*/*: sync with upstream

Taken from: HardenedBSD

archivers/py-borgbackup/Makefile

@@ -3,7 +3,7 @@
 
 PORTNAME=	borgbackup
 DISTVERSION=	1.1.5
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	archivers python
 MASTER_SITES=	CHEESESHOP
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -17,7 +17,7 @@ LICENSE_FILE=	${WRKSRC}/LICENSE
 BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}setuptools_scm>=1.7:devel/py-setuptools_scm@${PY_FLAVOR}
 LIB_DEPENDS=	liblz4.so:archivers/liblz4 \
 		libzstd.so:archivers/zstd
-RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}msgpack>=0.4.6:devel/py-msgpack@${PY_FLAVOR}
+RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}msgpack>=0.5.6:devel/py-msgpack@${PY_FLAVOR}
 
 OPTIONS_DEFINE=	FUSE
 FUSE_DESC=	Support to mount locally borg backup files
@@ -28,6 +28,9 @@ FUSE_RUN_DEPENDS=	${PYTHONPREFIX_SITELIBDIR}/llfuse.so:devel/py-llfuse@${PY_FLAV
 USES=		python:3.4+ ssl
 USE_PYTHON=	autoplist distutils
 
+post-patch:
+	@${REINPLACE_CMD} -i '' -e 's|msgpack-python>=0.4.6,<0.5.0|msgpack>=0.5.6|' ${WRKSRC}/setup.py ${WRKSRC}/src/borgbackup.egg-info/requires.txt
+
 post-install:
 	@${FIND} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/borg/ -name "*.so" \
 		-exec ${STRIP_CMD} {} \;

audio/cmus/files/patch-ip_ffmpeg.c

@@ -0,0 +1,15 @@
+https://github.com/cmus/cmus/commit/b595b8cd7fee
+
+--- ip/ffmpeg.c.orig	2016-11-20 12:29:46 UTC
++++ ip/ffmpeg.c
+@@ -252,8 +252,8 @@ static int ffmpeg_open(struct input_plugin_data *ip_da
+ 			break;
+ 		}
+
+-		if (codec->capabilities & CODEC_CAP_TRUNCATED)
+-			cc->flags |= CODEC_FLAG_TRUNCATED;
++		if (codec->capabilities & AV_CODEC_CAP_TRUNCATED)
++			cc->flags |= AV_CODEC_FLAG_TRUNCATED;
+
+ #if (LIBAVCODEC_VERSION_INT < ((53<<16)+(8<<8)+0))
+ 		if (avcodec_open(cc, codec) < 0) {

audio/moc/files/patch-decoder__plugins_ffmpeg_ffmpeg.c

@@ -0,0 +1,32 @@
+ffmpeg.c:996:34: error: use of undeclared identifier 'CODEC_CAP_TRUNCATED'
+        if (data->codec->capabilities & CODEC_CAP_TRUNCATED)
+                                        ^
+ffmpeg.c:997:23: error: use of undeclared identifier 'CODEC_FLAG_TRUNCATED'
+                data->enc->flags |= CODEC_FLAG_TRUNCATED;
+                                    ^
+ffmpeg.c:1028:34: error: use of undeclared identifier 'CODEC_CAP_DELAY'
+        if (data->codec->capabilities & CODEC_CAP_DELAY)
+                                        ^
+
+--- decoder_plugins/ffmpeg/ffmpeg.c.orig	2016-11-16 00:54:37 UTC
++++ decoder_plugins/ffmpeg/ffmpeg.c
+@@ -993,8 +993,8 @@ static void *ffmpeg_open (const char *file)
+ #endif
+
+ 	set_downmixing (data);
+-	if (data->codec->capabilities & CODEC_CAP_TRUNCATED)
+-		data->enc->flags |= CODEC_FLAG_TRUNCATED;
++	if (data->codec->capabilities & AV_CODEC_CAP_TRUNCATED)
++		data->enc->flags |= AV_CODEC_FLAG_TRUNCATED;
+
+ #ifdef HAVE_AVCODEC_OPEN2
+ 	if (avcodec_open2 (data->enc, data->codec, NULL) < 0)
+@@ -1025,7 +1025,7 @@ static void *ffmpeg_open (const char *file)
+
+ 	data->sample_width = sfmt_Bps (data->fmt);
+
+-	if (data->codec->capabilities & CODEC_CAP_DELAY)
++	if (data->codec->capabilities & AV_CODEC_CAP_DELAY)
+ 		data->delay = true;
+ 	data->seek_broken = is_seek_broken (data);
+ 	data->timing_broken = is_timing_broken (data->ic);

