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 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.mich...@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 I also think that the datalist file for pathprint is out of date.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.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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel