[Debian-med-packaging] [devteam-bioc] Test suite of snpStats 1.18.0 fails

[Martin Morgan]

On 05/09/2015 12:22 AM, Maintainer wrote:
> Hi,
>
> I want to upgrade the BioConductor packages in Debian to the latest
> versions and stumbled upon snpStats 1.18.0.  As a testsuite I try to
> build the vignettes this way:
>
> for rnw in *.Rnw ; do
> rfile=`basename $rnw nw`
> R --no-save <<EOT
>    Stangle("$rnw")
>    source("$rfile", echo=TRUE)
> EOT
>
> Unfortunately this ends up in:
>
>> allest["rs10882596"]
> Error in eval(expr, envir, enclos) : object 'allest' not found
> Calls: source -> withVisible -> eval -> eval
> Execution halted
>
> Any hint about this?

The problem would appear to be in the vignette 'snpStats-vignette.Rnw':

snpStats/vignettes$ grep allest\\[\"rs10882596\"\\] *Rnw
snpStats-vignette.Rnw:allest["rs10882596"]

The following

snpStats/vignettes$ Rrel --no-save <<EOT
 > Stangle("snpStats-vignette.Rnw")
 > source("snpStats-vignette.R", echo=TRUE)
 > EOT

'works for me' with the relevant code chunks

 > allest <- snp.rhs.estimates(cc ~ strata(stratum),
+     family = "binomial", sets = use, data = subject.support,
+     snp.data = snps.10)

 > length(allest)
[1] 28184

 > allest["rs10882596"]

      Model  Y-variable   Parameter    Estimate        S.E.     z-value
----------------------------------------------------------------------
rs10882596          cc  rs10882596      0.4575    0.094955       4.818
----------------------------------------------------------------------

The error 'object 'allest' not found' doesn't make sense at this point; it is 
clearly found in the previous line, for instance. It might help to see a little 
more of the output of the test script. Perhaps there is some memory corruption, 
but valgrind

   R -d valgrind -f snpStats-vignette.R

does not report any.

Martin

>
> Kind regards
>
>          Andreas.
>


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