*/*: sync with upstream

Taken from: FreeBSD

archivers/gtar/Makefile

@@ -36,13 +36,8 @@ NLS_CONFIGURE_ENABLE=	nls
 STATIC_LDFLAGS=	-static
 STATIC_CONFIGURE_ENV=	SHLIBEXT=""
 
-.include <bsd.port.options.mk>
-
-.if ${PORT_OPTIONS:MSTATIC}
-STATIC_ARGS=	build
-.else
-STATIC_ARGS=	lib
-.endif
+STATIC_VARS=	STATIC_ARGS=build
+STATIC_VARS_OFF=	STATIC_ARGS=lib
 
 # Tests 161 163 are known to fail because path resolution of ".."
 # in a removed directory fails.

audio/qmpdclient/Makefile

@@ -32,18 +32,16 @@ DBUS_USE=	QT4=dbus
 
 DEBUG_QMAKE_ON=	CONFIG+=debug
 
-.include  <bsd.port.options.mk>
-
 post-patch:
-.if ! ${PORT_OPTIONS:MNLS}
-	@${REINPLACE_CMD} -e '/INSTALLS += translations/d' \
-		${WRKSRC}/${PORTNAME}.pro
-.endif
 	@${REINPLACE_CMD} -e 's|/usr/local|${PREFIX}|' \
 		-e 's|lupdate|lupdate-qt4|' \
 		-e 's|lrelease|lrelease-qt4|' \
 		${WRKSRC}/${PORTNAME}.pro
 	@${REINPLACE_CMD} -e 's|/usr|${PREFIX}|' \
 		${WRKSRC}/src/notifications_dbus.cpp
 
+post-patch-NLS-off:
+	@${REINPLACE_CMD} -e '/INSTALLS += translations/d' \
+		${WRKSRC}/${PORTNAME}.pro
+
 .include <bsd.port.mk>

benchmarks/Makefile

@@ -70,6 +70,7 @@
     SUBDIR += smhasher
     SUBDIR += spp
     SUBDIR += stream
+    SUBDIR += stress-ng
     SUBDIR += super-smack
     SUBDIR += sysbench
     SUBDIR += tcpblast

benchmarks/stress-ng/Makefile

@@ -0,0 +1,29 @@
+# $FreeBSD$
+
+PORTNAME=	stress-ng
+PORTVERSION=	0.04.20
+CATEGORIES=	benchmarks
+MASTER_SITES=	http://kernel.ubuntu.com/~cking/tarballs/stress-ng/
+
+MAINTAINER=	[email protected]
+COMMENT=	Stress test benchmarks
+
+LICENSE=	GPLv2 # or later
+LICENSE_FILE=	${WRKSRC}/COPYING
+
+ALL_TARGET=	# empty
+
+PLIST_FILES=	bin/stress-ng man/man1/stress-ng.1.gz
+
+.include <bsd.port.pre.mk>
+
+.if ${OSVERSION} < 1000000
+EXTRA_PATCHES+=	${FILESDIR}/extrapatch-stress-cpu.c \
+		${FILESDIR}/extrapatch-Makefile
+.endif
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/stress-ng ${STAGEDIR}${PREFIX}/bin
+	${INSTALL_MAN} ${WRKSRC}/stress-ng.1 ${STAGEDIR}${MANDIRS}/man1
+
+.include <bsd.port.post.mk>

benchmarks/stress-ng/distinfo

@@ -0,0 +1,2 @@
+SHA256 (stress-ng-0.04.20.tar.gz) = 5b00c23325e46236466e598a977c8ebcd4f786cc0c2e15118004a0462bb6f47f
+SIZE (stress-ng-0.04.20.tar.gz) = 236074

benchmarks/stress-ng/files/extrapatch-Makefile

@@ -0,0 +1,11 @@
+--- Makefile.orig	2015-09-25 10:15:45 UTC
++++ Makefile
+@@ -165,7 +165,7 @@ OBJS = $(SRC:.c=.o)
+ 	@$(CC) $(CFLAGS) -c -o $@ $<
+
+ stress-ng: $(OBJS)
+-	$(CC) $(CPPFLAGS) $(CFLAGS) $(OBJS) -lm -pthread -lrt -lcrypt -o $@ $(LDFLAGS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(OBJS) -lm -pthread -lrt -lcrypt -lstdc++ -o $@ $(LDFLAGS)
+
+ stress-cpu.o: stress-cpu.c
+ 	@echo $(CC) $(CFLAGS) -c -o $@ $<

