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*/*: sync with upstream

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Taken from: HardenedBSD
This commit is contained in:
Franco Fichtner 2017-10-25 21:27:38 +02:00
parent e72aa8d7fe
commit 643fd91f32
117 changed files with 1019 additions and 1414 deletions
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6
archivers/kf5-karchive/Makefile
View file

@ -2,12 +2,16 @@
# $FreeBSD$
PORTNAME= karchive
PORTVERSION= ${KDE_FRAMEWORKS_VERSION}
DISTVERSION= ${KDE_FRAMEWORKS_VERSION}
CATEGORIES= archivers kde kde-frameworks
MAINTAINER= kde@FreeBSD.org
COMMENT= KF5 library that provides classes for handling archive formats
# Sources say LGPL20, KDE policy says LGPL21+, license file is LGPL21
LICENSE= LGPL20
LICENSE_FILE= ${WRKSRC}/COPYING.LIB
USES= cmake:outsource compiler:c++11-lib kde:5 tar:xz
USE_KDE= ecm
USE_QT5= buildtools_build core qmake_build

23
biology/bcftools/Makefile
View file

@ -2,8 +2,7 @@
# $FreeBSD$
PORTNAME= bcftools
PORTVERSION= 1.3.1
PORTREVISION= 2
PORTVERSION= 1.6
CATEGORIES= biology
MAINTAINER= cartwright@asu.edu
@ -12,7 +11,7 @@ COMMENT= Tools for manipulating next-generation sequencing data
LICENSE= MIT
# LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= htslib>=1.3:biology/htslib
BUILD_DEPENDS= htslib>=1.6:biology/htslib
LIB_DEPENDS= libhts.so:biology/htslib
TEST_DEPENDS= bash:shells/bash
@ -21,10 +20,12 @@ CONFLICTS_BUILD=openssl
USE_GITHUB= yes
GH_ACCOUNT= samtools
USES= gmake perl5 shebangfix
USES= autoreconf gmake perl5 python shebangfix
USE_PERL5= test
PYTHON_NO_DEPENDS= yes
GNU_CONFIGURE= yes
SUB_FILES= pkg-message
SHEBANG_FILES= vcfutils.pl plot-vcfstats plugins/color-chrs.pl test/test.pl
SHEBANG_FILES= misc/* test/test.pl
OPTIONS_DEFINE= GPL
GPL_DESC= Enable modules that rely on GPL code
@ -37,19 +38,15 @@ GPL_LIB_DEPENDS= libgsl.so:math/gsl
CPPFLAGS+= -I${LOCALBASE}/include
LDFLAGS+= -L${LOCALBASE}/lib
MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \
INSTALL_DATA="${INSTALL_DATA}" \
INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
INSTALL_DIR="${MKDIR}"
.if ${PORT_OPTIONS:MGPL}
MAKE_ENV+= USE_GPL=1
LICENSE= GPLv3
.endif
PLIST_SUB= PORTVERSION="${PORTVERSION}"
TEST_TARGET= test
post-patch:
@${GREP} -q '@PORTVERSION@' ${WRKSRC}/configure.ac || (echo "@PORTVERSION@ in file/patch-configure.ac is overwritten probably due to using 'make makepatch'"; exit 1)
@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac
.include <bsd.port.mk>

6
biology/bcftools/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1463692643
SHA256 (samtools-bcftools-1.3.1_GH0.tar.gz) = 99a5cc05faa974f5ddbeebf346bb51a806bdaaf8e2f6adc3bead28551983e77e
SIZE (samtools-bcftools-1.3.1_GH0.tar.gz) = 958207
TIMESTAMP = 1508307708
SHA256 (samtools-bcftools-1.6_GH0.tar.gz) = afb2a96d3419fbe77fab5c501dc28bc5e691145353ac5600909a75c0e625f025
SIZE (samtools-bcftools-1.6_GH0.tar.gz) = 2333330

91
biology/bcftools/files/patch-Makefile
View file

@ -1,18 +1,8 @@
--- Makefile.orig 2015-12-15 21:42:34 UTC
--- Makefile.orig 2017-09-28 11:22:48 UTC
+++ Makefile
@@ -29,16 +29,15 @@ TEST_PROG= test/test-rbuf
all: $(PROG) $(TEST_PROG)
# Adjust $(HTSDIR) to point to your top-level htslib directory
-HTSDIR = ../htslib
-include $(HTSDIR)/htslib.mk
-HTSLIB = $(HTSDIR)/libhts.a
-BGZIP = $(HTSDIR)/bgzip
-TABIX = $(HTSDIR)/tabix
+HTSDIR = $(prefix)/include
+HTSLIB = -lhts
+BGZIP = $(HTSDIR)/../bin/bgzip
+TABIX = $(HTSDIR)/../bin/tabix
@@ -22,10 +22,10 @@
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
-CC = gcc
-CPPFLAGS =
@ -24,17 +14,13 @@
+LDFLAGS +=
LIBS =
OBJS = main.o vcfindex.o tabix.o \
@@ -57,26 +56,20 @@ GSL_LIBS =
ifdef USE_GPL
EXTRA_CPPFLAGS += -DUSE_GPL
OBJS += polysomy.o peakfit.o
- GSL_LIBS = -lgsl -lcblas
+ GSL_LIBS = -lgsl -lgslcblas
endif
DYNAMIC_FLAGS = -rdynamic
@@ -42,26 +42,25 @@ OBJS = main.o vcfindex.o tabix.o \
vcfsort.o \
ccall.o em.o prob1.o kmin.o # the original samtools calling
-prefix = /usr/local
+prefix = ${STAGEDIR}${PREFIX}
+prefix = ${PREFIX}
exec_prefix = $(prefix)
bindir = $(exec_prefix)/bin
libdir = $(exec_prefix)/lib
@ -42,37 +28,52 @@
-mandir = $(prefix)/share/man
+mandir = $(prefix)/man
man1dir = $(mandir)/man1
# Installation location for $(PLUGINS)
plugindir = $(libexecdir)/bcftools
pluginpath = $(plugindir)
# Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
-misc_bindir = $(bindir)
+misc_bindir = $(bindir)/samtools_misc
-MKDIR_P = mkdir -p
MKDIR_P = mkdir -p
-INSTALL = install -p
-INSTALL_PROGRAM = $(INSTALL)
-INSTALL_DATA = $(INSTALL) -m 644
-INSTALL_DIR = $(MKDIR_P) -m 755
-
MISC_PROGRAMS = plot-vcfstats vcfutils.pl plugins/color-chrs.pl
-INSTALL_MAN = $(INSTALL_DATA)
-INSTALL_PROGRAM = $(INSTALL)
-INSTALL_SCRIPT = $(INSTALL_PROGRAM)
+INSTALL_DATA = ${BSD_INSTALL_DATA}
+INSTALL_DIR = $(MKDIR_P)
+INSTALL_MAN = ${BSD_INSTALL_MAN}
+INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
+INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT}
all:$(PROG) plugins
@@ -181,7 +174,7 @@ test/test-rbuf: test/test-rbuf.o
$(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS)
PROGRAMS = bcftools
MISC_SCRIPTS = \
@@ -77,7 +76,7 @@ all: $(PROGRAMS) $(TEST_PROGRAMS) plugin
bcftools: $(HTSLIB) $(OBJS)
- $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
+ $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -pthread -lz -lm $(GSL_LIBS) $(LIBS)
ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS)
-ALL_LIBS = -lz -ldl $(LIBS)
+ALL_LIBS = -lz $(LIBS)
doc/bcftools.1: doc/bcftools.txt
cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt
@@ -198,8 +191,9 @@ docs: doc/bcftools.1 doc/bcftools.html
# Usually config.mk and config.h are generated by running configure
# or config.status, but if those aren't used create defaults here.
@@ -131,7 +130,7 @@ print-version:
ifdef USE_GPL
main.o : EXTRA_CPPFLAGS += -DUSE_GPL
OBJS += polysomy.o peakfit.o
- GSL_LIBS ?= -lgsl -lcblas
+ GSL_LIBS ?= -lgsl -lgslcblas
endif
bcftools: $(OBJS) $(HTSLIB)
@@ -273,7 +272,7 @@ docs: doc/bcftools.1 doc/bcftools.html
# Since there is no make dependency, bcftools.1 can be out-of-date and
# make docs can be run to update if asciidoc is available
install: $(PROG)
install: $(PROG) $(PLUGINS)
- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
- $(INSTALL_PROGRAM) $(PROG) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
+ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
+ $(INSTALL_PROGRAM) $(PROG) $(DESTDIR)$(bindir)
+ $(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
$(INSTALL_DATA) doc/bcftools.1 $(DESTDIR)$(man1dir)
$(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)
+ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(misc_bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
$(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir)
$(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir)

11
biology/bcftools/files/patch-configure.ac Normal file
View file

@ -0,0 +1,11 @@
--- configure.ac.orig 2017-09-28 11:22:48 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([make print-version]),
+AC_INIT([BCFtools], [@PORTVERSION@],
[samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])
AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER
AC_CONFIG_SRCDIR([main.c])

11
biology/bcftools/files/patch-misc_run-roh.pl Normal file
View file

@ -0,0 +1,11 @@
--- misc/run-roh.pl.orig 2017-10-18 09:33:24 UTC
+++ misc/run-roh.pl
@@ -97,7 +97,7 @@ sub cmd
else
{
# child
- exec('/bin/bash', '-o','pipefail','-c', $cmd) or error("Failed to run the command [/bin/sh -o pipefail -c $cmd]: $!");
+ exec('/bin/sh', '-c', $cmd) or error("Failed to run the command [/bin/sh -c $cmd]: $!");
}
if ( exists($args{exit_on_error}) && !$args{exit_on_error} ) { return @out; }

2
biology/bcftools/files/patch-prob1.c
View file

@ -1,4 +1,4 @@
--- prob1.c.orig 2015-12-15 21:42:34 UTC
--- prob1.c.orig 2017-09-28 11:22:48 UTC
+++ prob1.c
@@ -33,6 +33,12 @@ THE SOFTWARE. */
#include <zlib.h>

8
biology/bcftools/files/patch-test_test.pl
View file

@ -1,6 +1,6 @@
--- test/test.pl.orig 2015-12-22 22:45:13 UTC
--- test/test.pl.orig 2017-10-18 09:33:24 UTC
+++ test/test.pl
@@ -290,7 +290,7 @@ sub _cmd
@@ -381,7 +381,7 @@ sub _cmd
else
{
# child
@ -9,7 +9,7 @@
}
return ($? >> 8, join('',@out));
}
@@ -657,7 +657,7 @@ sub test_usage
@@ -782,7 +782,7 @@ sub test_usage
my $command = $args{cmd};
my $commandpath = $$opts{bin}."/".$command;
my ($ret,$out) = _cmd("$commandpath $args{redirection} 2>&1");
@ -18,7 +18,7 @@
my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
@@ -708,7 +708,7 @@ sub test_usage_subcommand
@@ -833,7 +833,7 @@ sub test_usage_subcommand
my $subcommand = $args{subcmd};
my $commandpath = $$opts{bin}."/".$command;
my ($ret,$out) = _cmd("$commandpath $subcommand $args{redirection} 2>&1");

2
biology/bcftools/files/pkg-message.in
View file

@ -3,5 +3,5 @@ The miscellaneous tools included with Bcftools have been installed to
Add that directory to your path if you want to use these tools.
Some of these tools depend on Perl5, and it will need to be installed to
Some of these tools depend on Perl5/Python, and it will need to be installed to
use them.

15
biology/bcftools/pkg-plist
View file

@ -1,19 +1,32 @@
bin/bcftools
bin/samtools_misc/color-chrs.pl
bin/samtools_misc/guess-ploidy.py
bin/samtools_misc/plot-roh.py
bin/samtools_misc/plot-vcfstats
bin/samtools_misc/run-roh.pl
bin/samtools_misc/vcfutils.pl
libexec/bcftools/GTisec.so
libexec/bcftools/GTsubset.so
libexec/bcftools/ad-bias.so
libexec/bcftools/af-dist.so
libexec/bcftools/check-ploidy.so
libexec/bcftools/check-sparsity.so
libexec/bcftools/color-chrs.so
libexec/bcftools/counts.so
libexec/bcftools/dosage.so
libexec/bcftools/fill-AN-AC.so
libexec/bcftools/fill-from-fasta.so
libexec/bcftools/fill-tags.so
libexec/bcftools/fixploidy.so
libexec/bcftools/fixref.so
libexec/bcftools/frameshifts.so
libexec/bcftools/guess-ploidy.so
libexec/bcftools/impute-info.so
libexec/bcftools/isecGT.so
libexec/bcftools/mendelian.so
libexec/bcftools/missing2ref.so
libexec/bcftools/prune.so
libexec/bcftools/setGT.so
libexec/bcftools/tag2tag.so
libexec/bcftools/vcf2sex.so
libexec/bcftools/trio-switch-rate.so
man/man1/bcftools.1.gz

10
biology/htslib/Makefile
View file

@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= htslib
PORTVERSION= 1.3.1
PORTVERSION= 1.6
CATEGORIES= biology devel
MAINTAINER= cartwright@asu.edu
@ -34,16 +34,8 @@ CURL_CONFIGURE_ENABLE= libcurl
CPPFLAGS+= -I${LOCALBASE}/include
LDFLAGS+= -L${LOCALBASE}/lib
MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \
INSTALL_DATA="${INSTALL_DATA}" \
INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
INSTALL_DIR="${MKDIR}"
PLIST_SUB= PORTVERSION="${PORTVERSION}"
TEST_TARGET= test
post-patch:
@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac
.include <bsd.port.mk>

6
biology/htslib/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1463688817
SHA256 (samtools-htslib-1.3.1_GH0.tar.gz) = 3bbd04f9a0c4c301abd5d19a81920894ac2ee5e86e8aa977e8c2035e01d93ea7
SIZE (samtools-htslib-1.3.1_GH0.tar.gz) = 1065840
TIMESTAMP = 1508301522
SHA256 (samtools-htslib-1.6_GH0.tar.gz) = 4215c9153c27603cbaaf542f2ec128c5e839380d6df6edd4dbf67955170740c6
SIZE (samtools-htslib-1.6_GH0.tar.gz) = 1155672

