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(-)biology/ncbi-vdb/Makefile (+72 lines)
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# $FreeBSD$
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PORTNAME=	ncbi-vdb
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DISTVERSION=	2.8.2-2
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CATEGORIES=	biology
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MAINTAINER=	mzaki@niid.go.jp
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COMMENT=	NCBI's virtualized back-end for accessing Sequence Read Archive
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LICENSE=	PD LGPL21+
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LICENSE_COMB=	multi
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LICENSE_FILE_PD=	${WRKSRC}/LICENSE
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LICENSE_DISTFILES_LGPL21+ =	${DISTNAME}${EXTRACT_SUFX}
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# This port never use the bundled libraries otherwise licensed.
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BUILD_DEPENDS=	bash:shells/bash
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LIB_DEPENDS=	libxml2.so:textproc/libxml2 \
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		libhdf5.so:science/hdf5 \
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		libmbedtls.so:security/mbedtls
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USE_GITHUB=	yes
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GH_ACCOUNT=	ncbi
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GH_TUPLE+=	ncbi:ngs:1.3.0:ngs
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USES=		compiler gmake perl5 shebangfix
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USE_PERL5=	build
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SHEBANG_GLOB=	*.sh *.pl
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GNU_CONFIGURE=	yes
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CONFIGURE_ARGS=	--with-xml2-prefix=${LOCALBASE} \
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		--with-hdf5-prefix=${LOCALBASE} \
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		--with-mbedtls-prefix=${LOCALBASE} \
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		CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}"
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MAKE_ARGS+=	CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}"
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USE_LDCONFIG=	yes
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MAKE_JOBS_UNSAFE=	yes
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ONLY_FOR_ARCHS=	amd64 i386
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ONLY_FOR_ARCHS_REASON=	libs/search/nucstrstr.c requires SSE2 instructions
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# for port developpers, building with these options may fail
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OPTIONS_DEFINE=	DEBUG GCC OPTIMIZED_CFLAGS TEST
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DEBUG_PREVENTS=	OPTIMIZED_CFLAGS
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DEBUG_CONFIGURE_WITH=	debug
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GCC_USE=	gcc=yes
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OPTIMIZED_CFLAGS_MAKE_ARGS_OFF=	OPT=""
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TEST_TEST_TARGET=	test
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post-extract:
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	@${LN} -sf ${WRKSRC_ngs} ${WRKDIR}/ngs
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	@${LN} -sf ${WRKSRC} ${WRKDIR}/${PORTNAME}
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pre-patch:
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	@${CP} ${FILESDIR}/Makefile.bsd ${WRKSRC}/build/
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	@for f in ${WRKSRC}/build/ld.linux.*.sh; do ${CP} -p $${f} $${f%linux*}bsd$${f#*linux}; done
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	@${CP} -p ${WRKSRC}/build/ld.linux.gcc.sh ${WRKSRC}/build/ld.bsd.clang.sh
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	@${MKDIR} ${WRKSRC}/interfaces/os/bsd
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	@${CP} -p ${WRKSRC}/interfaces/os/mac/endian.h ${WRKSRC}/interfaces/os/bsd/
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	@${REINPLACE_CMD} -e 's/vdb_mbedtls_/mbedtls_/g' ${WRKSRC}/libs/kns/tls.c
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	@${RM} -rf ${WRKSRC}/interfaces/ext/mbedtls
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post-patch:
64
	@${GREP} -q '@@PREFIX@@' ${WRKSRC}/libs/kfg/config.c || (echo "@@PREFIX@@ in file/patch-libs_kfg_config.c is overwritten probably due to using 'make makepatch'"; exit 1)
65
	@${REINPLACE_CMD} -e 's#@@PREFIX@@#"${PREFIX}"#' ${WRKSRC}/libs/kfg/config.c
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post-configure:
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	@${ECHO} ${CHOSEN_COMPILER_TYPE} > ${WRKSRC}/build/COMP
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70
post-build-TEST-on:	do-test
71
72
.include <bsd.port.mk>
(-)biology/ncbi-vdb/distinfo (+5 lines)
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TIMESTAMP = 1505048188
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SHA256 (ncbi-ncbi-vdb-2.8.2-2_GH0.tar.gz) = 7866f7abf00e35faaa58eb3cdc14785e6d42bde515de4bb3388757eb0c8f3c95
3
SIZE (ncbi-ncbi-vdb-2.8.2-2_GH0.tar.gz) = 19348893
4
SHA256 (ncbi-ngs-1.3.0_GH0.tar.gz) = 803c650a6de5bb38231d9ced7587f3ab788b415cac04b0ef4152546b18713ef2
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SIZE (ncbi-ngs-1.3.0_GH0.tar.gz) = 1089187
(-)biology/ncbi-vdb/files/Makefile.bsd (+72 lines)
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# ===========================================================================
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#
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#                            PUBLIC DOMAIN NOTICE
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#               National Center for Biotechnology Information
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#
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#  This software/database is a "United States Government Work" under the
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#  terms of the United States Copyright Act.  It was written as part of
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#  the author's official duties as a United States Government employee and
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#  thus cannot be copyrighted.  This software/database is freely available
10
#  to the public for use. The National Library of Medicine and the U.S.
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#  Government have not placed any restriction on its use or reproduction.
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#
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#  Although all reasonable efforts have been taken to ensure the accuracy
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#  and reliability of the software and data, the NLM and the U.S.
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#  Government do not and cannot warrant the performance or results that
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#  may be obtained by using this software or data. The NLM and the U.S.
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#  Government disclaim all warranties, express or implied, including
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#  warranties of performance, merchantability or fitness for any particular
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#  purpose.
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#
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#  Please cite the author in any work or product based on this material.
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#
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# ===========================================================================
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25
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# default compiler
27
ifeq (,$(COMP))
28
	COMP = clang
29
endif
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# handle attempts to set cross-compilation architecture
32
# note that if your installation is set up for cross compilation,
33
# you can try to enable it on your own.
34
ifeq (i386,$(ARCH))
35
i386:
36
	@ true
37
x86_64:
38
	@ echo "FreeBSD builds do not support cross-compilation to this architecture"
39
endif
40
41
ifeq (x86_64,$(ARCH))
42
i386:
43
	@ echo "FreeBSD builds do not support cross-compilation to this architecture"
44
x86_64:
45
	@ true
46
endif
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.PHONY: i386 x86_64
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50
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# library prefix
52
LPFX = lib
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54
# file extensions
55
OBJX = o
56
LOBX = pic.o
57
LIBX = a
58
SHLX = so
59
60
# compilation defines
61
DEFINES	:= -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=bsd$(BITS)
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# FreeBSD is a Unix variant; for most cases, linux sources do well
64
OS_DAD = linux
65
OS_GDAD = unix
66
67
# flex+bison: on Mac, use source-controlled generated .c/.h files
68
YACC = @ true
69
LEX = @ true
70
71
# build matrix
72
COMPILERS = CLANG GCC
(-)biology/ncbi-vdb/files/patch-build_Makefile.clang (+35 lines)
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--- build/Makefile.clang.orig	2017-07-14 21:55:36 UTC
2
+++ build/Makefile.clang
3
@@ -22,25 +22,27 @@
4
 #
5
 # ===========================================================================
6
 
