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 I also think that the datalist file for pathprint is out of date.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.ramospe...@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.kario...@sheffield.ac.uk <mailto:s.kario...@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@r-project.org <mailto:Bioc-devel@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@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