48
biology/htslib/files/patch-Makefile
View file

@ -1,6 +1,6 @@
--- Makefile.orig 2016-04-22 08:45:12 UTC
--- Makefile.orig 2017-10-18 08:03:33 UTC
+++ Makefile
@@ -22,16 +22,7 @@
@@ -22,41 +22,26 @@
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
@ -8,16 +8,23 @@
-AR = ar
-RANLIB = ranlib
-
-# Default libraries to link if configure is not used
-htslib_default_libs = -lz -lm -lbz2 -llzma
-
-CPPFLAGS =
-# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
-# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
-#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
-CFLAGS = -g -Wall -O2
EXTRA_CFLAGS_PIC = -fpic
-LDFLAGS =
-LIBS =
-LIBS = $(htslib_default_libs)
# For now these don't work too well as samtools also needs to know to
# add -lbz2 and -llzma if linking against the static libhts.a library.
@@ -58,17 +49,11 @@ includedir = $(prefix)/include
-prefix = /usr/local
+prefix = ${PREFIX}
exec_prefix = $(prefix)
bindir = $(exec_prefix)/bin
includedir = $(prefix)/include
libdir = $(exec_prefix)/lib
libexecdir = $(exec_prefix)/libexec
datarootdir = $(prefix)/share
@ -27,30 +34,27 @@
man5dir = $(mandir)/man5
pkgconfigdir= $(prefix)/libdata/pkgconfig
-MKDIR_P = mkdir -p
MKDIR_P = mkdir -p
-INSTALL = install -p
-INSTALL_PROGRAM = $(INSTALL)
-INSTALL_DATA = $(INSTALL) -m 644
-INSTALL_DIR = $(MKDIR_P) -m 755
-
-INSTALL_LIB = $(INSTALL_DATA)
-INSTALL_MAN = $(INSTALL_DATA)
-INSTALL_PROGRAM = $(INSTALL)
+INSTALL_DATA = ${BSD_INSTALL_DATA}
+INSTALL_DIR = $(MKDIR_P)
+INSTALL_LIB = ${BSD_INSTALL_LIB}
+INSTALL_MAN = ${BSD_INSTALL_MAN}
+INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
# Set by config.mk if plugins are enabled
plugindir =
@@ -86,7 +71,7 @@ BUILT_TEST_PROGRAMS = \
test/test-vcf-api \
test/test-vcf-sweep
@@ -87,7 +72,7 @@ BUILT_THRASH_PROGRAMS = \
test/thrash_threads5 \
test/thrash_threads6
-all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
+all: lib-static lib-shared $(BUILT_PROGRAMS) plugins
HTSPREFIX =
include htslib_vars.mk
@@ -360,7 +345,7 @@ installdirs:
# and libhts.so.NN (used by client executables at runtime).
install-so: libhts.so installdirs
- $(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
+ $(INSTALL_LIB) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so
ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION)

11
biology/htslib/files/patch-configure.ac
View file

@ -1,11 +0,0 @@
--- configure.ac.orig 2015-12-15 16:34:33 UTC
+++ configure.ac
@@ -23,7 +23,7 @@
# DEALINGS IN THE SOFTWARE.
dnl Process this file with autoconf to produce a configure script
-AC_INIT([HTSlib], m4_esyscmd_s([make print-version]),
+AC_INIT([HTSlib], [1.3],
[samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])
AC_PREREQ(2.63) dnl This version introduced 4-argument AC_CHECK_HEADER
AC_CONFIG_SRCDIR(hts.c)

12
biology/htslib/files/patch-hfile__libcurl.c
View file

@ -1,13 +1,13 @@
--- hfile_libcurl.c.orig 2015-12-15 16:34:33 UTC
--- hfile_libcurl.c.orig 2017-09-28 11:20:23 UTC
+++ hfile_libcurl.c
@@ -39,6 +39,10 @@ DEALINGS IN THE SOFTWARE. */
#include <curl/curl.h>
@@ -49,6 +49,10 @@ typedef struct {
unsigned int size;
} hdrlist;
+#ifndef ENOTRECOVERABLE
+#define ENOTRECOVERABLE EIO
+#endif
+
typedef struct {
hFILE base;
CURL *easy;
hdrlist fixed; // List of headers supplied at hopen()
hdrlist extra; // List of headers from callback

6
biology/htslib/pkg-plist
View file

@ -7,6 +7,9 @@ include/htslib/faidx.h
include/htslib/hfile.h
include/htslib/hts.h
include/htslib/hts_defs.h
include/htslib/hts_endian.h
include/htslib/hts_log.h
include/htslib/hts_os.h
include/htslib/kbitset.h
include/htslib/kfunc.h
include/htslib/khash.h
@ -20,13 +23,14 @@ include/htslib/regidx.h
include/htslib/sam.h
include/htslib/synced_bcf_reader.h
include/htslib/tbx.h
include/htslib/thread_pool.h
include/htslib/vcf.h
include/htslib/vcf_sweep.h
include/htslib/vcfutils.h
lib/libhts.a
lib/libhts.so
lib/libhts.so.1
lib/libhts.so.%%PORTVERSION%%
lib/libhts.so.2
libdata/pkgconfig/htslib.pc
man/man1/htsfile.1.gz
man/man1/tabix.1.gz

22
biology/samtools/Makefile
View file

@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= samtools
PORTVERSION= 1.3.1
PORTVERSION= 1.6
CATEGORIES= biology
MAINTAINER= cartwright@asu.edu
@ -11,34 +11,22 @@ COMMENT= Tools for manipulating next-generation sequencing data
LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= htslib>=1.3:biology/htslib
BUILD_DEPENDS= htslib>=1.6:biology/htslib
LIB_DEPENDS= libhts.so:biology/htslib
TEST_DEPENDS= bash:shells/bash
USE_GITHUB= yes
USES= autoreconf gmake ncurses perl5 shebangfix
USES= autoreconf gmake ncurses perl5 python shebangfix
USE_PERL5= test
PYTHON_NO_DEPENDS= yes
GNU_CONFIGURE= yes
SUB_FILES= pkg-message
SHEBANG_FILES= misc/*.pl misc/plot-bamstats test/test.pl
SHEBANG_FILES= misc/*.pl misc/*.py misc/plot-bamstats test/test.pl
CPPFLAGS+= -I${LOCALBASE}/include
LDFLAGS+= -L${LOCALBASE}/lib
MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \
INSTALL_DATA="${INSTALL_DATA}" \
INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
INSTALL_DIR="${MKDIR}"
PLIST_SUB= PORTVERSION="${PORTVERSION}"
TEST_TARGET= test
post-patch:
@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac
${CP} ${FILESDIR}/ax_with_htslib.m4 ${WRKSRC}/
${CP} ${FILESDIR}/ax_with_curses.m4 ${WRKSRC}/
.include <bsd.port.mk>

6
biology/samtools/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1463691050
SHA256 (samtools-samtools-1.3.1_GH0.tar.gz) = 30752c7b92cd9e146f4017983b2a41beb58c8966e93572cea76a14719f95a768
SIZE (samtools-samtools-1.3.1_GH0.tar.gz) = 3757176
TIMESTAMP = 1508304738
SHA256 (samtools-samtools-1.6_GH0.tar.gz) = c0d1ffefe441297ee0eec0e032ac3131519f82fd1a11d38fbcec19e2d5822b28
SIZE (samtools-samtools-1.6_GH0.tar.gz) = 4014195