7
+CCNAME  ?= clang
8
+CXXNAME ?= clang++
9
 
10
 # compilers
11
-CC = @ $(TOP)/build/cc.sh $(OS) 'clang -c' \
12
+CC = @ $(TOP)/build/cc.sh $(OS) '$(CCNAME) -c' \
13
 	 $(CHECKSUM) --objx $(OBJX) --cflags "$(CFLAGS)" -MD
14
-CP = @ $(TOP)/build/cc.sh $(OS) 'clang++ -c' \
15
+CP = @ $(TOP)/build/cc.sh $(OS) '$(CXXNAME) -c' \
16
 	 $(CHECKSUM) --objx $(OBJX) --cflags "$(CPFLAGS)" -MD
17
 
18
 # C preprocessor
19
-PP = gcc -E $(CFLAGS)
20
+PP = $(CCNAME) -E $(CFLAGS)
21
 
22
 # linkers
23
-LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) clang \
24
+LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CCNAME) \
25
 	--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
26
 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
27
 	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
28
 
29
 LPFLAGS = $(LDFLAGS)
30
 
31
-LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) clang++ \
32
+LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CXXNAME) \
33
 	--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
34
 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
35
 	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
(-)biology/ncbi-vdb/files/patch-build_Makefile.env (+41 lines)
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--- build/Makefile.env.orig	2017-07-14 21:55:36 UTC
2
+++ build/Makefile.env
3
@@ -324,16 +324,35 @@ INCDIRS = \
4
 	$(addprefix -I,$(XTINC) $(NGSINC)) \
5
 	-I.
6
 
7
+# linker paths
8
+LDPATHS =
9
+
10
+ifneq (,$(HDF5_LIBDIR))
11
+	LDPATHS += -L$(HDF5_LIBDIR)
12
+endif
13
+ifneq (,$(XML2_LIBDIR))
14
+	LDPATHS += -L$(XML2_LIBDIR)
15
+endif
16
+ifneq (,$(MAGIC_LIBDIR))
17
+	LDPATHS += -L$(MAGIC_LIBDIR)
18
+endif
19
+ifneq (,$(MBEDTLS_LIBDIR))
20
+	LDPATHS += -L$(MBEDTLS_LIBDIR)
21
+endif
22
+ifneq (,$(FUSE_LIBDIR))
23
+	LDPATHS += -L$(FUSE_LIBDIR)
24
+endif
25
+
26
 
27
 # defines that describe os & architecture
28
 DLLX ?= $(SHLX)
29
 ARCHDEFS = -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=$(LPFX) -DSHLIBEXT=$(DLLX)
30
 
31
 # default tool parameters
32
-CFLAGS	= $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
33
-CPFLAGS = $(DEBUG) $(DBG) $(CARCH) $(PROF) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
34
+CFLAGS	= $(PKGCFLAGS) $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
35
+CPFLAGS = $(CXXFLAGS) $(DEBUG) $(DBG) $(CARCH) $(PROF) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
36
 # some LDFLAGS may have been specified in $(CONFIG_FILE)
37
-LDFLAGS += $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT)
38
+LDFLAGS += $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS)
39
 
40
 #-------------------------------------------------------------------------------
41
 # runtests
(-)biology/ncbi-vdb/files/patch-build_Makefile.gcc (+35 lines)
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--- build/Makefile.gcc.orig	2017-07-14 21:55:36 UTC
2
+++ build/Makefile.gcc
3
@@ -22,25 +22,27 @@
4
 #
5
 # ===========================================================================
6
 
7
+CCNAME  ?= gcc
8
+CXXNAME ?= g++
9
 
10
 # compilers
11
-CC = @ $(TOP)/build/cc.sh $(OS) 'gcc -c' \
12
+CC = @ $(TOP)/build/cc.sh $(OS) '$(CCNAME) -c' \
13
 	 $(CHECKSUM) --objx $(OBJX) --cflags "$(CFLAGS)" -MD
14
-CP = @ $(TOP)/build/cc.sh $(OS) 'g++ -c' \
15
+CP = @ $(TOP)/build/cc.sh $(OS) '$(CXXNAME) -c' \
16
 	 $(CHECKSUM) --objx $(OBJX) --cflags "$(CPFLAGS)" -MD
17
 
18
 # C preprocessor
19
-PP = gcc -E $(CFLAGS)
20
+PP = $(CCNAME) -E $(CFLAGS)
21
 
22
 # linkers
23
-LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) gcc \
24
+LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CCNAME) \
25
 	--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
26
 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
27
 	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
28
 
29
 LPFLAGS = $(LDFLAGS)
30
 
31
-LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) g++ \
32
+LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CXXNAME) \
33
 	--build $(BUILD) --ldflags "$(LPFLAGS)" $(STATIC) \
34
 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
35
 	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
(-)biology/ncbi-vdb/files/patch-build_Makefile.install (+11 lines)
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1
--- build/Makefile.install.orig	2017-07-14 21:55:36 UTC
2
+++ build/Makefile.install
3
@@ -58,7 +58,7 @@ LIBRARIES_TO_INSTALL = \
4
     ncbi-wvdb.$(VERSION_SHLX) \
5
     ncbi-ngs-c++.$(VERSION_LIBX) \
6
 
