diff options
Diffstat (limited to 'biology/sra-tools')
68 files changed, 897 insertions, 2194 deletions
diff --git a/biology/sra-tools/Makefile b/biology/sra-tools/Makefile index 0b6a54bd67ca..2b9eb8e674cb 100644 --- a/biology/sra-tools/Makefile +++ b/biology/sra-tools/Makefile @@ -1,105 +1,66 @@ PORTNAME= sra-tools -DISTVERSION= 2.11.0 -CATEGORIES= biology +DISTVERSION= 3.0.6 +CATEGORIES= biology java MAINTAINER= jwb@FreeBSD.org COMMENT= NCBI's toolkit for handling data in INSDC Sequence Read Archives +WWW= https://github.com/ncbi/sra-tools LICENSE= PD LGPL21+ LICENSE_COMB= multi LICENSE_FILE_PD= ${WRKSRC}/LICENSE LICENSE_DISTFILES_LGPL21+ = -ONLY_FOR_ARCHS= amd64 -ONLY_FOR_ARCHS_REASON= NCBI-VDB requires SSE2 instructions, no 32-bit support +# Untested on other platforms, aarch64 support was recently added upstream +ONLY_FOR_ARCHS= aarch64 amd64 +ONLY_FOR_ARCHS_REASON= Upstream explicitly supports specific platforms -BUILD_DEPENDS= bash:shells/bash \ - ${LOCALBASE}/lib/libngs-c++.a:biology/ngs-sdk +BUILD_DEPENDS= bash:shells/bash LIB_DEPENDS= libxml2.so:textproc/libxml2 \ libhdf5.so:science/hdf5 \ - libepoll-shim.so:devel/libepoll-shim + libepoll-shim.so:devel/libepoll-shim \ + libzstd.so:archivers/zstd -USES= compiler:c11 gmake localbase:ldflags perl5 shebangfix -USE_PERL5= build +USES= bison cmake shebangfix USE_GITHUB= yes +USE_LDCONFIG= ${PREFIX}/lib64 +USE_JAVA= yes -SHEBANG_GLOB= *.sh *.pl -GH_ACCOUNT= ncbi -GH_TUPLE+= ncbi:ngs:${DISTVERSION}:ngs/ngs # ported as biology/ngs-sdk -GH_TUPLE+= ncbi:ncbi-vdb:${DISTVERSION}:vdb/ncbi-vdb - -GNU_CONFIGURE= yes -CONFIGURE_ARGS= --with-ngs-sdk-prefix=${LOCALBASE} \ - --with-ncbi-vdb-sources=${NCBI_VDB_WRKSRC} \ - --with-xml2-prefix=${LOCALBASE} \ - --with-hdf5-prefix=${LOCALBASE} \ - CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}" \ - --with-ncbi-vdb-build=${NCBI_VDB_WRKSRC}/amd64-portbld-freebsd$$(${FREEBSD_RELEASE}) -MAKE_ARGS= CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}" \ - INST_ETCDIR=${STAGEDIR}${PREFIX}/etc - -NCBI_VDB_WRKSRC= ${WRKSRC}/ncbi-vdb -NCBI_VDB_FILESDIR= ${FILESDIR} -FREEBSD_RELEASE= uname -r | cut -d - -f 1 - -CFLAGS+= -I${WRKSRC}/interfaces/os/sun -CXXFLAGS+= -I${WRKSRC}/interfaces/os/sun - -BINARY_ALIAS= gcc=${CC} g++=${CXX} +# Builds with earlier versions, but ngs-doc plist differs if jdk17 is present +JAVA_VERSION= 17+ -# for port developers, building with these options may fail -OPTIONS_DEFINE= DEBUG OPTIMIZED_CFLAGS TEST -DEBUG_PREVENTS= OPTIMIZED_CFLAGS -DEBUG_CONFIGURE_WITH= debug -OPTIMIZED_CFLAGS_MAKE_ARGS_OFF= OPT="" -TEST_TEST_TARGET= test -TEST_USES= python +OPTIONS_DEFINE= EXAMPLES -# ncbi-vdb build extras -VDB_CONFIGURE_ARGS= \ - --with-xml2-prefix=${LOCALBASE} \ - --with-hdf5-prefix=${LOCALBASE} \ - --prefix=${PREFIX} \ - --build=amd64-portbld-freebsd$$(${FREEBSD_RELEASE}) \ - CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}" -VDB_MAKE_ARGS+= -j 1 CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}" -MAKE_ENV+= CPATH="${LOCALBASE}/include/libepoll-shim" -CFLAGS+= -I${WRKSRC}/lib - -pre-patch: - @${CP} ${FILESDIR}/Makefile.bsd ${NCBI_VDB_WRKSRC}/build/ - @${CP} ${FILESDIR}/ld.bsd.*.sh ${NCBI_VDB_WRKSRC}/build/ - @${MKDIR} ${NCBI_VDB_WRKSRC}/interfaces/os/bsd - @${CP} -p ${NCBI_VDB_WRKSRC}/interfaces/os/mac/endian.h \ - ${NCBI_VDB_WRKSRC}/interfaces/os/bsd/ +SHEBANG_GLOB= *.sh +GH_ACCOUNT= ncbi +GH_TUPLE+= ncbi:ncbi-vdb:${DISTVERSION}:vdb/ncbi-vdb -post-patch: - @${GREP} -q '@@PREFIX@@' ${WRKSRC}/ncbi-vdb/libs/kfg/config.c || (echo "@@PREFIX@@ in file/patch-libs_kfg_config.c is overwritten probably due to using 'make makepatch'"; exit 1) - @${REINPLACE_CMD} -e 's#@@PREFIX@@#"${PREFIX}"#' ${WRKSRC}/ncbi-vdb/libs/kfg/config.c - @${LN} -s ${WRKSRC}/ncbi-vdb/interfaces/cc/gcc/x86_64 ${WRKSRC}/ncbi-vdb/interfaces/cc/gcc/amd64 +CMAKE_ARGS+= -DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib -post-patch-TEST-on: - @${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|' ${WRKSRC}/test/kget/Makefile +post-extract: + @${MKDIR} ${WRKSRC}/ncbi-vdb/interfaces/os/bsd + @${CP} ${FILESDIR}/*.h ${WRKSRC}/ncbi-vdb/interfaces/os/bsd + # cd ${WRKDIR} && ${LN} -s ${WRKSRC}/ncbi-vdb . pre-configure: - @${CP} ${NCBI_VDB_WRKSRC}/setup/os-arch.prl ${WRKSRC}/setup/os-arch.prl - # same as in biology/ncbi-vdb - @${CP} ${NCBI_VDB_FILESDIR}/Makefile.bsd ${WRKSRC}/build/ - @${CP} ${NCBI_VDB_WRKSRC}/build/ld.bsd.*.sh ${WRKSRC}/build/ - @${MKDIR} ${WRKSRC}/interfaces/override - @${CP} ${NCBI_VDB_WRKSRC}/interfaces/os/sun/atomic32.h ${WRKSRC}/interfaces/override - @${CP} ${FILESDIR}/byteswap.h ${WRKSRC}/interfaces/override - @cd ${WRKSRC}/ncbi-vdb && ./configure ${VDB_CONFIGURE_ARGS} - @${ECHO} ${CHOSEN_COMPILER_TYPE} > ${WRKSRC}/ncbi-vdb/build/COMP - @cd ${WRKSRC}/ncbi-vdb && ${DO_MAKE_BUILD} ${VDB_MAKE_ARGS} - -post-build-TEST-on: do-test - -do-install: - cd ${WRKSRC}/amd64-portbld-freebsd*/sra-tools/bsd/clang/*/rel/bin && \ - for f in `ls *.${PORTVERSION}`; do \ - ${INSTALL_PROGRAM} $${f} \ - ${STAGEDIR}${PREFIX}/bin/`basename $${f%%.${PORTVERSION}}`; \ - done + # This follows a static patch. Run "make clean patch" before + # updating the patch. + ${REINPLACE_CMD} -e 's|/usr/local/etc/ncbi|${PREFIX}/etc/ncbi|g' \ + ${WRKSRC}/ncbi-vdb/libs/kfg/config.c + ${REINPLACE_CMD} -e 's|/usr/local/bin|${PREFIX}/bin|g' \ + ${WRKSRC}/tools/external/driver-tool/file-path.posix.cpp + cd ${WRKSRC}/ncbi-vdb/build && cmake .. && make + +post-stage: + ${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*.${DISTVERSION} + ${MV} ${STAGEDIR}${PREFIX}/share/examples ${STAGEDIR}${PREFIX}/share/examples-sratools + ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} + ${MV} ${STAGEDIR}${PREFIX}/share/examples-sratools/* ${STAGEDIR}${EXAMPLESDIR} + ${RMDIR} ${STAGEDIR}${PREFIX}/share/examples-sratools + ${MV} ${STAGEDIR}${PREFIX}/share/examples-java ${STAGEDIR}${EXAMPLESDIR}/java + ${MV} ${STAGEDIR}${PREFIX}/share/examples-python ${STAGEDIR}${EXAMPLESDIR}/python + +post-stage-EXAMPLES-off: + ${RM} -r ${STAGEDIR}${EXAMPLESDIR} .include <bsd.port.mk> diff --git a/biology/sra-tools/distinfo b/biology/sra-tools/distinfo index fa75acf23fe6..db2f69729c91 100644 --- a/biology/sra-tools/distinfo +++ b/biology/sra-tools/distinfo @@ -1,7 +1,5 @@ -TIMESTAMP = 1624382289 -SHA256 (ncbi-sra-tools-2.11.0_GH0.tar.gz) = 10ac0a4d1fafc274bc107de811891d3e803d0713a247581dece4448231883810 -SIZE (ncbi-sra-tools-2.11.0_GH0.tar.gz) = 8966605 -SHA256 (ncbi-ngs-2.11.0_GH0.tar.gz) = 5fde50784760c00b403c2cc42ead15a4e9477697ee439f0a16edb4de3f52dfcc -SIZE (ncbi-ngs-2.11.0_GH0.tar.gz) = 1100365 -SHA256 (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 9a65e3885b9ae1ebecbec871f04ce3162ac3764fb556ecdc8c1e61993e2164aa -SIZE (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 22277539 +TIMESTAMP = 1691599515 +SHA256 (ncbi-sra-tools-3.0.6_GH0.tar.gz) = 9fecfd819ee9beaf8a1d3e4b76a5d49e747bc064525b40416e0730a168986348 +SIZE (ncbi-sra-tools-3.0.6_GH0.tar.gz) = 44957431 +SHA256 (ncbi-ncbi-vdb-3.0.6_GH0.tar.gz) = 4b6f93336bf8664fdcc151d41ea0793f0b0f88cfcb7c2aa049f162a72f905223 +SIZE (ncbi-ncbi-vdb-3.0.6_GH0.tar.gz) = 18972238 diff --git a/biology/sra-tools/files/Makefile.bsd b/biology/sra-tools/files/Makefile.bsd deleted file mode 100644 index 7692ec277948..000000000000 --- a/biology/sra-tools/files/Makefile.bsd +++ /dev/null @@ -1,72 +0,0 @@ -# =========================================================================== -# -# 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 diff --git a/biology/sra-tools/files/byteswap.h b/biology/sra-tools/files/byteswap.h index ef07fe98db64..807bea1289b8 100644 --- a/biology/sra-tools/files/byteswap.h +++ b/biology/sra-tools/files/byteswap.h @@ -1,40 +1,15 @@ -/*=========================================================================== -* -* 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. -* -* =========================================================================== -* -*/ -#ifndef _h_byteswap_ -#define _h_byteswap_ +#ifndef _freebsd_byteswap_h_ +#define _freebsd_byteswap_h_ -#include <stdint.h> #include <sys/endian.h> -/* N.B. Sun's BSWAP seems to be macro-based, - meaning that (x) will be evaluated multiple times */ +#define __BYTE_ORDER _BYTE_ORDER +#define __BIG_ENDIAN _BIG_ENDIAN +#define __LITTLE_ENDIAN _LITTLE_ENDIAN #define bswap_16(x) bswap16 (x) #define bswap_32(x) bswap32 (x) #define bswap_64(x) bswap64 (x) -#endif /* _h_byteswap_ */ +#endif diff --git a/biology/sra-tools/files/endian.h b/biology/sra-tools/files/endian.h new file mode 100644 index 000000000000..c4b8fc49f735 --- /dev/null +++ b/biology/sra-tools/files/endian.h @@ -0,0 +1,2 @@ + +#include <sys/endian.h> diff --git a/biology/sra-tools/files/ld.bsd.clang.sh b/biology/sra-tools/files/ld.bsd.clang.sh deleted file mode 100755 index 61c7779adcf1..000000000000 --- a/biology/sra-tools/files/ld.bsd.clang.sh +++ /dev/null @@ -1,47 +0,0 @@ -#!/usr/local/bin/bash -# =========================================================================== -# -# 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. -# -# =========================================================================== - -# define linker params -LD_EXPORT_GLOBAL="-Wl,--export-dynamic" -LD_MULTIPLE_DEFS="-Wl,-zmuldefs" -LD_STATIC="-Wl,-Bstatic" -LD_DYNAMIC="-Wl,-Bdynamic" -LD_ALL_SYMBOLS="-Wl,-whole-archive" -LD_REF_SYMBOLS="-Wl,-no-whole-archive" - -# build command -DLIB_CMD="$LD -shared" -EXE_CMD="$LD" - -# versioned output -if [ "$VERS" = "" ] -then - DLIB_CMD="$DLIB_CMD -o $TARG" - EXE_CMD="$EXE_CMD -o $TARG" -else - set-vers $(echo $VERS | tr '.' ' ') - DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ" - EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS" -fi diff --git a/biology/sra-tools/files/ld.bsd.cmn.sh b/biology/sra-tools/files/ld.bsd.cmn.sh deleted file mode 100755 index a0a65f39884b..000000000000 --- a/biology/sra-tools/files/ld.bsd.cmn.sh +++ /dev/null @@ -1,158 +0,0 @@ -#!/usr/local/bin/bash -# =========================================================================== -# -# 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. -# -# =========================================================================== - -# script name -SELF_NAME="$(basename $0)" - -# parameters -LD="$1" -ARCH="$2" -BUILD="$3" -shift 3 - -SRCDIR="$1" -BINDIR="$2" -OUTDIR="$3" -TARG="$4" -NAME="$5" -DBGAP="$6" -shift 6 - -VERS="$1" -VERSFILE="$2" -DEPFILE="$3" -shift 3 - -MODE="$1" -SCMFLAGS="$2" -LDFLAGS="$3" -shift 3 - -LDIRS="$1" -XDIRS="$2" -shift 2 - -OBJS="$1" -LIBS="$2" - -# decode MODE -STATIC=$(expr $MODE % 2) -MODE=$(expr $MODE / 2) -DYLD=$(expr $MODE % 2) -MODE=$(expr $MODE / 2) -KPROC=$(expr $MODE % 2) -MODE=$(expr $MODE / 2) -THREADS=$(expr $MODE % 2) -MODE=$(expr $MODE / 2) -HAVE_M=$(expr $MODE % 2) -MODE=$(expr $MODE / 2) -HAVE_XML=$(expr $MODE % 2) - -# decode SCMFLAGS -CHECKSUM=$(expr $SCMFLAGS % 2) -STATICSYSLIBS=$(expr $SCMFLAGS / 2) - -# return parameter for find-lib -LIBPATH='' - -# initial command state -CMD='' -LD_STATIC_STATE=0 -LD_ALL_STATE=0 - -# for breaking out version -set-vers () -{ - MAJ=$1 - MIN=$2 - REL=$3 -} - -# for locating libraries -find-lib () -{ - _lib="lib$1" - _dirs="$2" - - LIBPATH='' - - while [ "$_dirs" != "" ] - do - _dir="${_dirs%%:*}" - - if [ "$_dir" != "" ] - then - if [ -e "$_dir/$_lib" ] - then - while [ -L "$_dir/$_lib" ] - do - _lib=$(readlink -n "$_dir/$_lib") - done - LIBPATH="$_dir/$_lib" - break; - fi - fi - - _dirs="${_dirs#$_dir}" - _dirs="${_dirs#:}" - done -} - -# setting state -load-static () -{ - if [ $LD_STATIC_STATE -eq 0 ] - then - CMD="$CMD $LD_STATIC" - LD_STATIC_STATE=1 - fi -} - -load-dynamic () -{ - if [ $LD_STATIC_STATE -eq 1 ] - then - CMD="$CMD $LD_DYNAMIC" - LD_STATIC_STATE=0 - fi -} - -load-all-symbols () -{ - if [ $LD_ALL_STATE -eq 0 ] - then - CMD="$CMD $LD_ALL_SYMBOLS" - LD_ALL_STATE=1 - fi -} - -load-ref-symbols () -{ - if [ $LD_ALL_STATE -eq 1 ] - then - CMD="$CMD $LD_REF_SYMBOLS" - LD_ALL_STATE=0 - fi -} diff --git a/biology/sra-tools/files/ld.bsd.dlib.sh b/biology/sra-tools/files/ld.bsd.dlib.sh deleted file mode 100755 index a74f2b006818..000000000000 --- a/biology/sra-tools/files/ld.bsd.dlib.sh +++ /dev/null @@ -1,308 +0,0 @@ -#!