSTLYCLEANFILES = *.log *.ps core FILE *~
+ CLEANFILES = *.log *.ps core FILE *~

cad/geda/files/patch-gsymcheck_src_Makefile.in

@@ -0,0 +1,11 @@
+--- gsymcheck/src/Makefile.in.orig	2013-09-25 21:55:33 UTC
++++ gsymcheck/src/Makefile.in
+@@ -428,7 +428,7 @@ gsymcheck_CPPFLAGS = -I$(top_srcdir)/libgeda/include -
+ gsymcheck_CFLAGS = $(GCC_CFLAGS) $(MINGW_CFLIGS) $(GLIB_CFLAGS) \
+ 	$(GUILE_CFLAGS) $(GDK_PIXBUF_CFLAGS)
+
+-gsymcheck_LDFLAGS = $(GLIB_LIBS) $(GUILE_LIBS) $(GDK_PIXBUF_LIBS)
++gsymcheck_LDFLAGS = $(GLIB_LIBS) -lgio-2.0 $(GUILE_LIBS) $(GDK_PIXBUF_LIBS)
+ gsymcheck_LDADD = $(top_builddir)/libgeda/src/libgeda.la
+ MOSTLYCLEANFILES = *.log *.ps core FILE *~
+ CLEANFILES = *.log *.ps core FILE *~