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

Michael Lawrence lawrence.michael at gene.com
Mon Mar 27 20:58:08 CEST 2017

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I also think that the datalist file for pathprint is out of date.


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]]
>     _______________________________________________
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> --
> Marcel Ramos
> Bioconductor Core Team Member
> Roswell Park Cancer Institute
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