/usr/local/bin/bash -# =========================================================================== -# -# PUBLIC DOMAIN NOTICE -# National Center for Biotechnology Information -# -# This software/database is a "United States Government Work" under the -# terms of the United States Copyright Act. It was written as part of -# the author's official duties as a United States Government employee and -# thus cannot be copyrighted. This software/database is freely available -# to the public for use. The National Library of Medicine and the U.S. -# Government have not placed any restriction on its use or reproduction. -# -# Although all reasonable efforts have been taken to ensure the accuracy -# and reliability of the software and data, the NLM and the U.S. -# Government do not and cannot warrant the performance or results that -# may be obtained by using this software or data. The NLM and the U.S. -# Government disclaim all warranties, express or implied, including -# warranties of performance, merchantability or fitness for any particular -# purpose. -# -# Please cite the author in any work or product based on this material. -# -# =========================================================================== - - -# =========================================================================== -# input library types, and their handling -# -# normal linkage -# -l : find shared or static -# -s : require static -# -d : require shared -# -# static linkage -# -l : require static -# -s : require static -# -d : ignore -# =========================================================================== - - -# script name -SELF_NAME="$(basename $0)" -BUILD_DIR="$(dirname $0)" - -# parameters and common functions -source "${0%dlib.sh}cmn.sh" - -# discover tool chain -case "$LD" in -g*) - source "${0%dlib.sh}gcc.sh" - ;; -c*) - source "${0%dlib.sh}clang.sh" - ;; - *) - echo "$SELF_NAME: unrecognized ld tool - '$LD'" - exit 5 -esac - -# DLIB_CMD was started in tool-specific source -CMD="$DLIB_CMD $LDFLAGS" - -# tack on object files -CMD="$CMD $OBJS" - -# list of static libraries used to create dynamic lib -SLIBS='' - -# initial dependency upon Makefile and vers file -DEPS="$SRCDIR/Makefile" -if [ "$LIBS" != "" ] -then - # tack on paths - DIRS="$LDIRS:$XDIRS" - while [ "$DIRS" != "" ] - do - DIR="${DIRS%%:*}" - [ "$DIR" != "" ] && CMD="$CMD -L$DIR" - DIRS="${DIRS#$DIR}" - DIRS="${DIRS#:}" - done - - # update LD_LIBRARY_PATH - unset LD_LIBRARY_PATH - export LD_LIBRARY_PATH="$LDIRS:$XDIRS" - - # tack on libraries, finding as we go - for LIB in $LIBS - do - - # strip off switch - LIBNAME="${LIB#-[lsd]}" - - # look at linkage - case "$LIB" in - -ldl|-ddl) - - # always load libdl as shared library - load-ref-symbols - load-dynamic -# CMD="$CMD -ldl" - ;; - - -l*) - - # normal or dynamic linkage - FOUND=0 - if [ $STATIC -eq 0 ] - then - find-lib $LIBNAME.so $LDIRS - if [ "$LIBPATH" != "" ] - then - - # found it - FOUND=1 - - # load normally - load-ref-symbols - load-dynamic - CMD="$CMD -l$LIBNAME" - - fi - fi - - # try static only - if [ $FOUND -eq 0 ] - then - find-lib $LIBNAME.a $LDIRS - if [ "$LIBPATH" != "" ] - then - - # found it - FOUND=1 - - # add it to dependencies - DEPS="$DEPS $LIBPATH" - SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a" - - # load static - load-static - load-all-symbols - CMD="$CMD -l$LIBNAME" - - fi - fi - - # not found within our directories - if [ $FOUND -eq 0 ] - then - - if [ $STATICSYSLIBS -eq 1 ] - then - case "$LIBNAME" in - z|bz2) - # set load to static - load-static - load-all-symbols - ;; - - *) - # set load to dynamic - load-ref-symbols - load-dynamic - ;; - - esac - else - # set load to normal - load-ref-symbols - load-dynamic - fi - - CMD="$CMD -l$LIBNAME" - fi - ;; - - -s*) - - # force static load - FOUND=0 - find-lib $LIBNAME.a $LDIRS - if [ "$LIBPATH" != "" ] - then - - # found it - FOUND=1 - - # add it to dependencies - DEPS="$DEPS $LIBPATH" - SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a" - - # load static - load-static - load-all-symbols - CMD="$CMD -l$LIBNAME" - - fi - - # not found within our directories - if [ $FOUND -eq 0 ] - then - - if [ $STATIC -eq 1 ] || [ $STATICSYSLIBS -eq 1 ] - then - # set load to static - load-static - load-all-symbols - else - - case "$LIBNAME" in - z|bz2) - # set load to dynamic - load-ref-symbols - load-dynamic - ;; - - *) - # set load to static - load-static - load-all-symbols - ;; - esac - fi - - CMD="$CMD -l$LIBNAME" - fi - ;; - - -d*) - - # only dynamic linkage - FOUND=0 - if [ $STATIC -eq 0 ] - then - find-lib $LIBNAME.so $LDIRS - if [ "$LIBPATH" != "" ] - then - - # found it - FOUND=1 - - # load normally - load-ref-symbols - load-dynamic - CMD="$CMD -l$LIBNAME" - - fi - fi - - # not found within our directories - if [ $FOUND -eq 0 ] - then - # set load to normal - load-ref-symbols - load-dynamic - CMD="$CMD -l$LIBNAME" - fi - ;; - - esac - - done -fi - -# put state back to normal -load-ref-symbols -load-dynamic - -# add in pthreads -if [ $THREADS -ne 0 ] -then - CMD="$CMD -lpthread" -fi - -# add in xml -if [ $HAVE_XML -ne 0 ] -then - CMD="$CMD -lxml2" -fi - -# add in math library -if [ $HAVE_M -ne 0 ] -then - CMD="$CMD -lm" -fi - -# produce shared library -echo "$CMD" -$CMD || exit $? - -# produce dependencies -if [ "$DEPFILE" != "" ] -then - echo "$TARG: $DEPS" > "$DEPFILE" -fi - -if [ $CHECKSUM -eq 1 ] -then - SCM_DIR="${BUILD_DIR%/*}/scm" - LOGFILE="$SCM_DIR/scm.log" - MSG=">>>>> scm: calling the collect script from ld.linux.dlib.sh <<<<<<" - #echo "$MSG" - echo "$MSG" >> $LOGFILE - - "$BUILD_DIR/scm-collect.sh" "$OBJS" "$SLIBS" | sort -u > "$TARG.md5" -fi diff --git a/biology/sra-tools/files/ld.bsd.exe.sh b/biology/sra-tools/files/ld.bsd.exe.sh deleted file mode 100755 index 650a212780c3..000000000000 --- a/biology/sra-tools/files/ld.bsd.exe.sh +++ /dev/null @@ -1,326 +0,0 @@ -#!/usr/local/bin/bash -# =========================================================================== -# -# PUBLIC DOMAIN NOTICE -# National Center for Biotechnology Information -# -# This software/database is a "United States Government Work" under the -# terms of the United States Copyright Act. It was written as part of -# the author's official duties as a United States Government employee and -# thus cannot be copyrighted. This software/database is freely available -# to the public for use. The National Library of Medicine and the U.S. -# Government have not placed any restriction on its use or reproduction. -# -# Although all reasonable efforts have been taken to ensure the accuracy -# and reliability of the software and data, the NLM and the U.S. -# Government do not and cannot warrant the performance or results that -# may be obtained by using this software or data. The NLM and the U.S. -# Government disclaim all warranties, express or implied, including -# warranties of performance, merchantability or fitness for any particular -# purpose. -# -# Please cite the author in any work or product based on this material. -# -# =========================================================================== - - -# =========================================================================== -# input library types, and their handling -# -# normal linkage -# -l : find shared or static -# -s : require static -# -d : ignore - will be dynamically loaded -# -# static linkage -# -l : require static -# -s : require static -# -d : require static -# =========================================================================== - - -# script name -SELF_NAME="$(basename $0)" -BUILD_DIR="$(dirname $0)" - -# parameters and common functions -source "${0%exe.sh}cmn.sh" - -# discover tool chain -case "$LD" in -g*) - source "${0%exe.sh}gcc.sh" - ;; -c*) - source "${0%exe.sh}clang.sh" - ;; -*) - echo "$SELF_NAME: unrecognized ld tool - '$LD'" - exit 5 -esac - -# EXE_CMD was started in tool-specific source -CMD="$EXE_CMD $LDFLAGS" - -# if building a static executable against dynamic libraries -# the main application will substitute for name lookup -if [ $STATIC -eq 1 ] && [ $DYLD -eq 1 ] -then -# CMD="$CMD $LD_EXPORT_GLOBAL $LD_MULTIPLE_DEFS" - CMD="$CMD $LD_EXPORT_GLOBAL" -fi - -# tack on object files -CMD="$CMD $OBJS" - -# list of static libraries used to create executable -SLIBS='' - -# initial dependency upon Makefile and vers file -DEPS="$SRCDIR/Makefile $VERSFILE" -if [ "$LIBS" != "" ] -then - # tack on paths - DIRS="$LDIRS:$XDIRS" - while [ "$DIRS" != "" ] - do - DIR="${DIRS%%:*}" - [ "$DIR" != "" ] && CMD="$CMD -L$DIR" - DIRS="${DIRS#$DIR}" - DIRS="${DIRS#:}" - done - - # update LD_LIBRARY_PATH - unset LD_LIBRARY_PATH - export LD_LIBRARY_PATH="$LDIRS:$XDIRS" - - # tack on libraries, finding as we go - for LIB in $LIBS - do - - # strip off switch - LIBNAME="${LIB#-[lsd]}" - - # look at linkage - case "$LIB" in - -ldl|-ddl) - - # always load libdl as shared library - load-ref-symbols - load-dynamic -# CMD="$CMD -ldl" - ;; - - -l*) - - # normal or dynamic linkage - FOUND=0 - if [ $STATIC -eq 0 ] - then - find-lib $LIBNAME.so $LDIRS - if [ "$LIBPATH" != "" ] - then - - # found it - FOUND=1 - - # load dynamic - load-dynamic - CMD="$CMD -l$LIBNAME" - - fi - fi - - # try static only - if [ $FOUND -eq 0 ] - then - find-lib $LIBNAME.a $LDIRS - if [ "$LIBPATH" != "" ] - then - - # found it - FOUND=1 - - # add it to dependencies - DEPS="$DEPS $LIBPATH" - SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a" - - # load static - load-static - [ $STATIC -eq 1 ] && load-all-symbols - CMD="$CMD -l$LIBNAME" - - fi - fi - - # not found within our directories - if [ $FOUND -eq 0 ] - then - - # do not need to load all symbols for external libs - [ $STATIC -eq 1 ] && load-ref-symbols - - if [ $STATICSYSLIBS -eq 1 ] - then - case "$LIBNAME" in - z|bz2) - # set load to static - load-static - ;; - - *) - # set load to dynamic - load-dynamic - ;; - - esac - else - # set load to normal - load-dynamic - fi - - CMD="$CMD -l$LIBNAME" - fi - ;; - - -s*) - - # force static load - FOUND=0 - find-lib $LIBNAME.a $LDIRS - if [ "$LIBPATH" != "" ] - then - - # found it - FOUND=1 - - # add it to dependencies - DEPS="$DEPS $LIBPATH" - SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a" - - # load static - load-static - [ $STATIC -eq 1 ] && load-all-symbols - CMD="$CMD -l$LIBNAME" - - fi - - # not found within our directories - if [ $FOUND -eq 0 ] - then - - # do not need to load all symbols for external libs - [ $STATIC -eq 1 ] && load-ref-symbols - - if [ $STATIC -eq 1 ] || [ $STATICSYSLIBS -eq 1 ] - then - - # set load to static - load-static - - else - - # special case for libs we have in "ext" - # that are sometimes requested as static - case "$LIBNAME" in - z|bz2) - # set load to dynamic - load-dynamic - ;; - *) - load-static - ;; - esac - fi - - CMD="$CMD -l$LIBNAME" - fi - ;; - - -d*) - - FOUND=0 - if [ $STATIC -eq 1 ] - then - find-lib $LIBNAME.a $LDIRS - if [ "$LIBPATH" != "" ] - then - - # found it - FOUND=1 - - # add it to dependencies - DEPS="$DEPS $LIBPATH" - SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a" - - # load static - load-static - load-all-symbols - - CMD="$CMD -l$LIBNAME" - - fi - - # not found within our directories - if [ $FOUND -eq 0 ] - then - load-static - load-all-symbols - - CMD="$CMD -l$LIBNAME" - fi - fi - ;; - - - esac - - done -fi - -# return to normal -load-ref-symbols -load-dynamic - -# add in pthreads -if [ $THREADS -ne 0 ] -then - CMD="$CMD -lpthread" -fi - -# add in xml -# Doesn't work since ld.sh uses HAVE_XML=32, passed here as part of MODE -if [ "$HAVE_XML2" = "1" ] -then - CMD="$CMD -lxml2" -fi - -# For sra-tools tools/* -CMD="$CMD -lepoll-shim -lxml2 -lbz2 -lz" - -# add in math library -if [ $HAVE_M -ne 0 ] -then - CMD="$CMD -lm" -fi - -# produce shared library -echo $CMD -$CMD || exit $? - -# produce dependencies -if [ "$DEPFILE" != "" ] -then - echo "$TARG: $DEPS" > "$DEPFILE" -fi - -if [ $CHECKSUM -eq 1 ] -then - SCM_DIR="${BUILD_DIR%/*}/scm" - LOGFILE="$SCM_DIR/scm.log" - MSG=">>>>> scm: calling the collect script from ld.linux.exe.sh <<<<<<" - #echo "$MSG" - echo "$MSG" >> $LOGFILE - - "$BUILD_DIR/scm-collect.sh" "$OBJS" "$SLIBS" | sort -u > "$TARG.md5" -fi diff --git a/biology/sra-tools/files/ld.bsd.gcc.sh b/biology/sra-tools/files/ld.bsd.gcc.sh deleted file mode 100755 index 61c7779adcf1..000000000000 --- a/biology/sra-tools/files/ld.bsd.gcc.sh +++ /dev/null @@ -1,47 +0,0 @@ -#!/usr/local/bin/bash -# =========================================================================== -# -# PUBLIC DOMAIN NOTICE -# National Center for Biotechnology Information -# -# This software/database is a "United States Government Work" under the -# terms of the United States Copyright Act. It was written as part of -# the author's official duties as a United States Government employee and -# thus cannot be copyrighted. This software/database is freely available -# to the public for use. The National Library of Medicine and the U.S. -# Government have not placed any restriction on its use or reproduction. -# -# Although all reasonable efforts have been taken to ensure the accuracy -# and reliability of the software and data, the NLM and the U.S. -# Government do not and cannot warrant the performance or results that -# may be obtained by using this software or data. The NLM and the U.S. -# Government disclaim all warranties, express or implied, including -# warranties of performance, merchantability or fitness for any particular -# purpose. -# -# Please cite the author in any work or product based on this material. -# -# =========================================================================== - -# define linker params -LD_EXPORT_GLOBAL="-Wl,--export-dynamic" -LD_MULTIPLE_DEFS="-Wl,-zmuldefs" -LD_STATIC="-Wl,-Bstatic" -LD_DYNAMIC="-Wl,-Bdynamic" -LD_ALL_SYMBOLS="-Wl,-whole-archive" -LD_REF_SYMBOLS="-Wl,-no-whole-archive" - -# build command -DLIB_CMD="$LD -shared" -EXE_CMD="$LD" - -# versioned output -if [ "$VERS" = "" ] -then - DLIB_CMD="$DLIB_CMD -o $TARG" - EXE_CMD="$EXE_CMD -o $TARG" -else - set-vers $(echo $VERS | tr '.' ' ') - DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ" - EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS" -fi diff --git a/biology/sra-tools/files/ld.bsd.ln.sh b/biology/sra-tools/files/ld.bsd.ln.sh deleted file mode 100755 index 4897950a2144..000000000000 --- a/biology/sra-tools/files/ld.bsd.ln.sh +++ /dev/null @@ -1,98 +0,0 @@ -#!/usr/local/bin/bash -# =========================================================================== -# -# 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. -# -# =========================================================================== - -# script name -SELF_NAME="$(basename $0)" - -# parameters -TYPE="$1" -OUTDIR="$2" -TARG="$3" -NAME="$4" -DBGAP="$5" -EXT="$6" -VERS="$7" - -# find target -TARG=$(basename "$TARG") - -# put extension back onto name -NAME="$NAME$DBGAP" -STATIC_NAME="$NAME-static" -if [ "$EXT" != "" ] -then - NAME="$NAME.$EXT" - STATIC_NAME="$STATIC_NAME.$EXT" -fi - -# break out version -set-vers () -{ - MAJ=$1 - MIN=$2 - REL=$3 -} - -set-vers $(echo $VERS | tr '.' ' ') - -cd "$OUTDIR" || exit 5 - -# create link -create-link () -{ - rm -f "$2" - local CMD="ln -s $1 $2" - echo $CMD - $CMD -} - -# test for version in target name -if [ "$TARG" != "$NAME.$MAJ.$MIN.$REL" ] -then - - # for simple name, create 2 links - if [ "$TARG" = "$NAME" ] - then - create-link "$NAME.$MAJ.$MIN.$REL" "$NAME.$MAJ" - create-link "$NAME.$MAJ" "$NAME" - - # for static libraries, create special link - if [ "$TYPE" = "slib" ] - then - create-link "$NAME" "$STATIC_NAME" - fi - - # for name with major version in it - elif [ "$TARG" = "$NAME.$MAJ" ] - then - create-link "$NAME.$MAJ.$MIN.$REL" "$NAME.$MAJ" - - - # for name with major & minor version in it - elif [ "$TARG" = "$NAME.$MAJ.$MIN" ] - then - create-link "$NAME.$MAJ.$MIN.$REL" "$NAME.$MAJ.$MIN" - fi -fi diff --git a/biology/sra-tools/files/ld.bsd.slib.sh b/biology/sra-tools/files/ld.bsd.slib.sh deleted file mode 100755 index c0e85183ea4e..000000000000 --- a/biology/sra-tools/files/ld.bsd.slib.sh +++ /dev/null @@ -1,146 +0,0 @@ -#!/usr/local/bin/bash -# =========================================================================== -# -# 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. -# -# =========================================================================== - - -# =========================================================================== -# input library types, and their handling -# -# normal or static linkage -# -l : require static -# -s : require static -# -d : ignore -# =========================================================================== - -# script name -SELF_NAME="$(basename $0)" -BUILD_DIR="$(dirname $0)" - -# parameters and common functions -source "${0%slib.sh}cmn.sh" - -# initialize command -CMD="ar -rc" - -# function to convert an archive into individual object files -convert-static () -{ - # list members - local path="$1" - local mbrs="$(ar -t $path)" - - # unpack archive into temporary directory - mkdir -p ld-tmp - if ! cd ld-tmp - then - echo "$SELF_NAME: failed to cd to ld-tmp" - exit 5 - fi - ar -x "$path" - - # rename and add to source files list - local m= - for m in $mbrs - do - mv $m $LIBNAME-$m - CMD="$CMD ld-tmp/$LIBNAME-$m" - done - - # return to prior location - cd - > /dev/null -} - -# versioned output -if [ "$VERS" = "" ] -then - CMD="$CMD $TARG" -else - set-vers $(echo $VERS | tr '.' ' ') - CMD="$CMD $OUTDIR/$NAME$DBGAP.a.$VERS" -fi - -# tack on object files -CMD="$CMD $OBJS" - -# list of static libraries used to create this lib -SLIBS='' - -# initial dependency upon Makefile and vers file -DEPS="$SRCDIR/Makefile" -if [ "$LIBS" != "" ] -then - # tack on libraries, finding as we go - for LIB in $LIBS - do - - # strip off switch - LIBNAME="${LIB#-[lsd]}" - - # look at linkage - case "$LIB" in - -s*) - - # force static load - find-lib $LIBNAME.a $LDIRS - if [ "$LIBPATH" != "" ] - then - - # add it to dependencies - DEPS="$DEPS $LIBPATH" - SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a" - - # convert to individual object files - convert-static "$LIBPATH" || exit $? - - fi - ;; - - esac - - done -fi - -# produce static library -echo $CMD -$CMD || exit $? - -# remove temporaries -rm -rf ld-tmp - -# produce dependencies -if [ "$DEPFILE" != "" ] && [ "$DEPS" != "" ] -then - echo "$TARG: $DEPS" > "$DEPFILE" -fi - -if [ $CHECKSUM -eq 1 ] -then - SCM_DIR="${BUILD_DIR%/*}/scm" - LOGFILE="$SCM_DIR/scm.log" - MSG=">>>>> scm: calling the collect script from ld.linux.slib.sh <<<<<<" - #echo "$MSG" - echo "$MSG" >> $LOGFILE - - "$BUILD_DIR/scm-collect.sh" "$OBJS" "$SLIBS" | sort -u > "$TARG.md5" -fi diff --git a/biology/sra-tools/files/os-native.h b/biology/sra-tools/files/os-native.h new file mode 100644 index 000000000000..7dc63e85c167 --- /dev/null +++ b/biology/sra-tools/files/os-native.h @@ -0,0 +1,43 @@ +/*=========================================================================== +* +* 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. +* +* =========================================================================== +* +*/ + +#ifndef _h_os_native_ +#define _h_os_native_ + +#ifndef _h_unix_native_ +#include "../unix/unix-native.h" +#endif + +#ifdef __cplusplus +extern "C" { +#endif + + +#ifdef __cplusplus +} +#endif + +#endif /* _h_os_native_ */ diff --git a/biology/sra-tools/files/patch-CMakeLists.txt b/biology/sra-tools/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..7c864a522b85 --- /dev/null +++ b/biology/sra-tools/files/patch-CMakeLists.txt @@ -0,0 +1,13 @@ +--- CMakeLists.txt.orig 2023-02-01 20:26:19 UTC ++++ CMakeLists.txt +@@ -54,8 +54,8 @@ set(CMAKE_MODULE_PATH + "${CMAKE_CURRENT_SOURCE_DIR}/build" + ) + +-set( VDB_BINDIR "${CMAKE_BINARY_DIR}/../ncbi-vdb" CACHE PATH "Location of NCBI VDB build directory" ) +-set( VDB_INCDIR "${CMAKE_SOURCE_DIR}/../ncbi-vdb/interfaces" CACHE PATH "Location of NCBI VDB include directory" ) ++set( VDB_BINDIR "${CMAKE_BINARY_DIR}/ncbi-vdb" CACHE PATH "Location of NCBI VDB build directory" ) ++set( VDB_INCDIR "${CMAKE_SOURCE_DIR}/ncbi-vdb/interfaces" CACHE PATH "Location of NCBI VDB include directory" ) + + include(CTest) + enable_testing() diff --git a/biology/sra-tools/files/patch-build_env.cmake b/biology/sra-tools/files/patch-build_env.cmake new file mode 100644 index 000000000000..be1423fb24c2 --- /dev/null +++ b/biology/sra-tools/files/patch-build_env.cmake @@ -0,0 +1,56 @@ +--- build/env.cmake.orig 2023-07-10 16:23:35 UTC ++++ build/env.cmake +@@ -69,11 +69,21 @@ if ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL "Darwin" ) + set(LIBPFX "lib") + set(SHLX "dylib") + set(STLX "a") ++elseif ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL "FreeBSD" ) ++ set(OS "bsd") ++ set(LIBPFX "lib") ++ set(SHLX "so") ++ set(STLX "a") + elseif ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL "Linux" ) + set(OS "linux") + set(LIBPFX "lib") + set(SHLX "so") + set(STLX "a") ++elseif ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL "NetBSD" ) ++ set(OS "bsd") ++ set(LIBPFX "lib") ++ set(SHLX "so") ++ set(STLX "a") + elseif ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL "Windows" ) + set(OS "windows") + set(LIBPFX "") +@@ -91,6 +101,8 @@ elseif ( ${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "aarc + set(ARCH "arm64") + elseif ( ${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "x86_64") + set(ARCH "x86_64") ++elseif ( ${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "amd64") ++ set(ARCH "x86_64") + elseif ( ${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "AMD64") + set(ARCH "x86_64") + else() +@@ -98,7 +110,11 @@ else() + endif () + + # create variables based entirely upon OS +-if ( "mac" STREQUAL ${OS} ) ++if ( "bsd" STREQUAL ${OS} ) ++ add_compile_definitions( BSD UNIX ) ++ set( LMCHECK "" ) ++ set( EXE "" ) ++elseif ( "mac" STREQUAL ${OS} ) + add_compile_definitions( MAC BSD UNIX ) + set( LMCHECK "" ) + set( EXE "" ) +@@ -380,6 +396,9 @@ endif() + + if ( "mac" STREQUAL ${OS} ) + include_directories(${VDB_INTERFACES_DIR}/os/mac) ++ include_directories(${VDB_INTERFACES_DIR}/os/unix) ++elseif( "bsd" STREQUAL ${OS} ) ++ include_directories(${VDB_INTERFACES_DIR}/os/bsd) + include_directories(${VDB_INTERFACES_DIR}/os/unix) + elseif( "linux" STREQUAL ${OS} ) + include_directories(${VDB_INTERFACES_DIR}/os/linux) diff --git a/biology/sra-tools/files/patch-build_ld.linux.exe.sh b/biology/sra-tools/files/patch-build_ld.linux.exe.sh deleted file mode 100644 index 970a7e10aac8..000000000000 --- a/biology/sra-tools/files/patch-build_ld.linux.exe.sh +++ /dev/null @@ -1,11 +0,0 @@ ---- build/ld.linux.exe.sh.orig 2021-06-20 16:32:05 UTC -+++ build/ld.linux.exe.sh -@@ -313,6 +313,8 @@ then - fi - fi - -+CMD="$CMD -lepoll-thread -lbz2 -lz" -+ - # add in math library - if [ $HAVE_M -ne 0 ] - then diff --git a/biology/sra-tools/files/patch-libs_ascp_CMakeLists.txt b/biology/sra-tools/files/patch-libs_ascp_CMakeLists.txt new file mode 100644 index 000000000000..25801b4ed932 --- /dev/null +++ b/biology/sra-tools/files/patch-libs_ascp_CMakeLists.txt @@ -0,0 +1,27 @@ +--- libs/ascp/CMakeLists.txt.orig 2023-07-10 16:23:35 UTC ++++ libs/ascp/CMakeLists.txt +@@ -23,12 +23,17 @@ + # =========================================================================== + + set ( UNIX_SRC unix/connect.c ) ++# FIXME: Add BSD-specific ascp-path.c ++# Aspera can be installed and run with linux compat ++set ( BSD_SRC ${UNIX_SRC} linux/ascp-path.c ) + set ( LINUX_SRC ${UNIX_SRC} linux/ascp-path.c ) + set ( MAC_SRC ${UNIX_SRC} mac/ascp-path.c ) + set ( WIN_SRC win/connect.c win/ascp-path.c ) + + if ( "windows" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${WIN_SRC} ) ++elseif( "bsd" STREQUAL ${OS} ) ++ set ( OS_SPECIFIC_SRC ${BSD_SRC} ) + elseif( "linux" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) + elseif( "mac" STREQUAL ${OS} ) +@@ -49,4 +54,4 @@ GenerateStaticLibs(ascp + ) + + add_compile_definitions( __mod__="libs/ascp" ) +-include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} ) +\ No newline at end of file ++include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} ) diff --git a/biology/sra-tools/files/patch-libs_general-writer_general-writer.cpp b/biology/sra-tools/files/patch-libs_general-writer_general-writer.cpp new file mode 100644 index 000000000000..b16584ab8dbf --- /dev/null +++ b/biology/sra-tools/files/patch-libs_general-writer_general-writer.cpp @@ -0,0 +1,10 @@ +--- libs/general-writer/general-writer.cpp.orig 2023-05-11 11:57:33 UTC ++++ libs/general-writer/general-writer.cpp +@@ -39,6 +39,7 @@ + #include <string.h> + + #define PROGRESS_EVENT 0 ++#define UNUSED(x) ((void)(x)) + + namespace ncbi + { diff --git a/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.clang b/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.clang deleted file mode 100644 index 99878e619099..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.clang +++ /dev/null @@ -1,30 +0,0 @@ ---- ncbi-vdb/build/Makefile.clang.orig 2021-03-15 18:16:43 UTC -+++ ncbi-vdb/build/Makefile.clang -@@ -24,23 +24,23 @@ - - - # 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 $(OBJX) -stdlib=libc++ --cflags "$(CPFLAGS)" -MD - - # C preprocessor - PP = gcc -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) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.env b/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.env deleted file mode 100644 index 4e0b80a9bf78..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.env +++ /dev/null @@ -1,25 +0,0 @@ ---- ncbi-vdb/build/Makefile.env.orig 2021-03-15 18:16:43 UTC -+++ ncbi-vdb/build/Makefile.env -@@ -333,6 +333,22 @@ 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$(MAGIC_LIBDIR) -+endif -+ifneq (,$(FUSE_LIBDIR)) -+ LDPATHS += -L$(FUSE_LIBDIR) -+endif -+ - - # defines that describe os & architecture - DLLX ?= $(SHLX) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.gcc b/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.gcc deleted file mode 100644 index d2fc4c4e04c6..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.gcc +++ /dev/null @@ -1,35 +0,0 @@ ---- ncbi-vdb/build/Makefile.gcc.orig 2017-07-14 21:55:36 UTC -+++ ncbi-vdb/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):$(ILIBDIR) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.install b/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.install deleted file mode 100644 index 143eb4d07868..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.install +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi-vdb/build/Makefile.install.orig 2021-03-15 18:16:43 UTC -+++ ncbi-vdb/build/Makefile.install -@@ -69,7 +69,7 @@ ifeq (1,$(HAVE_HDF5)) - endif - - --LIB_TARGET = $(INST_LIBDIR)$(BITS) -+LIB_TARGET = $(INST_LIBDIR) - - LIBRARIES_WITH_PREFIX = \ - $(addprefix $(LIB_TARGET)/$(LPFX),$(LIBRARIES_TO_INSTALL)) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.shell b/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.shell deleted file mode 100644 index fb98fc610def..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.shell +++ /dev/null @@ -1,31 +0,0 @@ ---- ncbi-vdb/build/Makefile.shell.orig 2017-07-14 21:55:36 UTC -+++ ncbi-vdb/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 diff --git a/biology/sra-tools/files/patch-ncbi-vdb_build_env.cmake b/biology/sra-tools/files/patch-ncbi-vdb_build_env.cmake new file mode 100644 index 000000000000..ead9978585e2 --- /dev/null +++ b/biology/sra-tools/files/patch-ncbi-vdb_build_env.cmake @@ -0,0 +1,47 @@ +--- ncbi-vdb/build/env.cmake.orig 2023-07-10 16:13:36 UTC ++++ ncbi-vdb/build/env.cmake +@@ -75,9 +75,15 @@ set(CMAKE_CXX_EXTENSIONS OFF) + if ( ${CMAKE_SYSTEM_NAME} STREQUAL "Darwin" ) + set(OS "mac") + set(SHLX "dylib") ++elseif ( ${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD" ) ++ set(OS "bsd") ++ set(SHLX "so") + elseif ( ${CMAKE_SYSTEM_NAME} STREQUAL "Linux" ) + set(OS "linux") + set(SHLX "so") ++elseif ( ${CMAKE_SYSTEM_NAME} STREQUAL "NetBSD" ) ++ set(OS "bsd") ++ set(SHLX "so") + elseif ( ${CMAKE_SYSTEM_NAME} STREQUAL "Windows" ) + set(OS "windows") + else() +@@ -99,6 +105,8 @@ elseif ( ${_system_processor} STREQUAL "x86_64") + set(ARCH "x86_64") + elseif ( ${_system_processor} STREQUAL "AMD64") + set(ARCH "x86_64") ++elseif ( ${_system_processor} STREQUAL "amd64") ++ set(ARCH "x86_64") + else () + message ( FATAL_ERROR "unknown architecture " ${_system_processor}) + endif () +@@ -110,6 +118,9 @@ if ( "mac" STREQUAL ${OS} ) + set(CMAKE_CXX_ARCHIVE_CREATE "<CMAKE_AR> Scr <TARGET> <LINK_FLAGS> <OBJECTS>") + set(CMAKE_C_ARCHIVE_FINISH "<CMAKE_RANLIB> -no_warning_for_no_symbols -c <TARGET>") + set(CMAKE_CXX_ARCHIVE_FINISH "<CMAKE_RANLIB> -no_warning_for_no_symbols -c <TARGET>") ++elseif( "bsd" STREQUAL ${OS} ) ++ add_compile_definitions( BSD UNIX ) ++ set( LMCHECK "" ) + elseif( "linux" STREQUAL ${OS} ) + add_compile_definitions( LINUX UNIX ) + set( LMCHECK -lmcheck ) +@@ -241,6 +252,9 @@ endif() + + if ( "mac" STREQUAL ${OS} ) + include_directories(interfaces/os/mac) ++ include_directories(interfaces/os/unix) ++elseif( "bsd" STREQUAL ${OS} ) ++ include_directories(interfaces/os/bsd) + include_directories(interfaces/os/unix) + elseif( "linux" STREQUAL ${OS} ) + include_directories(interfaces/os/linux) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_interfaces_os_sun_atomic32.h b/biology/sra-tools/files/patch-ncbi-vdb_interfaces_os_sun_atomic32.h deleted file mode 100644 index 3edaa3fa3fb3..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_interfaces_os_sun_atomic32.h +++ /dev/null @@ -1,85 +0,0 @@ ---- ncbi-vdb/interfaces/os/sun/atomic32.h.orig 2021-03-15 18:16:43 UTC -+++ ncbi-vdb/interfaces/os/sun/atomic32.h -@@ -1,3 +1,66 @@ -+#ifndef _h_atomic32_ -+#define _h_atomic32_ -+ -+#include <sys/types.h> -+#include <machine/atomic.h> -+ -+#ifdef __cplusplus -+extern "C" { -+#endif -+ -+/* -+ * /usr/src/sys/cddl/compat/opensolaris/sys/atomic.h -+ * BSD license -+ */ -+ -+#if defined(__i386__) || defined(__amd64__) || defined(__arm__) -+/* No spurious failures from fcmpset. */ -+#define STRONG_FCMPSET -+#endif -+ -+static inline uint32_t -+atomic_cas_32(volatile uint32_t *target, uint32_t cmp, uint32_t newval) -+{ -+#ifdef STRONG_FCMPSET -+ (void) atomic_fcmpset_32(target, &cmp, newval); -+#else -+ uint32_t expected = cmp; -+ -+ do { -+ if (atomic_fcmpset_32(target, &cmp, newval)) -+ break; -+ } while (cmp == expected); -+#endif -+ return (cmp); -+} -+ -+static inline void atomic_inc_32(volatile uint32_t *target) -+{ -+ atomic_add_32(target, 1); -+} -+ -+static __inline uint32_t atomic_add_32_nv(volatile uint32_t *target, int32_t delta) -+{ -+ return (atomic_fetchadd_32(target, delta) + delta); -+} -+ -+static __inline uint32_t atomic_inc_32_nv(volatile uint32_t *target) -+{ -+ return (atomic_add_32_nv(target, 1)); -+} -+ -+static __inline void -+atomic_dec_32(volatile uint32_t *target) -+{ -+ atomic_subtract_32(target, 1); -+} -+ -+static __inline uint32_t -+atomic_dec_32_nv(volatile uint32_t *target) -+{ -+ return (atomic_fetchadd_32(target, -1) - 1); -+} -+ - /*=========================================================================== - * - * PUBLIC DOMAIN NOTICE -@@ -23,15 +86,6 @@ - * =========================================================================== - * - */ -- --#ifndef _h_atomic32_ --#define _h_atomic32_ -- --#include <sys/atomic.h> -- --#ifdef __cplusplus --extern "C" { --#endif - - #ifndef __inline__ - #define __inline__ inline diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_align_samextract-lib.cpp b/biology/sra-tools/files/patch-ncbi-vdb_libs_align_samextract-lib.cpp new file mode 100644 index 000000000000..69973928e80f --- /dev/null +++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_align_samextract-lib.cpp @@ -0,0 +1,11 @@ +--- ncbi-vdb/libs/align/samextract-lib.cpp.orig 2023-07-10 16:13:36 UTC ++++ ncbi-vdb/libs/align/samextract-lib.cpp +@@ -48,7 +48,7 @@ + #include <stdlib.h> + #include <string.h> + +-#if LINUX ++#if BSD || LINUX + #include <unistd.h> + #define DFL_THREAD_COUNT ((int)sysconf( _SC_NPROCESSORS_ONLN ) - 1) + #else diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_ext_Makefile b/biology/sra-tools/files/patch-ncbi-vdb_libs_ext_Makefile deleted file mode 100644 index 4d3fae2846fd..