audio/pianobar/Makefile

@@ -6,6 +6,9 @@ PORTVERSION=	2017.08.30
 CATEGORIES=	audio
 MASTER_SITES=	https://6xq.net/${PORTNAME}/
 
+PATCH_SITES=	https://github.com/PromyLOPh/${PORTNAME}/commit/
+PATCHFILES=	38b16f9957a7.patch:-p1
+
 MAINTAINER=	[email protected]
 COMMENT=	Command-line Pandora online radio player
 

audio/pianobar/distinfo

@@ -1,3 +1,5 @@
 TIMESTAMP = 1504104262
 SHA256 (pianobar-2017.08.30.tar.bz2) = ec14db6cf1a7dbc1d8190b5ca0d256021e970587bcdaeb23904d4bca71a04674
 SIZE (pianobar-2017.08.30.tar.bz2) = 46664
+SHA256 (38b16f9957a7.patch) = cc90b0f0cd7b02a1a5470af2cb60e5dc6f45bcbc2302faba6502f2f6c9e73bf0
+SIZE (38b16f9957a7.patch) = 1040

biology/Makefile

@@ -128,6 +128,7 @@
     SUBDIR += trimadap
     SUBDIR += trimmomatic
     SUBDIR += ugene
+    SUBDIR += unanimity
     SUBDIR += vcftools
     SUBDIR += vcflib
     SUBDIR += velvet

biology/seaview/Makefile

@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	seaview
-PORTVERSION=	4.6.3
+PORTVERSION=	4.6.5
 PORTEPOCH=	1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/
@@ -14,13 +14,15 @@ COMMENT=	Multiple DNA/protein sequence alignment editor
 LICENSE=	GPLv3
 
 LIB_DEPENDS=	libfltk.so:x11-toolkits/fltk \
+		libfontconfig.so:x11-fonts/fontconfig \
 		libpng.so:graphics/png
 
 PORTSCOUT=	skipv:4.6.1.3
 WRKSRC=		${WRKDIR}/${PORTNAME}
 
-USES=		gmake
-USE_XORG=	xext xft xinerama
+USES=		gmake jpeg
+USE_XORG=	x11 xcursor xext xfixes xft xinerama xrender
+
 MAKE_ENV=	HELPFILE='-DDEFAULT_HELPFILE=\"${DATADIR}/seaview.html\"' \
 		PHYMLNAME='-DPHYMLNAME=\"phyml\"' \
 		IFLTK='-I${LOCALBASE}/include' \

biology/seaview/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1514962318
-SHA256 (seaview_4.6.3.tar.gz) = 36361f0f2950b9ec438823bbd7fc8ae67619837673fe3220b6dca97b7afad1bf
-SIZE (seaview_4.6.3.tar.gz) = 435155
+TIMESTAMP = 1524512448
+SHA256 (seaview_4.6.5.tar.gz) = 9663f4488ac32d8db27922923f525ad7ac8f650d4987e6e874567723f4713164
+SIZE (seaview_4.6.5.tar.gz) = 429108