518
biology/samtools/files/ax_with_curses.m4
View file

@ -1,518 +0,0 @@
# ===========================================================================
# http://www.gnu.org/software/autoconf-archive/ax_with_curses.html
# ===========================================================================
#
# SYNOPSIS
#
# AX_WITH_CURSES
#
# DESCRIPTION
#
# This macro checks whether a SysV or X/Open-compatible Curses library is
# present, along with the associated header file. The NcursesW
# (wide-character) library is searched for first, followed by Ncurses,
# then the system-default plain Curses. The first library found is the
# one returned.
#
# The following options are understood: --with-ncursesw, --with-ncurses,
# --without-ncursesw, --without-ncurses. The "--with" options force the
# macro to use that particular library, terminating with an error if not
# found. The "--without" options simply skip the check for that library.
# The effect on the search pattern is:
#
# (no options) - NcursesW, Ncurses, Curses
# --with-ncurses --with-ncursesw - NcursesW only [*]
# --without-ncurses --with-ncursesw - NcursesW only [*]
# --with-ncursesw - NcursesW only [*]
# --with-ncurses --without-ncursesw - Ncurses only [*]
# --with-ncurses - NcursesW, Ncurses [**]
# --without-ncurses --without-ncursesw - Curses only
# --without-ncursesw - Ncurses, Curses
# --without-ncurses - NcursesW, Curses
#
# [*] If the library is not found, abort the configure script.
#
# [**] If the second library (Ncurses) is not found, abort configure.
#
# The following preprocessor symbols may be defined by this macro if the
# appropriate conditions are met:
#
# HAVE_CURSES - if any SysV or X/Open Curses library found
# HAVE_CURSES_ENHANCED - if library supports X/Open Enhanced functions
# HAVE_CURSES_COLOR - if library supports color (enhanced functions)
# HAVE_CURSES_OBSOLETE - if library supports certain obsolete features
# HAVE_NCURSESW - if NcursesW (wide char) library is to be used
# HAVE_NCURSES - if the Ncurses library is to be used
#
# HAVE_CURSES_H - if <curses.h> is present and should be used
# HAVE_NCURSESW_H - if <ncursesw.h> should be used
# HAVE_NCURSES_H - if <ncurses.h> should be used
# HAVE_NCURSESW_CURSES_H - if <ncursesw/curses.h> should be used
# HAVE_NCURSES_CURSES_H - if <ncurses/curses.h> should be used
#
# (These preprocessor symbols are discussed later in this document.)
#
# The following output variable is defined by this macro; it is precious
# and may be overridden on the ./configure command line:
#
# CURSES_LIB - library to add to xxx_LDADD
#
# The library listed in CURSES_LIB is NOT added to LIBS by default. You
# need to add CURSES_LIB to the appropriate xxx_LDADD line in your
# Makefile.am. For example:
#
# prog_LDADD = @CURSES_LIB@
#
# If CURSES_LIB is set on the configure command line (such as by running
# "./configure CURSES_LIB=-lmycurses"), then the only header searched for
# is <curses.h>. The user may use the CPPFLAGS precious variable to
# override the standard #include search path. If the user needs to
# specify an alternative path for a library (such as for a non-standard
# NcurseW), the user should use the LDFLAGS variable.
#
# The following shell variables may be defined by this macro:
#
# ax_cv_curses - set to "yes" if any Curses library found
# ax_cv_curses_enhanced - set to "yes" if Enhanced functions present
# ax_cv_curses_color - set to "yes" if color functions present
# ax_cv_curses_obsolete - set to "yes" if obsolete features present
#
# ax_cv_ncursesw - set to "yes" if NcursesW library found
# ax_cv_ncurses - set to "yes" if Ncurses library found
# ax_cv_plaincurses - set to "yes" if plain Curses library found
# ax_cv_curses_which - set to "ncursesw", "ncurses", "plaincurses" or "no"
#
# These variables can be used in your configure.ac to determine the level
# of support you need from the Curses library. For example, if you must
# have either Ncurses or NcursesW, you could include:
#
# AX_WITH_CURSES
# if test "x$ax_cv_ncursesw" != xyes && test "x$ax_cv_ncurses" != xyes; then
# AC_MSG_ERROR([requires either NcursesW or Ncurses library])
# fi
#
# If any Curses library will do (but one must be present and must support
# color), you could use:
#
# AX_WITH_CURSES
# if test "x$ax_cv_curses" != xyes || test "x$ax_cv_curses_color" != xyes; then
# AC_MSG_ERROR([requires an X/Open-compatible Curses library with color])
# fi
#
# Certain preprocessor symbols and shell variables defined by this macro
# can be used to determine various features of the Curses library. In
# particular, HAVE_CURSES and ax_cv_curses are defined if the Curses
# library found conforms to the traditional SysV and/or X/Open Base Curses
# definition. Any working Curses library conforms to this level.
#
# HAVE_CURSES_ENHANCED and ax_cv_curses_enhanced are defined if the
# library supports the X/Open Enhanced Curses definition. In particular,
# the wide-character types attr_t, cchar_t and wint_t, the functions
# wattr_set() and wget_wch() and the macros WA_NORMAL and _XOPEN_CURSES
# are checked. The Ncurses library does NOT conform to this definition,
# although NcursesW does.
#
# HAVE_CURSES_COLOR and ax_cv_curses_color are defined if the library
# supports color functions and macros such as COLOR_PAIR, A_COLOR,
# COLOR_WHITE, COLOR_RED and init_pair(). These are NOT part of the
# X/Open Base Curses definition, but are part of the Enhanced set of
# functions. The Ncurses library DOES support these functions, as does
# NcursesW.
#
# HAVE_CURSES_OBSOLETE and ax_cv_curses_obsolete are defined if the
# library supports certain features present in SysV and BSD Curses but not
# defined in the X/Open definition. In particular, the functions
# getattrs(), getcurx() and getmaxx() are checked.
#
# To use the HAVE_xxx_H preprocessor symbols, insert the following into
# your system.h (or equivalent) header file:
#
# #if defined HAVE_NCURSESW_CURSES_H
# # include <ncursesw/curses.h>
# #elif defined HAVE_NCURSESW_H
# # include <ncursesw.h>
# #elif defined HAVE_NCURSES_CURSES_H
# # include <ncurses/curses.h>
# #elif defined HAVE_NCURSES_H
# # include <ncurses.h>
# #elif defined HAVE_CURSES_H
# # include <curses.h>
# #else
# # error "SysV or X/Open-compatible Curses header file required"
# #endif
#
# For previous users of this macro: you should not need to change anything
# in your configure.ac or Makefile.am, as the previous (serial 10)
# semantics are still valid. However, you should update your system.h (or
# equivalent) header file to the fragment shown above. You are encouraged
# also to make use of the extended functionality provided by this version
# of AX_WITH_CURSES, as well as in the additional macros
# AX_WITH_CURSES_PANEL, AX_WITH_CURSES_MENU and AX_WITH_CURSES_FORM.
#
# LICENSE
#
# Copyright (c) 2009 Mark Pulford <mark@kyne.com.au>
# Copyright (c) 2009 Damian Pietras <daper@daper.net>
# Copyright (c) 2012 Reuben Thomas <rrt@sc3d.org>
# Copyright (c) 2011 John Zaitseff <J.Zaitseff@zap.org.au>
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation, either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program. If not, see <http://www.gnu.org/licenses/>.
#
# As a special exception, the respective Autoconf Macro's copyright owner
# gives unlimited permission to copy, distribute and modify the configure
# scripts that are the output of Autoconf when processing the Macro. You
# need not follow the terms of the GNU General Public License when using
# or distributing such scripts, even though portions of the text of the
# Macro appear in them. The GNU General Public License (GPL) does govern
# all other use of the material that constitutes the Autoconf Macro.
#
# This special exception to the GPL applies to versions of the Autoconf
# Macro released by the Autoconf Archive. When you make and distribute a
# modified version of the Autoconf Macro, you may extend this special
# exception to the GPL to apply to your modified version as well.
#serial 15
AU_ALIAS([MP_WITH_CURSES], [AX_WITH_CURSES])
AC_DEFUN([AX_WITH_CURSES], [
AC_ARG_VAR([CURSES_LIB], [linker library for Curses, e.g. -lcurses])
AC_ARG_WITH([ncurses], [AS_HELP_STRING([--with-ncurses],
[force the use of Ncurses or NcursesW])],
[], [with_ncurses=check])
AC_ARG_WITH([ncursesw], [AS_HELP_STRING([--without-ncursesw],
[do not use NcursesW (wide character support)])],
[], [with_ncursesw=check])
ax_saved_LIBS=$LIBS
AS_IF([test "x$with_ncurses" = xyes || test "x$with_ncursesw" = xyes],
[ax_with_plaincurses=no], [ax_with_plaincurses=check])
ax_cv_curses_which=no
# Test for NcursesW
AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncursesw" != xno], [
LIBS="$ax_saved_LIBS -lncursesw"
AC_CACHE_CHECK([for NcursesW wide-character library], [ax_cv_ncursesw], [
AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])],
[ax_cv_ncursesw=yes], [ax_cv_ncursesw=no])
])
AS_IF([test "x$ax_cv_ncursesw" = xno && test "x$with_ncursesw" = xyes], [
AC_MSG_ERROR([--with-ncursesw specified but could not find NcursesW library])
])
AS_IF([test "x$ax_cv_ncursesw" = xyes], [
ax_cv_curses=yes
ax_cv_curses_which=ncursesw
CURSES_LIB="-lncursesw"
AC_DEFINE([HAVE_NCURSESW], [1], [Define to 1 if the NcursesW library is present])
AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present])
AC_CACHE_CHECK([for working ncursesw/curses.h], [ax_cv_header_ncursesw_curses_h], [
AC_LINK_IFELSE([AC_LANG_PROGRAM([[
@%:@define _XOPEN_SOURCE_EXTENDED 1
@%:@include <ncursesw/curses.h>
]], [[
chtype a = A_BOLD;
int b = KEY_LEFT;
chtype c = COLOR_PAIR(1) & A_COLOR;
attr_t d = WA_NORMAL;
cchar_t e;
wint_t f;
int g = getattrs(stdscr);
int h = getcurx(stdscr) + getmaxx(stdscr);
initscr();
init_pair(1, COLOR_WHITE, COLOR_RED);
wattr_set(stdscr, d, 0, NULL);
wget_wch(stdscr, &f);
]])],
[ax_cv_header_ncursesw_curses_h=yes],
[ax_cv_header_ncursesw_curses_h=no])
])
AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xyes], [
ax_cv_curses_enhanced=yes
ax_cv_curses_color=yes
ax_cv_curses_obsolete=yes
AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
AC_DEFINE([HAVE_NCURSESW_CURSES_H], [1], [Define to 1 if <ncursesw/curses.h> is present])
])
AC_CACHE_CHECK([for working ncursesw.h], [ax_cv_header_ncursesw_h], [
AC_LINK_IFELSE([AC_LANG_PROGRAM([[
@%:@define _XOPEN_SOURCE_EXTENDED 1
@%:@include <ncursesw.h>
]], [[
chtype a = A_BOLD;
int b = KEY_LEFT;
chtype c = COLOR_PAIR(1) & A_COLOR;
attr_t d = WA_NORMAL;
cchar_t e;
wint_t f;
int g = getattrs(stdscr);
int h = getcurx(stdscr) + getmaxx(stdscr);
initscr();
init_pair(1, COLOR_WHITE, COLOR_RED);
wattr_set(stdscr, d, 0, NULL);
wget_wch(stdscr, &f);
]])],
[ax_cv_header_ncursesw_h=yes],
[ax_cv_header_ncursesw_h=no])
])
AS_IF([test "x$ax_cv_header_ncursesw_h" = xyes], [
ax_cv_curses_enhanced=yes
ax_cv_curses_color=yes
ax_cv_curses_obsolete=yes
AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
AC_DEFINE([HAVE_NCURSESW_H], [1], [Define to 1 if <ncursesw.h> is present])
])
AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h_with_ncursesw], [
AC_LINK_IFELSE([AC_LANG_PROGRAM([[
@%:@define _XOPEN_SOURCE_EXTENDED 1
@%:@include <ncurses.h>
]], [[
chtype a = A_BOLD;
int b = KEY_LEFT;
chtype c = COLOR_PAIR(1) & A_COLOR;
attr_t d = WA_NORMAL;
cchar_t e;
wint_t f;
int g = getattrs(stdscr);
int h = getcurx(stdscr) + getmaxx(stdscr);
initscr();
init_pair(1, COLOR_WHITE, COLOR_RED);
wattr_set(stdscr, d, 0, NULL);
wget_wch(stdscr, &f);
]])],
[ax_cv_header_ncurses_h_with_ncursesw=yes],
[ax_cv_header_ncurses_h_with_ncursesw=no])
])
AS_IF([test "x$ax_cv_header_ncurses_h_with_ncursesw" = xyes], [
ax_cv_curses_enhanced=yes
ax_cv_curses_color=yes
ax_cv_curses_obsolete=yes
AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present])
])
AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xno && test "x$ax_cv_header_ncursesw_h" = xno && test "x$ax_cv_header_ncurses_h_with_ncursesw" = xno], [
AC_MSG_WARN([could not find a working ncursesw/curses.h, ncursesw.h or ncurses.h])
])
])
])
# Test for Ncurses
AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncurses" != xno && test "x$ax_cv_curses_which" = xno], [
LIBS="$ax_saved_LIBS -lncurses"
AC_CACHE_CHECK([for Ncurses library], [ax_cv_ncurses], [
AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])],
[ax_cv_ncurses=yes], [ax_cv_ncurses=no])
])
AS_IF([test "x$ax_cv_ncurses" = xno && test "x$with_ncurses" = xyes], [
AC_MSG_ERROR([--with-ncurses specified but could not find Ncurses library])
])
AS_IF([test "x$ax_cv_ncurses" = xyes], [
ax_cv_curses=yes
ax_cv_curses_which=ncurses
CURSES_LIB="-lncurses"
AC_DEFINE([HAVE_NCURSES], [1], [Define to 1 if the Ncurses library is present])
AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present])
AC_CACHE_CHECK([for working ncurses/curses.h], [ax_cv_header_ncurses_curses_h], [
AC_LINK_IFELSE([AC_LANG_PROGRAM([[
@%:@include <ncurses/curses.h>
]], [[
chtype a = A_BOLD;
int b = KEY_LEFT;
chtype c = COLOR_PAIR(1) & A_COLOR;
int g = getattrs(stdscr);
int h = getcurx(stdscr) + getmaxx(stdscr);
initscr();
init_pair(1, COLOR_WHITE, COLOR_RED);
]])],
[ax_cv_header_ncurses_curses_h=yes],
[ax_cv_header_ncurses_curses_h=no])
])
AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xyes], [
ax_cv_curses_color=yes
ax_cv_curses_obsolete=yes
AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
AC_DEFINE([HAVE_NCURSES_CURSES_H], [1], [Define to 1 if <ncurses/curses.h> is present])
])
AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h], [
AC_LINK_IFELSE([AC_LANG_PROGRAM([[
@%:@include <ncurses.h>
]], [[
chtype a = A_BOLD;
int b = KEY_LEFT;
chtype c = COLOR_PAIR(1) & A_COLOR;
int g = getattrs(stdscr);
int h = getcurx(stdscr) + getmaxx(stdscr);
initscr();
init_pair(1, COLOR_WHITE, COLOR_RED);
]])],
[ax_cv_header_ncurses_h=yes],
[ax_cv_header_ncurses_h=no])
])
AS_IF([test "x$ax_cv_header_ncurses_h" = xyes], [
ax_cv_curses_color=yes
ax_cv_curses_obsolete=yes
AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present])
])
AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xno && test "x$ax_cv_header_ncurses_h" = xno], [
AC_MSG_WARN([could not find a working ncurses/curses.h or ncurses.h])
])
])
])
# Test for plain Curses (or if CURSES_LIB was set by user)
AS_IF([test "x$with_plaincurses" != xno && test "x$ax_cv_curses_which" = xno], [
AS_IF([test "x$CURSES_LIB" != x], [
LIBS="$ax_saved_LIBS $CURSES_LIB"
], [
LIBS="$ax_saved_LIBS -lcurses"
])
AC_CACHE_CHECK([for Curses library], [ax_cv_plaincurses], [
AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])],
[ax_cv_plaincurses=yes], [ax_cv_plaincurses=no])
])
AS_IF([test "x$ax_cv_plaincurses" = xyes], [
ax_cv_curses=yes
ax_cv_curses_which=plaincurses
AS_IF([test "x$CURSES_LIB" = x], [
CURSES_LIB="-lcurses"
])
AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present])
# Check for base conformance (and header file)
AC_CACHE_CHECK([for working curses.h], [ax_cv_header_curses_h], [
AC_LINK_IFELSE([AC_LANG_PROGRAM([[
@%:@include <curses.h>
]], [[
chtype a = A_BOLD;
int b = KEY_LEFT;
initscr();
]])],
[ax_cv_header_curses_h=yes],
[ax_cv_header_curses_h=no])
])
AS_IF([test "x$ax_cv_header_curses_h" = xyes], [
AC_DEFINE([HAVE_CURSES_H], [1], [Define to 1 if <curses.h> is present])
# Check for X/Open Enhanced conformance
AC_CACHE_CHECK([for X/Open Enhanced Curses conformance], [ax_cv_plaincurses_enhanced], [
AC_LINK_IFELSE([AC_LANG_PROGRAM([[
@%:@define _XOPEN_SOURCE_EXTENDED 1
@%:@include <curses.h>
@%:@ifndef _XOPEN_CURSES
@%:@error "this Curses library is not enhanced"
"this Curses library is not enhanced"
@%:@endif
]], [[
chtype a = A_BOLD;
int b = KEY_LEFT;
chtype c = COLOR_PAIR(1) & A_COLOR;
attr_t d = WA_NORMAL;
cchar_t e;
wint_t f;
initscr();
init_pair(1, COLOR_WHITE, COLOR_RED);
wattr_set(stdscr, d, 0, NULL);
wget_wch(stdscr, &f);
]])],
[ax_cv_plaincurses_enhanced=yes],
[ax_cv_plaincurses_enhanced=no])
])
AS_IF([test "x$ax_cv_plaincurses_enhanced" = xyes], [
ax_cv_curses_enhanced=yes
ax_cv_curses_color=yes
AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
])
# Check for color functions
AC_CACHE_CHECK([for Curses color functions], [ax_cv_plaincurses_color], [
AC_LINK_IFELSE([AC_LANG_PROGRAM([[
@%:@define _XOPEN_SOURCE_EXTENDED 1
@%:@include <curses.h>
]], [[
chtype a = A_BOLD;
int b = KEY_LEFT;
chtype c = COLOR_PAIR(1) & A_COLOR;
initscr();
init_pair(1, COLOR_WHITE, COLOR_RED);
]])],
[ax_cv_plaincurses_color=yes],
[ax_cv_plaincurses_color=no])
])
AS_IF([test "x$ax_cv_plaincurses_color" = xyes], [
ax_cv_curses_color=yes
AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
])
# Check for obsolete functions
AC_CACHE_CHECK([for obsolete Curses functions], [ax_cv_plaincurses_obsolete], [
AC_LINK_IFELSE([AC_LANG_PROGRAM([[
@%:@include <curses.h>
]], [[
chtype a = A_BOLD;
int b = KEY_LEFT;
int g = getattrs(stdscr);
int h = getcurx(stdscr) + getmaxx(stdscr);
initscr();
]])],
[ax_cv_plaincurses_obsolete=yes],
[ax_cv_plaincurses_obsolete=no])
])
AS_IF([test "x$ax_cv_plaincurses_obsolete" = xyes], [
ax_cv_curses_obsolete=yes
AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
])
])
AS_IF([test "x$ax_cv_header_curses_h" = xno], [
AC_MSG_WARN([could not find a working curses.h])
])
])
])
AS_IF([test "x$ax_cv_curses" != xyes], [ax_cv_curses=no])
AS_IF([test "x$ax_cv_curses_enhanced" != xyes], [ax_cv_curses_enhanced=no])
AS_IF([test "x$ax_cv_curses_color" != xyes], [ax_cv_curses_color=no])
AS_IF([test "x$ax_cv_curses_obsolete" != xyes], [ax_cv_curses_obsolete=no])
LIBS=$ax_saved_LIBS
])dnl

