[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,

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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