7
-LIB_TARGET = $(INST_LIBDIR)$(BITS)
8
+LIB_TARGET = $(INST_LIBDIR)
9
 
10
 LIBRARIES_WITH_PREFIX = \
11
 	$(addprefix $(LIB_TARGET)/$(LPFX),$(LIBRARIES_TO_INSTALL))
(-)biology/ncbi-vdb/files/patch-build_Makefile.shell (+31 lines)
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1
--- build/Makefile.shell.orig	2017-07-14 21:55:36 UTC
2
+++ build/Makefile.shell
3
@@ -36,6 +36,9 @@ endif
4
 ifeq (Linux, $(UNAME))
5
 	HOST_OS = linux
6
 endif
7
+ifeq (FreeBSD, $(UNAME))
8
+	HOST_OS = bsd
9
+endif
10
 ifeq (SunOS, $(UNAME))
11
 	HOST_OS = sun
12
 	ARCHITECTURES = x86_64 i386
13
@@ -83,6 +86,9 @@ else
14
 	ifeq (x86_64, $(MARCH))
15
 		HOST_ARCH = x86_64
16
 	endif
17
+	ifeq (amd64, $(MARCH))
18
+		HOST_ARCH = x86_64
19
+	endif
20
 	ifeq (i86pc, $(MARCH))
21
 		HOST_ARCH = x86_64
22
 		ARCHITECTURES = x86_64 i386
23
@@ -93,7 +99,7 @@ else
24
 	endif
25
 endif
26
 
27
-ARCH = $(HOST_ARCH)
28
+override ARCH = $(HOST_ARCH)
29
 REMOTE_ARCH = $(ARCH)
30
 
31
 # pick up dependencies from object directory
(-)biology/ncbi-vdb/files/patch-build_ld.bsd.dlib.sh (+22 lines)
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1
--- build/ld.bsd.dlib.sh.orig	2017-10-27 07:23:08 UTC
2
+++ build/ld.bsd.dlib.sh
3
@@ -51,8 +51,8 @@ case "$LD" in
4
 g*)
5
     source "${0%dlib.sh}gcc.sh"
6
     ;;
7
-i*)
8
-    source "${0%dlib.sh}icc.sh"
9
+c*)
10
+    source "${0%dlib.sh}clang.sh"
11
     ;;
12
  *)
13
     echo "$SELF_NAME: unrecognized ld tool - '$LD'"
14
@@ -100,7 +100,7 @@ then
15
             # always load libdl as shared library
16
             load-ref-symbols
17
             load-dynamic
18
-            CMD="$CMD -ldl"
19
+#            CMD="$CMD -ldl"
20
             ;;
21
 
22
         -l*)
(-)biology/ncbi-vdb/files/patch-build_ld.bsd.exe.sh (+22 lines)
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1
--- build/ld.bsd.exe.sh.orig	2017-10-27 07:23:08 UTC
2
+++ build/ld.bsd.exe.sh
3
@@ -51,8 +51,8 @@ case "$LD" in
4
 g*)
5
     source "${0%exe.sh}gcc.sh"
6
     ;;
7
-i*)
8
-    source "${0%exe.sh}icc.sh"
9
+c*)
10
+    source "${0%exe.sh}clang.sh"
11
     ;;
12
 *)
13
     echo "$SELF_NAME: unrecognized ld tool - '$LD'"
14
@@ -108,7 +108,7 @@ then
15
             # always load libdl as shared library
16
             load-ref-symbols
17
             load-dynamic
18
-            CMD="$CMD -ldl"
19
+#            CMD="$CMD -ldl"
20
             ;;
21
 
22
         -l*)
(-)biology/ncbi-vdb/files/patch-build_ld.sh (+58 lines)
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1
--- build/ld.sh.orig	2017-10-27 07:23:08 UTC
2
+++ build/ld.sh
3
@@ -68,6 +68,8 @@ HAVE_M=0
4
 NEED_M=1
5
 HAVE_XML=0
6
 NEED_XML=0
7
+HAVE_MBEDTLS=0
8
+NEED_MBEDTLS=0
9
 HAVE_KFC=0
10
 HAVE_KAPP=0
11
 HAVE_NCBI_VDB=0
12
@@ -297,18 +299,19 @@ do
13
     -[lds]ncbi-vdb)
14
         HAVE_NCBI_VDB=1
15
         KPROC=4
16
-        HAVE_GZIP=1
17
-        HAVE_BZIP=1
18
+        NEED_GZIP=1
19
+        NEED_BZIP=1
20
         HAVE_KFC=1
21
         NEED_M=1
22
         NEED_XML=1
23
+        NEED_MBEDTLS=1
24
         LIBS="$LIBS $1"
25
         ;;
26
     -[lds]ncbi-ngs-c++)
27
         HAVE_NCBI_VDB=1
28
         KPROC=4
29
-        HAVE_GZIP=1
30
-        HAVE_BZIP=1
31
+        NEED_GZIP=1
32
+        NEED_BZIP=1
33
         HAVE_KFC=1
34
         NEED_M=1
35
         NEED_XML=1
36
@@ -317,11 +320,12 @@ do
37
     -[lds]ncbi-wvdb)
38
         HAVE_NCBI_WVDB=1
39
         KPROC=4
40
-        HAVE_GZIP=1
41
-        HAVE_BZIP=1
42
+        NEED_GZIP=1
43
+        NEED_BZIP=1
44
         HAVE_KFC=1
45
         NEED_M=16
46
         NEED_XML=1
47
+        NEED_MBEDTLS=1
48
         LIBS="$LIBS $1"
49
         ;;
50
 
