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5.8 years ago
Chvatil
▴
130
Hi, I'm trying to install SOAP from here: link
Then I made a tar xvzf SOAPdenovo2-src-r240.tgz
And made a make
And I got an error:
/usr/bin/X11/ld: final link failed: Symbol needs debug section which does not exist
collect2: error: ld returned 1 exit status
Makefile:65: recipe for target 'SOAPdenovo-63mer' failed
make: *** [SOAPdenovo-63mer] Error 1
Here is all the report from the make:
make[1]: Entering directory '/panhome/bguinet/TOOLS/SOAPdenovo2-src-r240/sparsePregraph'
pregraph_sparse_63mer.v1.0.3 cleaning done.
multi_threads.cpp: In function 'void* threadRoutine(void*)':
multi_threads.cpp:93:3: error: 'usleep' was not declared in this scope
usleep ( 1 );
^~~~~~
multi_threads.cpp:93:3: note: suggested alternative: 'fseek'
usleep ( 1 );
^~~~~~
fseek
multi_threads.cpp: In function 'void sendWorkSignal(unsigned char, unsigned char*)':
multi_threads.cpp:115:3: error: 'usleep' was not declared in this scope
usleep ( 10 );
^~~~~~
multi_threads.cpp:115:3: note: suggested alternative: 'fseek'
usleep ( 10 );
^~~~~~
fseek
Error in command: g++ -c -O4 -fomit-frame-pointer -D_63MER_ -m64 -I./inc multi_threads.cpp
build_preArc.cpp: In function 'void build_preArc_threaded(preArc_array*, vertex_hash2*, int, int, std::vector<std::__cxx11::basic_string<char> >*, int)':
build_preArc.cpp:1071:28: error: 'usleep' was not declared in this scope
while ( io_ready == 0 ) {usleep ( 1 );}
^~~~~~
build_preArc.cpp:1071:28: note: suggested alternative: 'beep'
while ( io_ready == 0 ) {usleep ( 1 );}
^~~~~~
beep
Error in command: g++ -c -O4 -fomit-frame-pointer -D_63MER_ -m64 -I./inc build_preArc.cpp
pregraph_sparse.cpp: In function 'int call_pregraph_sparse(int, char**)':
pregraph_sparse.cpp:171:31: error: 'usleep' was not declared in this scope
while ( io_ready == 0 ) {usleep ( 1 );}
^~~~~~
pregraph_sparse.cpp:171:31: note: suggested alternative: 'fseek'
while ( io_ready == 0 ) {usleep ( 1 );}
^~~~~~
fseek
pregraph_sparse.cpp:284:31: error: 'usleep' was not declared in this scope
while ( io_ready == 0 ) {usleep ( 1 );}
^~~~~~
pregraph_sparse.cpp:284:31: note: suggested alternative: 'fseek'
while ( io_ready == 0 ) {usleep ( 1 );}
^~~~~~
fseek
pregraph_sparse.cpp: In function 'void initenv(int, char**)':
pregraph_sparse.cpp:504:2: error: 'optind' was not declared in this scope
optind = 1;
^~~~~~
pregraph_sparse.cpp:504:2: note: suggested alternative: 'optarg'
optind = 1;
^~~~~~
optarg
pregraph_sparse.cpp:507:19: error: 'getopt' was not declared in this scope
while ( ( copt = getopt ( argc, argv, "s:o:K:g:z:d:e:p:m:r:R" ) ) != EOF )
^~~~~~
pregraph_sparse.cpp:507:19: note: suggested alternative: 'getpt'
while ( ( copt = getopt ( argc, argv, "s:o:K:g:z:d:e:p:m:r:R" ) ) != EOF )
^~~~~~
getpt
Error in command: g++ -c -O4 -fomit-frame-pointer -D_63MER_ -m64 -I./inc pregraph_sparse.cpp
make[1]: Leaving directory '/panhome/bguinet/TOOLS/SOAPdenovo2-src-r240/sparsePregraph'
make[1]: Entering directory '/panhome/bguinet/TOOLS/SOAPdenovo2-src-r240/standardPregraph'
SOAPdenovo-63mer cleaning done.
contig.c: In function 'call_heavygraph':
contig.c:78:2: warning: implicit declaration of function 'swapedge'; did you mean 'loadEdge'? [-Wimplicit-function-declaration]
swapedge();
^~~~~~~~
loadEdge
contig.c:79:2: warning: implicit declaration of function 'sortedge'; did you mean 'loadEdge'? [-Wimplicit-function-declaration]
sortedge();
^~~~~~~~
loadEdge
contig.c:80:2: warning: implicit declaration of function 'freshArc' [-Wimplicit-function-declaration]
freshArc();
^~~~~~~~
contig.c:144:3: warning: implicit declaration of function 'Iterate' [-Wimplicit-function-declaration]
Iterate ( shortrdsfile, graphfile, maxk, M ); //keepReadFile,
^~~~~~~
contig.c:154:3: warning: implicit declaration of function 'freshpreGraphBasic' [-Wimplicit-function-declaration]
freshpreGraphBasic ( iter, maxk, graphfile );
^~~~~~~~~~~~~~~~~~
cutTipPreGraph.c: In function 'clipTipFromNode':
cutTipPreGraph.c:127:3: warning: implicit declaration of function 'PrintKmer'; did you mean 'print_kmer'? [-Wimplicit-function-declaration]
PrintKmer ( stderr, word );
^~~~~~~~~
print_kmer
hashFunction.c: In function 'crc32cHardware64':
hashFunction.c:111:9: warning: implicit declaration of function '__builtin_ia32_crc32di'; did you mean '__builtin_ia32_bsrdi'? [-Wimplicit-function-declaration]
crc = __builtin_ia32_crc32di ( crc, * ( uint64_t * ) data );
^~~~~~~~~~~~~~~~~~~~~~
__builtin_ia32_bsrdi
loadPreGraph.c: In function 'kmer2vt':
loadPreGraph.c:222:4: warning: implicit declaration of function 'PrintKmer'; did you mean 'print_kmer'? [-Wimplicit-function-declaration]
PrintKmer ( stderr, kmer );
^~~~~~~~~
print_kmer
localAsm.c: In function 'traceAlongDBgraph':
localAsm.c:657:3: warning: implicit declaration of function 'PrintKmer'; did you mean 'print_kmer'? [-Wimplicit-function-declaration]
PrintKmer ( stderr, word );
^~~~~~~~~
print_kmer
node2edge.c: In function 'merge_linearV2':
node2edge.c:505:5: warning: implicit declaration of function 'PrintKmer'; did you mean 'print_kmer'? [-Wimplicit-function-declaration]
PrintKmer ( stderr, wordplus );
^~~~~~~~~
print_kmer
orderContig.c: In function 'score_pass':
orderContig.c:2411:15: warning: implicit declaration of function 'allConnect'; did you mean 'validConnect'? [-Wimplicit-function-declaration]
int outnum = allConnect ( id, NULL );
^~~~~~~~~~
validConnect
output_pregraph.c: In function 'output_1edge':
output_pregraph.c:92:2: warning: implicit declaration of function 'print_kmer_gz'; did you mean 'print_kmer'? [-Wimplicit-function-declaration]
print_kmer_gz ( fp, edge->from_node, ',' );
^~~~~~~~~~~~~
print_kmer
prlRead2path.c: In function 'searchKmer':
prlRead2path.c:356:3: warning: implicit declaration of function 'PrintKmer'; did you mean 'print_kmer'? [-Wimplicit-function-declaration]
PrintKmer ( stderr, kmerBuffer[t] );
^~~~~~~~~
print_kmer
scaffold.c: In function 'call_scaffold':
scaffold.c:90:2: warning: implicit declaration of function 'ScafStat' [-Wimplicit-function-declaration]
ScafStat ( 100, graphfile );
^~~~~~~~
cutTip_graph2.c: In function 'removeLowCovEdges2':
cutTip_graph2.c:231:2: warning: implicit declaration of function 'linearConcatenate2'; did you mean 'linearConcatenate'? [-Wimplicit-function-declaration]
linearConcatenate2 ( last );
^~~~~~~~~~~~~~~~~~
linearConcatenate
read2edge.c: In function 'Read2edge':
read2edge.c:960:19: warning: implicit declaration of function 'read1seqInLibpos'; did you mean 'read1seqInLib'? [-Wimplicit-function-declaration]
