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

Ulrich Bodenhofer bodenhofer at bioinf.jku.at
Tue Jan 23 10:56:12 CET 2018

Thanks for your thoughts, Martin!
> It's very easy for 'pictures of code' (unevaluated code chunks in 
> vignettes) to drift from the actual implementation. So I'd really 
> encourage your conditional evaluation to be as narrow as possible -- 
> during CRAN or even CRAN fedora checks. Certainly trying to use 
> uninstalled Suggest'ed packages in vignettes should provide an error 
> message that is informative to users. Presumably the developer or user 
> intends actually to execute the code, and needs to struggle through 
> whatever issues come up.
I understand your point and I agree.
> I'm not sure whether my comments are consistent with Writing R 
> Extensions or not.
I doubt that. My understanding of the section " Suggested 
packages" is that conditional usage of suggested non-CRAN packages is 
more or less required.
> There is a fundamental tension between the CRAN and Bioconductor 
> release models. The Bioconductor 'devel' package repositories and 
> nightly builds are meant to be a place where new features and breaking 
> changes can be introduced and problems resolved before being exposed 
> to general users as a stable 'release' branch, once every six months. 
> This means that the Bioconductor devel branch periodically (as 
> recently and I suspect over the next several days) contains 
> considerable carnage that propagates to CRAN devel builds, creating 
> additional work for CRAN maintainers.
I am aware of these different philosophies. Though I have an opinion 
about this matter, it is pointless which model I like better. As a 
developer, I have to respect the rules, period. It seems that I can 
avoid trouble by avoiding any dependency to Bioconductor in my CRAN 
packages. In the case of the 'apcluster' package, I deliberately chose 
trouble ;-)   because I think that exemplar-based clustering of 
biological sequences by means of sequence kernels is a very cool thing 
that users should be made aware of.

If I could make a wish to a fairy, I'd ask her to initiate a 
constructive discussion between the R Core Team and the Bioconductor 
Core Team to sort these things out, such that the "tensions" (as you 
have put it) are no longer left as a burden to the package developers.

Thanks and best regards,

>> 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 § 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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