140
biology/samtools/files/ax_with_htslib.m4
View file

@ -1,140 +0,0 @@
# ===========================================================================
# http://www.gnu.org/software/autoconf-archive/ax_with_htslib.html
# ===========================================================================
#
# SYNOPSIS
#
# AX_WITH_HTSLIB
#
# DESCRIPTION
#
# This macro checks whether HTSlib <http://www.htslib.org/> is installed
# or nearby, and adds a --with-htslib=DIR option to the configure script
# for specifying the location. It locates either an installation prefix
# (with 'include' and 'lib' subdirectories) or an HTSlib source tree, as
# HTSlib is fast-moving and users may wish to use an in-development tree.
#
# Different checks occur depending on the --with-htslib argument given:
#
# With --with-htslib=DIR, checks whether DIR is a source tree or contains
# a working installation.
# By default, searches for a source tree (with a name matching htslib*)
# within or alongside $srcdir. Produces AC_MSG_ERROR if there are
# several equally-likely candidates. If there are none, checks for
# a working default installation.
# With --with-htslib=system, checks for a working default installation.
#
# If a source tree is found or specified, it is added to AC_CONFIG_SUBDIRS
# (which unfortunately may cause a "you should use literals" warning when
# autoconf is run).
#
# The following output variables are set by this macro:
#
# HTSDIR Directory containing HTSlib source tree
# HTSLIB_CPPFLAGS Preprocessor flags for compiling with HTSlib
# HTSLIB_LDFLAGS Linker flags for linking with HTSlib
#
# The following shell variables may be defined:
#
# ax_cv_htslib Set to "yes" if HTSlib was found
# ax_cv_htslib_which Set to "source", "install", or "none"
#
# LICENSE
#
# Copyright (C) 2015 Genome Research Ltd
#
# Copying and distribution of this file, with or without modification, are
# permitted in any medium without royalty provided the copyright notice
# and this notice are preserved. This file is offered as-is, without any
# warranty.
#serial 1
AC_DEFUN([AX_WITH_HTSLIB],
[AC_ARG_WITH([htslib],
[AS_HELP_STRING([--with-htslib=DIR],
[use the HTSlib source tree or installation in DIR])
dnl Not indented, to avoid extra whitespace outwith AS_HELP_STRING()
AS_HELP_STRING([--with-htslib=system],
[use only a system HTSlib installation])],
[], [with_htslib=search])
case $with_htslib in
yes|search)
AC_MSG_CHECKING([location of HTSlib source tree])
case $srcdir in
.) srcp= ;;
*) srcp=$srcdir/ ;;
esac
found=
for dir in ${srcp}htslib* -- ${srcp}../htslib -- ${srcp}../htslib*
do
if test "$dir" = "--"; then
test -n "$found" && break
elif test -f "$dir/hts.c" && test -f "$dir/htslib/hts.h"; then
found="${found}1"
HTSDIR=$dir
fi
done
if test -z "$found"; then
AC_MSG_RESULT([none found])
ax_cv_htslib_which=system
elif test "$found" = 1; then
AC_MSG_RESULT([$HTSDIR])
ax_cv_htslib_which=source
else
AC_MSG_RESULT([several directories found])
AC_MSG_ERROR([use --with-htslib=DIR to select which HTSlib to use])
fi
;;
no) ax_cv_htslib_which=none ;;
system) ax_cv_htslib_which=system ;;
*)
HTSDIR=$with_htslib
if test -f "$HTSDIR/hts.c" && test -f "$HTSDIR/htslib/hts.h"; then
ax_cv_htslib_which=source
else
ax_cv_htslib_which=install
fi
;;
esac
case $ax_cv_htslib_which in
#source)
# ax_cv_htslib=yes
# HTSLIB_CPPFLAGS="-I$HTSDIR"
# HTSLIB_LDFLAGS="-L$HTSDIR"
# # We can't use a literal, because $HTSDIR is user-provided and variable
# AC_CONFIG_SUBDIRS($HTSDIR)
# ;;
system)
AC_CHECK_HEADER([htslib/sam.h],
[AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])],
[ax_cv_htslib=no], [;])
ax_cv_htslib_which=install
HTSDIR=
HTSLIB_CPPFLAGS=
HTSLIB_LDFLAGS=
;;
install)
ax_saved_CPPFLAGS=$CPPFLAGS
ax_saved_LDFLAGS=$LDFLAGS
HTSLIB_CPPFLAGS="-I$HTSDIR/include"
HTSLIB_LDFLAGS="-L$HTSDIR/lib"
CPPFLAGS="$CPPFLAGS $HTSLIB_CPPFLAGS"
LDFLAGS="$LDFLAGS $HTSLIB_LDFLAGS"
AC_CHECK_HEADER([htslib/sam.h],
[AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])],
[ax_cv_htslib=no], [;])
HTSDIR=
CPPFLAGS=$ax_saved_CPPFLAGS
LDFLAGS=$ax_saved_LDFLAGS
;;
none)
ax_cv_htslib=no
;;
esac
AC_SUBST([HTSDIR])
AC_SUBST([HTSLIB_CPPFLAGS])
AC_SUBST([HTSLIB_LDFLAGS])])

58
biology/samtools/files/patch-Makefile
View file

@ -1,11 +1,11 @@
--- Makefile.orig 2016-04-22 09:22:44 UTC
--- Makefile.orig 2017-09-28 11:12:01 UTC
+++ Makefile
@@ -38,18 +38,18 @@ AOBJS= bam_index.o bam_plcmd.o sam_
@@ -40,23 +40,22 @@ AOBJS= bam_index.o bam_plcmd.o sam_
bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \
bam_quickcheck.o bam_addrprg.o
bam_quickcheck.o bam_addrprg.o bam_markdup.o
-prefix = /usr/local
+prefix = ${STAGEDIR}${PREFIX}
+prefix = ${PREFIX}
exec_prefix = $(prefix)
bindir = $(exec_prefix)/bin
datarootdir = $(prefix)/share
@ -13,46 +13,22 @@
+mandir = $(prefix)/man
man1dir = $(mandir)/man1
-MKDIR_P = mkdir -p
# Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
-misc_bindir = $(bindir)
+misc_bindir = $(bindir)/samtools_misc
MKDIR_P = mkdir -p
-INSTALL = install -p
-INSTALL_PROGRAM = $(INSTALL)
-INSTALL_DATA = $(INSTALL) -m 644
-INSTALL_DIR = $(MKDIR_P) -m 755
+#MKDIR_P = mkdir -p
+#INSTALL = install -p
+#INSTALL_PROGRAM = $(INSTALL)
+#INSTALL_DATA = $(INSTALL) -m 644
+#INSTALL_DIR = $(MKDIR_P) -m 755
-INSTALL_MAN = $(INSTALL_DATA)
-INSTALL_PROGRAM = $(INSTALL)
-INSTALL_SCRIPT = $(INSTALL_PROGRAM)
+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 = samtools
@@ -59,7 +59,6 @@ BUILT_MISC_PROGRAMS = \
misc/md5fa misc/md5sum-lite misc/wgsim
MISC_PROGRAMS = \
- $(BUILT_MISC_PROGRAMS) \
misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \
misc/interpolate_sam.pl misc/novo2sam.pl \
misc/plot-bamstats misc/psl2sam.pl \
@@ -82,7 +81,7 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
# TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally
ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS)
-ALL_LIBS = -lz -ldl $(LIBS)
+ALL_LIBS = -lz $(LIBS)
# Usually config.mk and config.h are generated by running configure
# or config.status, but if those aren't used create defaults here.
@@ -280,8 +279,10 @@ misc/maq2sam-long.o: misc/maq2sam.c conf
install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir)
- $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
+ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir)
+ $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
+ $(INSTALL_PROGRAM) $(BUILT_MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
+ $(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
$(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir)

19
biology/samtools/files/patch-configure.ac
View file

@ -1,19 +0,0 @@
--- configure.ac.orig 2015-12-15 21:26:20 UTC
+++ configure.ac
@@ -23,12 +23,15 @@
# DEALINGS IN THE SOFTWARE.
dnl Process this file with autoconf to produce a configure script
-AC_INIT([Samtools], m4_esyscmd_s([make print-version]),
+AC_INIT([Samtools], [1.3],
[samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])
AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER
AC_CONFIG_SRCDIR([bamtk.c])
AC_CONFIG_HEADERS([config.h])
+m4_include([ax_with_htslib.m4])
+m4_include([ax_with_curses.m4])
+
dnl Copyright notice to be copied into the generated configure script
AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd.

10
biology/samtools/files/patch-dict.c
View file

@ -1,10 +0,0 @@
--- dict.c.orig 2015-12-15 21:26:20 UTC
+++ dict.c
@@ -25,6 +25,7 @@ DEALINGS IN THE SOFTWARE. */
#include <stdio.h>
#include <zlib.h>
#include <getopt.h>
+#include <unistd.h>
#include "htslib/kseq.h"
#include "htslib/hts.h"

16
biology/samtools/files/patch-errmod.c
View file

@ -1,16 +0,0 @@
--- errmod.c.orig 2015-12-15 21:26:20 UTC
+++ errmod.c
@@ -24,6 +24,13 @@ FROM, OUT OF OR IN CONNECTION WITH THE S
DEALINGS IN THE SOFTWARE. */
#include <math.h>
+
+#include <sys/param.h>
+#if defined(__FreeBSD__) && (__FreeBSD_version < 1000034)
+# define logl(x) log(x)
+# define expl(x) exp(x)
+#endif
+
#include "errmod.h"
#include "htslib/ksort.h"
KSORT_INIT_GENERIC(uint16_t)

15
biology/samtools/files/patch-test_test.pl
View file

@ -1,15 +1,6 @@
--- test/test.pl.orig 2015-12-22 22:43:15 UTC
--- test/test.pl.orig 2017-10-18 06:08:39 UTC
+++ test/test.pl
@@ -136,7 +136,7 @@ sub _cmd
else
{
# child
- exec('/bin/bash', '-o','pipefail','-c', "($cmd) 2> $err_filename") or error("Cannot execute the command [/bin/sh -o pipefail -c $cmd]: $!");
+ exec('/usr/local/bin/bash', '-o','pipefail','-c', "($cmd) 2> $err_filename") or error("Cannot execute the command [/usr/local/bin/bash -o pipefail -c $cmd]: $!");
}
}
sub cmd
@@ -560,7 +560,7 @@ sub test_usage
@@ -636,7 +636,7 @@ sub test_usage
my $command = $args{cmd};
my $commandpath = $$opts{bin}."/".$command;
my ($ret,$out,$err) = _cmd("$commandpath $args{redirection}");
@ -18,7 +9,7 @@
my @sections = ($err =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
@@ -615,7 +615,7 @@ sub test_usage_subcommand
@@ -694,7 +694,7 @@ sub test_usage_subcommand
my $commandpath = $$opts{bin}."/".$command;
my ($ret,$out,$err) = _cmd("$commandpath $subcommand $args{redirection}");

2
biology/samtools/files/pkg-message.in
View file

@ -3,5 +3,5 @@ The miscellaneous tools included with Samtools have been installed to
Add that directory to your path if you want to use these tools.
Some of these tools depend on Perl5, and it will need to be installed to
Some of these tools depend on Perl5/Python, and it will need to be installed to
use them.

7
cad/iverilog/Makefile
View file

@ -2,9 +2,9 @@
# $FreeBSD$
PORTNAME= iverilog
PORTVERSION= 10.1.1
PORTVERSION= 10.2
CATEGORIES= cad
MASTER_SITES= ftp://icarus.com/pub/eda/verilog/v${PORTVERSION:C,\.[0-9]\.[0-9]$,,}/
MASTER_SITES= ftp://icarus.com/pub/eda/verilog/v10/
DISTNAME= verilog-${PORTVERSION}
MAINTAINER= zeising@FreeBSD.org
@ -14,8 +14,7 @@ LICENSE= GPLv2
GNU_CONFIGURE= yes
CONFIGURE_ARGS= --disable-suffix
USES= bison gmake
MAKE_JOBS_UNSAFE= yes
USES= bison gmake readline
.include <bsd.port.mk>

6
cad/iverilog/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1464367614
SHA256 (verilog-10.1.1.tar.gz) = fdaa75dfe7c58cbc471fc12710ee49b3f32fd6cc055d9181b5190cbcbbd6cada
SIZE (verilog-10.1.1.tar.gz) = 1684925
TIMESTAMP = 1508676832
SHA256 (verilog-10.2.tar.gz) = 96dedbddb12d375edb45a144a926a3ba1e3e138d6598b18e7d79f2ae6de9e500
SIZE (verilog-10.2.tar.gz) = 1695227

10
cad/iverilog/files/patch-load_module.cc
View file

@ -1,10 +0,0 @@
--- load_module.cc.orig 2015-08-23 21:41:41 UTC
+++ load_module.cc
@@ -21,6 +21,7 @@
# include "util.h"
# include "parse_api.h"
# include "compiler.h"
+# include <assert.h>
# include <iostream>
# include <map>
# include <cstdlib>

3
databases/galera/Makefile
View file

@ -2,9 +2,8 @@
# $FreeBSD$
PORTNAME= galera
PORTVERSION?= 25.3.21
PORTVERSION?= 25.3.22
DISTVERSIONPREFIX?= release_
PORTREVISION= 2
CATEGORIES= databases
MAINTAINER= devel@galeracluster.com

6
databases/galera/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1501158019
SHA256 (codership-galera-release_25.3.21_GH0.tar.gz) = dc0d8e9bcbd16de98c3ee558f7e7e2cf4596670a2e2e38a03d3e45bf5c9ebd5e
SIZE (codership-galera-release_25.3.21_GH0.tar.gz) = 3276033
TIMESTAMP = 1508930849
SHA256 (codership-galera-release_25.3.22_GH0.tar.gz) = cf9d13af44411c8e09222554eb7b6dd82896ad4fe8c2cb54066862abbefef8fb
SIZE (codership-galera-release_25.3.22_GH0.tar.gz) = 3278520