while ( ( flag = read1seqInLibpos ( seqBuffer[read_c], next_name, & ( lenBuffer[read_c] ), //file,
^~~~~~~~~~~~~~~~
read1seqInLib
iterate.c: In function 'update1Edge':
iterate.c:406:3: warning: implicit declaration of function 'destroyEdge2'; did you mean 'destroyArcMem'? [-Wimplicit-function-declaration]
destroyEdge2 ( index );
^~~~~~~~~~~~
destroyArcMem
iterate.c: In function 'addArc':
iterate.c:780:3: warning: implicit declaration of function 'Read2edge2'; did you mean 'prlRead2edge'? [-Wimplicit-function-declaration]
Read2edge2 ( libfile, graph, last, maxk ); //, keepReadFile
^~~~~~~~~~
prlRead2edge
iterate.c:783:5: warning: implicit declaration of function 'Read2edge'; did you mean 'prlRead2edge'? [-Wimplicit-function-declaration]
{ Read2edge ( libfile, graph, maxk ); }
^~~~~~~~~
prlRead2edge
iterate.c:795:2: warning: implicit declaration of function 'removeDeadArcs2'; did you mean 'removeDeadArcs'? [-Wimplicit-function-declaration]
removeDeadArcs2();
^~~~~~~~~~~~~~~
removeDeadArcs
iterate.c: In function 'checkindegree':
iterate.c:1169:3: warning: implicit declaration of function 'arcCount2'; did you mean 'arcCount'? [-Wimplicit-function-declaration]
arcCount2 ( from_ed, &arcRight_n );
^~~~~~~~~
arcCount
iterate.c: In function 'swapedge':
iterate.c:1653:5: warning: implicit declaration of function 'copyEdge'; did you mean 'copy1Edge'? [-Wimplicit-function-declaration]
copyEdge ( i, num_ed + 1 + 1 );
^~~~~~~~
copy1Edge
iterate.c: In function 'Iterate':
iterate.c:2566:4: warning: implicit declaration of function 'removeWeakEdges2'; did you mean 'removeWeakEdges'? [-Wimplicit-function-declaration]
removeWeakEdges2 ( cutlen, 1, mink );
^~~~~~~~~~~~~~~~
removeWeakEdges
iterate.c:2567:4: warning: implicit declaration of function 'removeLowCovEdges2'; did you mean 'removeLowCovEdges'? [-Wimplicit-function-declaration]
removeLowCovEdges2 ( cutlen, deLowEdge, mink, 0 );
^~~~~~~~~~~~~~~~~~
removeLowCovEdges
iterate.c:2576:4: warning: implicit declaration of function 'cutTipsInGraph2'; did you mean 'cutTipsInGraph'? [-Wimplicit-function-declaration]
cutTipsInGraph2 ( cutlen, 0, 0 );
^~~~~~~~~~~~~~~
cutTipsInGraph
make[1]: Leaving directory '/panhome/bguinet/TOOLS/SOAPdenovo2-src-r240/standardPregraph'
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(bam.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(bam_import.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(sam.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(bam_pileup.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(faidx.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(knetfile.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(sam_header.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(bgzf.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(kstring.o): relocation R_X86_64_32 against `.text' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(bam_aux.o): relocation R_X86_64_32S against `.rodata' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(razf.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
standardPregraph/main.o: In function `main':
main.c:(.text.startup+0xee): undefined reference to `call_pregraph_sparse'
/usr/bin/X11/ld: final link failed: Symbol needs debug section which does not exist
collect2: error: ld returned 1 exit status
Makefile:65: recipe for target 'SOAPdenovo-63mer' failed
make: *** [SOAPdenovo-63mer] Error 1
Does someone have any idea why it does not work? And what could I do to fix it?
Thank you.
