[Rd] How to address the following: CRAN packages not using Suggests conditionally
Ulrich Bodenhofer
bodenhofer at bioinf.jku.at
Mon Jan 22 14:40:39 CET 2018
Thanks a lot, Iñaki, this is a perfect solution! I already implemented
it and it works great. I'll wait for 2 more days before I submit the
revised package to CRAN - in order to give others to comment on it.
Best regards,
Ulrich
On 01/22/2018 10:16 AM, Iñaki Úcar wrote:
> 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
> <mailto:i.ucar86 at gmail.com>> escribió:
>
>
>
> El 22 ene. 2018 8:12, "Ulrich Bodenhofer"
> <bodenhofer at bioinf.jku.at <mailto: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
> <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
> <mailto:bodenhofer at bioinf.jku.at>>
> To: Prof Brian Ripley <ripley at stats.ox.ac.uk
> <mailto: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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