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] S4 accessor conflict (MoleculeExperiement)

Hi Nick, Git blame says the 'molecules' method and generic have been in SpatialExperiment for at least 2 years. It looks like the maintainers of MoleculeExperiment should import the molecules generic and export only their method. The other option is to have a separate package with only

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?

Hi, Sorry... it looks like I replied to the wrong email De : Bioc-devel de la part de Julien Wollbrett Envoyé : mardi 31 octobre 2023 16:04 À : Wolfgang Huber ; Christian Arnold Cc : bioc-devel@r-project.org Objet : Re: [Bioc-devel] Package problems due

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

Bonjour, Quelle magnifique nouvelle. Nous ne serons malheureusement pas disponible avant le 30 novembre car nous partons ce vendredi pour un mois de vacances dans nos familles respectives.Nous serions potentiellement disponibles demain ou jeudi mais j'imagine que cela n'est pas du tout

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] Summer school on computational cytometry

Dear Bioconductor community, Next year, from April 29 to May 1, 2024, we will organize a Computational Cytometry Summer School in Ghent, Belgium. We will explore and demonstrate several R packages available for cytometry data, many of which are available on Bioconductor. If you have programming