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_ext_Makefile +++ /dev/null @@ -1,12 +0,0 @@ ---- ncbi-vdb/libs/ext/Makefile.orig 2021-03-15 18:16:43 UTC -+++ ncbi-vdb/libs/ext/Makefile -@@ -32,9 +32,6 @@ include $(TOP)/build/Makefile.shell - # default - # - SUBDIRS = \ -- zlib \ -- bzip2 \ -- magic \ - mbedtls - - include $(TOP)/build/Makefile.targets diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kapp_CMakeLists.txt b/biology/sra-tools/files/patch-ncbi-vdb_libs_kapp_CMakeLists.txt new file mode 100644 index 000000000000..4815ee9bdcbd --- /dev/null +++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_kapp_CMakeLists.txt @@ -0,0 +1,19 @@ +--- ncbi-vdb/libs/kapp/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC ++++ ncbi-vdb/libs/kapp/CMakeLists.txt +@@ -23,12 +23,16 @@ + # =========================================================================== + + set ( UNIX_SRC unix/args-conv-os.c unix/sysmain.c ) ++# Must patch hw.memsize -> hw.usermem ++set ( BSD_SRC ${UNIX_SRC} mac/ram.c ) + set ( LINUX_SRC ${UNIX_SRC} linux/ram.c ) + set ( MAC_SRC ${UNIX_SRC} mac/ram.c ) + set ( WIN_SRC win/args-conv-os.c win/ram.c win/sysmain.c ) + + if ( "windows" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${WIN_SRC} ) ++elseif( "bsd" STREQUAL ${OS} ) ++ set ( OS_SPECIFIC_SRC ${BSD_SRC} ) + elseif( "linux" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) + elseif( "mac" STREQUAL ${OS} ) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kapp_mac_ram.c b/biology/sra-tools/files/patch-ncbi-vdb_libs_kapp_mac_ram.c new file mode 100644 index 000000000000..67d836a71d38 --- /dev/null +++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_kapp_mac_ram.c @@ -0,0 +1,17 @@ +--- ncbi-vdb/libs/kapp/mac/ram.c.orig 2023-07-10 16:13:36 UTC ++++ ncbi-vdb/libs/kapp/mac/ram.c +@@ -46,7 +46,14 @@ rc_t KAppGetTotalRam ( uint64_t * totalRam ) + + assert ( totalRam != 0 ); + ++// FIXME: This file should probably be moved to bsd/ram.c ++#if defined(__APPLE__) + ret = sysctlbyname("hw.memsize", totalRam, &len, NULL, 0 ); ++#elif defined(__FreeBSD__) || defined(__NetBSD__) ++ ret = sysctlbyname("hw.usermem", totalRam, &len, NULL, 0 ); ++#else ++ #error "You need to add a sysctl for this platform." ++#endif + if ( ret < 0 ) + { + int status = errno; diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kfc_CMakeLists.txt b/biology/sra-tools/files/patch-ncbi-vdb_libs_kfc_CMakeLists.txt new file mode 100644 index 000000000000..05d204e31147 --- /dev/null +++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_kfc_CMakeLists.txt @@ -0,0 +1,25 @@ +--- ncbi-vdb/libs/kfc/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC ++++ ncbi-vdb/libs/kfc/CMakeLists.txt +@@ -23,12 +23,15 @@ + # =========================================================================== + + set ( UNIX_SRC unix/sysctx.c unix/sysrsrc.c ) ++set ( BSD_SRC ${UNIX_SRC} ) + set ( LINUX_SRC ${UNIX_SRC} ) + set ( MAC_SRC ${UNIX_SRC} ) + set ( WIN_SRC win/sysctx.c win/sysrsrc.c ) + + if ( "windows" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${WIN_SRC} ) ++elseif( "bsd" STREQUAL ${OS} ) ++ set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) + elseif( "linux" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) + elseif( "mac" STREQUAL ${OS} ) +@@ -48,4 +51,4 @@ set( SRC + GenerateStaticLibs( kfc "${SRC}" ) + + add_compile_definitions (__mod__="libs/kfc") +-include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} ) +\ No newline at end of file ++include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} ) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kfg_config.c b/biology/sra-tools/files/patch-ncbi-vdb_libs_kfg_config.c index f454a2b79c16..8d9268922948 100644 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_kfg_config.c +++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_kfg_config.c @@ -1,20 +1,31 @@ ---- ncbi-vdb/libs/kfg/config.c.orig 2021-03-15 18:16:43 UTC +--- ncbi-vdb/libs/kfg/config.c.orig 2023-07-10 16:13:36 UTC +++ ncbi-vdb/libs/kfg/config.c -@@ -2577,7 +2577,7 @@ bool load_from_std_location ( KConfig *self, const KDi +@@ -2574,7 +2574,7 @@ bool load_from_std_location ( KConfig *self, const KDi const char * std_locs [] = { #if ! WINDOWS - "/etc/ncbi", -+ @@PREFIX@@ "/etc/ncbi", ++ "/usr/local/etc/ncbi", #else "/c/ncbi", #endif -@@ -2850,6 +2850,8 @@ void add_predefined_nodes ( KConfig * self, const char - #define OS "win" - #elif SUN - #define OS "sun" -+#elif BSD +@@ -2588,7 +2588,7 @@ bool load_from_std_location ( KConfig *self, const KDi + NCBI_VDB_NO_ETC_NCBI_KFG[0] != '\0') + { + DBGMSG(DBG_KFG, DBG_FLAG(DBG_KFG), +- ("KFG: load from std. location /etc/ncbi is disabled. " ++ ("KFG: load from std. location /usr/local/etc/ncbi is disabled. " + "NCBI_VDB_NO_ETC_NCBI_KFG='%s'\n", NCBI_VDB_NO_ETC_NCBI_KFG)); + return loaded; + } +@@ -2839,7 +2839,9 @@ void add_predefined_nodes ( KConfig * self, const char + update_node ( self, "kfg/arch/bits", buf, true ); + + /* *OS */ +-#if LINUX ++#if BSD + #define OS "bsd" - #else - #error unrecognized OS - #endif ++#elif LINUX + #define OS "linux" + #elif MAC + #define OS "mac" diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kfs_CMakeLists.txt b/biology/sra-tools/files/patch-ncbi-vdb_libs_kfs_CMakeLists.txt new file mode 100644 index 000000000000..c6b4801f527d --- /dev/null +++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_kfs_CMakeLists.txt @@ -0,0 +1,35 @@ +--- ncbi-vdb/libs/kfs/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC ++++ ncbi-vdb/libs/kfs/CMakeLists.txt +@@ -23,6 +23,7 @@ + # =========================================================================== + + set ( UNIX_SRC unix/sysdir.c unix/sysdll.c unix/sysfile.c unix/syslockfile.c unix/sysmmap.c ) ++set ( BSD_SRC ${UNIX_SRC} ) + set ( LINUX_SRC ${UNIX_SRC} ) + set ( MAC_SRC ${UNIX_SRC} ) + set ( WIN_SRC win/directory-path.c win/sysdir.c win/sysdll.c win/sysfile.c win/syslockfile.c win/sysmmap.c +@@ -30,6 +31,7 @@ set ( WIN_SRC win/directory-path.c win/sysdir.c win/sy + ) + + set ( UNIX_SRC_V2 unix/sysfile-v2.c ) ++set ( BSD_SRC_V2 ${UNIX_SRC_V2} ) + set ( LINUX_SRC_V2 ${UNIX_SRC_V2} ) + set ( MAC_SRC_V2 ${UNIX_SRC_V2} ) + set ( WIN_SRC_V2 win/sysfile-v2.c ) +@@ -37,6 +39,9 @@ set ( WIN_SRC_V2 win/sysfile-v2.c ) + if ( "windows" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${WIN_SRC} ) + include_directories( win ) ++elseif( "bsd" STREQUAL ${OS} ) ++ set ( OS_SPECIFIC_SRC ${BSD_SRC} ) ++ include_directories( unix ) + elseif( "linux" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) + include_directories( unix ) +@@ -106,4 +111,4 @@ GenerateStaticLibsWithDefs( kfs-nommap ${KFS_NOMMAP_SR + GenerateStaticLibs( kfs "${KFS_SRC}" ) + + add_compile_definitions (__mod__="libs/kfs") +-include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} ) +\ No newline at end of file ++include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} ) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kfs_unix_sysdir.c b/biology/sra-tools/files/patch-ncbi-vdb_libs_kfs_unix_sysdir.c new file mode 100644 index 000000000000..b128f98c29eb --- /dev/null +++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_kfs_unix_sysdir.c @@ -0,0 +1,11 @@ +--- ncbi-vdb/libs/kfs/unix/sysdir.c.orig 2023-07-10 16:13:36 UTC ++++ ncbi-vdb/libs/kfs/unix/sysdir.c +@@ -2291,6 +2291,8 @@ rc_t KSysDirOpenDirRead_v1 ( const KSysDir_v1 * self, + rc_t rc; + + rc = KSysDirMakePath_v1 ( self, rcOpening, true, full, sizeof full, path, args ); ++ // FIXME: Remove this debug statement ++ // fprintf(stderr, "path = %s full = %s\n", path, full); + if ( rc == 0 ) + { + int t; diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_CMakeLists.txt b/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_CMakeLists.txt new file mode 100644 index 000000000000..a854e97d5480 --- /dev/null +++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_CMakeLists.txt @@ -0,0 +1,18 @@ +--- ncbi-vdb/libs/klib/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC ++++ ncbi-vdb/libs/klib/CMakeLists.txt +@@ -24,12 +24,15 @@ + + set ( UNIX_BASE_SRC unix/misc.c unix/syslog.c unix/systime.c unix/syswriter.c ) + set ( UNIX_SRC ${UNIX_BASE_SRC} unix/syserrcode.c ) ++set ( BSD_SRC ${UNIX_SRC} ) + set ( LINUX_SRC ${UNIX_BASE_SRC} linux/syserrcode.c ) + set ( MAC_SRC ${UNIX_SRC} ) + set ( WIN_SRC win/misc.c win/sysalloc.c win/syserrcode.c win/syslog.c win/systime.c win/syswriter.c ) + + if ( "windows" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${WIN_SRC} ) ++elseif( "bsd" STREQUAL ${OS} ) ++ set ( OS_SPECIFIC_SRC ${BSD_SRC} ) + elseif( "linux" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) + elseif( "mac" STREQUAL ${OS} ) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_hashfile.c b/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_hashfile.c new file mode 100644 index 000000000000..205569c40a3e --- /dev/null +++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_hashfile.c @@ -0,0 +1,20 @@ +--- ncbi-vdb/libs/klib/hashfile.c.orig 2023-07-10 16:13:36 UTC ++++ ncbi-vdb/libs/klib/hashfile.c +@@ -35,7 +35,7 @@ + #include <stdio.h> + #include <stdlib.h> + #include <string.h> +-#if LINUX ++#if BSD || LINUX + #include <sys/mman.h> + #endif + +@@ -346,7 +346,7 @@ static void * map_calloc( KHashFile * self, size_t siz + KLockUnlock( self->alloc_lock ); + return NULL; + } +-#if LINUX ++#if BSD || LINUX + /* Not sure this helps */ + madvise( (void *)self->alloc_base, req, MADV_RANDOM ); + #endif diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_unix_systime.c b/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_unix_systime.c index 3732c47ce93a..193f584e41fe 100644 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_unix_systime.c +++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_unix_systime.c @@ -1,11 +1,16 @@ ---- ncbi-vdb/libs/klib/unix/systime.c.orig 2017-07-14 21:55:36 UTC +--- ncbi-vdb/libs/klib/unix/systime.c.orig 2023-07-10 16:13:36 UTC +++ ncbi-vdb/libs/klib/unix/systime.c -@@ -142,7 +142,7 @@ LIB_EXPORT KTime_t CC KTimeMakeTime ( co +@@ -142,7 +142,13 @@ LIB_EXPORT KTime_t CC KTimeMakeTime ( const KTime *sel t . tm_isdst = self -> dst; ts = mktime ( &t ); -- ts -= timezone; -+ ts += localtime(&ts)->tm_gmtoff; ++#ifdef __FreeBSD__ ++ // This might be portable to all platforms ++ ts += localtime(&ts)->tm_gmtoff; ++#else ++ // extern global in sys/time.h on Linux and some other platforms + ts -= timezone; ++#endif } return ts; diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_CMakeLists.txt b/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_CMakeLists.txt new file mode 100644 index 000000000000..c85b1b6631ca --- /dev/null +++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_CMakeLists.txt @@ -0,0 +1,20 @@ +--- ncbi-vdb/libs/kns/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC ++++ ncbi-vdb/libs/kns/CMakeLists.txt +@@ -23,6 +23,7 @@ + # =========================================================================== + + set ( UNIX_SRC unix/sysmgr.c unix/syssock.c unix/sysstream.c ) ++set ( BSD_SRC ${UNIX_SRC} mac/sysendpoint.c mac/syspoll.c ) + set ( LINUX_SRC ${UNIX_SRC} linux/sysendpoint.c linux/syspoll.c ) + set ( MAC_SRC ${UNIX_SRC} mac/sysendpoint.c mac/syspoll.c ) + set ( WIN_SRC win/sysendpoint.c win/sysmgr.c win/syssock.c win/sysstream.c ) +@@ -30,6 +31,9 @@ set ( WIN_SRC win/sysendpoint.c win/sysmgr.c win/sysso + if ( "windows" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${WIN_SRC} ) + include_directories( win ) ++elseif( "bsd" STREQUAL ${OS} ) ++ set ( OS_SPECIFIC_SRC ${BSD_SRC} ) ++ include_directories( unix ) + elseif( "linux" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) + include_directories( unix ) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_manager.c b/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_manager.c new file mode 100644 index 000000000000..816454bea102 --- /dev/null +++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_manager.c @@ -0,0 +1,11 @@ +--- ncbi-vdb/libs/kns/manager.c.orig 2023-07-10 16:13:36 UTC ++++ ncbi-vdb/libs/kns/manager.c +@@ -58,7 +58,7 @@ + #if HAVE_GNU_LIBC_VERSION_H + #include <gnu/libc-version.h> + #endif +-#if LINUX ++#if BSD || LINUX + #include <arpa/inet.h> + #include <netinet/in.h> + #endif diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_unix_syssock.c b/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_unix_syssock.c index 50484bb1d503..313461f90846 100644 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_unix_syssock.c +++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_unix_syssock.c @@ -1,4 +1,4 @@ ---- ncbi-vdb/libs/kns/unix/syssock.c.orig 2017-07-14 21:55:36 UTC +--- ncbi-vdb/libs/kns/unix/syssock.c.orig 2023-08-07 20:34:54 UTC +++ ncbi-vdb/libs/kns/unix/syssock.c @@ -66,6 +66,7 @@ #include <sys/types.h> diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kproc_CMakeLists.txt b/biology/sra-tools/files/patch-ncbi-vdb_libs_kproc_CMakeLists.txt new file mode 100644 index 000000000000..2f4e808e2d65 --- /dev/null +++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_kproc_CMakeLists.txt @@ -0,0 +1,21 @@ +--- ncbi-vdb/libs/kproc/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC ++++ ncbi-vdb/libs/kproc/CMakeLists.txt +@@ -23,6 +23,7 @@ + # =========================================================================== + + set ( UNIX_SRC unix/syscond.c unix/systhread.c unix/systimeout.c ) ++set ( BSD_SRC ${UNIX_SRC} bsd/syslock.c bsd/sysmgr.c) + set ( LINUX_SRC ${UNIX_SRC} linux/sysbarrier.c linux/syslock.c linux/sysmgr.c ) + set ( MAC_SRC ${UNIX_SRC} bsd/syslock.c bsd/sysmgr.c) + set ( WIN_SRC win/syscond.c win/syslock.c win/sysmgr.c win/systhread.c win/systimeout.c ) +@@ -30,6 +31,10 @@ set ( WIN_SRC win/syscond.c win/syslock.c win/sysmgr.c + if ( "windows" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${WIN_SRC} ) + include_directories( win ) ++elseif( "bsd" STREQUAL ${OS} ) ++ set ( OS_SPECIFIC_SRC ${BSD_SRC} ) ++ include_directories( bsd ) ++ include_directories( unix ) + elseif( "linux" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) + include_directories( linux ) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_ktst_CMakeLists.txt b/biology/sra-tools/files/patch-ncbi-vdb_libs_ktst_CMakeLists.txt new file mode 100644 index 000000000000..78926849f124 --- /dev/null +++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_ktst_CMakeLists.txt @@ -0,0 +1,18 @@ +--- ncbi-vdb/libs/ktst/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC ++++ ncbi-vdb/libs/ktst/CMakeLists.txt +@@ -23,12 +23,15 @@ + # =========================================================================== + + set ( UNIX_SRC unix/systestenv ) ++set ( BSD_SRC ${UNIX_SRC} ) + set ( LINUX_SRC ${UNIX_SRC} ) + set ( MAC_SRC ${UNIX_SRC} ) + set ( WIN_SRC win/systestenv ) + + if ( "windows" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${WIN_SRC} ) ++elseif( "bsd" STREQUAL ${OS} ) ++ set ( OS_SPECIFIC_SRC ${BSD_SRC} ) + elseif( "linux" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) + elseif( "mac" STREQUAL ${OS} ) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_ncbi-vdb_Makefile b/biology/sra-tools/files/patch-ncbi-vdb_libs_ncbi-vdb_Makefile deleted file mode 100644 index 7f5ad0a8802f..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_ncbi-vdb_Makefile +++ /dev/null @@ -1,20 +0,0 @@ ---- ncbi-vdb/libs/ncbi-vdb/Makefile.orig 2021-06-20 15:15:25 UTC -+++ ncbi-vdb/libs/ncbi-vdb/Makefile -@@ -138,9 +138,7 @@ VDB_LIB_CMN = \ - klib \ - kproc \ - $(LIBKQ) \ -- kfc \ -- bz2 \ -- z \ -+ kfc - - VDB_LIB_RD = \ - align-reader \ -@@ -198,4 +196,4 @@ fuzz: - $(TOP)/build/ld.sh linux x86_64 gcc --build dbg --ldflags "-g -m64" --objx o --shlx so --libx a --srcdir $(SRCDIR) --bindir $(BINDIR) --slib -o $(FLIBDIR)/libncbi-vdb.$(LIBX) -L$(FLIBDIR) $(VDB_LIB) $(VDB_NGS_LIB) - - cleanfuzz: -- rm -rf $(FLIBDIR)/* -\ No newline at end of file -+ rm -rf $(FLIBDIR)/* diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_search_Makefile b/biology/sra-tools/files/patch-ncbi-vdb_libs_search_Makefile deleted file mode 100644 index b1c52cb7ecf4..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_search_Makefile +++ /dev/null @@ -1,12 +0,0 @@ ---- ncbi-vdb/libs/search/Makefile.orig 2017-07-14 21:55:36 UTC -+++ ncbi-vdb/libs/search/Makefile -@@ -39,6 +39,9 @@ OBJFILES = \ - - include $(TOP)/build/Makefile.env - -+CARCH += -msse2 -+# nucstrstr.c requires SSE2 -+ - #------------------------------------------------------------------------------- - # outer targets - # diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_vfs_CMakeLists.txt b/biology/sra-tools/files/patch-ncbi-vdb_libs_vfs_CMakeLists.txt new file mode 100644 index 000000000000..5d670acdbe4b --- /dev/null +++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_vfs_CMakeLists.txt @@ -0,0 +1,25 @@ +--- ncbi-vdb/libs/vfs/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC ++++ ncbi-vdb/libs/vfs/CMakeLists.txt +@@ -23,12 +23,15 @@ + # =========================================================================== + + set ( UNIX_SRC unix/syskeyring.c unix/syspath.c ) ++set ( BSD_SRC ${UNIX_SRC} ) + set ( LINUX_SRC ${UNIX_SRC} ) + set ( MAC_SRC ${UNIX_SRC} ) + set ( WIN_SRC win/syskeyring.c win/syspath.c ) + + if ( "windows" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${WIN_SRC} ) ++elseif( "bsd" STREQUAL ${OS} ) ++ set ( OS_SPECIFIC_SRC ${BSD_SRC} ) + elseif( "linux" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) + elseif( "mac" STREQUAL ${OS} ) +@@ -54,4 +57,4 @@ set( SRC + GenerateStaticLibs( vfs "${SRC}" ) + + add_compile_definitions (__mod__="libs/vfs") +-include_directories(${CMAKE_CURRENT_SOURCE_DIR}) +\ No newline at end of file ++include_directories(${CMAKE_CURRENT_SOURCE_DIR}) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_setup_konfigure.perl b/biology/sra-tools/files/patch-ncbi-vdb_setup_konfigure.perl deleted file mode 100644 index 8d293bbd71cc..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_setup_konfigure.perl +++ /dev/null @@ -1,243 +0,0 @@ ---- ncbi-vdb/setup/konfigure.perl.orig 2021-03-15 18:16:43 UTC -+++ ncbi-vdb/setup/konfigure.perl -@@ -192,7 +192,7 @@ 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 $PACKAGE_NAME package"; -@@ -204,7 +204,7 @@ print "checking system type... " unless ($AUTORUN); - 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; - } -@@ -225,7 +225,7 @@ if ($OS eq 'linux') { - - print "checking machine architecture... " unless ($AUTORUN); - println $MARCH unless ($AUTORUN); --unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i || $MARCH =~ /aarch64/) { -+unless ($MARCH =~ /x86_64/i || $MARCH =~ /amd64/i || $MARCH =~ /i?86/i || $MARCH =~ /aarch64/) { - println "configure: error: unsupported architecture '$OSTYPE':'$MARCH'"; - exit 1; - } -@@ -310,7 +310,7 @@ print "checking for supported architecture... " unless - - my $BITS; - --if ($MARCH =~ /x86_64/i) { -+if ($MARCH =~ /(x86_|amd)64/i) { - $BITS = 64; - } elsif ($MARCH eq 'fat86') { - $BITS = '32_64'; -@@ -337,6 +337,19 @@ if ($OSTYPE =~ /linux/i) { - $OSINC = 'unix'; - $TOOLS = 'gcc' unless ($TOOLS); - $PYTHON = 'python'; -+} elsif ($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}); -+ } -+ $PYTHON = $ENV{FREEBSD_PYTHON_CMD}; - } elsif ($OSTYPE =~ /darwin/i) { - $LPFX = 'lib'; - $OBJX = 'o'; -@@ -362,17 +375,19 @@ my ($ARCH_FL, $DBG, $OPT, $PIC, $INC, $MD, $LDFLAGS) = - - print "checking for supported tool chain... " unless ($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; - - $DBG = '-g -DDEBUG'; -@@ -382,21 +397,24 @@ if ($TOOLS =~ /gcc$/) { - $MD = '-MD'; - } elsif ($TOOLS eq 'clang') { - $CPP = 'clang++' unless ($CPP); -- $CC = 'clang -c'; -- my $versionMin = '-mmacosx-version-min=10.10'; -+ $CC = 'clang' unless ($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"; - } - $ARX = 'ar x'; -@@ -826,13 +844,13 @@ OS_ARCH = \$(shell perl \$(TOP)/setup/os-arch.perl) - # install paths - EndText - -- L($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); -@@ -896,7 +914,7 @@ 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 $MARCH); -@@ -932,7 +950,7 @@ EndText - } - L($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 $(VERSION) \\'); -@@ -1043,7 +1061,7 @@ EndText - L($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 -@@ -1073,12 +1091,12 @@ 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),%$(LIBX),$@) ' -@@ -1087,7 +1105,7 @@ 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($F, ' else \\'); -@@ -1097,15 +1115,15 @@ EndText - L($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 $(@F) ' -@@ -1124,7 +1142,7 @@ EndText - - L($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),%$(EXEX),$@); \\'); -@@ -1406,7 +1424,7 @@ 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 $f) { -@@ -1628,12 +1646,12 @@ sub find_lib { - - sub check_compiler { - my ($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; -@@ -1706,7 +1724,7 @@ sub check_compiler { - } - } - 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; diff --git a/biology/sra-tools/files/patch-ncbi-vdb_setup_os-arch.prl b/biology/sra-tools/files/patch-ncbi-vdb_setup_os-arch.prl deleted file mode 100644 index 01cb9824ff7b..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_setup_os-arch.prl +++ /dev/null @@ -1,20 +0,0 @@ ---- ncbi-vdb/setup/os-arch.prl.orig 2021-03-15 18:16:43 UTC -+++ ncbi-vdb/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/) { -@@ -48,6 +50,8 @@ sub OsArch { - $HOST_ARCH = 'i386'; - } - } elsif ($MARCH =~ /x86_64/) { -+ $HOST_ARCH = 'x86_64'; -+ } elsif ($MARCH =~ /amd64/) { - $HOST_ARCH = 'x86_64'; - } elsif ($MARCH =~ /i86pc/) { - $HOST_ARCH = 'x86_64'; diff --git a/biology/sra-tools/files/patch-ncbi-vdb_test_kfg_kfgtest.cpp b/biology/sra-tools/files/patch-ncbi-vdb_test_kfg_kfgtest.cpp index 468483b89535..ce1bb1b02508 100644 --- a/biology/sra-tools/files/patch-ncbi-vdb_test_kfg_kfgtest.cpp +++ b/biology/sra-tools/files/patch-ncbi-vdb_test_kfg_kfgtest.cpp @@ -1,11 +1,11 @@ ---- ncbi-vdb/test/kfg/kfgtest.cpp.orig 2019-08-20 18:27:10 UTC +--- ncbi-vdb/test/kfg/kfgtest.cpp.orig 2023-07-10 16:13:36 UTC +++ ncbi-vdb/test/kfg/kfgtest.cpp -@@ -280,6 +280,8 @@ FIXTURE_TEST_CASE(predef_OS, KfgFixture) +@@ -282,6 +282,8 @@ FIXTURE_TEST_CASE(predef_ARCHBITS, KfgFixture) + FIXTURE_TEST_CASE(predef_OS, KfgFixture) + { CreateAndLoad(GetName(), "var=$(OS)\n"); ++ #if BSD ++ #define OS "bsd" #if LINUX #define OS "linux" -+ #elif BSD -+ #define OS "bsd" #elif SUN - #define OS "sun" - #elif MAC diff --git a/biology/sra-tools/files/patch-ncbi-vdb_test_klib_printf-test.c b/biology/sra-tools/files/patch-ncbi-vdb_test_klib_printf-test.c index 76b1210a7ae7..0ce58974e6ed 100644 --- a/biology/sra-tools/files/patch-ncbi-vdb_test_klib_printf-test.c +++ b/biology/sra-tools/files/patch-ncbi-vdb_test_klib_printf-test.c @@ -1,11 +1,11 @@ ---- ncbi-vdb/test/klib/printf-test.c.orig 2019-08-20 18:27:10 UTC +--- ncbi-vdb/test/klib/printf-test.c.orig 2023-07-10 16:13:36 UTC +++ ncbi-vdb/test/klib/printf-test.c -@@ -503,7 +503,7 @@ rc_t run ( const char *progname ) +@@ -504,7 +504,7 @@ 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 + #if 0 + /* The standard says this result is undefined, we shouldn't test for it, it is not consistent */ diff --git a/biology/sra-tools/files/patch-ncbi-vdb_test_kns_Makefile b/biology/sra-tools/files/patch-ncbi-vdb_test_kns_Makefile deleted file mode 100644 index 958399985cc9..