[Rd] How to address the following: CRAN packages not using Suggests conditionally

[Iñaki Úcar]

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.ucar86 at gmail.com> escribió:

>
>
> El 22 ene. 2018 8:12, "Ulrich Bodenhofer" <bodenhofer at 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 <bodenhofer at bioinf.jku.at>
> To:     Prof Brian Ripley <ripley at 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.
>>
>>
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