[Bioc-devel] Reproducing erros on build and check

[Dan Tenenbaum]

2011/10/18 Martin Morgan <mtmorgan at fhcrc.org>:
> On 10/17/2011 11:59 PM, Stefan McKinnon Høj-Edwards wrote:
>>
>> Hi,
>>
>> I have just noticed that my package AnnotationFuncs does pass build and
>> check for the next release on the Windows hosts. On the Linux and Max OS X
>> hosts there are no problems.
>> The error logs are these:
>> -
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/AnnotationFuncs/liverpool-buildsrc.html
>> -
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/AnnotationFuncs/moscato1-checksrc.html
>>
>> My personal workstation is also running Windows (7), and I have checked
>> and built the package using the latest R release (R version 2.14.0 alpha
>> (2011-10-04 r57169)), but I am not able to reproduce the errors displayed on
>> the log at BioConductor.
>>
>> I have also been looking through my code, and I cannot trace the error
>> giving problems in the build and check above:
>>
>> Error in function (x)  : no function to return from, jumping to top level
>> Execution halted
>> Error in function (x)  : attempt to apply non-function
>> Execution halted
>
> These errors seem to be an issue with the build system  / R. They show up
> intermitently on all platforms, but much more commonly on our windows build
> machines. We don't know what the precise issue is (maybe contention of
> multiple installation threads for some R-wide resource? a memory allocation
> bug in R?) but these seem to be on our side of the fence and not yours.
> Actually, though, we are quite stumped about the root cause so any insights
> from the broader community would be great...

Yesterday I installed on moscato1 an R build without byte-compilation,
and in today's build report all of these errors have disappeared.

Further investigation is required to figure out exactly what is going
on, but I think we can reasonably say that byte-compilation has
something to do with it.

Dan



>
> While on the topic, it can also be disconcerting to see your package fail,
> but tracing to some dependency -- all authors should check carefully,
> especially at this point in the release cycle, that their changes work. The
> recommended strategy for PkgA is to make a local svn export
>
>  cd /tmp
>  svn export /home/mtmorgan/mypkgs/PkgA
>
> then in the /tmp directory build
>
>  R CMD build PkgA
>
> then check
>
>  R CMD check PkgA_0.99.0.tar.gz
>
> The local svn export makes sure that everything you think is in svn actually
> is. R CMD build creates the vignette; the --no-vignette flag can be useful
> to speed things up for other-than-final checks.
>
> Martin
>
>>
>>
>> Any suggestions?
>>
>> Kind regards,
>>
>> Stefan McKinnon Høj-Edwards              Dept. of Molecular Biology and
>> Genetics
>> Ph.D. Fellow                             Aarhus University
>>                                          Blichers Allé 20, Postboks 50
>>                                          DK-8830 Tjele
>> Tel.: +45 8715 7969                      Tel.: +45 8715 6000
>> Email: Stefan.Hoj-Edwards at agrsci.dk      Web: www.agrsci.dk
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>