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Makefile:65: recipe for target 'SOAPdenovo-63mer' failed

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.

assembly soapdenovo
• 455 views • link
updated by h.mon h.mon • written by Chvatil Chvatil

This could be due to compiler incompatibility. What OS and version of GCC compiler are you using?

• 1 views • link
written by GenoMax GenoMax

In fact it is in my lab server, how can I know the version you are asking for, I'm not admin.

• 1 views • link
written by Chvatil Chvatil

Can you ask the admin to compile and install in that case?

• 1 views • link
written by GenoMax GenoMax

cat /etc/issue will tell which operating system, gcc -v will tell the version of GCC.

• 1 views • link
written by h.mon h.mon

Hello Toto, If u are using Ubuntu use the command below

sudo apt-get install gcc-c++

Or if u r using fedora use the below command

sudo dnf install gcc-c++

Then use 'make' command

• 1 views • link
written by mks002 mks002

1 answer

Make your life simpler, either download the pre-compiled SOAPdenovo2-bin-LINUX-generic-r240 binary, or use conda to install it.

• 1 views • link
written by h.mon h.mon

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