115
databases/galera/files/patch-gcomm__src__asio_tcp.cpp
View file

@ -1,115 +0,0 @@
--- gcomm/src/asio_tcp.cpp.orig 2017-01-25 07:55:06 UTC
+++ gcomm/src/asio_tcp.cpp
@@ -231,10 +231,18 @@ void gcomm::AsioTcpSocket::close()
}
}
+// Enable to introduce random errors for write handler
+// #define GCOMM_ASIO_TCP_SIMULATE_WRITE_HANDLER_ERROR
void gcomm::AsioTcpSocket::write_handler(const asio::error_code& ec,
size_t bytes_transferred)
{
+#ifdef GCOMM_ASIO_TCP_SIMULATE_WRITE_HANDLER_ERROR
+ static const long empty_rate(10000);
+ static const long bytes_transferred_less_than_rate(10000);
+ static const long bytes_transferred_not_zero_rate(10000);
+#endif // GCOMM_ASIO_TCP_SIMULATE_WRITE_HANDLER_ERROR
+
Critical<AsioProtonet> crit(net_);
if (state() != S_CONNECTED && state() != S_CLOSING)
@@ -252,34 +260,70 @@ void gcomm::AsioTcpSocket::write_handler
if (!ec)
{
- gcomm_assert(send_q_.empty() == false);
- gcomm_assert(send_q_.front().len() >= bytes_transferred);
-
- while (send_q_.empty() == false &&
- bytes_transferred >= send_q_.front().len())
+ if (send_q_.empty() == true
+#ifdef GCOMM_ASIO_TCP_SIMULATE_WRITE_HANDLER_ERROR
+ || ::rand() % empty_rate == 0
+#endif // GCOMM_ASIO_TCP_SIMULATE_WRITE_HANDLER_ERROR
+ )
{
- const Datagram& dg(send_q_.front());
- bytes_transferred -= dg.len();
- send_q_.pop_front();
+ log_warn << "write_handler() called with empty send_q_. "
+ << "Transport may not be reliable, closing the socket";
+ FAILED_HANDLER(asio::error_code(EPROTO,
+ asio::error::system_category));
}
- gcomm_assert(bytes_transferred == 0);
-
- if (send_q_.empty() == false)
+ else if (send_q_.front().len() < bytes_transferred
+#ifdef GCOMM_ASIO_TCP_SIMULATE_WRITE_HANDLER_ERROR
+ || ::rand() % bytes_transferred_less_than_rate == 0
+#endif // GCOMM_ASIO_TCP_SIMULATE_WRITE_HANDLER_ERROR
+ )
{
- const Datagram& dg(send_q_.front());
- boost::array<asio::const_buffer, 2> cbs;
- cbs[0] = asio::const_buffer(dg.header()
- + dg.header_offset(),
- dg.header_len());
- cbs[1] = asio::const_buffer(&dg.payload()[0],
- dg.payload().size());
- write_one(cbs);
+ log_warn << "write_handler() bytes_transferred "
+ << bytes_transferred
+ << " less than sent "
+ << send_q_.front().len()
+ << ". Transport may not be reliable, closing the socket";
+ FAILED_HANDLER(asio::error_code(EPROTO,
+ asio::error::system_category));
}
- else if (state_ == S_CLOSING)
+ else
{
- log_debug << "deferred close of " << id();
- close_socket();
- state_ = S_CLOSED;
+ while (send_q_.empty() == false &&
+ bytes_transferred >= send_q_.front().len())
+ {
+ const Datagram& dg(send_q_.front());
+ bytes_transferred -= dg.len();
+ send_q_.pop_front();
+ }
+ if (bytes_transferred != 0
+#ifdef GCOMM_ASIO_TCP_SIMULATE_WRITE_HANDLER_ERROR
+ || ::rand() % bytes_transferred_not_zero_rate == 0
+#endif // GCOMM_ASIO_TCP_SIMULATE_WRITE_HANDLER_ERROR
+ )
+ {
+ log_warn << "write_handler() bytes_transferred "
+ << bytes_transferred
+ << " after processing the send_q_. "
+ << "Transport may not be reliable, closing the socket";
+ FAILED_HANDLER(asio::error_code(EPROTO,
+ asio::error::system_category));
+ }
+ else if (send_q_.empty() == false)
+ {
+ const Datagram& dg(send_q_.front());
+ boost::array<asio::const_buffer, 2> cbs;
+ cbs[0] = asio::const_buffer(dg.header()
+ + dg.header_offset(),
+ dg.header_len());
+ cbs[1] = asio::const_buffer(&dg.payload()[0],
+ dg.payload().size());
+ write_one(cbs);
+ }
+ else if (state_ == S_CLOSING)
+ {
+ log_debug << "deferred close of " << id();
+ close_socket();
+ state_ = S_CLOSED;
+ }
}
}
else if (state_ == S_CLOSING)

5
databases/mysqlwsrep56-server/Makefile
View file

@ -2,10 +2,9 @@
# $FreeBSD$
PORTNAME= mysqlwsrep
PORTVERSION?= 5.6.36
PORTVERSION?= 5.6.38
DISTVERSIONPREFIX?= wsrep_
DISTVERSIONSUFFIX?= -25.20
PORTREVISION?= 2
DISTVERSIONSUFFIX?= -25.21
CATEGORIES= databases ipv6
PKGNAMESUFFIX= 56-server

6
databases/mysqlwsrep56-server/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1501158237
SHA256 (codership-mysql-wsrep-wsrep_5.6.36-25.20_GH0.tar.gz) = b40e01d95d8ccc5c23b9f1bf6c43c93776a7f542d57c14da661191b5a656754b
SIZE (codership-mysql-wsrep-wsrep_5.6.36-25.20_GH0.tar.gz) = 32374284
TIMESTAMP = 1508939312
SHA256 (codership-mysql-wsrep-wsrep_5.6.38-25.21_GH0.tar.gz) = 9fcad79b2a8940c5a16077790f2b0eebc9ca5c75679f010cfe78ec6d939e965a
SIZE (codership-mysql-wsrep-wsrep_5.6.38-25.21_GH0.tar.gz) = 32414996

2
devel/kf5-extra-cmake-modules/Makefile
View file

@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= extra-cmake-modules
PORTVERSION= ${KDE_FRAMEWORKS_VERSION}
DISTVERSION= ${KDE_FRAMEWORKS_VERSION}
CATEGORIES= devel kde kde-frameworks
MAINTAINER= kde@FreeBSD.org

5
devel/kf5-kapidox/Makefile
View file

@ -2,12 +2,15 @@
# $FreeBSD$
PORTNAME= kapidox
PORTVERSION= ${KDE_FRAMEWORKS_VERSION}
DISTVERSION= ${KDE_FRAMEWORKS_VERSION}
CATEGORIES= devel kde kde-frameworks
MAINTAINER= kde@FreeBSD.org
COMMENT= KF5 API Documentation Tools
LICENSE= BSD2CLAUSE
LICENSE_FILE= ${WRKSRC}/LICENSE
USES= cmake:outsource kde:5 python tar:xz
USE_KDE= archive ecm
USE_QT5= buildtools_build qmake_build

6
devel/kf5-kconfig/Makefile
View file

@ -2,12 +2,16 @@
# $FreeBSD$
PORTNAME= kconfig
PORTVERSION= ${KDE_FRAMEWORKS_VERSION}
DISTVERSION= ${KDE_FRAMEWORKS_VERSION}
CATEGORIES= devel kde kde-frameworks
MAINTAINER= kde@FreeBSD.org
COMMENT= KF5 widgets for configuration dialogs
# Sources say LGPL20+, KDE policy says LGPL21+, license file is LGPL21
LICENSE= LGPL21+
LICENSE_FILE= ${WRKSRC}/COPYING.LIB
USES= cmake:outsource compiler:c++11-lib kde:5 tar:xz
USE_KDE= ecm
USE_QT5= buildtools_build concurrent core gui linguisttools \

7
devel/kf5-kcoreaddons/Makefile
View file

@ -2,12 +2,17 @@
# $FreeBSD$
PORTNAME= kcoreaddons
PORTVERSION= ${KDE_FRAMEWORKS_VERSION}
DISTVERSION= ${KDE_FRAMEWORKS_VERSION}
CATEGORIES= devel kde kde-frameworks
MAINTAINER= kde@FreeBSD.org
COMMENT= KF5 addons to QtCore
LICENSE= LGPL21+ BSD3CLAUSE
LICENSE_COMB= multi
LICENSE_FILE_LGPL21+= ${WRKSRC}/COPYING.LIB
LICENSE_FILE_BSD3CLAUSE= ${WRKSRC}/COPYING-CMAKE-SCRIPTS
USES= cmake:outsource compiler:c++11-lib kde:5 shared-mime-info tar:xz
USE_KDE= ecm
USE_QT5= buildtools_build core linguisttools qmake_build

5
devel/kf5-kdbusaddons/Makefile
View file

@ -2,12 +2,15 @@
# $FreeBSD$
PORTNAME= kdbusaddons
PORTVERSION= ${KDE_FRAMEWORKS_VERSION}
DISTVERSION= ${KDE_FRAMEWORKS_VERSION}
CATEGORIES= devel kde kde-frameworks
MAINTAINER= kde@FreeBSD.org
COMMENT= KF5 addons to QtDBus
LICENSE= LGPL21+
LICENSE_FILE= ${WRKSRC}/COPYING.LIB
USES= cmake:outsource compiler:c++11-lib kde:5 tar:xz
USE_KDE= ecm
USE_QT5= buildtools_build core dbus gui linguisttools \

2
devel/py-apscheduler/Makefile
View file

@ -1,7 +1,7 @@
# $FreeBSD$
PORTNAME= apscheduler
PORTVERSION= 3.3.1
PORTVERSION= 3.4.0
CATEGORIES= devel python
MASTER_SITES= CHEESESHOP
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}

6
devel/py-apscheduler/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1482877432
SHA256 (APScheduler-3.3.1.tar.gz) = f68874dff1bdffcc6ce3adb7840c1e4d162c609a3e3f831351df30b75732767b
SIZE (APScheduler-3.3.1.tar.gz) = 84198
TIMESTAMP = 1508593119
SHA256 (APScheduler-3.4.0.tar.gz) = b51118a8ed014104f7e440456dcbd90f2015aea7bcc34c57e307fb34bc746316
SIZE (APScheduler-3.4.0.tar.gz) = 85878

3
devel/sdl20/Makefile
View file

@ -1,8 +1,7 @@
# $FreeBSD$
PORTNAME= sdl2
PORTVERSION= 2.0.6
PORTREVISION= 1
PORTVERSION= 2.0.7
CATEGORIES= devel
MASTER_SITES= http://www.libsdl.org/release/
DISTNAME= SDL2-${PORTVERSION}

6
devel/sdl20/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1506106261
SHA256 (SDL2-2.0.6.tar.gz) = 03658b5660d16d7b31263a691e058ed37acdab155d68dabbad79998fb552c5df
SIZE (SDL2-2.0.6.tar.gz) = 4420311
TIMESTAMP = 1508786865
SHA256 (SDL2-2.0.7.tar.gz) = ee35c74c4313e2eda104b14b1b86f7db84a04eeab9430d56e001cea268bf4d5e
SIZE (SDL2-2.0.7.tar.gz) = 4432499

31
devel/sdl20/files/patch-src_video_SDL__surface.c
View file

@ -1,31 +0,0 @@
SDL_FreeSurface deallocates surface->map even if the surface is not yet freed
https://bugzilla.libsdl.org/show_bug.cgi?id=3852
Memory leak in SDL_FreeSurface (after bug 3852 fix)
https://bugzilla.libsdl.org/show_bug.cgi?id=3855
--- src/video/SDL_surface.c.orig 2017-09-22 18:51:01 UTC
+++ src/video/SDL_surface.c
@@ -1198,10 +1198,8 @@ SDL_FreeSurface(SDL_Surface * surface)
if (surface->flags & SDL_DONTFREE) {
return;
}
- if (surface->map != NULL) {
- SDL_FreeBlitMap(surface->map);
- surface->map = NULL;
- }
+ SDL_InvalidateMap(surface->map);
+
if (--surface->refcount > 0) {
return;
}
@@ -1219,6 +1217,9 @@ SDL_FreeSurface(SDL_Surface * surface)
if (!(surface->flags & SDL_PREALLOC)) {
SDL_free(surface->pixels);
}
+ if (surface->map) {
+ SDL_FreeBlitMap(surface->map);
+ }
SDL_free(surface);
}

3
devel/sdl20/pkg-plist
View file

@ -60,6 +60,7 @@ include/SDL2/SDL_test_harness.h
include/SDL2/SDL_test_images.h
include/SDL2/SDL_test_log.h
include/SDL2/SDL_test_md5.h
include/SDL2/SDL_test_memory.h
include/SDL2/SDL_test_random.h
include/SDL2/SDL_thread.h
include/SDL2/SDL_timer.h
@ -72,7 +73,7 @@ include/SDL2/begin_code.h
include/SDL2/close_code.h
lib/cmake/SDL2/sdl2-config.cmake
lib/libSDL2-2.0.so.0
lib/libSDL2-2.0.so.0.6.0
lib/libSDL2-2.0.so.0.7.0
lib/libSDL2.a
lib/libSDL2.so
lib/libSDL2_test.a

6
dns/bind9-devel/Makefile
View file

@ -8,7 +8,7 @@ PORTVERSION= ${ISCVERSION:S/-P/P/:S/b/.b/:S/a/.a/:S/rc/.rc/}
PORTREVISION= 0
.else
# dns/bind9xx here
PORTREVISION= 0
PORTREVISION= 1
.endif
CATEGORIES= dns net ipv6
MASTER_SITES= LOCAL/mat/bind
@ -269,8 +269,8 @@ post-install:
${INSTALL_DATA} ${FILESDIR}/empty.db ${STAGEDIR}${ETCDIR}/master
${INSTALL_DATA} ${FILESDIR}/localhost-forward.db ${STAGEDIR}${ETCDIR}/master
${INSTALL_DATA} ${FILESDIR}/localhost-reverse.db ${STAGEDIR}${ETCDIR}/master
${INSTALL_DATA} ${FILESDIR}/BIND.chroot.dist ${STAGEDIR}${PREFIX}/etc/mtree
${INSTALL_DATA} ${FILESDIR}/BIND.chroot.local.dist ${STAGEDIR}${PREFIX}/etc/mtree
${INSTALL_DATA} ${FILESDIR}/BIND.chroot.dist ${STAGEDIR}${PREFIX}/etc/mtree/BIND.chroot.dist.sample
${INSTALL_DATA} ${FILESDIR}/BIND.chroot.local.dist ${STAGEDIR}${PREFIX}/etc/mtree/BIND.chroot.local.dist.sample
${INSTALL_DATA} ${WRKSRC}/bin/rndc/rndc.conf \
${STAGEDIR}${ETCDIR}/rndc.conf.sample

4
dns/bind9-devel/pkg-plist
View file

@ -9,8 +9,8 @@ bin/mdig
bin/named-rrchecker
bin/nslookup
bin/nsupdate
etc/mtree/BIND.chroot.dist
etc/mtree/BIND.chroot.local.dist
@sample etc/mtree/BIND.chroot.dist.sample
@sample etc/mtree/BIND.chroot.local.dist.sample
%%ETCDIR%%/bind.keys
%%ETCDIR%%/master/empty.db
%%ETCDIR%%/master/localhost-forward.db

6
dns/bind910/Makefile
View file

@ -3,7 +3,7 @@
PORTNAME= bind
PORTVERSION= ${ISCVERSION:S/-P/P/:S/b/.b/:S/a/.a/:S/rc/.rc/}
PORTREVISION= 0
PORTREVISION= 1
CATEGORIES= dns net ipv6
MASTER_SITES= ISC/bind9/${ISCVERSION}
PKGNAMESUFFIX= 910
@ -219,8 +219,8 @@ post-install:
${INSTALL_DATA} ${FILESDIR}/empty.db ${STAGEDIR}${ETCDIR}/master
${INSTALL_DATA} ${FILESDIR}/localhost-forward.db ${STAGEDIR}${ETCDIR}/master
${INSTALL_DATA} ${FILESDIR}/localhost-reverse.db ${STAGEDIR}${ETCDIR}/master
${INSTALL_DATA} ${FILESDIR}/BIND.chroot.dist ${STAGEDIR}${PREFIX}/etc/mtree
${INSTALL_DATA} ${FILESDIR}/BIND.chroot.local.dist ${STAGEDIR}${PREFIX}/etc/mtree
${INSTALL_DATA} ${FILESDIR}/BIND.chroot.dist ${STAGEDIR}${PREFIX}/etc/mtree/BIND.chroot.dist.sample
${INSTALL_DATA} ${FILESDIR}/BIND.chroot.local.dist ${STAGEDIR}${PREFIX}/etc/mtree/BIND.chroot.local.dist.sample
${INSTALL_DATA} ${WRKSRC}/bin/rndc/rndc.conf \
${STAGEDIR}${ETCDIR}/rndc.conf.sample