biology/unanimity/Makefile

@@ -0,0 +1,40 @@
+# $FreeBSD$
+
+PORTNAME=	unanimity
+DISTVERSION=	g20180307
+CATEGORIES=	biology
+
+MAINTAINER=	[email protected]
+COMMENT=	Pacific Biosciences consensus library and applications
+
+LICENSE=	BSD3CLAUSE
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+# Sensitive to dependency versions, use latest commit for everything
+BUILD_DEPENDS=	pbseqan==g20171002:biology/pbseqan \
+		pbbam==g20180416:biology/pbbam \
+		pbcopper==g20180413:biology/pbcopper
+LIB_DEPENDS=	libhts.so:biology/htslib \
+		libboost_regex.so:devel/boost-libs
+
+USES=		cmake pkgconfig python
+USE_GITHUB=	yes
+GH_ACCOUNT=	PacificBiosciences
+GH_TAGNAME=	6f11a13e1472b8c00337ba8c5e94bf83bdab31d6
+
+CMAKE_ARGS+=	-DHTSLIB_INCLUDE_DIRS:STRING=${LOCALBASE}/include/htslib \
+		-DHTSLIB_LIBRARIES:STRING="-L${LOCALBASE}/lib -lhts" \
+		-DPacBioBAM_INCLUDE_DIRS:STRING=${LOCALBASE}/include/pbbam \
+		-DPacBioBAM_LIBRARIES:STRING="-L${LOCALBASE}/lib -lpbbam" \
+		-DSEQAN_INCLUDE_DIRS:STRING=${LOCALBASE}/include/PacBio \
+		-Dpbcopper_INCLUDE_DIRS=${LOCALBASE}/include \
+		-Dpbcopper_LIBRARIES="-L${LOCALBASE}/lib -lpbcopper"
+CFLAGS_i386=	-msse2 -Wno-c++11-narrowing
+
+PLIST_FILES=	bin/arrow bin/ccs bin/gcpp lib/libcc2.a lib/libunanimity.a
+
+post-install:
+	${INSTALL_DATA} ${WRKSRC}/src/libcc2.a ${WRKSRC}/src/libunanimity.a \
+		${STAGEDIR}${PREFIX}/lib
+
+.include <bsd.port.mk>

biology/unanimity/distinfo

@@ -0,0 +1,3 @@
+TIMESTAMP = 1524324354
+SHA256 (PacificBiosciences-unanimity-g20180307-6f11a13e1472b8c00337ba8c5e94bf83bdab31d6_GH0.tar.gz) = 20ed61c46afcfe86403a564136b96f909149208c51fde16f608e924ad4c59e38
+SIZE (PacificBiosciences-unanimity-g20180307-6f11a13e1472b8c00337ba8c5e94bf83bdab31d6_GH0.tar.gz) = 6492231

biology/unanimity/files/patch-CMakeLists.txt

@@ -0,0 +1,11 @@
+--- CMakeLists.txt.orig	2018-03-07 23:10:34 UTC
++++ CMakeLists.txt
+@@ -37,7 +37,7 @@ include(uny-ccache)
+ include(uny-releasewithassert)
+ include(uny-dependencies)
+ include(uny-compilerflags)
+-include(uny-gitsha1)
++# include(uny-gitsha1)
+ include(uny-config)
+
+ # Build library

biology/unanimity/files/patch-cmake_uny-config.cmake

@@ -0,0 +1,10 @@
+--- cmake/uny-config.cmake.orig	2016-09-12 19:55:43 UTC
++++ cmake/uny-config.cmake
+@@ -1,6 +1,6 @@
+ # Config generation
+
+-find_git_sha1(UNANIMITY_GIT_SHA1)
++# find_git_sha1(UNANIMITY_GIT_SHA1)
+
+ file (STRINGS "${UNY_RootDir}/CHANGELOG.md" UNANIMITY_CHANGELOG)
+

biology/unanimity/files/patch-cmake_uny-gitsha1.cmake

@@ -0,0 +1,11 @@
+--- cmake/uny-gitsha1.cmake.orig	2018-03-07 23:10:34 UTC
++++ cmake/uny-gitsha1.cmake
+@@ -7,7 +7,7 @@ set(__find_git_sha1 YES)
+ function(find_git_sha1 _GIT_SHA1)
+     find_package(Git QUIET REQUIRED)
+     execute_process(COMMAND
+-        "${GIT_EXECUTABLE}" "describe" "--always" "--dirty=-dirty"
++        echo 6f11a13e1472b8c00337ba8c5e94bf83bdab31d6
+         WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+         RESULT_VARIABLE res
+         OUTPUT_VARIABLE out

