[Debian-med-packaging] [devteam-bioc] Problems with test suite of new verison of Rsamtools

[Andreas Tille]

[sorry for my last empty mail - please ignore]

On Tue, Nov 03, 2015 at 04:23:43PM +0000, Morgan, Martin wrote:
> > 
> > I tried this:
> > 
> > > Rsamtools::indexBam(fl)
> > [bam_index_core] the alignment is not sorted (EAS218_4:1:9:206:901): 2-th
> > chr > 1-th chr [bam_index_build2] fail to index the BAM file.
> 
> the messages above are not being reported as warnings, just messages (on stderr, I guess)...

I was just copying the output after starting R from a terminal - no idea
whether this was stderr or some other stream.
 
> > 
> > Trying to reproduce:
> > 
> > > warn <- FALSE
> > > tryCatch(Rsamtools::indexBam(fl), warning=function(msg) warn <<- TRUE)
> > [bam_index_core] the alignment is not sorted (EAS218_4:1:9:206:901): 2-th
> > chr > 1-th chr [bam_index_build2] fail to index the BAM file.
> > Error in FUN(X[[i]], ...) : failed to build index
> >   file: /usr/lib/R/site-library/Rsamtools/unitTests/cases/ex1_unsort.bam
> > > warn
> > [1] FALSE
> > 
> > 
> > > Have you set some R option related to warning and error handlers?
> > 
> > No, no special handlers applied here.  I think the problem is to write a file to a
> > non-writeable dir.

Could you please comment on my assumption that the test tries to write
to a non-writeable dir?
 
> the test could be written as
> 
> warn <- FALSE
> tryCatch(Rsamtools::indexBam(fl, tempfile()), warning=function(msg) warn <<- TRUE)
> warn
> 
> (expecting the value of warn changed to TRUE).
> 
> If the test above is not successful, then can you please provide the transcript of the package installation? Rsamtools re-directs fprintf calls in the samtools library, and I believe that some compiler flags will prohibit this re-direction. This is what Rsamtools tries to impose (from src/Makevars.common)
> 
> DFLAGS = -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 \
>   -U_FORTIFY_SOURCE -DBGZF_CACHE \
>   -Dfprintf=_samtools_fprintf \
>   -Dexit=_samtools_exit \
>   -Dabort=_samtools_abort

I have attached the full build log of the Debian package which contains
all flags.

Hope this helps

      Andreas.

-- 
http://fam-tille.de
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