4
dns/bind910/pkg-plist
View file

@ -7,8 +7,8 @@ bin/isc-config.sh
bin/named-rrchecker
bin/nslookup
bin/nsupdate
etc/mtree/BIND.chroot.dist
etc/mtree/BIND.chroot.local.dist
@sample etc/mtree/BIND.chroot.dist.sample
@sample etc/mtree/BIND.chroot.local.dist.sample
%%ETCDIR%%/bind.keys
%%ETCDIR%%/master/empty.db
%%ETCDIR%%/master/localhost-forward.db

6
dns/bind99/Makefile
View file

@ -3,7 +3,7 @@
PORTNAME= bind
PORTVERSION= ${ISCVERSION:S/-P/P/:S/b/.b/:S/a/.a/:S/rc/.rc/}
PORTREVISION= 0
PORTREVISION= 1
CATEGORIES= dns net ipv6
MASTER_SITES= ISC/bind9/${ISCVERSION}
PKGNAMESUFFIX= 99
@ -202,8 +202,8 @@ post-install:
${INSTALL_DATA} ${FILESDIR}/empty.db ${STAGEDIR}${ETCDIR}/master
${INSTALL_DATA} ${FILESDIR}/localhost-forward.db ${STAGEDIR}${ETCDIR}/master
${INSTALL_DATA} ${FILESDIR}/localhost-reverse.db ${STAGEDIR}${ETCDIR}/master
${INSTALL_DATA} ${FILESDIR}/BIND.chroot.dist ${STAGEDIR}${PREFIX}/etc/mtree
${INSTALL_DATA} ${FILESDIR}/BIND.chroot.local.dist ${STAGEDIR}${PREFIX}/etc/mtree
${INSTALL_DATA} ${FILESDIR}/BIND.chroot.dist ${STAGEDIR}${PREFIX}/etc/mtree/BIND.chroot.dist.sample
${INSTALL_DATA} ${FILESDIR}/BIND.chroot.local.dist ${STAGEDIR}${PREFIX}/etc/mtree/BIND.chroot.local.dist.sample
${INSTALL_DATA} ${WRKSRC}/bin/rndc/rndc.conf \
${STAGEDIR}${ETCDIR}/rndc.conf.sample

4
dns/bind99/pkg-plist
View file

@ -5,8 +5,8 @@ bin/host
bin/isc-config.sh
bin/nslookup
bin/nsupdate
etc/mtree/BIND.chroot.dist
etc/mtree/BIND.chroot.local.dist
@sample etc/mtree/BIND.chroot.dist.sample
@sample etc/mtree/BIND.chroot.local.dist.sample
%%ETCDIR%%/bind.keys
%%ETCDIR%%/master/empty.db
%%ETCDIR%%/master/localhost-forward.db

2
emulators/fuse/Makefile
View file

@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= fuse
PORTVERSION= 1.4.0
PORTVERSION= 1.4.1
CATEGORIES= emulators
MASTER_SITES= SF/${PORTNAME}-emulator/${PORTNAME}/${PORTVERSION}

6
emulators/fuse/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1505558455
SHA256 (fuse-1.4.0.tar.gz) = 75ac811534c7e352f238b1959a7f6478661bc4103f96dd1166ec395ad7523d97
SIZE (fuse-1.4.0.tar.gz) = 1652821
TIMESTAMP = 1508788895
SHA256 (fuse-1.4.1.tar.gz) = 817d57db6da95a411b5b44ccae2a00fff332b251b502957a8a886d794d475aa3
SIZE (fuse-1.4.1.tar.gz) = 1654522

2
emulators/libspectrum/Makefile
View file

@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= libspectrum
PORTVERSION= 1.4.0
PORTVERSION= 1.4.1
CATEGORIES= emulators devel
MASTER_SITES= SF/fuse-emulator/${PORTNAME}/${PORTVERSION}

6
emulators/libspectrum/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1505638448
SHA256 (libspectrum-1.4.0.tar.gz) = 6207d60e259fac2c2074b2149ff64914d656b658fb002d002a2be30bf0e6185f
SIZE (libspectrum-1.4.0.tar.gz) = 514972
TIMESTAMP = 1508788575
SHA256 (libspectrum-1.4.1.tar.gz) = 025a1663491cc58174e91df77d82b28782310f6831485cb14291ce774f23c729
SIZE (libspectrum-1.4.1.tar.gz) = 516697

2
emulators/libspectrum/pkg-plist
View file

@ -2,7 +2,7 @@ include/libspectrum.h
lib/libspectrum.a
lib/libspectrum.so
lib/libspectrum.so.8
lib/libspectrum.so.8.7.10
lib/libspectrum.so.8.7.11
libdata/pkgconfig/libspectrum.pc
man/man3/libspectrum.3.gz
%%PORTDOCS%%%%DOCSDIR%%/AUTHORS

2
emulators/virtualbox-ose-kmod/Makefile
View file

@ -3,6 +3,7 @@
PORTNAME= virtualbox-ose
PORTVERSION= 5.2.0
PORTREVISION= 1
CATEGORIES= emulators
MASTER_SITES= http://download.virtualbox.org/virtualbox/${PORTVERSION}/
PKGNAMESUFFIX= -kmod
@ -41,6 +42,7 @@ CONFLICTS_INSTALL= virtualbox-ose-kmod-devel-* \
virtualbox-ose-kmod-legacy-*
OPTIONS_DEFINE= DEBUG VIMAGE
OPTIONS_DEFAULT=VIMAGE
OPTIONS_SUB= yes
DEBUG_DESC= Debug symbols, additional logs and assertions
VIMAGE_DESC= VIMAGE virtual networking support

4
emulators/virtualbox-ose/Makefile
View file

@ -3,6 +3,7 @@
PORTNAME= virtualbox-ose
PORTVERSION= 5.2.0
PORTREVISION= 1
CATEGORIES= emulators
MASTER_SITES= http://download.virtualbox.org/virtualbox/${PORTVERSION}/
DISTFILES= VirtualBox-${PORTVERSION}${EXTRACT_SUFX} ${GUESTADDITIONS}
@ -30,7 +31,7 @@ CPE_PRODUCT= vm_virtualbox
WRKSRC= ${WRKDIR}/VirtualBox-${PORTVERSION}
ONLY_FOR_ARCHS= i386 amd64
USES= compiler:c++11-lang cpe iconv pkgconfig ssl tar:bzip2
USES= compiler:c++14-lang cpe iconv pkgconfig ssl tar:bzip2
USE_GNOME= libidl libxml2
HAS_CONFIGURE= yes
@ -276,7 +277,6 @@ post-patch:
${WRKSRC}/LocalConfig.kmk
@${ECHO} 'VBOX_GCC_PEDANTIC_CXX = -Wshadow $$(VBOX_GCC_WARN) -Wno-long-long' >> \
${WRKSRC}/LocalConfig.kmk
@${ECHO} 'VBOX_GCC_std = -std=c++11' >> ${WRKSRC}/LocalConfig.kmk
.endif
.if ${COMPILER_TYPE} == clang
@${REINPLACE_CMD} -e 's| -finline-limit=8000||' \

10
emulators/virtualbox-ose/files/patch-src_VBox_Debugger_Makefile.kmk Normal file
View file

@ -0,0 +1,10 @@
--- src/VBox/Debugger/Makefile.kmk.orig 2017-10-18 07:09:03 UTC
+++ src/VBox/Debugger/Makefile.kmk
@@ -109,6 +109,7 @@ VBoxDbg_SOURCES = \
VBoxDbgBase.cpp \
VBoxDbgConsole.cpp \
VBoxDbgStatsQt.cpp
+VBoxDbg_CXXFLAGS.freebsd += -std=c++11
VBoxDbg_LIBS = \
$(VBOX_LIB_VMM_LAZY)
VBoxDbg_LDFLAGS.darwin = \

18
emulators/virtualbox-ose/files/patch-src_VBox_Frontends_VirtualBox_Makefile.kmk Normal file
View file

@ -0,0 +1,18 @@
--- src/VBox/Frontends/VirtualBox/Makefile.kmk.orig 2017-10-18 07:12:20 UTC
+++ src/VBox/Frontends/VirtualBox/Makefile.kmk
@@ -895,6 +895,7 @@ if defined(VBOX_WITH_VIDEOHWACCEL) || defined(VBOX_GUI
VirtualBox_SOURCES += \
src/VBoxFBOverlay.cpp \
src/VBoxGLSupportInfo.cpp
+ VirtualBox_CXXFLAGS.freebsd += -std=c++11
endif
#
@@ -1217,6 +1218,7 @@ if defined(VBOX_WITH_VIDEOHWACCEL)
VBoxOGL2D_SOURCES = \
src/VBoxGLSupportInfo.cpp
VBoxOGL2D_INCS = include
+ VBoxOGL2D_CXXFLAGS.freebsd += -std=c++11
endif
endif

37
emulators/virtualbox-ose/files/patch-src_VBox_HostServices_SharedClipboard_x11-stub.cpp Normal file
View file

@ -0,0 +1,37 @@
--- src/VBox/HostServices/SharedClipboard/x11-stub.cpp.orig 2017-10-18 07:12:48 UTC
+++ src/VBox/HostServices/SharedClipboard/x11-stub.cpp
@@ -55,7 +55,7 @@ void vboxClipboardDestroy (void)
int vboxClipboardConnect (VBOXCLIPBOARDCLIENTDATA *pClient,
bool fHeadless)
{
- NOREF(pClient, fHeadless);
+ RT_NOREF2(pClient, fHeadless);
LogFlowFunc(("called, returning VINF_SUCCESS.\n"));
return VINF_SUCCESS;
}
@@ -91,7 +91,7 @@ void vboxClipboardDisconnect (VBOXCLIPBOARDCLIENTDATA
void vboxClipboardFormatAnnounce (VBOXCLIPBOARDCLIENTDATA *pClient,
uint32_t u32Formats)
{
- NOREF(pClient, u32Formats);
+ RT_NOREF2(pClient, u32Formats);
LogFlowFunc(("called, returning.\n"));
}
@@ -107,7 +107,7 @@ void vboxClipboardFormatAnnounce (VBOXCLIPBOARDCLIENTD
int vboxClipboardReadData (VBOXCLIPBOARDCLIENTDATA *pClient, uint32_t u32Format,
void *pv, uint32_t cb, uint32_t *pcbActual)
{
- NOREF(pClient, u32Format, pv, cb);
+ RT_NOREF4(pClient, u32Format, pv, cb);
LogFlowFunc(("called, returning VINF_SUCCESS.\n"));
/* No data available. */
*pcbActual = 0;
@@ -125,6 +125,6 @@ int vboxClipboardReadData (VBOXCLIPBOARDCLIENTDATA *pC
void vboxClipboardWriteData (VBOXCLIPBOARDCLIENTDATA *pClient, void *pv,
uint32_t cb, uint32_t u32Format)
{
- NOREF(pClient, pv, cb, u32Format);
+ RT_NOREF4(pClient, pv, cb, u32Format);
LogFlowFunc(("called, returning.\n"));
}

10
emulators/virtualbox-ose/files/patch-src_VBox_HostServices_SharedOpenGL_Makefile.kmk Normal file
View file

@ -0,0 +1,10 @@
--- src/VBox/HostServices/SharedOpenGL/Makefile.kmk.orig 2017-10-18 07:12:48 UTC
+++ src/VBox/HostServices/SharedOpenGL/Makefile.kmk
@@ -436,6 +436,7 @@ if ( defined(VBOX_WITH_QTGUI) \
$(if $(VBOX_WITH_CROGL), VBOX_WITH_CROGL,) \
$(if $(VBOX_WITH_VIDEOHWACCEL), VBOX_WITH_VIDEOHWACCEL,)
ifdef VBOX_WITH_VIDEOHWACCEL
+ VBoxTestOGL_CXXFLAGS.freebsd += -std=c++11
VBoxTestOGL_QT_MODULES += Core Gui OpenGL Widgets
VBoxTestOGL_LIBS.linux += xcb
VBoxTestOGL_LIBS.solaris += xcb

12
lang/erlang-runtime20/Makefile
View file

@ -2,21 +2,24 @@
# $FreeBSD$
PORTNAME= erlang
PORTVERSION= 20.1
PORTVERSION= 20.1.3
CATEGORIES= lang parallel java
MASTER_SITES= http://www.erlang.org/download/:erlangorg \
http://erlang.stacken.kth.se/download/:erlangorg \
http://www.csd.uu.se/ftp/mirror/erlang/download/:erlangorg
http://www.csd.uu.se/ftp/mirror/erlang/download/:erlangorg \
http://olgeni.olgeni.com/~olgeni/distfiles/:local \
LOCAL/olgeni:local
PKGNAMESUFFIX= -runtime20
DISTNAME= otp_src_${ERL_RELEASE}
DISTFILES= ${DISTNAME}${EXTRACT_SUFX}:erlangorg \
${ERLANG_MAN}:erlangorg
${ERLANG_MAN}:erlangorg \
preloaded-${PORTVERSION}${EXTRACT_SUFX}:local
DIST_SUBDIR= erlang
EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX}
PATCH_SITES= http://olgeni.olgeni.com/~olgeni/distfiles/ \
LOCAL/olgeni
PATCHFILES=
PATCHFILES= patch-otp-20.1.1 patch-otp-20.1.2 patch-otp-20.1.3
MAINTAINER= olgeni@FreeBSD.org
COMMENT= Functional programming language from Ericsson
@ -192,6 +195,7 @@ pre-configure:
.if ! ${PORT_OPTIONS:MWX}
echo "disabled by port options" > ${WRKSRC}/lib/wx/SKIP
.endif
cd ${WRKSRC} && ${TAR} --unlink -xzpf ${DISTDIR}/${DIST_SUBDIR}/preloaded-${PORTVERSION}${EXTRACT_SUFX}
post-configure:
.if ${PORT_OPTIONS:MODBC}