biology/unanimity/files/patch-include_pacbio_genomicconsensus_Input.h

@@ -0,0 +1,16 @@
+--- include/pacbio/genomicconsensus/Input.h.orig	2018-03-07 23:10:34 UTC
++++ include/pacbio/genomicconsensus/Input.h
+@@ -25,7 +25,12 @@ namespace GenomicConsensus {
+ class Input
+ {
+ public:
+-    explicit Input(const Settings& settings) : settings_{settings} {}
++    // Original
++    //explicit Input(const Settings& settings) : settings_{settings} {}
++    // Probably OK
++    //explicit Input(const Settings& settings) { settings_ = settings; }
++    // https://forums.freebsd.org/threads/compile-error-with-clang-3-4.65595/#post-385293
++    explicit Input(const Settings& settings) : settings_(settings) {}
+
+     Input() = delete;
+     Input(const Input&) = delete;

biology/unanimity/files/patch-include_pacbio_genomicconsensus_Output.h

@@ -0,0 +1,19 @@
+--- include/pacbio/genomicconsensus/Output.h.orig	2018-03-07 23:10:34 UTC
++++ include/pacbio/genomicconsensus/Output.h
+@@ -80,8 +80,15 @@ inline void PrintVcfLite(const Variant& 
+         << "\tPASS\n";
+ }
+
+-inline Output::Output(const Settings& settings) : settings_{settings}
++// Original
++//inline Output::Output(const Settings& settings) : settings_{settings}
++// Probably OK patch
++//inline Output::Output(const Settings& settings)
++// https://forums.freebsd.org/threads/compile-error-with-clang-3-4.65595/#post-385293
++inline Output::Output(const Settings& settings) : settings_(settings)
+ {
++    // Probably OK patch
++    //settings_ = settings;
+     // initialize maps
+     PacBio::BAM::FastaSequenceQuery fasta{settings_.referenceFilename};
+     for (const auto& seq : fasta) {

biology/unanimity/files/patch-src_CMakeLists.txt

@@ -0,0 +1,15 @@
+--- src/CMakeLists.txt.orig	2018-03-07 23:10:34 UTC
++++ src/CMakeLists.txt
+@@ -53,11 +53,11 @@ configure_file(
+
+ # includes
+ set(UNY_INCLUDE_DIRS
++    ${SEQAN_INCLUDE_DIRS}
+     ${UNY_IncludeDir}
+     ${CMAKE_BINARY_DIR}/generated
+     ${Boost_INCLUDE_DIRS}
+     ${HTSLIB_INCLUDE_DIRS}
+-    ${SEQAN_INCLUDE_DIRS}
+     ${CPPOPTPARSE_IncludeDir}
+     ${PacBioBAM_INCLUDE_DIRS}
+     ${pbcopper_INCLUDE_DIRS}

biology/unanimity/files/patch-src_Recursor.h

@@ -0,0 +1,12 @@
+# Type mismatch on 11.0 i386
+--- src/Recursor.h.orig	2018-03-07 23:10:34 UTC
++++ src/Recursor.h
+@@ -708,7 +708,7 @@ size_t Recursor<Derived>::FillAlphaBeta(
+     size_t J = tpl.Length();
+     int flipflops = 0;
+     size_t maxSize =
+-        std::max(100ul, static_cast<size_t>(0.5 + REBANDING_THRESHOLD * (I + 1) * (J + 1)));
++        std::max(100ul, static_cast<unsigned long>(0.5 + REBANDING_THRESHOLD * (I + 1) * (J + 1)));
+
+     // if we use too much space, do at least one more round
+     // to take advantage of rebanding

biology/unanimity/pkg-descr

@@ -0,0 +1,8 @@
+Unanimity is a C++ library + applications to generate and process accurate
+consensus sequences from Pacific Biosciences sequence data.
+
+The core binary, CCS (circular consensus calling) takes multiple reads of the
+same SMRTbell sequence and combines them, employing a statistical model, to
+produce one high quality consensus sequence.
+
+WWW: https://github.com/PacificBiosciences/unanimity

