[Bioc-devel] Cannot find SummarizedExperiment's function assays()
Martin Morgan
martin.morgan at roswellpark.org
Fri Mar 31 12:02:13 CEST 2017
On 03/31/2017 05:29 AM, Sokratis Kariotis wrote:
> 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?
Your experiment data package doesn't have an R/ directory so no R code
(this is normal for experiment data packages). There is therefore no
need to import(SummarizedExperiment) in your NAMESPACE, so remove it
there. The warning will then go away.
Martin
>
> Regards,
>
> Sokratis
>
>
> On 30 March 2017 at 12:05, Martin Morgan <martin.morgan at roswellpark.org
> <mailto: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 <mailto: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
> <mailto: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>
> <mailto: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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