10
lang/erlang-runtime20/distinfo
View file

@ -1,7 +1,15 @@
TIMESTAMP = 1506693440
TIMESTAMP = 1508934381
SHA256 (erlang/otp_src_20.1.tar.gz) = 900d35eb563607785a8e27f4b4c03cf6c98b4596028c5d6958569ddde5d4ddbf
SIZE (erlang/otp_src_20.1.tar.gz) = 87342296
SHA256 (erlang/otp_doc_man_20.1.tar.gz) = 05ccf82ff85316e2eb1bebf1a1741dfac1ee450ed49cf0be365f9d4fec6d7b46
SIZE (erlang/otp_doc_man_20.1.tar.gz) = 1334036
SHA256 (erlang/preloaded-20.1.3.tar.gz) = cf16dc6424772116612736bfa023fa11456380f76834b80e14246590300dbffc
SIZE (erlang/preloaded-20.1.3.tar.gz) = 335118
SHA256 (erlang/otp_doc_html_20.1.tar.gz) = 442c9b75a33be685a1af67414cc8758a4ef40e27cdcab9e432d4d9c6f3254dcf
SIZE (erlang/otp_doc_html_20.1.tar.gz) = 33059931
SHA256 (erlang/patch-otp-20.1.1) = 013f887a7773667b07a8bdd60b91df0c259931d54cd1f9e609c2832193c9f329
SIZE (erlang/patch-otp-20.1.1) = 27377
SHA256 (erlang/patch-otp-20.1.2) = df8f2d0cce45e277bc102d625e64ce57f6b0a3be710426570bc5cf837132f82f
SIZE (erlang/patch-otp-20.1.2) = 13450
SHA256 (erlang/patch-otp-20.1.3) = 01452c3b8f24bff90c390e7efdf7830e070dcb0fcb9b11709cee18a689d379ed
SIZE (erlang/patch-otp-20.1.3) = 23545

3
lang/erlang-wx/Makefile
View file

@ -2,6 +2,7 @@
PORTNAME= erlang
PORTVERSION= 19.3.6.2
PORTREVISION= 1
PORTEPOCH= 1
CATEGORIES= lang parallel
MASTER_SITES= http://www.erlang.org/download/:erlangorg \
@ -62,6 +63,8 @@ do-build:
cd ${WRKSRC}/lib/wx && ${GMAKE} ERL_TOP=${WRKSRC} TARGET=${CONFIGURE_TARGET}
${STRIP_CMD} ${WRKSRC}/lib/wx/priv/${CONFIGURE_TARGET}/erl_gl.so
${STRIP_CMD} ${WRKSRC}/lib/wx/priv/${CONFIGURE_TARGET}/wxe_driver.so
${MV} ${WRKSRC}/lib/wx/priv/${CONFIGURE_TARGET}/*.so ${WRKSRC}/lib/wx/priv
${RMDIR} ${WRKSRC}/lib/wx/priv/${CONFIGURE_TARGET}
do-install:
@${MKDIR} ${STAGEDIR}${APP_DIR}

4
lang/erlang-wx/pkg-plist
View file

@ -483,11 +483,11 @@ lib/erlang/lib/wx-%%APP_VERSION%%/ebin/wxe_util.beam
lib/erlang/lib/wx-%%APP_VERSION%%/include/gl.hrl
lib/erlang/lib/wx-%%APP_VERSION%%/include/glu.hrl
lib/erlang/lib/wx-%%APP_VERSION%%/include/wx.hrl
lib/erlang/lib/wx-%%APP_VERSION%%/priv/%%CONFIGURE_TARGET%%/erl_gl.so
lib/erlang/lib/wx-%%APP_VERSION%%/priv/%%CONFIGURE_TARGET%%/wxe_driver.so
lib/erlang/lib/wx-%%APP_VERSION%%/priv/erl_gl.so
lib/erlang/lib/wx-%%APP_VERSION%%/priv/erlang-logo128.png
lib/erlang/lib/wx-%%APP_VERSION%%/priv/erlang-logo32.png
lib/erlang/lib/wx-%%APP_VERSION%%/priv/erlang-logo64.png
lib/erlang/lib/wx-%%APP_VERSION%%/priv/wxe_driver.so
lib/erlang/lib/wx-%%APP_VERSION%%/src/Makefile
lib/erlang/lib/wx-%%APP_VERSION%%/src/gen/gl.erl
lib/erlang/lib/wx-%%APP_VERSION%%/src/gen/glu.erl

9
lang/see/Makefile
View file

@ -13,7 +13,12 @@ MASTER_SITES= http://download.openpkg.org/components/cache/see/ \
MAINTAINER= numisemis@yahoo.com
COMMENT= Simple ECMAScript Engine (SEE)
LICENSE= BSD
LICENSE= BSD3CLAUSE DTOA.C
LICENSE_COMB= multi
LICENSE_NAME_DTOA.C= License of dtoa.c
LICENSE_FILE_BSD3CLAUSE= ${WRKSRC}/COPYING
LICENSE_FILE_DTOA.C= ${WRKSRC}/COPYING
LICENSE_PERMS_DTOA.C= ${_LICENSE_PERMS_DEFAULT}
BROKEN_aarch64= fails to configure: floating point not detected: Exactly one of IEEE_8087, IEEE_MC68k, VAX, or IBM should be defined
BROKEN_armv6= fails to configure: floating point not detected: Exactly one of IEEE_8087, IEEE_MC68k, VAX, or IBM should be defined
@ -25,8 +30,8 @@ DEBUG_DESC= Internal SEE library debugging
CONFLICTS= see-devel-[0-9]*
USE_LDCONFIG= yes
USES= libtool pathfix perl5
USE_LDCONFIG= yes
USE_PERL5= build
GNU_CONFIGURE= yes
INSTALL_TARGET= install-strip

6
lang/see/files/patch-libsee_dtoa.c
View file

@ -1,6 +1,6 @@
--- libsee/dtoa.c.orig 2009-04-26 23:04:58.000000000 +0200
+++ libsee/dtoa.c 2015-03-16 15:46:21.218950229 +0100
@@ -252,6 +252,14 @@
--- libsee/dtoa.c.orig 2009-04-26 21:04:58 UTC
+++ libsee/dtoa.c
@@ -252,6 +252,14 @@ static double private_mem[PRIVATE_mem],
#include "math.h"
#endif

3
math/octave-forge-gsl/Makefile
View file

@ -2,8 +2,7 @@
# $FreeBSD$
PORTNAME= octave-forge-gsl
PORTVERSION= 2.0.0
PORTREVISION= 5
PORTVERSION= 2.1.0
CATEGORIES= math
MAINTAINER= stephen@FreeBSD.org

6
math/octave-forge-gsl/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1480110430
SHA256 (octave-forge/gsl-2.0.0.tar.gz) = 4a93623745024a7617eef435b99a03aaebece3d7967771518197f150746f58b1
SIZE (octave-forge/gsl-2.0.0.tar.gz) = 111757
TIMESTAMP = 1508897264
SHA256 (octave-forge/gsl-2.1.0.tar.gz) = 940142b7d655d9196e1ec5197b4176388c69671e03ba8da717782d9f040fcedb
SIZE (octave-forge/gsl-2.1.0.tar.gz) = 117838

3
math/octave-forge-interval/Makefile
View file

@ -2,8 +2,7 @@
# $FreeBSD$
PORTNAME= octave-forge-interval
PORTVERSION= 2.1.0
PORTREVISION= 1
PORTVERSION= 3.0.0
CATEGORIES= math
MAINTAINER= stephen@FreeBSD.org

6
math/octave-forge-interval/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1497920403
SHA256 (octave-forge/interval-2.1.0.tar.gz) = c2754e4216e768b5f2e76bae34233a9a97cb36b20a7f5f23603b74193947a4b0
SIZE (octave-forge/interval-2.1.0.tar.gz) = 2853637
TIMESTAMP = 1508897358
SHA256 (octave-forge/interval-3.0.0.tar.gz) = 879c3bd443ac9470756cf671118dbf281d84149dfced62d7947074ff3a801a5b
SIZE (octave-forge/interval-3.0.0.tar.gz) = 2835125

3
math/octave-forge-io/Makefile
View file

@ -2,8 +2,7 @@
# $FreeBSD$
PORTNAME= octave-forge-io
PORTVERSION= 2.4.7
PORTREVISION= 1
PORTVERSION= 2.4.8
PORTEPOCH= 1
CATEGORIES= math

6
math/octave-forge-io/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1497927062
SHA256 (octave-forge/io-2.4.7.tar.gz) = 9a926c5eb0ae6e101b1ab999ce9c09d1b4339e1dc578e5ad3f5d760e9787bf9a
SIZE (octave-forge/io-2.4.7.tar.gz) = 207855
TIMESTAMP = 1508892648
SHA256 (octave-forge/io-2.4.8.tar.gz) = 75733f711b8d0e820a13e9ce66020c0c392522f6d0c3fdbb7927848ad500096c
SIZE (octave-forge/io-2.4.8.tar.gz) = 231933

3
math/octave-forge-stk/Makefile
View file

@ -2,8 +2,7 @@
# $FreeBSD$
PORTNAME= octave-forge-stk
PORTVERSION= 2.4.2
PORTREVISION= 1
PORTVERSION= 2.5.0
CATEGORIES= math
MAINTAINER= stephen@FreeBSD.org

6
math/octave-forge-stk/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1497927848
SHA256 (octave-forge/stk-2.4.2.tar.gz) = cef2e4d40012a9fe8ff690efb0b78527eedbe9514e39432e76968875e0d9e874
SIZE (octave-forge/stk-2.4.2.tar.gz) = 315557
TIMESTAMP = 1508897414
SHA256 (octave-forge/stk-2.5.0.tar.gz) = fb189a80bdd34c80cdba75ff52344b80266effa5b67230aae97f34f8479a5b88
SIZE (octave-forge/stk-2.5.0.tar.gz) = 358164

22
misc/mmv/Makefile
View file

@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= mmv
PORTVERSION= 1.01b.15
PORTVERSION= 1.01b.19
CATEGORIES= misc
MASTER_SITES= DEBIAN_POOL
DISTNAME= ${PORTNAME}_1.01b.orig
@ -11,24 +11,26 @@ PATCH_SITES= ${MASTER_SITES}
PATCHFILES= ${PORTNAME}_1.01b-15.diff.gz
PATCH_DIST_STRIP= -p1
MAINTAINER= ports@FreeBSD.org
MAINTAINER= se@FreeBSD.org
COMMENT= Move/Copy/Append/Link multiple files
LICENSE= Freeware
LICENSE_NAME= MMV
LICENSE_FILE= ${PATCHDIR}/LICENSE
LICENSE_PERMS= dist-mirror pkg-mirror auto-accept
CFLAGS+= -DHAS_DIRENT
WRKSRC= ${WRKDIR}/${PORTNAME}-1.01b.orig
do-build:
@(cd ${WRKSRC} ; \
${CC} ${CFLAGS} -o ${PORTNAME} ${PORTNAME}.c ; )
cd ${WRKSRC}; ${CC} ${CFLAGS} -o ${PORTNAME} ${PORTNAME}.c
do-install:
@${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME} \
${STAGEDIR}${PREFIX}/bin/${PORTNAME}
@${INSTALL_MAN} ${WRKSRC}/mmv.1 \
${STAGEDIR}${PREFIX}/man/man1/${PORTNAME}.1
${INSTALL_PROGRAM} ${WRKSRC}/mmv ${STAGEDIR}${PREFIX}/bin/
${INSTALL_MAN} ${WRKSRC}/mmv.1 ${STAGEDIR}${PREFIX}/man/man1/
.for i in mcp mad mln
@${LN} -sf ${PORTNAME} ${STAGEDIR}${PREFIX}/bin/${i}
@${LN} -sf ${PORTNAME}.1 ${STAGEDIR}${PREFIX}/man/man1/${i}.1
${LN} -sf ${PORTNAME} ${STAGEDIR}${PREFIX}/bin/${i}
${LN} -sf ${PORTNAME}.1 ${STAGEDIR}${PREFIX}/man/man1/${i}.1
.endfor
.include <bsd.port.mk>

10
misc/mmv/files/LICENSE Normal file
View file

@ -0,0 +1,10 @@
Copyright (c) 1989 Vladimir Lanin
Mmv is freeware. That means that the entire package of software and
documentation is copyrighted, and may not be distributed with any
modifications or for any charge (without the author's explicit written
permission). Other than that, it may be used and distributed freely.
Vladimir Lanin
330 Wadsworth Ave, Apt 6F
New York, NY 10040

94
misc/mmv/files/patch-mmv.1
View file

@ -1,6 +1,77 @@
--- mmv.1 Thu Oct 5 19:09:58 2006
+++ mmv.1 Thu Oct 5 19:12:46 2006
@@ -345,7 +345,7 @@
--- mmv.1.orig 2017-10-24 14:25:26 UTC
+++ mmv.1
@@ -35,6 +35,43 @@ mmv \- move/copy/append multiple files by wildcard pat
.B mmvpatch
[\fBexecutable\fP]
\}
+.SH "EXAMPLES"
+Rename all
+.I *.jpeg
+files in the current directory to
+\fI*.jpg\fR:
+
+.in +3
+mmv '*.jpeg' '#1.jpg'
+.in -3
+
+Replace the first occurrence of
+.I abc
+with
+.I xyz
+in all files in the current directory:
+
+.in +3
+mmv '*abc*' '#1xyz#2'
+.in -3
+
+Rename files ending in \fI.html.en\fR, \fI.html.de\fR, etc. to ending
+in \fI.en.html\fR, \fI.de.html\fR, etc. in the current directory:
+
+.in +3
+mmv '*.html.??' '#1.#2#3.html'
+.in -3
+
+Rename music files from
+.I <track no.> - <interpreter> - <song title>.ogg
+to
+.I <interpreter> - <track no.> - <song title>.ogg
+in the current directory:
+
+.in +3
+mmv '* - * - *.ogg' '#2 - #1 - #3.ogg'
+.in -3
+
.SH "DESCRIPTION"
.I Mmv
moves (or copies,
@@ -196,8 +233,13 @@ and it applies to all matching files.
Remaining options need not be given separately,
i.e. "mmv \-mk" is allowed.
+\fBWARNING:\fR This operation mode does \fBnot\fR work if the patterns
+itself contain \fBspaces\fR. See
+.I http://bugs.debian.org/149873
+for details.
+
.ce
-Multiple Pattern Pairs
+Multiple Pattern Pairs / Reading Patterns from STDIN
.PP
Multiple
.I from
@@ -240,6 +282,11 @@ would give the error message "a \-> c : no match" beca
(even if it exists)
was already matched by the first pattern pair.
+\fBWARNING:\fR This operation mode does \fBnot\fR work if the patterns
+itself contain \fBspaces\fR. See
+.I http://bugs.debian.org/149873
+for details.
+
.ce
The \fIFrom\fP Pattern
.PP
@@ -350,7 +397,7 @@ pattern is a filename
with embedded
.I wildcard
.IR indexes ,
@ -9,7 +80,7 @@
followed by a string of digits.
When a source file matches a
.I from
@@ -406,7 +406,7 @@
@@ -411,7 +458,7 @@ if "dir2" is indeed a directory, actually move "dir1\*
However, if "dir2\*(SLa" already exists and is itself a directory,
this is considered an error.
.PP
@ -18,7 +89,20 @@
of its special meaning to
.IR mmv ,
as when the actual replacement name must contain the character '#',
@@ -639,6 +639,15 @@
@@ -555,6 +602,12 @@ and will accept pattern pairs with or without the inte
Lines with "(*)" after the target pattern have the effect of enabling \-d
for the files matching this pattern only,
so that such deletions are done silently.
+
+\fBWARNING:\fR This means that \fBunexpected things\fR may happen if
+\fBfiles\fR matched by the patterns contain \fBspaces\fR. See
+.I http://bugs.debian.org/149873
+for details.
+
When feeding
.I mmv
its own output,
@@ -644,6 +697,15 @@ and with status 0 otherwise.
.SH "SEE ALSO"
mv(1), cp(1), ln(1), umask(1)
\}