cad/Makefile

@@ -4,6 +4,7 @@
     COMMENT = CAD tools
 
     SUBDIR += NASTRAN-95
+    SUBDIR += abc
     SUBDIR += admesh
     SUBDIR += adms
     SUBDIR += alliance

cad/abc/Makefile

@@ -0,0 +1,48 @@
+# $FreeBSD$
+
+PORTNAME=	abc
+DISTVERSION=	g20180420
+CATEGORIES=	cad
+
+MAINTAINER=	[email protected]
+COMMENT=	System for sequential synthesis and verification
+
+LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/copyright.txt
+
+USES=		gmake localbase:ldflags
+USE_GITHUB=	yes
+GH_ACCOUNT=	berkeley-abc
+GH_TAGNAME=	0e15e4d
+USE_LDCONFIG=	yes
+
+MAKE_ENV=	ABC_USE_STDINT_H=1 ABC_MAKE_VERBOSE=1
+CFLAGS+=	-fPIC
+CXXFLAGS+=	-fPIC
+
+PLIST_FILES=	bin/${PORTNAME} lib/lib${PORTNAME}.so
+
+OPTIONS_DEFINE=	DEBUG DOCS READLINE THREADS
+OPTIONS_DEFAULT=	READLINE THREADS
+
+READLINE_USES=	readline
+READLINE_MAKE_ENV=	ABC_READLINE_LIBRARIES="-L${LOCALBASE}/lib -lreadline"
+READLINE_MAKE_ENV_OFF=	ABC_USE_NO_READLINE=1
+
+THREADS_MAKE_ENV_OFF=	ABC_USE_NO_PTHREADS=1
+
+PORTDOCS=	README.md readmeaig
+
+post-build:
+	cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ABC_USE_PIC=1 lib${PORTNAME}.so
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME} ${STAGEDIR}${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/lib${PORTNAME}.so ${STAGEDIR}${PREFIX}/lib
+
+do-install-DOCS-on:
+	@${MKDIR} ${STAGEDIR}${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/README.md ${STAGEDIR}${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/readmeaig ${STAGEDIR}${DOCSDIR}
+
+.include <bsd.port.mk>

cad/abc/distinfo

@@ -0,0 +1,3 @@
+TIMESTAMP = 1524554306
+SHA256 (berkeley-abc-abc-g20180420-0e15e4d_GH0.tar.gz) = ec291913390100d8b91264cba754fdf00274516d5f81d8b6ae2838d4489d0384
+SIZE (berkeley-abc-abc-g20180420-0e15e4d_GH0.tar.gz) = 5591634

cad/abc/files/patch-Makefile

@@ -0,0 +1,18 @@
+--- Makefile.orig	2018-03-30 08:04:05 UTC
++++ Makefile
+@@ -1,6 +1,4 @@
+
+-CC   := gcc
+-CXX  := g++
+ LD   := $(CXX)
+
+ MSG_PREFIX ?=
+@@ -52,8 +50,6 @@ endif
+
+ ARCHFLAGS := $(ARCHFLAGS)
+
+-OPTFLAGS  ?= -g -O
+-
+ CFLAGS    += -Wall -Wno-unused-function -Wno-write-strings -Wno-sign-compare $(ARCHFLAGS)
+ ifneq ($(findstring arm,$(shell uname -m)),)
+ 	CFLAGS += -DABC_MEMALIGN=4

cad/abc/files/patch-src_misc_util_abc__global.h

@@ -0,0 +1,18 @@
+--- src/misc/util/abc_global.h.orig	2018-04-10 14:33:45 UTC
++++ src/misc/util/abc_global.h
+@@ -97,6 +97,15 @@ ABC_NAMESPACE_HEADER_START
+ ////////////////////////////////////////////////////////////////////////
+
+ #ifdef ABC_USE_STDINT_H
++
++#ifndef __STDC_LIMIT_MACROS
++  #define __STDC_LIMIT_MACROS
++#endif
++
++#ifndef __STDC_CONSTANT_MACROS
++  #define __STDC_CONSTANT_MACROS
++#endif
++
+ // If there is stdint.h, assume this is a reasonably-modern platform that
+ // would also have stddef.h and limits.h
+ #include <limits.h>