Thanks Ali! Only problem is that I have too much control on too many infrastructure components so it's too easy for me to mess up other people's stuff :-(
On 10/31/23 14:00, Ali Sajid Imami wrote: > Herve, I see the work you do and stand in awe. I can only wish I could > some day be in a similar place. For now, I am content with submitting > packages for 3.19. :) > >> On Oct 31, 2023, at 4:49 PM, Hervé Pagès <hpages.on.git...@gmail.com> >> wrote: >> >> Hmm.. so I was curious and did a little bit more investigation about >> this. >> >> The other package that also defines a results() function is DESeq2, and >> it gets attached to the search path after calling analyzeSNPhood(). You >> can actually observe this phenomena with the following code: >> >> library(SNPhood) >> library(SNPhoodData) >> search() # DESeq2 is NOT attached >> example(analyzeSNPhood) >> search() # DESeq2 is attached >> >> What's intriguing is that this only happens in BioC 3.18. In BioC 3.17, >> running the analyzeSNPhood example does NOT alter the search path. After >> spending some time tracking this down, it turns out that the reason for >> this change of behaviour is a small tweak I made recently to the >> updateObject() generic in BiocGenerics. An unfortunate one that I will >> correct now. >> >> @Christian: A fix is on its way so you have nothing to do. >> >> Sorry for the trouble. >> >> H. >> >> On 10/31/23 09:44, Hervé Pagès wrote: >>> >>> On 10/31/23 07:22, Wolfgang Huber wrote: >>> >>>> Dear Christian >>>> >>>> If your vignette attaches another package that exports a “results” >>>> function, after it attached SNPhood which defines its own results >>>> function, then the R interpreter has no other choice than doing >>>> what it does. >>>> >>>> Other people adding additional functionality to their packages is >>>> probably not something one can really complain about, so I see >>>> three options >>>> - you use SNPhood::results in your vignette >>>> - you don’t attach the other package, and rather just use what you >>>> need from it using “::” >>>> - you convince Hervé to add ‘results' to BiocGenerics and everyone >>>> who exports such a function converts it to a method for that generic. >>> >>> My pleasure, and that's the cleanest solution. But it will only help >>> if the package that defines the "other" results() function is a >>> Bioconductor package and not a CRAN package. Has this package been >>> identified? >>> >>> A 4th option is to make sure that the other package gets loaded >>> _before_ SNPhood e.g. by putting an explicit library(<the other >>> package>) before library(SNPhood) in your vignette, even though that's >>> kind of hacky. >>> >>> Best, >>> >>> H. >>> >>>> Thank you and kind regards >>>> Wolfgang >>>> >>>> -- >>>> Wolfgang Huber >>>> EMBL >>>> https://www.huber.embl.de/ >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>>> Il giorno 2023-10-28, alle ore 16:15, Christian >>>>> Arnold<chrarn...@web.de> ha scritto: >>>>> >>>>> For my package SNPhood that did not receive any code changes or >>>>> updates >>>>> in quite a while, I suddenly see errors with Bioc 3.18: >>>>> https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/SNPhood/nebbiolo2-buildsrc.html >>>>> >>>>> Error: processing vignette 'workflow.Rmd' failed with diagnostics: >>>>> unused argument (type = "allelicBias") >>>>> >>>>> This comes from this line I think: >>>>> >>>>> names(results(SNPhood.o, type = "allelicBias")) >>>>> >>>>> For literally years, this didnt cause any problems, and the results >>>>> function is actually (re)defined in the SNPhood package: >>>>> >>>>> results <- function(SNPhood.o, type, elements = NULL) >>>>> >>>>> I am not sure now what causes this. Should I use the syntax >>>>> SNPhood::results to make it clear, or I am wrongly assuming that the >>>>> wrong result function is taken that causes the error? >>>>> >>>>> Any pointers? >>>>> >>>>> >>>>> Best >>>>> >>>>> Christian >>>>> >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> 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 >>> -- >>> Hervé Pagès >>> >>> Bioconductor Core Team >>> hpages.on.git...@gmail.com >> >> -- >> Hervé Pagès >> >> Bioconductor Core Team >> hpages.on.git...@gmail.com >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.orgmailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