37
misc/mmv/files/patch-mmv.c
View file

@ -1,6 +1,6 @@
--- mmv.c Thu Oct 5 10:36:36 2006
+++ mmv.c Thu Oct 5 10:38:31 2006
@@ -73,7 +73,8 @@
--- mmv.c.orig 2017-10-24 14:25:26 UTC
+++ mmv.c
@@ -73,7 +73,8 @@ Use -- as the end of options.\n";
%s [-m|x|r|c|o|a|l%s] [-h] [-d|p] [-g|t] [-v|n] [from to]\n\
\n\
Use #[l|u]N in the ``to'' pattern to get the [lowercase|uppercase of the]\n\
@ -10,7 +10,7 @@
\n\
A ``from'' pattern containing wildcards should be quoted when given\n\
on the command line. Also you may need to quote ``to'' pattern.\n\
@@ -976,6 +977,9 @@
@@ -977,6 +978,9 @@ static int parsepat()
lastname = p + 1;
break;
case '#':
@ -20,7 +20,7 @@
c = *(++p);
if (c == 'l' || c == 'u') {
#ifdef IS_MSDOS
@@ -986,8 +990,8 @@
@@ -987,8 +991,8 @@ static int parsepat()
#endif
}
if (!isdigit(c)) {
@ -31,7 +31,7 @@
return(-1);
}
for(x = 0; ;x *= 10) {
@@ -998,8 +1002,8 @@
@@ -999,8 +1003,8 @@ static int parsepat()
p++;
}
if (x < 1 || x > totwilds) {
@ -42,7 +42,7 @@
return(-1);
}
#ifdef IS_MSDOS
@@ -1007,6 +1011,7 @@
@@ -1008,6 +1012,7 @@ static int parsepat()
havedot = 1;
#endif
break;
@ -50,7 +50,19 @@
case ESC:
if ((c = *(++p)) == '\0') {
printf(TRAILESC, from, to, ESC);
@@ -2029,7 +2034,7 @@
@@ -1215,7 +1220,11 @@ static int keepmatch(ffrom, pathend, pk, needslash, di
getstat(pathbuf, ffrom);
if ((ffrom->fi_stflags & FI_ISDIR) ? !dirs : !fils)
#endif
+ {
+ if (verbose)
+ printf("ignoring directory %s\n", ffrom->fi_name);
return(0);
+ }
if (needslash) {
strcpy(pathend + *pk, SLASHSTR);
@@ -2030,7 +2039,7 @@ static void makerep()
repbad = 0;
p = fullrep;
for (pat = to, l = 0; (c = *pat) != '\0'; pat++, l++) {
@ -59,3 +71,12 @@
c = *(++pat);
#ifndef IS_MSDOS
if (c == 'l') {
@@ -2828,7 +2837,7 @@ static int getreply(m, failact)
static FILE *tty = NULL;
int c, r;
- fprintf(stderr, m);
+ fprintf(stderr, "%s", m);
if (tty == NULL && (tty = fopen(TTY, "r")) == NULL) {
fprintf(stderr, "Can not open %s to get reply.\n", TTY);
if (failact == -1)

6
misc/rump/Makefile
View file

@ -24,12 +24,12 @@ USE_LDCONFIG= yes
.include <bsd.port.pre.mk>
.if ${ARCH} == "i386" || ${ARCH} == "amd64"
PLIST_SUB+= X8664=""
PLIST_SUB+= X8664=""
.else
PLIST_SUB+= X8664="@comment "
PLIST_SUB+= X8664="@comment "
.endif
.if ${OSVERSION} >= 1100121
.if ${OSVERSION} >= 1100508
CFLAGS+= -Wno-address-of-packed-member
.endif

2
multimedia/rage/pkg-descr
View file

@ -1,4 +1,4 @@
Rage is a video and audio player written with Enlightenment Foundation
Libraries with some extra bells and whistles.
WWW: http://www.enlightenment.org/
WWW: https://www.enlightenment.org/

2
net-im/py-fbmq/Makefile
View file

@ -1,7 +1,7 @@
# $FreeBSD$
PORTNAME= fbmq
PORTVERSION= 2.3.1
PORTVERSION= 2.3.2
CATEGORIES= net-im devel python
MASTER_SITES= CHEESESHOP
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}

6
net-im/py-fbmq/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1506412442
SHA256 (fbmq-2.3.1.tar.gz) = 1dd8bf49a0d85ea397e4afbc7c0f6fbccaafd49d0c776357bb187430b627b4c4
SIZE (fbmq-2.3.1.tar.gz) = 5818
TIMESTAMP = 1508937681
SHA256 (fbmq-2.3.2.tar.gz) = 680d5cca973657affac562605962f27f3977e13285b663d6632bf8bcb1fc1107
SIZE (fbmq-2.3.2.tar.gz) = 5859

2
net-mgmt/cacti/Makefile
View file

@ -1,7 +1,7 @@
# $FreeBSD$
PORTNAME= cacti
PORTVERSION= 1.1.26
PORTVERSION= 1.1.27
CATEGORIES= net-mgmt www
MASTER_SITES= http://www.cacti.net/downloads/ \
ftp://ftpmirror.uk/freebsd-ports/cacti/

6
net-mgmt/cacti/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1508315864
SHA256 (cacti-1.1.26.tar.gz) = ad94d8b70a34efdc6132bd13706773878c0330be6eb891cf597ea75060627393
SIZE (cacti-1.1.26.tar.gz) = 8940185
TIMESTAMP = 1508833051
SHA256 (cacti-1.1.27.tar.gz) = b4a5aa2a772aff7eb5abae31d07ed86a1c00300094d3c3c63091554fbb0deea9
SIZE (cacti-1.1.27.tar.gz) = 8947294

1
net/Makefile
View file

@ -138,6 +138,7 @@
SUBDIR += exabgp
SUBDIR += exaddos
SUBDIR += fb
SUBDIR += file2pcap
SUBDIR += findmtu
SUBDIR += flower
SUBDIR += flowgrep

31
net/file2pcap/Makefile Normal file
View file

@ -0,0 +1,31 @@
# Created by: Nobutaka Mantani <nobutaka@FreeBSD.org>
# $FreeBSD$
PORTNAME= file2pcap
PORTVERSION= 1.25
CATEGORIES= net
MAINTAINER= nobutaka@FreeBSD.org
COMMENT= Tool to make packet captures containing the content of specified file
LICENSE= GPLv2
LICENSE_FILE= ${WRKSRC}/LICENSE
GH_ACCOUNT= Cisco-Talos
GH_PROJECT= file2pcap
USE_GITHUB= yes
ALL_TARGET= file2pcap
PLIST_FILES= bin/file2pcap
PORTDOCS= Changelog README.md TODO
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/file2pcap ${STAGEDIR}/${PREFIX}/bin
${MKDIR} ${STAGEDIR}/${DOCSDIR}
${INSTALL_DATA} ${WRKSRC}/Changelog ${STAGEDIR}/${DOCSDIR}
${INSTALL_DATA} ${WRKSRC}/README.md ${STAGEDIR}/${DOCSDIR}
${INSTALL_DATA} ${WRKSRC}/TODO ${STAGEDIR}/${DOCSDIR}
.include <bsd.port.mk>

3
net/file2pcap/distinfo Normal file
View file

@ -0,0 +1,3 @@
TIMESTAMP = 1508678999
SHA256 (Cisco-Talos-file2pcap-1.25_GH0.tar.gz) = 77a9cc8e2bf70fb88c140785a3f3f964aba16ed34844d12987a19cabf7b43d48
SIZE (Cisco-Talos-file2pcap-1.25_GH0.tar.gz) = 27561

7
net/file2pcap/files/patch-Makefile Normal file
View file

@ -0,0 +1,7 @@
--- Makefile.orig 2017-10-22 15:06:28 UTC
+++ Makefile
@@ -1,4 +1,3 @@
-CC = gcc

6
net/file2pcap/pkg-descr Normal file
View file

@ -0,0 +1,6 @@
The File2pcap tool allows you to make various types of packet captures
containing the content of any file that you specify.
Supported protocols: HTTP, HTTP/2, SMTP, POP3, IMAP, FTP
WWW: https://github.com/Cisco-Talos/file2pcap

5
ports-mgmt/porttree/Makefile
View file

@ -3,6 +3,7 @@
PORTNAME= porttree
PORTVERSION= 0.3.r${SVN_REV}
PORTREVISION= 1
CATEGORIES= ports-mgmt python
MASTER_SITES= SF
MASTER_SITE_SUBDIR= ${PORTNAME}
@ -12,7 +13,7 @@ COMMENT= Show dependences of FreeBSD port as pseudo graphical tree
LICENSE= MIT
USES= python tar:bzip2
USES= python tar:bzip2 shebangfix
RUN_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}networkx>=1.5:math/py-networkx
@ -26,6 +27,8 @@ NO_BUILD= yes
PLIST_FILES= bin/porttree man/man1/porttree.1.gz
NO_ARCH= yes
SHEBANG_FILES= src/porttree.py
do-install:
${INSTALL_SCRIPT} ${WRKSRC}/src/porttree.py ${STAGEDIR}${PREFIX}/bin/porttree
${INSTALL_MAN} ${WRKSRC}/src/porttree.1 ${STAGEDIR}${MANPREFIX}/man/man1

1
sysutils/Makefile
View file

@ -627,6 +627,7 @@
SUBDIR += minimunin
SUBDIR += minirsyslogd
SUBDIR += mixer
SUBDIR += mkdesktop
SUBDIR += mkfile
SUBDIR += mkfwimage
SUBDIR += mkntpwd

4
sysutils/intel-pcm/Makefile
View file

@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= intel-pcm
PORTVERSION= 201705
PORTVERSION= 201710
CATEGORIES= sysutils
MAINTAINER= imp@FreeBSD.org
@ -18,7 +18,7 @@ ONLY_FOR_ARCHS= i386 amd64
USE_GITHUB= yes
GH_ACCOUNT= opcm
GH_PROJECT= pcm
GH_TAGNAME= 201705
GH_TAGNAME= 201710
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/*.x ${STAGEDIR}${PREFIX}/sbin

6
sysutils/intel-pcm/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1505629521
SHA256 (opcm-pcm-201705_GH0.tar.gz) = ad101e3803def846b0203a481fa73e97451d7b432b90e775f4109815343099b9
SIZE (opcm-pcm-201705_GH0.tar.gz) = 1085327
TIMESTAMP = 1508899852
SHA256 (opcm-pcm-201710_GH0.tar.gz) = 772c7b6310ba9c89931ff6108cc71fa0cbe20540ab6a53503f5f61594c9f661d
SIZE (opcm-pcm-201710_GH0.tar.gz) = 1103994

12
sysutils/intel-pcm/files/patch-cpucounters.cpp
View file

@ -1,12 +0,0 @@
--- cpucounters.cpp.orig 2017-09-17 06:31:28 UTC
+++ cpucounters.cpp
@@ -192,6 +192,9 @@ class InstanceLock (public)
};
#endif // end of _MSC_VER else
+#if defined(__FreeBSD__)
+#define cpu_set_t cpuset_t
+#endif
class TemporalThreadAffinity // speedup trick for Linux, FreeBSD, DragonFlyBSD
{

2
sysutils/intel-pcm/pkg-plist
View file

@ -1,4 +1,6 @@
sbin/pcm-core.x
sbin/pcm-iio.x
sbin/pcm-lspci.x
sbin/pcm-memory.x
sbin/pcm-msr.x
sbin/pcm-numa.x

28
sysutils/mkdesktop/Makefile Normal file
View file

@ -0,0 +1,28 @@
# $FreeBSD$
PORTNAME= mkdesktop
PORTVERSION= 1.6
CATEGORIES= sysutils
MAINTAINER= bourne.identity@hotmail.com
COMMENT= Powerful, flexible utility to setup a FreeBSD desktop
RUN_DEPENDS= pkg>0:ports-mgmt/pkg
USE_GITHUB= yes
GH_ACCOUNT= bourne-again
NO_BUILD= yes
NO_ARCH= yes
DATA1= stage-definitions
DATA2= mkdesktop.help
PLIST_FILES= bin/${PORTNAME} ${DATADIR}/${DATA1} ${DATADIR}/${DATA2}
do-install:
${MKDIR} ${STAGEDIR}${DATADIR}
${INSTALL_DATA} ${WRKSRC}/${DATA1} ${STAGEDIR}${DATADIR}
${INSTALL_DATA} ${WRKSRC}/${DATA2} ${STAGEDIR}${DATADIR}
${INSTALL_SCRIPT} ${WRKSRC}/${PORTNAME} ${STAGEDIR}${PREFIX}/bin
.include <bsd.port.mk>

3
sysutils/mkdesktop/distinfo Normal file
View file

@ -0,0 +1,3 @@
TIMESTAMP = 1508900370
SHA256 (bourne-again-mkdesktop-1.6_GH0.tar.gz) = 11c9af79b78e6b6d9a92b7c2558e01855333b32db8208b12fa75df9f9345051c
SIZE (bourne-again-mkdesktop-1.6_GH0.tar.gz) = 10034

10
sysutils/mkdesktop/pkg-descr Normal file
View file

@ -0,0 +1,10 @@
mkdesktop is a Bourne script that helps to standardize the process of FreeBSD
desktop installation as much as possible per user, with plenty of flexibility as
well as modularity. By default, you get 5 distinct stages for defining your
desktop environment. But you can always add/subtract/customize the stages as
much as you wish. Once you start using mkdesktop, you will pretty soon love it -
particularly its post-processor which automatically kicks in once the stages
have been processed - it sets up emulation layers and configuration of system
files, if the user so desires.
WWW: https://github.com/bourne-again/mkdesktop

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