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_test_kns_Makefile +++ /dev/null @@ -1,19 +0,0 @@ ---- ncbi-vdb/test/kns/Makefile.orig 2021-03-15 18:16:43 UTC -+++ ncbi-vdb/test/kns/Makefile -@@ -25,7 +25,7 @@ - - default: runtests - --runtests: run-tests run-test-proxy-with-scheme -+runtests: - - TOP ?= $(abspath ../..) - MODULE = test/kns -@@ -133,6 +133,7 @@ $(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 - - #---------------------------------------------------------------- diff --git a/biology/sra-tools/files/patch-ncbi-vdb_test_vdb_test-dependencies.cpp b/biology/sra-tools/files/patch-ncbi-vdb_test_vdb_test-dependencies.cpp deleted file mode 100644 index 52bcf0460632..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_test_vdb_test-dependencies.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi-vdb/test/vdb/test-dependencies.cpp.orig 2019-08-20 18:27:10 UTC -+++ ncbi-vdb/test/vdb/test-dependencies.cpp -@@ -115,7 +115,7 @@ class EmptyFixture : public DepFixture { (public) - - class RefseqFixture : public DepFixture { - -- #if LINUX -+ #if LINUX || BSD - #define PATH "kfg/linux" - #elif MAC - #define PATH "kfg/mac" diff --git a/biology/sra-tools/files/patch-ncbi-vdb_test_vdb_test-dependencies__dflt.cpp b/biology/sra-tools/files/patch-ncbi-vdb_test_vdb_test-dependencies__dflt.cpp new file mode 100644 index 000000000000..b063ef020502 --- /dev/null +++ b/biology/sra-tools/files/patch-ncbi-vdb_test_vdb_test-dependencies__dflt.cpp @@ -0,0 +1,12 @@ +--- ncbi-vdb/test/vdb/test-dependencies_dflt.cpp.orig 2023-07-10 16:13:36 UTC ++++ ncbi-vdb/test/vdb/test-dependencies_dflt.cpp +@@ -139,6 +139,9 @@ class EmptyFixture : public DepFixture { (public) + + class RefseqFixture : public DepFixture { + ++ #if BSD ++ // FIXME: Should there be a separate kfg/freebsd? ++ #define PATH "kfg/linux" + #if LINUX + #define PATH "kfg/linux" + #elif MAC diff --git a/biology/sra-tools/files/patch-ncbi-vdb_test_vfs_redirect-rejected-names-cgi-http-to-https.cpp b/biology/sra-tools/files/patch-ncbi-vdb_test_vfs_redirect-rejected-names-cgi-http-to-https.cpp deleted file mode 100644 index 12780a95a08a..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_test_vfs_redirect-rejected-names-cgi-http-to-https.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi-vdb/test/vfs/redirect-rejected-names-cgi-http-to-https.cpp.orig 2017-07-14 21:55:36 UTC -+++ ncbi-vdb/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 diff --git a/biology/sra-tools/files/patch-setup_install.perl b/biology/sra-tools/files/patch-setup_install.perl deleted file mode 100644 index cc2eade52c15..000000000000 --- a/biology/sra-tools/files/patch-setup_install.perl +++ /dev/null @@ -1,13 +0,0 @@ ---- setup/install.perl.orig 2021-03-15 18:25:25 UTC -+++ setup/install.perl -@@ -1283,8 +1283,8 @@ sub prepare { - ' $_{INST_JARDIR } = "$_{PREFIX}/jar"; ' . - ' $_{INST_SHAREDIR} = "$_{PREFIX}/share"; ' . - ' $_{INCDIR } = "$Bin/../include"; ' . -- ' $_{LIBDIR64 } = "$Bin/../lib64"; ' . -- ' $_{LIBDIR32 } = "$Bin/../lib32"; '; -+ ' $_{LIBDIR64 } = "$Bin/../lib"; ' . -+ ' $_{LIBDIR32 } = "$Bin/../lib"; '; - if ($HAVE{TWO_LIBS}) { - $code .= - '$_{INST_NGSLIBDIR} = "' . "$root/usr/local/ngs/ngs-sdk/lib\";" diff --git a/biology/sra-tools/files/patch-setup_konfigure.perl b/biology/sra-tools/files/patch-setup_konfigure.perl deleted file mode 100644 index aacfe898be6d..000000000000 --- a/biology/sra-tools/files/patch-setup_konfigure.perl +++ /dev/null @@ -1,121 +0,0 @@ ---- setup/konfigure.perl.orig 2021-03-15 18:25:25 UTC -+++ setup/konfigure.perl -@@ -204,7 +204,7 @@ print "checking system type... " unless ($AUTORUN); - 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 =~ /darwin/i || $OSTYPE eq 'win' || $OSTYPE =~ /freebsd/i) { - println "configure: error: unsupported system '$OSTYPE'"; - exit 1; - } -@@ -225,7 +225,7 @@ if ($OS eq 'linux') { - - print "checking machine architecture... " unless ($AUTORUN); - println $MARCH unless ($AUTORUN); --unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i || $MARCH =~ /aarch64/) { -+unless ($MARCH =~ /x86_64/i || $MARCH =~ /amd64/i || $MARCH =~ /i?86/i || $MARCH =~ /aarch64/) { - println "configure: error: unsupported architecture '$OSTYPE':'$MARCH'"; - exit 1; - } -@@ -310,7 +310,7 @@ print "checking for supported architecture... " unless - - my $BITS; - --if ($MARCH =~ /x86_64/i) { -+if ($MARCH =~ /x86_64/i || $MARCH =~ /amd64/i) { - $BITS = 64; - } elsif ($MARCH eq 'fat86') { - $BITS = '32_64'; -@@ -337,6 +337,16 @@ if ($OSTYPE =~ /linux/i) { - $OSINC = 'unix'; - $TOOLS = 'gcc' unless ($TOOLS); - $PYTHON = 'python'; -+} elsif ($OSTYPE =~ /freebsd/i) { -+ $LPFX = 'lib'; -+ $OBJX = 'o'; -+ $LOBX = 'pic.o'; -+ $LIBX = 'a'; -+ $SHLX = 'so'; -+ $EXEX = ''; -+ $OSINC = 'unix'; -+ $TOOLS = 'clang' unless ($TOOLS); -+ $PYTHON = 'python'; - } elsif ($OSTYPE =~ /darwin/i) { - $LPFX = 'lib'; - $OBJX = 'o'; -@@ -512,7 +522,7 @@ foreach my $href (DEPENDS()) { - $I = $t if (-e $t); - } - push ( @L, File::Spec->catdir($OPT{$o}, 'lib') ); -- push ( @L, File::Spec->catdir($OPT{$o}, 'lib64') ); -+ #push ( @L, File::Spec->catdir($OPT{$o}, 'lib64') ); - } - my ($i, $l) = find_lib($_, $I, @L); - if (defined $i || $l) { -@@ -934,7 +944,7 @@ EndText - if ($PKG{LNG} eq 'C') { - if ($TOOLS =~ /clang/i) { - L($F, 'SONAME = -install_name ' . -- '$(INST_LIBDIR)$(BITS)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\'); -+ '$(INST_LIBDIR)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\'); - L($F, ' -compatibility_version $(MAJMIN) -current_version $(VERSION) \\'); - L($F, ' -flat_namespace -undefined suppress'); - } else { -@@ -1043,7 +1053,7 @@ EndText - L($F, '# directory rules'); - if ($PKG{LNG} eq 'C') { - L($F, '$(BINDIR) $(LIBDIR) $(ILIBDIR) ' -- . '$(OBJDIR) $(INST_LIBDIR) $(INST_LIBDIR)$(BITS):'); -+ . '$(OBJDIR) $(INST_LIBDIR) $(INST_LIBDIR):'); - T($F, 'mkdir -p $@'); - } elsif ($PKG{LNG} eq 'JAVA') { - # test if we have jni header path -@@ -1076,7 +1086,7 @@ EndText - if ($OS eq 'linux' || $OS eq 'mac') { - L($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, ' then \\'); -@@ -1087,7 +1097,7 @@ 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($F, ' else \\'); -@@ -1097,7 +1107,7 @@ EndText - L($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, ' then \\'); -@@ -1168,9 +1178,9 @@ EndText - print $F " \$_{INCDIR } = '" . expand("$Bin/.." ) . "';\n"; - if ($PKG{LNG} ne 'PYTHON') { - print $F " \$_{BINDIR$BITS} = '" . expand($E_BINDIR ) . "';\n"; -- print $F " \$_{LIBDIR$BITS} = '" . expand($E_LIBDIR ) . "';\n"; -+ print $F " \$_{LIBDIR} = '" . expand($E_LIBDIR ) . "';\n"; - } elsif ($OPT{PYTHON_LIB_PATH}) { -- print $F " \$_{LIBDIR$BITS} = '$OPT{PYTHON_LIB_PATH}';\n"; -+ print $F " \$_{LIBDIR} = '$OPT{PYTHON_LIB_PATH}';\n"; - } - print $F " \$_{OTHER_PREFIX } = '$PKG{UPATH}';\n"; - print $F " \$_{PREFIX } = '$OPT{'prefix'}';\n"; -@@ -1406,7 +1416,7 @@ 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) { diff --git a/biology/sra-tools/files/patch-tools_bam-loader_loader-imp.c b/biology/sra-tools/files/patch-tools_bam-loader_loader-imp.c deleted file mode 100644 index 9b78a578a601..000000000000 --- a/biology/sra-tools/files/patch-tools_bam-loader_loader-imp.c +++ /dev/null @@ -1,10 +0,0 @@ ---- tools/bam-loader/loader-imp.c.orig 2021-06-20 16:59:47 UTC -+++ tools/bam-loader/loader-imp.c -@@ -71,6 +71,7 @@ - #include <sysalloc.h> - #include <atomic32.h> - -+#include <sys/stat.h> - #include <unistd.h> - #include <fcntl.h> - #include <sys/mman.h> diff --git a/biology/sra-tools/files/patch-tools_copycat_Makefile b/biology/sra-tools/files/patch-tools_copycat_Makefile deleted file mode 100644 index fb24ac9e5d4e..000000000000 --- a/biology/sra-tools/files/patch-tools_copycat_Makefile +++ /dev/null @@ -1,11 +0,0 @@ ---- tools/copycat/Makefile.orig 2021-06-20 17:45:49 UTC -+++ tools/copycat/Makefile -@@ -92,7 +92,7 @@ COPYCAT_LIB = \ - -stk-version \ - -sncbi-vdb \ - -skff \ -- -smagic-static -+ -smagic - - - $(BINDIR)/copycat: $(COPYCAT_OBJ) diff --git a/biology/sra-tools/files/patch-tools_driver-tool_Makefile b/biology/sra-tools/files/patch-tools_driver-tool_Makefile deleted file mode 100644 index 408b82819a43..000000000000 --- a/biology/sra-tools/files/patch-tools_driver-tool_Makefile +++ /dev/null @@ -1,16 +0,0 @@ ---- tools/driver-tool/Makefile.orig 2021-03-15 18:25:25 UTC -+++ tools/driver-tool/Makefile -@@ -97,7 +97,12 @@ SRATOOLS_OBJ = \ - SRATOOLS_LIB = \ - -sncbi-vdb \ - -sjson \ -- -lm -+ -lepoll-shim \ -+ -lmbedtls \ -+ -lm \ -+ -lexecinfo \ -+ -lz \ -+ -lbz2 - - $(BINDIR)/sratools: $(SRATOOLS_OBJ) $(ILIBDIR)/libjson.$(LIBX) - $(LP) --exe --vers $(SRCDIR)/../../shared/toolkit.vers -o $@ $^ $(SRATOOLS_LIB) diff --git a/biology/sra-tools/files/patch-tools_driver-tool_cmdline.cpp b/biology/sra-tools/files/patch-tools_driver-tool_cmdline.cpp deleted file mode 100644 index 46747e4840e5..000000000000 --- a/biology/sra-tools/files/patch-tools_driver-tool_cmdline.cpp +++ /dev/null @@ -1,13 +0,0 @@ ---- tools/driver-tool/cmdline.cpp.orig 2021-04-21 19:42:12 UTC -+++ tools/driver-tool/cmdline.cpp -@@ -50,6 +50,10 @@ - #define environ (*_NSGetEnviron()) - #endif - -+#if defined(__FreeBSD__) -+extern char **environ; -+#endif -+ - #define TRACE( lvl, ... ) /* ignore */ - - namespace ncbi diff --git a/biology/sra-tools/files/patch-tools_driver-tool_utf8proc_Makefile b/biology/sra-tools/files/patch-tools_driver-tool_utf8proc_Makefile deleted file mode 100644 index c5c827645c95..000000000000 --- a/biology/sra-tools/files/patch-tools_driver-tool_utf8proc_Makefile +++ /dev/null @@ -1,11 +0,0 @@ ---- tools/driver-tool/utf8proc/Makefile.orig 2021-04-29 14:50:48 UTC -+++ tools/driver-tool/utf8proc/Makefile -@@ -79,7 +79,7 @@ libutf8proc.a: utf8proc.o - - libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH): utf8proc.o - $(CC) $(LDFLAGS) -shared -o $@ -Wl,-soname -Wl,libutf8proc.so.