benchmarks/stress-ng/files/extrapatch-stress-cpu.c

@@ -0,0 +1,10 @@
+--- stress-cpu.c.orig	2015-09-18 14:50:12 UTC
++++ stress-cpu.c
+@@ -23,6 +23,7 @@
+  *
+  */
+ #define _GNU_SOURCE
++#define _DECLARE_C99_LDBL_MATH 1
+
+ #include <stdio.h>
+ #include <stdlib.h>

benchmarks/stress-ng/files/patch-stress-cpu.c

@@ -0,0 +1,38 @@
+--- stress-cpu.c.orig	2015-09-18 14:50:12 UTC
++++ stress-cpu.c
+@@ -57,7 +58,6 @@
+ #define	ccosl	ccos
+ #define	csinl	csin
+ #define cpow	pow
+-#define powl	pow
+ #endif
+
+ /*
+@@ -866,6 +866,7 @@ stress_cpu_fp(_Decimal128, decimal128, s
+ /* Append floating point literal specifier to literal value */
+ #define FP(val, ltype)	val ## ltype
+
++#if defined(__STDC_IEC_559_COMPLEX__)
+ /*
+  *  Generic complex stressor macro
+  */
+@@ -891,6 +892,7 @@ static void HOT OPTIMIZE3 stress_cpu_ ##
+ stress_cpu_complex(complex float, f, complex_float, csinf, ccosf)
+ stress_cpu_complex(complex double, , complex_double, csin, ccos)
+ stress_cpu_complex(complex long double, l, complex_long_double, csinl, ccosl)
++#endif /* __STDC_IEC_559_COMPLEX__ */
+
+ #define int_float_ops(_ftype, flt_a, flt_b, flt_c, flt_d,	\
+ 	_sin, _cos, int_a, int_b, _c1, _c2, _c3)		\
+@@ -2058,9 +2060,11 @@ static stress_cpu_stressor_info_t cpu_me
+ 	{ "ackermann",		stress_cpu_ackermann },
+ 	{ "bitops",		stress_cpu_bitops },
+ 	{ "callfunc",		stress_cpu_callfunc },
++#if defined(__STDC_IEC_559_COMPLEX__)
+ 	{ "cdouble",		stress_cpu_complex_double },
+ 	{ "cfloat",		stress_cpu_complex_float },
+ 	{ "clongdouble",	stress_cpu_complex_long_double },
++#endif /* __STDC_IEC_559_COMPLEX__ */
+ 	{ "correlate",		stress_cpu_correlate },
+ 	{ "crc16",		stress_cpu_crc16 },
+ #if defined(STRESS_FLOAT_DECIMAL)

benchmarks/stress-ng/pkg-descr

@@ -0,0 +1,5 @@
+This stress test suite will stress a computer system in various selectable ways
+It was designed to exercise various physical subsystems of a computer as well
+as various operating system kernel interfaces.
+
+WWW: http://kernel.ubuntu.com/~cking/stress-ng/

biology/Makefile

@@ -11,7 +11,9 @@
     SUBDIR += biococoa
     SUBDIR += biojava
     SUBDIR += blat
+    SUBDIR += bwa
     SUBDIR += cd-hit
+    SUBDIR += cdbfasta
     SUBDIR += chemeq
     SUBDIR += clustalw
     SUBDIR += consed
@@ -20,6 +22,9 @@
     SUBDIR += fasta
     SUBDIR += fasta3
     SUBDIR += fastdnaml
+    SUBDIR += fastool
+    SUBDIR += fasttree
+    SUBDIR += fastx-toolkit
     SUBDIR += fluctuate
     SUBDIR += garlic
     SUBDIR += gff2ps
@@ -32,6 +37,7 @@
     SUBDIR += jalview
     SUBDIR += lagan
     SUBDIR += lamarc
+    SUBDIR += libgtextutils
     SUBDIR += libsbml
     SUBDIR += linux-foldingathome
     SUBDIR += mafft

biology/bwa/Makefile

@@ -0,0 +1,28 @@
+# Created by: Jason Bacon <[email protected]>
+# $FreeBSD$
+
+PORTNAME=	bwa
+PORTVERSION=	0.7.9a
+CATEGORIES=	biology
+MASTER_SITES=	SF/bio-bwa/
+
+MAINTAINER=	[email protected]
+COMMENT=	Burrows-Wheeler sequence aligner
+
+LICENSE=	GPLv3
+
+USES=		perl5 shebangfix tar:bzip2
+SHEBANG_FILES=	qualfa2fq.pl xa2multi.pl
+USE_PERL5=	run
+
+PLIST_FILES=	bin/bwa bin/qualfa2fq.pl bin/xa2multi.pl man/man1/bwa.1.gz
+
+# Avoid #error in emmintrin.h
+CFLAGS+=	-msse2
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/bwa ${STAGEDIR}${PREFIX}/bin
+	${INSTALL_SCRIPT} ${WRKSRC}/*.pl ${STAGEDIR}${PREFIX}/bin
+	${INSTALL_MAN} ${WRKSRC}/*.1 ${STAGEDIR}${MAN1PREFIX}/man/man1
+
+.include <bsd.port.mk>

