[Bioc-devel] Reproducing erros on build and check
dtenenba at fhcrc.org
Tue Oct 18 19:05:10 CEST 2011
2011/10/18 Martin Morgan <mtmorgan at fhcrc.org>:
> On 10/17/2011 11:59 PM, Stefan McKinnon Høj-Edwards wrote:
>> 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:
>> 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.
> 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.
>> Any suggestions?
>> Kind regards,
>> Stefan McKinnon Høj-Edwards Dept. of Molecular Biology and
>> 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
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