SOAPdenovo2 installation error #88
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pregraph_sparse_63mer.v1.0.3 cleaning done. |
This solved the problem for me. Thanks a lot! |
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Hello I tried to install SOAPdenovo2 using the following in ubuntu (22.04.2 LTS) terminal
$ git https://github.com/aquaskyline/SOAPdenovo2.git
$ cd SOAPdenovo2
Then tried to install using make and make clean but got error related to multiple definition as shown below
SOAPdenovo2$ sudo make
pregraph_sparse_63mer.v1.0.3 cleaning done.
pregraph_sparse_63mer.v1.0.3 objects generated.
SOAPdenovo-63mer cleaning done.
SOAPdenovo-63mer objects generated.
/usr/bin/ld: standardPregraph/attachPEinfo.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/bubble.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/check.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/compactEdge.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/concatenateEdge.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/connect.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/contig.o:(.bss+0x100): multiple definition of
shortrdsfile'; sparsePregraph/global.o:(.bss+0x1e0): first defined here /usr/bin/ld: standardPregraph/contig.o:(.bss+0x0): multiple definition ofgraphfile'; sparsePregraph/global.o:(.bss+0xe0): first defined here/usr/bin/ld: standardPregraph/contig.o:(.bss+0x200): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/cutTipPreGraph.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/cutTip_graph.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/cutTip_graph2.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/hashFunction.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/iterate.o:(.bss+0x48): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/kmer.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/kmerhash.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/lib.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/linearEdge.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/loadGraph.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/loadPath.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/loadPreGraph.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/localAsm.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/main.o:(.bss+0x32c): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/map.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/mem_manager.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/newhash.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/node2edge.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/orderContig.o:(.bss+0xc): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/output_contig.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/output_pregraph.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/output_scaffold.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/pregraph.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/prlHashCtg.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/prlHashReads.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/prlRead2Ctg.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/prlRead2path.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/prlReadFillGap.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/read2edge.o:(.bss+0x0): multiple definition oflocks'; sparsePregraph/global.o:(.bss+0x70): first defined here/usr/bin/ld: standardPregraph/read2edge.o:(.bss+0x40): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/read2scaf.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/readInterval.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/readseq1by1.o:(.bss+0x8): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/scaffold.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/searchPath.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/ld: standardPregraph/seq.o:(.bss+0x0): multiple definition of
b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here /usr/bin/ld: standardPregraph/splitReps.o:(.bss+0x0): multiple definition ofb_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here/usr/bin/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 -fPIE
/usr/bin/ld: failed to set dynamic section sizes: bad value
collect2: error: ld returned 1 exit status
make: *** [Makefile:58: SOAPdenovo-63mer] Error 1
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Could anyone help in solving the installation issue.
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