51
@@ -512,6 +516,7 @@ fi
52
 # supply missing libraries
53
 [ $HAVE_GZIP -eq 0 ] && [ $NEED_GZIP -ne 0 ] && LIBS="$LIBS -lz"
54
 [ $HAVE_BZIP -eq 0 ] && [ $NEED_BZIP -ne 0 ] && LIBS="$LIBS -lbz2"
55
+[ $HAVE_MBEDTLS -eq 0 ] && [ $NEED_MBEDTLS -ne 0 ] && LIBS="$LIBS -lmbedtls -lmbedcrypto -lmbedx509"
56
 [ $HAVE_DL -eq 0 ] && [ $NEED_DL -ne 0 ] && LIBS="$LIBS -ldl"
57
 [ $HAVE_M -eq 0 ] && [ $NEED_M -ne 0 ] && HAVE_M=16
58
 [ $HAVE_XML -eq 0 ] && [ $NEED_XML -ne 0 ] && HAVE_XML=32
(-)biology/ncbi-vdb/files/patch-libs_Makefile (+12 lines)
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1
To omit building bundled libraries.
2
3
--- libs/Makefile.orig	2017-07-14 21:55:36 UTC
4
+++ libs/Makefile
5
@@ -35,7 +35,6 @@ include $(TOP)/build/Makefile.config
6
 # default
7
 #
8
 SUBDIRS =    \
9
-	ext      \
10
 	kfc      \
11
 	klib     \
12
 	kproc    \
(-)biology/ncbi-vdb/files/patch-libs_kfg_config.c (+20 lines)
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1
--- libs/kfg/config.c.orig	2017-07-14 21:55:36 UTC
2
+++ libs/kfg/config.c
3
@@ -2558,7 +2558,7 @@ bool load_from_std_location ( KConfig *s
4
     const char * std_locs [] =
5
     {
6
 #if ! WINDOWS
7
-        "/etc/ncbi",
8
+        @@PREFIX@@ "/etc/ncbi",
9
 #else
10
         "/c/ncbi",
11
 #endif
12
@@ -2816,6 +2816,8 @@ void add_predefined_nodes ( KConfig * se
13
     #define OS "win"
14
 #elif SUN
15
     #define OS "sun"
16
+#elif BSD
17
+    #define OS "bsd"
18
 #else
19
     #error unrecognized OS
20
 #endif
(-)biology/ncbi-vdb/files/patch-libs_klib_unix_systime.c (+11 lines)
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1
--- libs/klib/unix/systime.c.orig	2017-07-14 21:55:36 UTC
2
+++ libs/klib/unix/systime.c
3
@@ -142,7 +142,7 @@ LIB_EXPORT KTime_t CC KTimeMakeTime ( co
4
         t . tm_isdst = self -> dst;
5
 
6
         ts = mktime ( &t );
7
-        ts -= timezone;
8
+        ts += localtime(&ts)->tm_gmtoff;
9
     }
10
 
11
     return ts;
(-)biology/ncbi-vdb/files/patch-libs_kns_Makefile (+13 lines)
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1
--- libs/kns/Makefile.orig	2017-07-14 21:55:36 UTC
2
+++ libs/kns/Makefile
3
@@ -39,6 +39,10 @@ OBJFILES = \
4
 
5
 include $(TOP)/build/Makefile.env
6
 
7
+ifdef MBEDTLS_INCDIR
8
+	INCDIRS += $(addprefix -I,$(MBEDTLS_INCDIR))
9
+endif
10
+
11
 RWORKDIR = $(TOP)/$(MODULE)
12
 
13
 #-------------------------------------------------------------------------------
(-)biology/ncbi-vdb/files/patch-libs_kns_unix_syssock.c (+10 lines)
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1
--- libs/kns/unix/syssock.c.orig	2017-07-14 21:55:36 UTC
2
+++ libs/kns/unix/syssock.c
3
@@ -66,6 +66,7 @@
4
 #include <sys/types.h>
5
 #include <sys/socket.h>
6
 #include <sys/un.h>
7
+#include <netinet/in.h>
8
 #include <netinet/tcp.h>
9
 #include <poll.h>
10
 #include <unistd.h>
(-)biology/ncbi-vdb/files/patch-libs_ncbi-vdb_Makefile (+32 lines)
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1
--- libs/ncbi-vdb/Makefile.orig	2017-07-14 21:55:36 UTC
2
+++ libs/ncbi-vdb/Makefile
3
@@ -87,14 +87,15 @@ LDFLAGS += -L$(XML2_LIBDIR)
4
 endif
5
 endif
6
 
7
+ifneq (,$(MBEDTLS_LIBDIR))
8
+LDFLAGS += -L$(MBEDTLS_LIBDIR)
9
+endif
10
+
11
 VDB_LIB_CMN =    \
12
 	align-access \
13
 	ncbi-bam     \
14
 	vfs          \
15
 	$(LIBKXML)   \
16
-	mbedx509     \
17
-	mbedtls      \
18
-	mbedcrypto   \
19
 	kns          \
20
 	kfg          \
21
 	krypto       \
22
@@ -103,9 +104,7 @@ VDB_LIB_CMN =    \
23
 	klib         \
24
 	kproc        \
25
 	$(LIBKQ)     \
26
-	kfc          \
27
-	bz2          \
28
-	z
29
+	kfc
30
 
31
 VDB_LIB_RD =              \
32
 	align-reader          \
(-)biology/ncbi-vdb/files/patch-libs_search_Makefile (+12 lines)
Line 0 Link Here
1
--- libs/search/Makefile.orig	2017-07-14 21:55:36 UTC
2
+++ libs/search/Makefile
3
@@ -39,6 +39,9 @@ OBJFILES = \
4
 
5
 include $(TOP)/build/Makefile.env
6
 
7
+CARCH += -msse2
8
+# nucstrstr.c requires SSE2
9
+
10
 #-------------------------------------------------------------------------------
11
 # outer targets
12
 #
(-)biology/ncbi-vdb/files/patch-setup_konfigure.perl (+252 lines)
Line 0 Link Here
1
--- setup/konfigure.perl.orig	2017-07-14 21:55:36 UTC
2
+++ setup/konfigure.perl
3
@@ -186,7 +186,7 @@ if ($OPT{'help'}) {
4
 foreach (@ARGV) {
5
     @_ = split('=');
6
     next if ($#_ != 1);
7
-    $OPT{$_[0]} = $_[1] if ($_[0] eq 'CXX' || $_[0] eq 'LDFLAGS');
8
+    $OPT{$_[0]} = $_[1] if ($_[0] eq 'CC' || $_[0] eq 'CXX' || $_[0] eq 'LDFLAGS' || $_[0] eq 'TOOLS');
9
 }
10
 
11
 println "Configuring $PACKAGE_NAME package";
12
@@ -198,7 +198,7 @@ print "checking system type... " unless 
13
 my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch();
14
 println $OSTYPE unless ($AUTORUN);
15
 
