aquaskyline / SOAPdenovo2

Next generation sequencing reads de novo assembler.
GNU General Public License v3.0
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compilation is not working on EL/rocky 9 #96

Open eylenth opened 5 months ago

eylenth commented 5 months ago

I'm trying to compile SOAPdenovo2 from source on a RedHat9 server, but it seems not to work. I'm getting a lot of multiple definition ofb_ban'` error messages

[eylenbt@by3acs] SOAPdenovo2 $ /usr/bin/ld --version
GNU ld version 2.35.2-37.el9
Copyright (C) 2020 Free Software Foundation, Inc.
This program is free software; you may redistribute it under the terms of
the GNU General Public License version 3 or (at your option) a later version.
This program has absolutely no warranty.
[eylenbt@by3acs] SOAPdenovo2 $ make -j 1
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 of `b_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 of `b_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 of `b_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 of `graphfile'; 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/cutTip_graph2.o:(.bss+0x0): multiple definition of `b_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/cutTipPreGraph.o:(.bss+0x0): multiple definition of `b_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 of `b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here
/usr/bin/ld: standardPregraph/kmerhash.o:(.bss+0x0): multiple definition of `b_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/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 of `b_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 of `b_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 of `b_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 of `b_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 of `b_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 of `b_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 of `b_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 of `b_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 of `b_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 of `b_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 of `locks'; 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 of `b_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 of `b_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 of `b_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 of `b_ban'; standardPregraph/arc.o:(.bss+0x0): first defined here
collect2: error: ld returned 1 exit status
make: *** [Makefile:58: SOAPdenovo-63mer] Error 1

On a Redhat7 server, this is working fine.