Re: [Bioc-devel] Package problems due to results() function from other package?

Fine with me to make results() into a generic. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Package problems due to results() function from other package?

Fixed in BiocGenerics 0.48.1: https://github.com/Bioconductor/BiocGenerics/commit/5fd6dfe93786292484dc53023ec681391f4559e0 With this version of BiocGenerics, SNPhood passes CHECK on my laptop (Ubuntu Linux). We'll see how it goes on Thursday's report. (The fix was too late for today's builds

Re: [Bioc-devel] Package problems due to results() function from other package?

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

Re: [Bioc-devel] Package problems due to results() function from other package?

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 On Tue, Oct 31, 2023 at 4:50 PM

Re: [Bioc-devel] Package problems due to results() function from other package?

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:    

Re: [Bioc-devel] Package problems due to results() function from other package?

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

Re: [Bioc-devel] Package problems due to results() function from other package?

� : mardi 31 octobre 2023 15:22 � : Christian Arnold Cc : bioc-devel@r-project.org Objet : Re: [Bioc-devel] Package problems due to results() function from other package? Dear Christian If your vignette attaches another package that exports a �results� function, after it attached SNPhood which

Re: [Bioc-devel] Package problems due to results() function from other package?

Arnold Cc : bioc-devel@r-project.org Objet : Re: [Bioc-devel] Package problems due to results() function from other package? 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

Re: [Bioc-devel] Package problems due to results() function from other package?

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

[Bioc-devel] Package problems due to results() function from other package?

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