[Debian-med-packaging] Bug#847171: Different output, still FTBFS

[Andreas Tille]

tags 847171 help
thanks

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.

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