$(MAJOR) utf8proc.o -- chmod a-x $@ -+ # FIX .so build so this will work: chmod a-x $@ - - libutf8proc.so: libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH) - ln -f -s libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH) $@ diff --git a/biology/sra-tools/files/patch-tools_external_driver-tool_file-path.posix.cpp b/biology/sra-tools/files/patch-tools_external_driver-tool_file-path.posix.cpp new file mode 100644 index 000000000000..9c995dcdbc51 --- /dev/null +++ b/biology/sra-tools/files/patch-tools_external_driver-tool_file-path.posix.cpp @@ -0,0 +1,20 @@ +--- tools/external/driver-tool/file-path.posix.cpp.orig 2023-07-10 16:23:35 UTC ++++ tools/external/driver-tool/file-path.posix.cpp +@@ -193,7 +193,16 @@ static char const *find_executable_path(char const *co + FilePath FilePath::fullPathToExecutable(char const *const *const argv, char const *const *const envp, char const *const *const extra) + { + char const *path; +-#if LINUX ++// Assume sra-tools is installed by FreeBSD ports. FreeBSD users ++// don't often install software by other means. Default prefix ++// is /usr/local, but this can be overridden by the user building ++// the port. The port can replace /usr/local using sed if that's the ++// case. ++#if BSD ++ char full_path[PATH_MAX]; ++ snprintf(full_path, PATH_MAX, "/usr/local/bin/%s", argv[0]); ++ path = full_path; ++#elif LINUX + path = "/proc/self/exe"; + #elif MAC + path = find_executable_path(extra, argv[0]); diff --git a/biology/sra-tools/files/patch-tools_external_driver-tool_sratools.cpp b/biology/sra-tools/files/patch-tools_external_driver-tool_sratools.cpp new file mode 100644 index 000000000000..bea51c07e42e --- /dev/null +++ b/biology/sra-tools/files/patch-tools_external_driver-tool_sratools.cpp @@ -0,0 +1,25 @@ +--- tools/external/driver-tool/sratools.cpp.orig 2023-07-10 16:23:35 UTC ++++ tools/external/driver-tool/sratools.cpp +@@ -420,6 +420,7 @@ static int main(CommandLine const &argv) + enableLogging(argv.toolName.c_str()); + #endif + LOG(7) << "executable path: " << (std::string)argv.fullPathToExe << std::endl; ++ // std::cerr << "executable path: " << (std::string)argv.fullPathToExe << std::endl; + + config = new Config(); + struct Defer { ~Defer() { delete config; config = nullptr; } } freeConfig; +@@ -576,6 +577,14 @@ static int main(CommandLine const &argv) + } + + } // namespace sratools ++ ++#if BSD ++int main(int argc, char *argv[], char *envp[]) ++{ ++ auto const invocation = CommandLine(argc, argv, envp, nullptr); ++ return sratools::main(invocation); ++} ++#endif + + #if MAC + int main(int argc, char *argv[], char *envp[], char *apple[]) diff --git a/biology/sra-tools/files/patch-tools_external_vdb-config_tui_CMakeLists.txt b/biology/sra-tools/files/patch-tools_external_vdb-config_tui_CMakeLists.txt new file mode 100644 index 000000000000..d3627cbbc42a --- /dev/null +++ b/biology/sra-tools/files/patch-tools_external_vdb-config_tui_CMakeLists.txt @@ -0,0 +1,20 @@ +--- tools/external/vdb-config/tui/CMakeLists.txt.orig 2023-07-10 16:23:35 UTC ++++ tools/external/vdb-config/tui/CMakeLists.txt +@@ -25,6 +25,7 @@ + include_directories( ${CMAKE_CURRENT_SOURCE_DIR}/.. ) + + set ( UNIX_SRC unix/systui.c ) ++set ( BSD_SRC bsd/systui.c ) + set ( LINUX_SRC linux/systui.c ) + set ( MAC_SRC bsd/systui.c ) + set ( WIN_SRC win/systui.c ) +@@ -32,6 +33,9 @@ set ( WIN_SRC win/systui.c ) + if ( "windows" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${WIN_SRC} ) + #include_directories( win ) ++elseif( "bsd" STREQUAL ${OS} ) ++ set ( OS_SPECIFIC_SRC ${BSD_SRC} ) ++ #include_directories( unix ) + elseif( "linux" STREQUAL ${OS} ) + set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) + #include_directories( unix ) diff --git a/biology/sra-tools/files/patch-tools_fastq-loader_spot-assembler.c b/biology/sra-tools/files/patch-tools_fastq-loader_spot-assembler.c deleted file mode 100644 index 0a8f0fd3ccb1..000000000000 --- a/biology/sra-tools/files/patch-tools_fastq-loader_spot-assembler.c +++ /dev/null @@ -1,11 +0,0 @@ ---- tools/fastq-loader/spot-assembler.c.orig 2021-06-20 17:00:29 UTC -+++ tools/fastq-loader/spot-assembler.c -@@ -26,6 +26,8 @@ - - #include "spot-assembler.h" - -+#include <sys/stat.h> -+ - #include <klib/status.h> - #include <klib/printf.h> - diff --git a/biology/sra-tools/files/patch-tools_loaders_fastq-loader_spot-assembler.c b/biology/sra-tools/files/patch-tools_loaders_fastq-loader_spot-assembler.c new file mode 100644 index 000000000000..2b337b2116e5 --- /dev/null +++ b/biology/sra-tools/files/patch-tools_loaders_fastq-loader_spot-assembler.c @@ -0,0 +1,17 @@ +--- tools/loaders/fastq-loader/spot-assembler.c.orig 2023-08-08 12:26:35 UTC ++++ tools/loaders/fastq-loader/spot-assembler.c +@@ -1,3 +1,4 @@ ++ + /*=========================================================================== + * + * PUBLIC DOMAIN NOTICE +@@ -25,6 +26,9 @@ + */ + + #include "spot-assembler.h" ++ ++// FIXME: Unsure if this is still necessary ++#include <sys/stat.h> + + #include <klib/status.h> + #include <klib/printf.h> diff --git a/biology/sra-tools/files/patch-tools_sra-sort_Makefile b/biology/sra-tools/files/patch-tools_sra-sort_Makefile deleted file mode 100644 index 8e96b1a43f97..000000000000 --- a/biology/sra-tools/files/patch-tools_sra-sort_Makefile +++ /dev/null @@ -1,13 +0,0 @@ ---- tools/sra-sort/Makefile.orig 2021-06-20 22:24:20 UTC -+++ tools/sra-sort/Makefile -@@ -135,7 +135,9 @@ DBB_OBJ = \ - $(addsuffix .$(OBJX),$(DBB_SRC)) - - DBB_LIB = \ -- -lncbi-vdb \ -+ -sncbi-vdb \ - - $(BINDIR)/dump-blob-boundaries: $(DBB_OBJ) -+ @echo "LD = ${LD}" -+ @echo "DBB_LIB = ${DBB_LIB}" - $(LD) --exe -o $@ $^ $(DBB_LIB) diff --git a/biology/sra-tools/files/patch-tools_util_validate-names4.c b/biology/sra-tools/files/patch-tools_util_validate-names4.c deleted file mode 100644 index 5d66976db304..000000000000 --- a/biology/sra-tools/files/patch-tools_util_validate-names4.c +++ /dev/null @@ -1,13 +0,0 @@ ---- tools/util/validate-names4.c.orig 2021-06-20 17:53:25 UTC -+++ tools/util/validate-names4.c -@@ -30,8 +30,8 @@ - #include <klib/rc.h> /* RC */ - #include <vfs/path.h> /* VPath */ - --#include "../../../ncbi-vdb/libs/vfs/json-response.h" /* Response4Make4 */ --#include "../../../ncbi-vdb/libs/vfs/services-priv.h"/*KServiceGetKSrvResponse*/ -+#include "../libs/vfs/json-response.h" /* Response4Make4 */ -+#include "../libs/vfs/services-priv.h"/*KServiceGetKSrvResponse*/ - - #define RELEASE(type, obj) do { rc_t rc2 = type##Release(obj); \ - if (rc2 && !rc) { rc = rc2; } obj = NULL; } while (false) diff --git a/biology/sra-tools/pkg-descr b/biology/sra-tools/pkg-descr index e9324dc5a96a..06ed34546192 100644 --- a/biology/sra-tools/pkg-descr +++ b/biology/sra-tools/pkg-descr @@ -1,18 +1,13 @@ SRA tools is a toolkit for using data in the INSDC Sequence Read Archives. - SRAs operated by International Nucleotide Sequence Database Collaboration houses sequence reads and alignments generated by "next-gen" sequencers. SRA tools allows conversion of .sra files, which INSDC SRAs maintain, from/to other formats that the 'next-gen' sequenecers generate including: - * csfasta/csqual (ABI SOLiD) * fastq (and fasta for writing) * hdf5 (PacBio, reading only) * qseq (older Illumina) * sam (writing only) / bam (reading only) * sff - The toolkit uses NCBI-VDB back-end enabling seamless access to remote SRA data and local SRA files. - -WWW: https://github.com/ncbi/sra-tools/wiki diff --git a/biology/sra-tools/pkg-plist b/biology/sra-tools/pkg-plist index dad924be78f4..20e3af7ac25d 100644 --- a/biology/sra-tools/pkg-plist +++ b/biology/sra-tools/pkg-plist @@ -1,57 +1,282 @@ bin/abi-dump -bin/abi-load -bin/align-cache +bin/abi-dump.3 +bin/abi-dump.3.0.6 bin/align-info -bin/bam-load +bin/align-info.3 +bin/align-info.3.0.6 bin/cache-mgr -bin/ccextract -bin/cg-load +bin/cache-mgr.3 +bin/cache-mgr.3.0.6 bin/check-corrupt -bin/copycat +bin/check-corrupt.3 +bin/check-corrupt.3.0.6 bin/fasterq-dump +bin/fasterq-dump-orig.3.0.6 +bin/fasterq-dump.3 +bin/fasterq-dump.3.0.6 bin/fastq-dump -bin/fastq-load -bin/helicos-load +bin/fastq-dump-orig.3.0.6 +bin/fastq-dump.3 +bin/fastq-dump.3.0.6 bin/illumina-dump -bin/illumina-load -bin/kar -bin/kar+ -bin/kar+meta -bin/kdb-index +bin/illumina-dump.3 +bin/illumina-dump.3.0.6 bin/kdbmeta -bin/kget -bin/latf-load -bin/make-read-filter -bin/md5cp +bin/kdbmeta.3 +bin/kdbmeta.3.0.6 bin/ngs-pileup -bin/pacbio-correct -bin/pacbio-loadxml +bin/ngs-pileup.3 +bin/ngs-pileup.3.0.6 bin/prefetch -bin/qual-recalib-stat +bin/prefetch-orig.3.0.6 +bin/prefetch.3 +bin/prefetch.3.0.6 bin/rcexplain -bin/read-filter-redact +bin/rcexplain.3 +bin/rcexplain.3.0.6 +bin/ref-variation +bin/ref-variation.3 +bin/ref-variation.3.0.6 bin/sam-dump -bin/samview -bin/schema-replace +bin/sam-dump-orig.3.0.6 +bin/sam-dump.3 +bin/sam-dump.3.0.6 bin/sff-dump -bin/sff-load +bin/sff-dump.3 +bin/sff-dump.3.0.6 +bin/sra-info +bin/sra-info.3 +bin/sra-info.3.0.6 bin/sra-pileup -bin/sra-sort -bin/sra-sort-cg +bin/sra-pileup-orig.3.0.6 +bin/sra-pileup.3 +bin/sra-pileup.3.0.6 +bin/sra-search +bin/sra-search.3 +bin/sra-search.3.0.6 bin/sra-stat +bin/sra-stat.3 +bin/sra-stat.3.0.6 bin/srapath +bin/srapath-orig.3.0.6 +bin/srapath.3 +bin/srapath.3.0.6 bin/sratools -bin/srf-load -bin/test-read-write-cursor +bin/sratools.3 +bin/sratools.3.0.6 bin/test-sra +bin/test-sra.3 +bin/test-sra.3.0.6 +bin/var-expand +bin/var-expand.3 +bin/var-expand.3.0.6 bin/vdb-config -bin/vdb-copy +bin/vdb-config.3 +bin/vdb-config.3.0.6 bin/vdb-decrypt -bin/vdb-diff +bin/vdb-decrypt.3 +bin/vdb-decrypt.3.0.6 bin/vdb-dump +bin/vdb-dump-orig.3.0.6 +bin/vdb-dump.3 +bin/vdb-dump.3.0.6 bin/vdb-encrypt -bin/vdb-lock -bin/vdb-passwd -bin/vdb-sql -bin/vdb-unlock +bin/vdb-encrypt.3 +bin/vdb-encrypt.3.0.6 bin/vdb-validate +bin/vdb-validate.3 +bin/vdb-validate.3.0.6 +include/ncbi-vdb/NGS.hpp +include/ngs/Alignment.hpp +include/ngs/AlignmentIterator.hpp +include/ngs/ErrorMsg.hpp +include/ngs/Fragment.hpp +include/ngs/FragmentIterator.hpp +include/ngs/Package.hpp +include/ngs/Pileup.hpp +include/ngs/PileupEvent.hpp +include/ngs/PileupEventIterator.hpp +include/ngs/PileupIterator.hpp +include/ngs/Read.hpp +include/ngs/ReadCollection.hpp +include/ngs/ReadGroup.hpp +include/ngs/ReadGroupIterator.hpp +include/ngs/ReadIterator.hpp +include/ngs/Reference.hpp +include/ngs/ReferenceIterator.hpp +include/ngs/ReferenceSequence.hpp +include/ngs/Statistics.hpp +include/ngs/StringRef.hpp +include/ngs/adapter/AlignmentItf.hpp +include/ngs/adapter/ErrorMsg.hpp +include/ngs/adapter/FragmentItf.hpp +include/ngs/adapter/PileupEventItf.hpp +include/ngs/adapter/PileupItf.hpp +include/ngs/adapter/ReadCollectionItf.hpp +include/ngs/adapter/ReadGroupItf.hpp +include/ngs/adapter/ReadItf.hpp +include/ngs/adapter/Refcount.hpp +include/ngs/adapter/ReferenceItf.hpp +include/ngs/adapter/ReferenceSequenceItf.hpp +include/ngs/adapter/StatisticsItf.hpp +include/ngs/adapter/StringItf.hpp +include/ngs/adapter/defs.h +include/ngs/inl/Alignment.hpp +include/ngs/inl/AlignmentIterator.hpp +include/ngs/inl/Fragment.hpp +include/ngs/inl/FragmentIterator.hpp +include/ngs/inl/Package.hpp +include/ngs/inl/Pileup.hpp +include/ngs/inl/PileupEvent.hpp +include/ngs/inl/PileupEventIterator.hpp +include/ngs/inl/PileupIterator.hpp +include/ngs/inl/Read.hpp +include/ngs/inl/ReadCollection.hpp +include/ngs/inl/ReadGroup.hpp +include/ngs/inl/ReadGroupIterator.hpp +include/ngs/inl/ReadIterator.hpp +include/ngs/inl/Reference.hpp +include/ngs/inl/ReferenceIterator.hpp +include/ngs/inl/ReferenceSequence.hpp +include/ngs/inl/Statistics.hpp +include/ngs/inl/StringRef.hpp +include/ngs/itf/AlignmentItf.h +include/ngs/itf/AlignmentItf.hpp +include/ngs/itf/ErrBlock.h +include/ngs/itf/ErrBlock.hpp +include/ngs/itf/ErrorMsg.hpp +include/ngs/itf/FragmentItf.h +include/ngs/itf/FragmentItf.hpp +include/ngs/itf/PackageItf.hpp +include/ngs/itf/PileupEventItf.h +include/ngs/itf/PileupEventItf.hpp 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