[Bioc-devel] Cannot find SummarizedExperiment's function assays()

[Sokratis Kariotis]

Hey all,

Thanks for the input! I followed Marcel's advice and included the library
in my vignette. Also, I replaced lazyData with a datalist. The datalist
file includes "compressed_result : result" which is in turn loaded in the
vignette using "data(compressed_result)". However, I got:

Warning in data(compressed_result) :
  data set ‘compressed_result’ not found

Error: processing vignette 'usingPathprintGEOData.Rnw' failed with diagnostics:
 chunk 1
Error in assays(result) : object 'result' not found

So the dataset is still not loaded (again, these errors did not exist
prior to package acceptance). I have been using devtools to
build/check the package (since the github issue was closed) and these
warnings/errors dont show up, which imakes it difficult for me to fix
them. Thanks again for any input!

Regards,

Sokratis


On 27 March 2017 at 19:58, Michael Lawrence <lawrence.michael at gene.com>
wrote:

> Actually, I don't see where the package itself is loaded in the
> vignette. If it were, this error would not occur.
>
> Unsurprisingly, I get this when trying to run the vignette code:
>
> Warning message:
> In data(list = ds) : data set ‘pathprintSummarizedGEOData’ not found
>
> I noticed that pathprintGEOData just provides compressed_result, not
> the "pathprintSummarizedGEOData" so I'm not sure where that lives now.
> You might also consider turning off lazy data and using a datalist
> file for that package since the file is somewhat large.
>
> I also think that the datalist file for pathprint is out of date.
>
> Michael
>
> On Mon, Mar 27, 2017 at 11:26 AM, Marcel Ramos
> <marcel.ramosperez at roswellpark.org> wrote:
> > Hi Sokratis,
> >
> > You can resolve this issue by moving `SummarizedExperiment` to the
> > Suggests field and
> >
> > including a `library(SummarizedExperiment)` call in your vignette.
> >
> > Best regards,
> >
> > Marcel
> >
> >
> > On Mon, Mar 27, 2017 at 11:09 AM Sokratis Kariotis
> > <s.kariotis at sheffield.ac.uk <mailto:s.kariotis at sheffield.ac.uk>> wrote:
> >
> >     Hey,
> >
> >     I have submitted the package pathprintGEOData, which got accepted,
> >     but the
> >     build/check report is now producing the following error:
> >
> >
> >
> >     *Error: processing vignette 'usingPathprintGEOData.Rnw' failed with
> >     diagnostics:  chunk 1 Error in assays(result) : could not find
> function
> >     "assays"*
> >
> >     *assays *is a function from the SummarizedExperiment package which I
> >     have
> >     added on my Depends in DESCRIPTION. This error was not present during
> >     building/checking before this package was accepted. Besides adding
> >     SummarizedExperiment
> >     to my Imports what else might be responsible for that error?
> >
> >     Thank you for any help on the matter!
> >
> >     -Sokratis
> >
> >              [[alternative HTML version deleted]]
> >
> >     _______________________________________________
> >     Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>mailing
> list
> >     https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >     <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
> >
> > --
> > Marcel Ramos
> > Bioconductor Core Team Member
> > Roswell Park Cancer Institute
> >
> >
> >
> > This email message may contain legally privileged and/or...{{dropped:4}}
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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