*/*: sync with upstream

Taken from: HardenedBSD

benchmarks/phoronix-test-suite/Makefile

@@ -3,7 +3,7 @@
 
 PORTNAME=	phoronix-test-suite
 DISTVERSIONPREFIX=	v
-DISTVERSION=	8.8.1
+DISTVERSION=	9.0.0
 CATEGORIES=	benchmarks
 PKGNAMESUFFIX=	${PHP_PKGNAMESUFFIX}
 

benchmarks/phoronix-test-suite/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1560783124
-SHA256 (phoronix-test-suite-phoronix-test-suite-v8.8.1_GH0.tar.gz) = d51a0749c8d93767686e36a93214d66cd1657c189b68fd61f4dff84fdce2fd5e
-SIZE (phoronix-test-suite-phoronix-test-suite-v8.8.1_GH0.tar.gz) = 890982
+TIMESTAMP = 1569412239
+SHA256 (phoronix-test-suite-phoronix-test-suite-v9.0.0_GH0.tar.gz) = 041aebe9e3828bb41dfd51c57446a5d215b38a7cd1830bee8154a73a0d384129
+SIZE (phoronix-test-suite-phoronix-test-suite-v9.0.0_GH0.tar.gz) = 1261557

biology/Makefile

@@ -158,6 +158,7 @@
     SUBDIR += tRNAscan-SE
     SUBDIR += t_coffee
     SUBDIR += tabixpp
+    SUBDIR += tophat
     SUBDIR += treekin
     SUBDIR += treepuzzle
     SUBDIR += trimadap

biology/tophat/Makefile

@@ -0,0 +1,34 @@
+# $FreeBSD$
+
+PORTNAME=	tophat
+DISTVERSION=	2.1.1
+CATEGORIES=	biology python
+MASTER_SITES=	http://ccb.jhu.edu/software/tophat/downloads/
+
+MAINTAINER=	[email protected]
+COMMENT=	Fast splice junction mapper for RNA-Seq reads
+
+LICENSE=	BSL
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+LIB_DEPENDS=	libboost_iostreams.so:devel/boost-libs
+RUN_DEPENDS=	bowtie2:biology/bowtie2
+
+USES=		gmake python:2.7 shebangfix
+
+SHEBANG_FILES=	src/contig_to_chr_coords \
+		src/bed_to_juncs \
+		src/sra_to_solid \
+		src/tophat-fusion-post \
+		src/tophat.py \
+		src/tophat2.sh
+
+GNU_CONFIGURE=		yes
+CFLAGS+=		-Wno-unused
+INSTALL_TARGET=		install-strip
+MAKE_JOBS_UNSAFE=	yes
+
+post-install:
+	${INSTALL_SCRIPT} ${FILESDIR}/tophat-test ${STAGEDIR}${PREFIX}/bin
+
+.include <bsd.port.mk>

biology/tophat/distinfo

@@ -0,0 +1,3 @@
+TIMESTAMP = 1522620646
+SHA256 (tophat-2.1.1.tar.gz) = 37840b96f3219630082b15642c47f5ef95d14f6ee99c06a369b08b3d05684da5
+SIZE (tophat-2.1.1.tar.gz) = 2259554

biology/tophat/files/patch-configure

@@ -0,0 +1,22 @@
+--- configure.orig	2016-02-24 02:55:11 UTC
++++ configure
+@@ -6886,7 +6886,7 @@ case $host_os in *\ *) host_os=`echo "$h
+ # set CFLAGS and CXXFLAGS
+ #user_CFLAGS="${CXXFLAGS}"
+ user_CFLAGS=${CFLAGS}
+-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
++generic_CFLAGS="-Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
+ ext_CFLAGS=""
+ debug_CFLAGS=""
+ user_LDFLAGS="$LDFLAGS"
+@@ -6922,8 +6922,8 @@ else
+ fi
+
+ CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}"
+-CXXFLAGS="$CFLAGS"
+-CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS -I./SeqAn-1.4.2"
++CXXFLAGS="-std=gnu++98 $CFLAGS"
++CXXFLAGS="-I./SeqAn-1.4.2 $CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS"
+ LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS"
+
+ if test "`cd $srcdir && pwd`" != "`pwd`"; then

biology/tophat/files/patch-src-samtools-0.1.18-Makefile

@@ -0,0 +1,25 @@
+--- src/samtools-0.1.18/Makefile.orig	2016-02-14 18:21:17 UTC
++++ src/samtools-0.1.18/Makefile
+@@ -1,5 +1,10 @@
+-CC=			gcc
+-CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
++CC?=			gcc
++CFLAGS?=		-g -Wall -O2 #-m64 #-arch ppc
++CC?=           gcc
++CFLAGS?=       -g -Wall -O2
++# Link fails with clang on inlined functions with no -O
++CFLAGS+=       -O
++RANLIB?=       /usr/bin/ranlib
+ DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0
+ KNETFILE_O=	knetfile.o
+ LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
+@@ -38,7 +43,8 @@ all:$(PROG)
+ lib:libbam.a
+
+ libbam.a:$(LOBJS)
+-		$(AR) -csru $@ $(LOBJS)
++		$(AR) cr $@ $(LOBJS)
++		$(RANLIB) $@
+
+ samtools_0.1.18:lib-recur $(AOBJS)
+ 		$(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf -lm -lz #$(LIBCURSES)

biology/tophat/files/patch-src_Makefile.in

@@ -0,0 +1,51 @@
+--- src/Makefile.in.orig	2016-02-24 03:08:32 UTC
++++ src/Makefile.in
+@@ -1207,10 +1207,15 @@ libgc.a: $(libgc_a_OBJECTS) $(libgc_a_DE
+ 	-rm -f libgc.a
+ 	$(libgc_a_AR) libgc.a $(libgc_a_OBJECTS) $(libgc_a_LIBADD)
+ 	$(RANLIB) libgc.a
++
++# $(SAMLIB) and $(SAMPROG) are being mysteriously deleted sometime after they
++# are copied to src.  The cp below is a hack to allow the port to build.
+ libtophat.a: $(libtophat_a_OBJECTS) $(libtophat_a_DEPENDENCIES) $(EXTRA_libtophat_a_DEPENDENCIES) 
+ 	-rm -f libtophat.a
+ 	$(libtophat_a_AR) libtophat.a $(libtophat_a_OBJECTS) $(libtophat_a_LIBADD)
+ 	$(RANLIB) libtophat.a
++	cp $(SAMDIR)/$(SAMLIB) $(SAMDIR)/$(SAMPROG) .
++
+ install-binPROGRAMS: $(bin_PROGRAMS)
+ 	@$(NORMAL_INSTALL)
+ 	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
+@@ -1281,9 +1286,11 @@ prep_reads$(EXEEXT): $(prep_reads_OBJECT
+ sam_juncs$(EXEEXT): $(sam_juncs_OBJECTS) $(sam_juncs_DEPENDENCIES) $(EXTRA_sam_juncs_DEPENDENCIES) 
+ 	@rm -f sam_juncs$(EXEEXT)
+ 	$(sam_juncs_LINK) $(sam_juncs_OBJECTS) $(sam_juncs_LDADD) $(LIBS)
++
+ samtools_0.1.18$(EXEEXT): $(samtools_0_1_18_OBJECTS) $(samtools_0_1_18_DEPENDENCIES) $(EXTRA_samtools_0_1_18_DEPENDENCIES) 
+-	@rm -f samtools_0.1.18$(EXEEXT)
+-	$(LINK) $(samtools_0_1_18_OBJECTS) $(samtools_0_1_18_LDADD) $(LIBS)
++	#rm -f samtools_0.1.18$(EXEEXT)
++	#$(LINK) $(samtools_0_1_18_OBJECTS) $(samtools_0_1_18_LDADD) $(LIBS)
++
+ segment_juncs$(EXEEXT): $(segment_juncs_OBJECTS) $(segment_juncs_DEPENDENCIES) $(EXTRA_segment_juncs_DEPENDENCIES) 
+ 	@rm -f segment_juncs$(EXEEXT)
+ 	$(segment_juncs_LINK) $(segment_juncs_OBJECTS) $(segment_juncs_LDADD) $(LIBS)
+@@ -1658,7 +1665,7 @@ uninstall-am: uninstall-binPROGRAMS unin
+
+
+ clean-local:
+-	cd $(SAMDIR) && make clean
++	cd $(SAMDIR) && ${MAKE} clean
+
+ tophat2: tophat2.sh
+ 	cp tophat2.sh tophat2 && chmod 755 tophat2
+@@ -1669,7 +1676,8 @@ tophat: tophat.py
+ $(SAMPROG): $(SAMLIB)
+
+ $(SAMLIB):
+-	cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) ..
++	cd $(SAMDIR) && ${MAKE} $(SAMPROG)
++	cp $(SAMDIR)/$(SAMLIB) $(SAMDIR)/$(SAMPROG) .
+
+ install-data-hook:
+ 	cp -r intervaltree sortedcontainers $(DESTDIR)$(bindir)

