[Debian-med-packaging] Bug#812767: [devteam-bioc] Bug#812767: r-bioc-genefilter: conflicting declarations of function gf_distance

[Morgan, Martin]

Thanks Andreas; that's a strange thing to have been around for all these years. It's fixed in version 1.53.1 (devel) and will be ported to release later today. Martin

________________________________________
From: devteam-bioc-bounces at lists.fhcrc.org <devteam-bioc-bounces at lists.fhcrc.org> on behalf of Maintainer <maintainer at bioconductor.org>
Sent: Wednesday, January 27, 2016 8:55 AM
To: 812767 at bugs.debian.org; Bioconductor Package Maintainer
Subject: Re: [devteam-bioc] Bug#812767: r-bioc-genefilter: conflicting declarations of function gf_distance

Hi,

I would like to let you know that a build test in Debian has uncovered a
problem in genefilter.  Please let me know if you need more information
to track down this issue.

Kind regards

       Andreas.

On Tue, Jan 26, 2016 at 11:59:33AM +0000, Michael Tautschnig wrote:
> Package: r-bioc-genefilter
> Version: 1.52.0-1
> Usertags: goto-cc
>
> During a rebuild of all Debian packages in a clean sid chroot (using cowbuilder
> and pbuilder) the build failed with the following error. Please note that we
> use our research compiler tool-chain (using tools from the cbmc package), which
> permits extended reporting on type inconsistencies at link time.
>
> g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
>
> file nd.c line 270: error: conflicting parameter counts of function declarations `gf_distance'
> old definition in module `init' file genefilter.h line 5
> void (double *, double *, signed int *, signed int *, double *, signed int *, signed int *)
> new definition in module `nd' file nd.c line 270
> void (double *x, signed int *nr, signed int *nc, signed int *g, double *d, signed int *iRow, signed int *nInterest, signed int *nResults, signed int *method, double *wval)
>
> /usr/share/R/share/make/shlib.mk:6: recipe for target 'genefilter.so' failed
> make[1]: *** [genefilter.so] Error 1
> make[1]: Leaving directory '/srv/jenkins-slave/workspace/sid-goto-cc-r-bioc-genefilter/r-bioc-genefilter-1.52.0/src'
>
> It seems the declaration in genefilter.h and the definition in nd.c are highly
> inconsistent as not only the number, but also the individual types do not match
> up. This will cause misaligned stack accesses.
>
> Best,
> Michael
>



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