biology/bwa/distinfo

@@ -0,0 +1,2 @@
+SHA256 (bwa-0.7.9a.tar.bz2) = f5ad30e4e5ea86a8dcd6febcb6f620a75c82b03024f64a572017c295a962eadc
+SIZE (bwa-0.7.9a.tar.bz2) = 166193

biology/bwa/files/patch-Makefile

@@ -0,0 +1,11 @@
+--- Makefile.orig	2014-05-19 13:11:41 UTC
++++ Makefile
+@@ -1,6 +1,6 @@
+-CC=			gcc
++CC?=			gcc
+ #CC=			clang --analyze
+-CFLAGS=		-g -Wall -Wno-unused-function -O2
++CFLAGS?=		-g -Wall -Wno-unused-function -O2
+ WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
+ AR=			ar
+ DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)

biology/bwa/files/patch-bwt_lite.c

@@ -0,0 +1,11 @@
+--- bwt_lite.c.orig	2014-05-19 13:11:41 UTC
++++ bwt_lite.c
+@@ -48,7 +48,7 @@ bwtl_t *bwtl_seq2bwtl(int len, const uin
+ 	}
+ 	{ // generate cnt_table
+ 		for (i = 0; i != 256; ++i) {
+-			u_int32_t j, x = 0;
++			uint32_t j, x = 0;
+ 			for (j = 0; j != 4; ++j)
+ 				x |= (((i&3) == j) + ((i>>2&3) == j) + ((i>>4&3) == j) + (i>>6 == j)) << (j<<3);
+ 			b->cnt_table[i] = x;

biology/bwa/files/patch-bwtgap.c

@@ -0,0 +1,11 @@
+--- bwtgap.c.orig	2014-02-25 21:20:01 UTC
++++ bwtgap.c
+@@ -58,7 +58,7 @@ static inline void gap_push(gap_stack_t 
+ 		q->stack = (gap_entry_t*)realloc(q->stack, sizeof(gap_entry_t) * q->m_entries);
+ 	}
+ 	p = q->stack + q->n_entries;
+-	p->info = (u_int32_t)score<<21 | i; p->k = k; p->l = l;
++	p->info = (uint32_t)score<<21 | i; p->k = k; p->l = l;
+ 	p->n_mm = n_mm; p->n_gapo = n_gapo; p->n_gape = n_gape;
+ 	p->n_ins = n_ins; p->n_del = n_del;
+ 	p->state = state; 

biology/bwa/files/patch-bwtgap.h

@@ -0,0 +1,15 @@
+--- bwtgap.h.orig	2014-02-25 21:20:01 UTC
++++ bwtgap.h
+@@ -5,9 +5,9 @@
+ #include "bwtaln.h"
+
+ typedef struct { // recursion stack
+-	u_int32_t info; // score<<21 | i
+-	u_int32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6;
+-	u_int32_t n_ins:16, n_del:16;
++	uint32_t info; // score<<21 | i
++	uint32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6;
++	uint32_t n_ins:16, n_del:16;
+ 	int last_diff_pos;
+ 	bwtint_t k, l; // (k,l) is the SA region of [i,n-1]
+ } gap_entry_t;

biology/bwa/pkg-descr

@@ -0,0 +1,5 @@
+BWA is a program for aligning sequencing reads against a large reference
+genome (e.g. human genome). It has two major components, one for read shorter
+than 150bp and the other for longer reads.
+
+WWW: http://sourceforge.net/projects/bio-bwa/

biology/cdbfasta/Makefile

@@ -0,0 +1,25 @@
+# Created by: Dan Siercks <[email protected]>
+# $FreeBSD$
+
+PORTNAME=	cdbfasta
+PORTVERSION=	2010.07.22
+CATEGORIES=	biology
+MASTER_SITES=	http://acadix.biz/Ports/distfiles/ \
+		http://personalpages.tds.net/~jwbacon/Ports/distfiles/
+
+MAINTAINER=	[email protected]
+COMMENT=	Fast indexing and retrieval of FASTA records from flat file databases
+
+# LICENSE=	unspecified
+
+WRKSRC=		${WRKDIR}/${PORTNAME}
+
+USES=		gmake
+
+PLIST_FILES=	bin/cdbfasta bin/cdbyank
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/cdbfasta ${STAGEDIR}${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/cdbyank ${STAGEDIR}${PREFIX}/bin
+
+.include <bsd.port.mk>