biology/tophat/files/tophat-test

@@ -0,0 +1,16 @@
+#!/bin/sh -e
+
+if [ ! -e test_data.tar.gz ]; then
+    fetch https://ccb.jhu.edu/software/tophat/downloads/test_data.tar.gz
+fi
+if [ -e test_data ]; then
+    cat << EOM
+
+test_data already exists.  Remove it or run $0 from a different directory.
+
+EOM
+    exit 1
+fi
+tar zxvf test_data.tar.gz
+cd test_data
+tophat -r 20 test_ref reads_1.fq reads_2.fq

biology/tophat/pkg-descr

@@ -0,0 +1,11 @@
+TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq
+reads to mammalian-sized genomes using the ultra high-throughput short read
+aligner Bowtie, and then analyzes the mapping results to identify splice
+junctions between exons.
+
+Note:
+
+TopHat has been Superseded by HISAT2 and is no longer maintained upstream.
+This port is provided mainly for revisiting old studies where TopHat was used.
+
+WWW: http://ccb.jhu.edu/software/tophat/index.shtml

biology/tophat/pkg-plist

@@ -0,0 +1,29 @@
+bin/bam2fastx
+bin/bam_merge
+bin/bed_to_juncs
+bin/contig_to_chr_coords
+bin/fix_map_ordering
+bin/gtf_juncs
+bin/gtf_to_fasta
+bin/intervaltree/__init__.py
+bin/intervaltree/interval.py
+bin/intervaltree/intervaltree.py
+bin/intervaltree/node.py
+bin/juncs_db
+bin/long_spanning_reads
+bin/map2gtf
+bin/prep_reads
+bin/sam_juncs
+bin/samtools_0.1.18
+bin/segment_juncs
+bin/sortedcontainers/__init__.py
+bin/sortedcontainers/sorteddict.py
+bin/sortedcontainers/sortedlist.py
+bin/sortedcontainers/sortedlistwithkey.py
+bin/sortedcontainers/sortedset.py
+bin/sra_to_solid
+bin/tophat
+bin/tophat-fusion-post
+bin/tophat-test
+bin/tophat2
+bin/tophat_reports

chinese/librime/Makefile

@@ -4,7 +4,7 @@
 PORTNAME=	librime
 PORTVERSION=	1.2.9
 DISTVERSIONPREFIX=	rime-
-PORTREVISION=	18
+PORTREVISION=	19
 CATEGORIES=	chinese textproc
 
 MAINTAINER=	[email protected]

comms/Makefile

@@ -39,6 +39,7 @@
     SUBDIR += dump1090
     SUBDIR += ebook2cw
     SUBDIR += ebook2cwgui
+    SUBDIR += ebusd
     SUBDIR += echolinux
     SUBDIR += efax
     SUBDIR += ems-flasher

comms/ebusd/Makefile

@@ -0,0 +1,47 @@
+# $FreeBSD$
+
+PORTNAME=	ebusd
+PORTVERSION=	3.3
+CATEGORIES=	comms
+
+MAINTAINER=	[email protected]
+COMMENT=	Daemon for communication with eBUS heating systems
+
+LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+LIB_DEPENDS=	libargp.so:devel/argp-standalone
+
+USES=		autoreconf localbase:ldflags
+
+OPTIONS_DEFINE=	MQTT
+OPTIONS_DEFAULT=MQTT
+MQTT_DESC=	MQTT protocol support
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	john30
+GH_TAGNAME=	v${PORTVERSION}
+
+USE_RC_SUBR=	ebusd
+
+USERS=		ebusd
+GROUPS=		ebusd
+
+LOGDIR=		/var/log/${PORTNAME}
+RUNDIR=		/var/run/${PORTNAME}
+CPPFLAGS+=	-I${LOCALBASE}/include
+GNU_CONFIGURE=	yes
+
+PLIST_SUB=	USER=${USERS} GROUP=${GROUPS} \
+		LOGDIR=${LOGDIR} \
+		RUNDIR=${RUNDIR}
+
+MQTT_CONFIGURE_WITH=	mqtt
+MQTT_LIB_DEPENDS=	libmosquitto.so:net/mosquitto
+MQTT_VARS=		LIBS+=-lmosquitto
+
+post-install:
+	${MKDIR} ${STAGEDIR}${LOGDIR}
+	${MKDIR} ${STAGEDIR}${RUNDIR}
+
+.include <bsd.port.mk>

