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