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