comms/ebusd/distinfo

@@ -0,0 +1,3 @@
+TIMESTAMP = 1565559816
+SHA256 (john30-ebusd-3.3-v3.3_GH0.tar.gz) = 48669140cfafbe060c765b4530018b30f07e1b074dbce00b205a8f2a22dee573
+SIZE (john30-ebusd-3.3-v3.3_GH0.tar.gz) = 696172

comms/ebusd/files/ebusd.in

@@ -0,0 +1,37 @@
+#!/bin/sh
+
+# $FreeBSD$
+# 
+# PROVIDE: ebusd
+# REQUIRE: LOGIN cleanvar
+# KEYWORD: shutdown
+
+#
+# Add the following lines to /etc/rc.conf to enable ebusd:
+#
+#ebusd_enable (bool): set to "YES" to start domotics at boot
+#ebusd_user (str):    Default to ebusd, user for starting ebusd
+#ebusd_group (str):   Default to ebusd, group for stating ebusd
+#ebusd_pidfile (str): Custum PID file path and name
+#                        Default to "/var/run/ebusd/${hostname}.pid".
+#ebusd_args (str):    Custom additional arguments to be passed
+#                        Default to "-d /dev/ttyU0 --scanconfig --localhost"
+
+. /etc/rc.subr
+
+name="ebusd"
+rcvar="ebusd_enable"
+
+load_rc_config $name
+
+: ${ebusd_user:=ebusd}
+: ${ebusd_group:=ebusd}
+: ${ebusd_enable:=NO}
+: ${ebusd_args:="-d /dev/ttyU0 --scanconfig --localhost"}
+
+pidfile=${ebusd_pidfile:-"/var/run/ebusd/${hostname}.pid"}
+
+command="%%PREFIX%%/bin/ebusd"
+command_args="--pidfile ${pidfile} ${ebusd_args}"
+
+run_rc_command "$1"

comms/ebusd/files/patch-configure.ac

@@ -0,0 +1,19 @@
+--- configure.ac.orig	2018-12-26 15:38:15 UTC
++++ configure.ac
+@@ -36,6 +36,7 @@ AC_SUBST(EXTRA_LIBS)
+ AC_CHECK_FUNC([pselect], [AC_DEFINE(HAVE_PSELECT, [1], [Defined if pselect() is available.])])
+ AC_CHECK_FUNC([ppoll], [AC_DEFINE(HAVE_PPOLL, [1], [Defined if ppoll() is available.])])
+ AC_CHECK_HEADER([linux/serial.h], [AC_DEFINE(HAVE_LINUX_SERIAL, [1], [Defined if linux/serial.h is available.])])
++AC_CHECK_HEADER([dev/usb/uftdiio.h], [AC_DEFINE(HAVE_FREEBSD_UFTDI, [1], [Defined if dev/usb/uftdiio.h is available.])])
+
+ AC_ARG_ENABLE(coverage, AS_HELP_STRING([--enable-coverage], [enable code coverage tracking]), [CXXFLAGS+=" -coverage -O0"], [])
+ AC_ARG_WITH(contrib, AS_HELP_STRING([--without-contrib], [disable inclusion of contributed sources]), [], [with_contrib=yes])
+@@ -118,7 +119,7 @@ AM_COND_IF([CONTRIB], [AC_CONFIG_FILES([
+ 	])])
+
+ AC_DEFINE_UNQUOTED(PACKAGE_PIDFILE, LOCALSTATEDIR "/run/" PACKAGE ".pid", [The path and name of the PID file.])
+-AC_DEFINE_UNQUOTED(PACKAGE_LOGFILE, LOCALSTATEDIR "/log/" PACKAGE ".log", [The path and name of the log file.])
++AC_DEFINE_UNQUOTED(PACKAGE_LOGFILE, LOCALSTATEDIR "/log/" PACKAGE "/" PACKAGE ".log", [The path and name of the log file.])
+ AC_DEFINE(SCAN_VERSION, "[m4_esyscmd_s([sed -e 's#^\([0-9]*\.[0-9]*\).*#\1#' -e 's#\.\([0-9]\)$#0\1#' -e 's#\.##' VERSION])]", [The version of the package formatted for the scan result.])
+ AC_DEFINE(REVISION, "[m4_esyscmd_s([git describe --always 2>/dev/null || (date +p%Y%m%d)])]", [The revision of the package.])
+