biology/cdbfasta/distinfo

@@ -0,0 +1,2 @@
+SHA256 (cdbfasta-2010.07.22.tar.gz) = 68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c
+SIZE (cdbfasta-2010.07.22.tar.gz) = 59735

biology/cdbfasta/files/patch-Makefile

@@ -0,0 +1,54 @@
+--- Makefile.orig	2009-12-03 20:17:51 UTC
++++ Makefile
+@@ -18,7 +18,10 @@ else
+     MARCH = 
+ endif    
+
+-CC      := g++
++# Use the correct compiler (CXX, not CC) and respect the environment
++# by using ?=
++CXX	?= g++
++
+ BASEFLAGS  = -Wall ${SEARCHDIRS} $(MARCH) -DENABLE_COMPRESSION=0 -D_FILE_OFFSET_BITS=64 \
+ -D_LARGEFILE_SOURCE -fno-exceptions -fno-rtti -fno-strict-aliasing \
+ -D_REENTRANT 
+@@ -33,30 +36,30 @@ else
+ endif
+
+ ifeq ($(findstring nommap,$(MAKECMDGOALS)),)
+-  CFLAGS = $(DBGFLAGS) $(BASEFLAGS)
++  CXXFLAGS = $(DBGFLAGS) $(BASEFLAGS)
+ else
+-  CFLAGS = $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP
++  CXXFLAGS = $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP
+ endif
+
+ %.o : %.c
+-	${CC} ${CFLAGS} -c $< -o $@
++	${CXX} ${CXXFLAGS} -c $< -o $@
+
+ %.o : %.cc
+-	${CC} ${CFLAGS} -c $< -o $@
++	${CXX} ${CXXFLAGS} -c $< -o $@
+
+ %.o : %.C
+-	${CC} ${CFLAGS} -c $< -o $@
++	${CXX} ${CXXFLAGS} -c $< -o $@
+
+ %.o : %.cpp
+-	${CC} ${CFLAGS} -c $< -o $@
++	${CXX} ${CXXFLAGS} -c $< -o $@
+
+ %.o : %.cxx
+-	${CC} ${CFLAGS} -c $< -o $@
++	${CXX} ${CXXFLAGS} -c $< -o $@
+
+ # C/C++ linker
+
+-LINKER    := g++
+-LDFLAGS    = -lz
++LINKER	:= ${CXX}
++LDFLAGS	= -lz
+ #if ENABLE_COMPRESSION is not needed,
+ # LDFLAGS = 
+

biology/cdbfasta/pkg-descr

@@ -0,0 +1,3 @@
+Fast indexing and retrieval of FASTA records from flat file data bases.
+
+WWW: http://sourceforge.net/projects/cdbfasta/

biology/fastool/Makefile

@@ -0,0 +1,33 @@
+# Created by: Jason Bacon <[email protected]>
+# $FreeBSD$
+
+PORTNAME=	fastool
+PORTVERSION=	0.1.4
+CATEGORIES=	biology
+
+MAINTAINER=	[email protected]
+COMMENT=	Simple and quick FastQ and FastA tool for file reading and conversion
+
+LICENSE=	BSD2CLAUSE
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	fstrozzi
+GH_PROJECT=	Fastool
+
+WRKSRC=		${WRKDIR}/Fastool-${PORTVERSION}
+
+PLIST_FILES=	bin/fastool
+
+CFLAGS+=	-std=c99
+
+post-patch:
+	${REINPLACE_CMD} \
+		-e 's|CC *=|CC ?=|g' \
+		-e 's|CFLAGS *=|CFLAGS ?=|g' \
+		${WRKSRC}/Makefile
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/fastool \
+		${STAGEDIR}${PREFIX}/bin
+
+.include <bsd.port.mk>

biology/fastool/distinfo

@@ -0,0 +1,2 @@
+SHA256 (fstrozzi-Fastool-0.1.4_GH0.tar.gz) = f86f02fced9479b77d6d27a442b66e66f0c55d40d5ad2ddd91a752de57024540
+SIZE (fstrozzi-Fastool-0.1.4_GH0.tar.gz) = 6346

biology/fastool/pkg-descr

@@ -0,0 +1,3 @@
+Simple and quick FastQ and FastA tool for file reading and conversion.
+
+WWW: https://github.com/fstrozzi/Fastool