Urgent: Spades Update before freeze
Hi folks,
I think we should urgently upgrade spades before the freeze. I've
commited the latest upstream version to Git but it has Build-Issues:
...
cd /build/spades-3.15.0+dfsg/assembler/build_spades/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-core.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -Wl,-z, relro -Wl,-z,now CMakeFiles/spades-core.dir/pipeline.cpp.o CMakeFiles/spades-core.dir/main.cpp.o CMakeFiles/spades-core.dir/series_analysis.cpp.o CMakeFiles/spades-core.dir/__/mts/ contig_abundance.cpp.o ../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o -o ../../bin/spades-core libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/ libcommon_modules.a ../../common/hmm/libhmmercpp.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/gfa1/libgfa1.a ../../ common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/ libBamTools.a /usr/lib/x86_64-linux-gnu/libz.so ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/ libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/ libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa ../../ ext/hmmer/libhmmer.a ../../ext/easel/libeasel.a -lm
/usr/bin/ld: ../../ext/llvm/libllvm-support.a(JSON.cpp.o): in function `llvm::json::isUTF8(llvm::StringRef, unsigned long*)':
./assembler/build_spades/ext/llvm/./assembler/ext/src/llvm/JSON.cpp:538: undefined reference to `llvm::isLegalUTF8String(unsigned char const**, unsigned char const*)'
/usr/bin/ld: ./assembler/build_spades/ext/llvm/./assembler/ext/src/llvm/JSON.cpp:538: undefined reference to `llvm::isLegalUTF8String(unsigned char const**, unsigned char const*)'
/usr/bin/ld: ../../ext/llvm/libllvm-support.a(JSON.cpp.o): in function `llvm::json::fixUTF8[abi:cxx11](llvm::StringRef)':
./assembler/build_spades/ext/llvm/./assembler/ext/src/llvm/JSON.cpp:551: undefined reference to `llvm::ConvertUTF8toUTF32(unsigned char const**, unsigned char const*, unsigned int**, unsigned int*, llvm::ConversionFlags)'
/usr/bin/ld: ./assembler/build_spades/ext/llvm/./assembler/ext/src/llvm/JSON.cpp:557: undefined reference to `llvm::ConvertUTF32toUTF8(unsigned int const**, unsigned int const*, unsigned char**, unsigned char*, llvm::ConversionFlags)'
/usr/bin/ld: ../../ext/llvm/libllvm-support.a(JSON.cpp.o): in function `llvm::json::isUTF8(llvm::StringRef, unsigned long*)':
./assembler/build_spades/ext/llvm/./assembler/ext/src/llvm/JSON.cpp:538: undefined reference to `llvm::isLegalUTF8String(unsigned char const**, unsigned char const*)'
/usr/bin/ld: ./assembler/build_spades/ext/llvm/./assembler/ext/src/llvm/JSON.cpp:538: undefined reference to `llvm::isLegalUTF8String(unsigned char const**, unsigned char const*)'
/usr/bin/ld: ../../ext/llvm/libllvm-support.a(Unicode.cpp.o): in function `llvm::sys::unicode::columnWidthUTF8(llvm::StringRef)':
./assembler/build_spades/ext/llvm/./assembler/ext/src/llvm/Unicode.cpp:346: undefined reference to `llvm::getNumBytesForUTF8(unsigned char)'
/usr/bin/ld: ./assembler/build_spades/ext/llvm/./assembler/ext/src/llvm/Unicode.cpp:352: undefined reference to `llvm::ConvertUTF8toUTF32(unsigned char const**, unsigned char const*, unsigned int**, unsigned int*, llvm::ConversionFlags)'
collect2: error: ld returned 1 exit status
I think its just a matter of proper linking, Could someone
please have a helping hand?
Kind regards
Andreas.
--
http://fam-tille.de
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