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. :)
Regards, Dr. Ali Sajid Imami LinkedIn <https://pk.linkedin.com/pub/ali-sajid-imami/50/956/2a6> On Tue, Oct 31, 2023 at 4:50 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.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
