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

Fri Mar 31 11:29:25 CEST 2017

Hey all,

Following your advice, the package now builds successfully! However, I got
this error while checking:

* checking package dependencies ... ERROR
Namespace dependency not required: ‘SummarizedExperiment’

Should I add *Imports :**SummarizedExperiment* in my DESCRIPTION file?

Regards,

Sokratis

On 30 March 2017 at 12:05, Martin Morgan <martin.morgan at roswellpark.org>
wrote:

> 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
>>>>
>>>>
>>>>
>>>> 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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>>
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