Re-sending, since I forgot to include the list, sorry. I'm including r-package-devel too this time, as it seems more appropriate for this list.
El 22 ene. 2018 10:11, "Iñaki Úcar" <i.uca...@gmail.com> escribió: > > > El 22 ene. 2018 8:12, "Ulrich Bodenhofer" <bodenho...@bioinf.jku.at> > escribió: > > Dear colleagues, dear members of the R Core Team, > > This was an issue raised by Prof. Brian Ripley and sent privately to all > developers of CRAN packages that suggest Bioconductor packages (see > original message below). As mentioned in my message enclosed below, it was > easy for me to fix the error in examples (new version not submitted to CRAN > yet), but it might turn into a major effort for the warnings raised by the > package vignette. Since I have not gotten any advice yet, I take the > liberty to post it here on this list - hoping that we reach a conclusion > here how to deal with this matter. > > > Just disable code chunk evaluation if suggested packages are missing (see > [1]). As explained by Prof. Ripley, it will only affect Fedora checks on > r-devel, i.e., your users will still see fully evaluated vignettes on CRAN. > > [1] https://www.enchufa2.es/archives/suggests-and-vignettes.html > > Iñaki > > > Thanks in advance for your kind assistance, > Ulrich Bodenhofer > > > > -------- Forwarded Message -------- > Subject: Re: CRAN packages not using Suggests conditionally > Date: Mon, 15 Jan 2018 08:44:40 +0100 > From: Ulrich Bodenhofer <bodenho...@bioinf.jku.at> > To: Prof Brian Ripley <rip...@stats.ox.ac.uk> > CC: [...stripped for the sake of privacy ...] > > > > Dear Prof. Ripley, > > Thank you very much for bringing this important issue to my attention. I > am the maintainer of the 'apcluster' package. My package refers to > 'Biostrings' in an example section of a help page (a quite insignificant > one, by the way), which creates errors on some platforms. It also refers > to 'kebabs' in the package vignette, which leads to warnings. > > I could fix the first, more severe, problem quite easily, (1) since it > is relatively easy to wrap an entire examples section in a conditional, > and (2), as I have mentioned, it is not a particularly important help page. > > Regarding the vignette, I want to ask for your advice now, since the > situation appears more complicated to me. While it is, of course, only > one code chunk that loads the 'kebabs' package, five more code chunks > depend on the package (more specifically, the data objects created by a > method implemented in the package) - with quite some text in between. So > the handling of the conditional loading of the package would propagate > to multiple code chunks and also affect the validity of the explanations > in between. I would see the following options: > > 1. Remove the entire section of the vignette. That would be a pity, > since I can no longer point the users to an otherwise interesting > application of my package. > 2. Replace the code chunks by static LaTeX code such that it appears in > the PDF as if there were code chunks that had been run. This sort of > undermines the philosophy of vignettes and also creates extra effort for > me to maintain the vignette. > 3. Use the functionality of 'kernlab' instead of 'kebabs' if the latter > is not available. This would be technically possible, but (1) the code > in the vignette will look much more complicated to the user and (2) > 'kernlab' does not implement the necessary functionality fully correctly > and also has much longer run times. Needless to say, the issue with > conditional loading will then simply propagate to 'kernlab'. > > Which of the three solutions would you prefer? Do you see any fourth > alternative? Or would you tolerate the warnings on some platforms > arising from the non-availability of packages suggested by the package > vignette? > > Thanks for your time and best regards, > Ulrich Bodenhofer > > P.S.: @all: I hope it is acceptable that I replied to all. I thought the > discussion would be interesting for some of you having similar issues. > > > > On 01/14/2018 09:20 AM, Prof Brian Ripley wrote: > >> as required by §1.1.3.1 of the manual. >> >> The Bioconductor branch used by R-devel has been very unstable recently, >> and it has been decided not to use it for the Fedora checks on R-devel. As >> you can see from the CRAN results pages (at least at the time of writing), >> packages >> >> ACMEeqtl BoSSA CNVassoc CorShrink GRANBase GenCAT GiANT NMF PlackettLuce >> ProFit ProFound RNAseqNet SIBERG antaresRead apcluster cherry clValid coloc >> colorhcplot entropart filematrix fuzzyforest fuzzyjoin glycanr hexbin loon >> nscancor ordinalgmifs penalized phangorn propr shiftR switchr tcgsaseq >> tileHMM tmod >> >> then give ERRORs or (new) WARNINGs on their checks. Please correct ASAP, >> and by Feb 20 to safely retain the package on CRAN. >> >> > ______________________________________________ > r-de...@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
