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Help needed for Bug#847171 soapdenovo2: Different output, still FTBFS



Hi,

it seems there are different ways how the build fails but its totally
unclear to me why this happens.

On Tue, Dec 06, 2016 at 11:33:14AM +0000, Ghislain Vaillant wrote:
> I could not repeat the exact output Chris got.
> 
> Still FTBFS on my end in a clean chroot, with the following output:
> 
> standardPregraph/contig.o: In function `call_heavygraph':
> contig.c:(.text+0x8a6): undefined reference to `I'
> contig.c:(.text+0x91f): undefined reference to `no symbol'
> contig.c:(.text+0x994): undefined reference to `no symbol'
> contig.c:(.text+0xa0a): undefined reference to `no symbol'
> contig.c:(.text+0xa68): undefined reference to `'
> collect2: error: ld returned 1 exit status
> Makefile:70: recipe for target 'SOAPdenovo-63mer' failed
> make[1]: *** [SOAPdenovo-63mer] Error 1
> make[1]: *** Waiting for unfinished jobs....
> make[2]: Leaving directory '/<<BUILDDIR>>/soapdenovo2-
> 240+dfsg1/standardPregraph'
> standardPregraph/contig.o: In function `call_heavygraph':
> contig.c:(.text+0x8a6): undefined reference to `I'
> contig.c:(.text+0x91f): undefined reference to `no symbol'
> contig.c:(.text+0x994): undefined reference to `no symbol'
> contig.c:(.text+0xa0a): undefined reference to `no symbol'
> contig.c:(.text+0xa68): undefined reference to `'
> collect2: error: ld returned 1 exit status
> Makefile:74: recipe for target 'SOAPdenovo-127mer' failed
> make[1]: *** [SOAPdenovo-127mer] Error 1
> make[1]: Leaving directory '/<<BUILDDIR>>/soapdenovo2-240+dfsg1'
> 
> Hope this helps.

Thanks for confirming the build issue.  I can only say that in the clean
unstable chroot I used at 2016-12-04 the package has built fine but now
I can contribute just another way of failure:

...
iterate.c:2567:4: warning: implicit declaration of function 'removeLowCovEdges2' [-Wimplicit-function-declaration]
    removeLowCovEdges2 ( cutlen, deLowEdge, mink, 0 );
    ^~~~~~~~~~~~~~~~~~
iterate.c:2576:4: warning: implicit declaration of function 'cutTipsInGraph2' [-Wimplicit-function-declaration]
    cutTipsInGraph2 ( cutlen, 0, 0 );
    ^~~~~~~~~~~~~~~
make[2]: Leaving directory '/build/soapdenovo2-240+dfsg1/standardPregraph'
/usr/bin/ld: error: sparsePregraph/build_graph.o: ELF section name out of range
collect2: error: ld returned 1 exit status
Makefile:70: recipe for target 'SOAPdenovo-63mer' failed


It seems, that in the last two days something has changed that
leads to random build errors in this package.  When I try to
compare the build logs the visible changes are these:

Additional package due to dependencies of Build-Depends installed:

    libtimedate-perl 2.3000-2

Debian revision of libc-bin bumped

-Processing triggers for libc-bin (2.24-7) ...
+Processing triggers for libc-bin (2.24-8) ...
 

I do not have any idea how to proceed from here.

Any help is welcome

     Andreas.


-- 
http://fam-tille.de


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