16
-unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
17
+unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /freebsd/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
18
     println "configure: error: unsupported system '$OSTYPE'";
19
     exit 1;
20
 }
21
@@ -213,7 +213,7 @@ if ($OS eq 'linux') {
22
 
23
 print "checking machine architecture... " unless ($AUTORUN);
24
 println $MARCH unless ($AUTORUN);
25
-unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) {
26
+unless ($MARCH =~ /x86_64/i || $MARCH =~ /amd64/i || $MARCH =~ /i?86/i) {
27
     println "configure: error: unsupported architecture '$OSTYPE'";
28
     exit 1;
29
 }
30
@@ -298,7 +298,7 @@ print "checking for supported architectu
31
 
32
 my $BITS;
33
 
34
-if ($MARCH =~ /x86_64/i) {
35
+if ($MARCH =~ /(x86_|amd)64/i) {
36
     $BITS = 64;
37
 } elsif ($MARCH eq 'fat86') {
38
     $BITS = '32_64';
39
@@ -331,6 +331,18 @@ if ($OSTYPE =~ /linux/i) {
40
     $EXEX = '';
41
     $OSINC = 'unix';
42
     $TOOLS = 'clang' unless ($TOOLS);
43
+} elsif ($OSTYPE =~ /freebsd/i) {
44
+    $LPFX = 'lib';
45
+    $OBJX = 'o';
46
+    $LOBX = 'pic.o';
47
+    $LIBX = 'a';
48
+    $SHLX = 'so';
49
+    $EXEX = '';
50
+    $OSINC = 'unix';
51
+    unless ($TOOLS) {
52
+        $TOOLS = 'clang';
53
+        $TOOLS = $OPT{TOOLS} if ($OPT{TOOLS});
54
+    }
55
 } elsif ($OSTYPE eq 'win') {
56
     $TOOLS = 'vc++';
57
 } else {
58
@@ -346,17 +358,19 @@ my ($ARCH_FL, $DBG, $OPT, $PIC, $INC, $M
59
 
60
 print "checking for supported tool chain... " unless ($AUTORUN);
61
 
62
+$CC      = $OPT{CC     } if ($OPT{CC     });
63
 $CPP     = $OPT{CXX    } if ($OPT{CXX    });
64
 $LDFLAGS = $OPT{LDFLAGS} if ($OPT{LDFLAGS});
65
 
66
 if ($TOOLS =~ /gcc$/) {
67
     $CPP  = 'g++' unless ($CPP);
68
-    $CC   = "$TOOLS -c";
69
+    $CC   = 'gcc' unless ($CC);
70
+    $LD   = $CC;
71
+    $CC   = "$CC -c";
72
     $CP   = "$CPP -c";
73
     $AR   = 'ar rc';
74
     $ARX  = 'ar x';
75
     $ARLS = 'ar t';
76
-    $LD   = $TOOLS;
77
     $LP   = $CPP;
78
 
79
     $DBG = '-g -DDEBUG';
80
@@ -366,21 +380,24 @@ if ($TOOLS =~ /gcc$/) {
81
     $MD  = '-MD';
82
 } elsif ($TOOLS eq 'clang') {
83
     $CPP  = 'clang++' unless ($CPP);
84
-    $CC   = 'clang -c';
85
-    my $versionMin = '-mmacosx-version-min=10.6';
86
+    $CC   = 'clang' unless ($CC);
87
+    $LD   = $CC;
88
+    $CC   = "$CC -c";
89
+    my $versionMin = '';
90
+    $versionMin = '-mmacosx-version-min=10.6' if ($OSTYPE =~ /darwin/i);
91
     $CP   = "$CPP -c $versionMin";
92
     if ($BITS ne '32_64') {
93
         $ARCH_FL = '-arch i386' if ($BITS == 32);
94
         $OPT = '-O3';
95
         $AR      = 'ar rc';
96
-        $LD      = "clang $ARCH_FL";
97
+        $LD      = "$LD $ARCH_FL";
98
         $LP      = "$CPP $versionMin $ARCH_FL";
99
     } else {
100
         $MAKE_MANIFEST = '( echo "$^" > $@/manifest )';
101
         $ARCH_FL       = '-arch i386 -arch x86_64';
102
         $OPT    = '-O3';
103
         $AR     = 'libtool -static -o';
104
-        $LD     = "clang -Wl,-arch_multiple $ARCH_FL -Wl,-all_load";
105
+        $LD     = "$LD -Wl,-arch_multiple $ARCH_FL -Wl,-all_load";
106
         $LP     = "$CPP $versionMin -Wl,-arch_multiple $ARCH_FL -Wl,-all_load";
107
     }
108
     $ARX  = 'ar x';
109
@@ -762,13 +779,13 @@ OS_ARCH = \$(shell perl \$(TOP)/setup/os
110
 # install paths
111
 EndText
112
 
113
-    L($F, "INST_BINDIR = $OPT{'bindir'}"      ) if ($OPT{'bindir'});
114
-    L($F, "INST_LIBDIR = $OPT{'libdir'}"      ) if ($OPT{'libdir'});
115
-    L($F, "INST_INCDIR = $OPT{'includedir'}"  ) if ($OPT{'includedir'});
116
-    L($F, "INST_SCHEMADIR = $OPT{'shemadir'}" ) if ($OPT{'shemadir'});
117
-    L($F, "INST_SHAREDIR = $OPT{'sharedir'}"  ) if ($OPT{'sharedir'});
118
-    L($F, "INST_JARDIR = $OPT{'javadir'}"     ) if ($OPT{'javadir'});
119
-    L($F, "INST_PYTHONDIR = $OPT{'pythondir'}") if ($OPT{'pythondir'});
120
+    L($F, "INST_BINDIR = \$(DESTDIR)$OPT{'bindir'}"      ) if ($OPT{'bindir'});
121
+    L($F, "INST_LIBDIR = \$(DESTDIR)$OPT{'libdir'}"      ) if ($OPT{'libdir'});
122
+    L($F, "INST_INCDIR = \$(DESTDIR)$OPT{'includedir'}"  ) if ($OPT{'includedir'});
123
+    L($F, "INST_SCHEMADIR = \$(DESTDIR)$OPT{'shemadir'}" ) if ($OPT{'shemadir'});
124
+    L($F, "INST_SHAREDIR = \$(DESTDIR)$OPT{'sharedir'}"  ) if ($OPT{'sharedir'});
125
+    L($F, "INST_JARDIR = \$(DESTDIR)$OPT{'javadir'}"     ) if ($OPT{'javadir'});
126
+    L($F, "INST_PYTHONDIR = \$(DESTDIR)$OPT{'pythondir'}") if ($OPT{'pythondir'});
127
 
