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.mor...@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.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 >> >> > > This email message may contain legally privileged and/or confidential > information. 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