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

[Martin Morgan]

On 03/30/2017 05:21 AM, Sokratis Kariotis wrote:
> 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


I Stangle'd the vignette

   cd pathprintGEOData/vignettes
   R CMD Stangle usingPathprintGEOData.Rnw

and then walked through the lines of R code. I got to

 > data(compressed_result)
Warning message:
In data(compressed_result) : data set 'compressed_result' not found

The data 'compressed_result' is not found, because it is in the 
pathprintGEOData package, and the pathprintGEOData package is not on the 
search path.

 > search()
  [1] ".GlobalEnv"                   "package:SummarizedExperiment"
  [3] "package:DelayedArray"         "package:matrixStats"
  [5] "package:Biobase"              "package:GenomicRanges"
  [7] "package:GenomeInfoDb"         "package:IRanges"
  [9] "package:S4Vectors"            "package:BiocGenerics"
[11] "package:parallel"             "package:stats4"
[13] "package:pathprint"            "ESSR"
[15] "package:BiocInstaller"        "package:stats"
[17] "package:graphics"             "package:grDevices"
[19] "package:utils"                "package:datasets"
[21] "package:methods"              "Autoloads"
[23] "package:base"

It is not on the search path because, originally, pathprint had Depends: 
pathprintGEOData, but that was modified, as you know, to Suggests: 
pathprintGEOData, to avoid circular dependencies that thwart our build 
system. So previously library(pathprint) was enough to make the data 
available, but now you must either load the package

   library(pathprintGEOData)
   data(compressed_result)

or tell data() where the data set is

   data(compressed_result, package="pathprintGEOData")

One would still like to use an informative name for the data (first 
argument of data) and presumably an identical name for the object that 
is loaded.

Martin


>
> 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
>>>
>>>
>>>
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>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
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>>
>
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>
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