128
     my ($E_VERSION_SHLX, $VERSION_SHLX,
129
         $E_MAJVERS_SHLX , $MAJMIN_SHLX, $MAJVERS_SHLX);
130
@@ -832,7 +849,7 @@ MAJMIN_EXEX  = \$(EXEX).\$(MAJMIN)
131
 MAJVERS_EXEX = \$(EXEX).\$(MAJVERS)
132
 
133
 # system architecture and wordsize
134
-ARCH = $ARCH
135
+override ARCH = $ARCH
136
 EndText
137
 
138
     L($F, "# ARCH = $ARCH ( $MARCH )") if ($ARCH ne $MARCH);
139
@@ -867,7 +884,7 @@ EndText
140
     }
141
     L($F, "PIC     = $PIC") if ($PIC);
142
     if ($PKG{LNG} eq 'C') {
143
-        if ($TOOLS =~ /clang/i) {
144
+        if ($OSTYPE =~ /darwin/i) {
145
    L($F, 'SONAME  = -install_name ' .
146
                '$(INST_LIBDIR)$(BITS)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\');
147
    L($F, '    -compatibility_version $(MAJMIN) -current_version $(VERSION) \\');
148
@@ -978,7 +995,7 @@ EndText
149
     L($F, '# directory rules');
150
     if ($PKG{LNG} eq 'C') {
151
         L($F, '$(BINDIR) $(LIBDIR) $(ILIBDIR) '
152
-            . '$(OBJDIR) $(INST_LIBDIR) $(INST_LIBDIR)$(BITS):');
153
+            . '$(OBJDIR) $(INST_LIBDIR):');
154
         T($F, 'mkdir -p $@');
155
     } elsif ($PKG{LNG} eq 'JAVA') {
156
         # test if we have jni header path
157
@@ -1008,12 +1025,12 @@ EndText
158
     L($F, 'export CONFIGURE_FOUND_XML2');
159
     L($F);
160
 
161
-    if ($OS eq 'linux' || $OS eq 'mac') {
162
+    if ($OS eq 'linux' || $OS eq 'bsd' || $OS eq 'mac') {
163
         L($F, '# installation rules');
164
         L($F,
165
-        '$(INST_LIBDIR)$(BITS)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)');
166
+        '$(INST_LIBDIR)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)');
167
         T($F, '@ echo -n "installing \'$(@F)\'... "');
168
-        T($F, '@ if cp $^ $@ && chmod 644 $@;                         \\');
169
+        T($F, '@ if $(BSD_INSTALL_DATA) $^ $@;                        \\');
170
         T($F, '  then                                                 \\');
171
         T($F, '      rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) '
172
                      . '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@) '
173
@@ -1022,7 +1039,7 @@ EndText
174
         T($F, '      ln -s $(patsubst %$(VERSION),%$(MAJVERS),$(@F)) '
175
                       . '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@); \\');
176
         T($F, '      ln -s $(patsubst %$(VERSION_LIBX),%$(LIBX),$(@F)) ' .
177
-   '$(INST_LIBDIR)$(BITS)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));'
178
+   '$(INST_LIBDIR)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));'
179
                                                               . ' \\');
180
         T($F, '      echo success;                                    \\');
181
         T($F, '  else                                                 \\');
182
@@ -1032,15 +1049,15 @@ EndText
183
         L($F);
184
 
185
         L($F,
186
-        '$(INST_LIBDIR)$(BITS)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)');
187
+        '$(INST_LIBDIR)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)');
188
         T($F, '@ echo -n "installing \'$(@F)\'... "');
189
-        T($F, '@ if cp $^ $@ && chmod 755 $@;                         \\');
190
+        T($F, '@ if $(BSD_INSTALL_LIB) $^ $@;                         \\');
191
         T($F, '  then                                                 \\');
192
         if ($OS ne 'mac') {
193
           T($F, '      rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) '
194
                       . '$(patsubst %$(VERSION_SHLX),%$(SHLX),$@);    \\');
195
         }
196
-        if ($OS eq 'linux') {
197
+        if ($OS eq 'linux' || $OS eq 'bsd') {
198
           T($F, '      ln -s $(@F) $(patsubst %$(VERSION),%$(MAJVERS),$@); \\');
199
         } elsif ($OS eq 'mac') {
200
           T($F, '      ln -sf $(@F) '
201
@@ -1059,7 +1076,7 @@ EndText
202
 
203
         L($F, '$(INST_BINDIR)/%$(VERSION_EXEX): $(BINDIR)/%$(VERSION_EXEX)');
204
         T($F, '@ echo -n "installing \'$(@F)\'... "');
205
-        T($F, '@ if cp $^ $@ && chmod 755 $@;                         \\');
206
+        T($F, '@ if $(BSD_INSTALL_PROGRAM) $^ $@;                     \\');
207
         T($F, '  then                                                 \\');
208
         T($F, '      rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) '
209
                       . '$(patsubst %$(VERSION_EXEX),%$(EXEX),$@);     \\');
210
@@ -1341,7 +1358,7 @@ sub find_in_dir {
211
                 ++$found;
212
             }
213
             if (! $found) {
214
-                my $libdir = File::Spec->catdir($dir, 'lib' . $BITS);
215
+                my $libdir = File::Spec->catdir($dir, 'lib');
216
                 my $f = File::Spec->catdir($libdir, $lib);
217
                 print "\tchecking $f\n\t" if ($OPT{'debug'});
218
                 if (-e $f) {
219
@@ -1483,12 +1500,12 @@ sub find_lib {
220
 
221
 sub check_compiler {
222
     my ($t, $n, $I, @l) = @_;
223
-    my $tool = $TOOLS;
224
+    my $tool = $CC;
225
 
226
     if ($t eq 'L') {
227
         print "checking for $n library... ";
228
     } elsif ($t eq 'O') {
229
-        if ($tool && ($tool =~ /gcc$/ || $tool =~ /g\+\+$/)) {
230
+        if ($tool && ($tool =~ /gcc/ || $tool =~ /g\+\+/)) {
231
             print "checking whether $tool accepts $n... ";
232
         } else {
233
             return;
234
@@ -1518,6 +1535,9 @@ sub check_compiler {
235
         } elsif ($n eq 'magic') {
236
             $library = '-lmagic';
237
             $log = '#include <magic.h> \n int main() { magic_open     (0); }\n'
238
+        } elsif ($n eq 'mbedtls') {
239
+            $library = '-lmbedtls';
240
+            $log = '#include <mbedtls/version.h> \n int main() { mbedtls_version_get_string(0); }\n'
241
         } elsif ($n eq 'xml2') {
242
             $library  = '-lxml2';
243
             $library .=       ' -liconv' if ($OS eq 'mac');
244
@@ -1554,7 +1574,7 @@ sub check_compiler {
245
             my $l = $l [ $i ];
246
             next if ( $l && ! -d $l );
247
             my $gcc = "| $tool -xc $flags " . ($I ? "-I$I " : ' ')
248
-                                      . ($l ? "-L$l " : ' ') . "- $library";
249
+                                      . ($l ? "-L$l " : ' ') . "-o a.out - $library";
250
             $gcc .= ' 2> /dev/null' unless ($OPT{'debug'});
251
 
252
             open GCC, $gcc or last;
(-)biology/ncbi-vdb/files/patch-setup_os-arch.prl (+20 lines)
Line 0 Link Here
1
--- setup/os-arch.prl.orig	2017-07-14 21:55:36 UTC
2
+++ setup/os-arch.prl
3
@@ -11,6 +11,8 @@ sub OsArch {
4
         chomp $UNAME;
5
         if ($UNAME =~ /Darwin/) {
6
             $HOST_OS = 'mac';
7
+        } elsif ($UNAME =~ /.*BSD/) {
8
+            $HOST_OS = 'bsd';
9
         } elsif ($UNAME =~ /Linux/) {
10
             $HOST_OS = 'linux';
11
         } elsif ($UNAME =~ /SunOS/) {
12
@@ -49,6 +51,8 @@ sub OsArch {
13
                 }
14
             } elsif ($MARCH =~ /x86_64/) {
15
                 $HOST_ARCH = 'x86_64';
16
+            } elsif ($MARCH =~ /amd64/) {
17
+                $HOST_ARCH = 'x86_64';
18
             } elsif ($MARCH =~ /i86pc/) {
19
                 $HOST_ARCH = 'x86_64';
20
                 @ARCHITECTURES = qw(x86_64 i386);
(-)biology/ncbi-vdb/files/patch-setup_package.prl (+26 lines)
Line 0 Link Here
1
--- setup/package.prl.orig	2017-07-14 21:55:36 UTC
2
+++ setup/package.prl
3
@@ -12,6 +12,7 @@ sub PKG { ( LNG   => 'C',
4
 sub DEPENDS { ( { name => 'fuse' , Include => '/usr/include'        , },
5
                 { name => 'hdf5' , Include => '/usr/include'        , },
6
                 { name => 'magic', Include => '/usr/include'        , },
7
+                { name => 'mbedtls', Include => '/usr/include'        , },
8
                 { name => 'xml2' , Include => '/usr/include/libxml2', } ) }
9
 sub REQ { ( { name    => 'ngs-sdk',
10
               aname   => 'NGS',
11
@@ -55,6 +56,15 @@ sub REQ { ( { name    => 'ngs-sdk',
12
               include => 'magic.h',
13
               lib     => 'libmagic.so',
14
             },
15
+            { name    => 'mbedtls',
16
+              option  => 'with-mbedtls-prefix',
17
+              origin  => 'E',
18
+              type    => 'LIO',
19
+              pkgpath => '/usr',
20
+              usrpath => '$HOME',
21
+              include => 'mbedtls/config.h',
22
+              lib     => 'libmbedtls.so',
23
+            },
24
             { name    => 'xml2',
25
               option  => 'with-xml2-prefix',
26
               origin  => 'E',
(-)biology/ncbi-vdb/files/patch-test_kapp_run-sig-core.sh (+49 lines)
Line 0 Link Here
1
--- test/kapp/run-sig-core.sh.orig	2017-10-27 07:23:08 UTC
2
+++ test/kapp/run-sig-core.sh
3
@@ -29,12 +29,12 @@ BUILD_TYPE="$3"
4
 
5
 SIGQUIT=3
6
 
7
-function killFromBackground ()
8
+killFromBackground ()
9
 {
10
     PARENT_PID=$1
11
     for I in 1 2 3 4 5
12
     do
13
-        COMMAND="ps -ef|awk '\$3==${PARENT_PID} && \$8==\"${BINARY_PATH}\"  {print \$2}'"
14
+        COMMAND="ps awwo pid,ppid,command|awk '\$2==${PARENT_PID} && \$3==\"${BINARY_PATH}\"  {print \$1}'"
15
         eval PID=\`${COMMAND}\`
16
         if [ "$PID" = "" ]; then
17
             sleep 1
18
@@ -44,7 +44,7 @@ function killFromBackground ()
19
     done
20
 
21
     if [ "$PID" != "" ]; then
22
-        kill -s $SIGQUIT $PID
23
+        kill -s QUIT $PID
24
     fi
25
 
26
     echo $PID > killed.pid
27
@@ -63,6 +63,13 @@ if [ "$HOST_OS" = "mac" ]; then
28
    fi
29
 
30
    CORE_FOLDER="/core/"
31
+elif [ "$HOST_OS" = "bsd" ]; then
32
+   if [ "`ulimit -c`" = "0" ] || [ "`/sbin/sysctl -n kern.coredump`" != "1" ]; then
33
+       echo "Core files are disabled. Skipping core file tests"
34
+       exit 0
35
+   fi
36
+
37
+   CORE_FOLDER="./"
38
 elif [ "$HOST_OS" = "linux" ]; then
39
    if [ "`ulimit -c`" = "0" ]; then
40
        echo "Core files are disabled. Skipping core file tests"
41
@@ -92,7 +99,7 @@ wait
42
 BINARY_PID=`cat killed.pid`
43
 rm killed.pid
44
 
45
-CORE_FILE="${CORE_FOLDER}core.${BINARY_PID}"
46
+CORE_FILE="${CORE_FOLDER}${BINARY_PATH##*/}.core"
47
 
48
 if [ "$BUILD_TYPE" = "dbg" ]; then
49
    if [ -f $CORE_FILE ]; then
(-)biology/ncbi-vdb/files/patch-test_kfg_kfgtest.cpp (+11 lines)
Line 0 Link Here
1
--- test/kfg/kfgtest.cpp.orig	2017-07-14 21:55:36 UTC
2
+++ test/kfg/kfgtest.cpp
3
@@ -443,6 +443,8 @@ FIXTURE_TEST_CASE(predef_OS, KfgFixture)
4
     CreateAndLoad(GetName(), "var=$(OS)\n");
5
     #if LINUX
6
         #define OS "linux"
7
+    #elif BSD
8
+        #define OS "bsd"    
9
     #elif SUN
10
         #define OS "sun"    
11
     #elif MAC 
(-)biology/ncbi-vdb/files/patch-test_klib_printf-test.c (+11 lines)
Line 0 Link Here
1
--- test/klib/printf-test.c.orig	2017-07-14 21:55:36 UTC
2
+++ test/klib/printf-test.c
3
@@ -503,7 +503,7 @@ rc_t run ( const char *progname )
4
         if ( rc == 0 )
5
         {
6
             rc = make_initial_test ( field_width, precision, " ", "s", "Kurt is having a fit" );
7
-#if !defined(__SunOS)  &&  !defined(__sun__)
8
+#if !defined(__SunOS)  &&  !defined(__sun__) && !defined(__FreeBSD__)
9
             /* Solaris printf doesn't cope with NULLs */
10
             rc = make_initial_test ( field_width, precision, " ", "s", NULL );
11
 #endif            
(-)biology/ncbi-vdb/files/patch-test_kns_Makefile (+32 lines)
Line 0 Link Here
1
run-test-proxy-with-scheme requires a web proxy server.
2
3
--- test/kns/Makefile.orig	2017-07-14 21:55:36 UTC
4
+++ test/kns/Makefile
5
@@ -25,7 +25,7 @@
6
 
7
 default: runtests
8
 
9
-runtests: run-test-proxy-with-scheme
10
+runtests:
11
 
12
 TOP ?= $(abspath ../..)
13
 MODULE = test/kns
14
@@ -39,6 +39,10 @@ TEST_TOOLS = \
15
 
16
 include $(TOP)/build/Makefile.env
17
 
18
+ifdef MBEDTLS_INCDIR
19
+	INCDIRS += $(addprefix -I,$(MBEDTLS_INCDIR))
20
+endif
21
+
22
 EXT_TOOLS = \
23
 	test-proxy-with-env \
24
 	test-proxy-with-scheme \
25
@@ -124,6 +128,7 @@ $(TEST_BINDIR)/test-kns: $(KNSTEST_OBJ)
26
 	$(LP) --exe -o $@ $^ $(KNSTEST_LIB)
27
 
28
 kns: test-kns
29
+	if [ ! -d $(HOME)/.ncbi ]; then mkdir $(HOME)/.ncbi; fi
30
 	$(TEST_BINDIR)/test-kns  #-l=all
31
 
32
 #----------------------------------------------------------------
(-)biology/ncbi-vdb/files/patch-test_vdb_test-dependencies.cpp (+11 lines)
Line 0 Link Here
1
--- test/vdb/test-dependencies.cpp.orig	2017-07-14 21:55:36 UTC
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+++ test/vdb/test-dependencies.cpp
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@@ -115,7 +115,7 @@ public:
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 class RefseqFixture : public DepFixture {
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-  #if LINUX
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+  #if LINUX || BSD
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     #define PATH "kfg/linux"
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   #elif MAC
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     #define PATH "kfg/mac"
(-)biology/ncbi-vdb/files/patch-test_vfs_redirect-rejected-names-cgi-http-to-https.cpp (+11 lines)
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--- test/vfs/redirect-rejected-names-cgi-http-to-https.cpp.orig	2017-07-14 21:55:36 UTC
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+++ test/vfs/redirect-rejected-names-cgi-http-to-https.cpp
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@@ -148,7 +148,7 @@ struct Test : protected ncbi :: NK :: Sh
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 TEST_CASE(TEST) {
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-#define RESOLVER_CGI_HEAD "test.ncbi.nlm.nih."
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+#define RESOLVER_CGI_HEAD "www.ncbi.nlm.nih."
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 #ifdef VDB_3162
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 #else
(-)biology/ncbi-vdb/pkg-descr (+7 lines)
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NCBI-VDB is a virtualized back-end engine library for Sequencing Read Archives.
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The 'front-end' API are provided by biology/ngs-sdk port.
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Although the GitHub repository also contains Java and Python codes,
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this port currently builds only C- and C++-based libraries.
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WWW: https://github.com/ncbi/ncbi-vdb/wiki
(-)biology/ncbi-vdb/pkg-plist (+21 lines)
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include/ncbi-vdb/NGS.hpp
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lib/libncbi-ngs-c++-static.a
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lib/libncbi-ngs-c++.a
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lib/libncbi-ngs-c++.a.2
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lib/libncbi-ngs-c++.a.2.8.2
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lib/libncbi-vdb-static.a
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lib/libncbi-vdb.a
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lib/libncbi-vdb.a.2
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lib/libncbi-vdb.a.2.8.2
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lib/libncbi-vdb.so
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lib/libncbi-vdb.so.2
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lib/libncbi-vdb.so.2.8.2
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lib/libncbi-wvdb-static.a
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lib/libncbi-wvdb.a
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lib/libncbi-wvdb.a.2
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lib/libncbi-wvdb.a.2.8.2
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lib/libncbi-wvdb.so
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lib/libncbi-wvdb.so.2
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lib/libncbi-wvdb.so.2.8.2
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lib/ncbi/certs.kfg
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lib/ncbi/default.kfg

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