[R-pkg-devel] [Rd] How to address the following: CRAN packages not using Suggests conditionally

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, "I?aki ?car" <i.ucar86 at gmail.com 
<mailto:i.ucar86 at gmail.com>> escribi?:



    El 22 ene. 2018 8:12, "Ulrich Bodenhofer"
    <bodenhofer at bioinf.jku.at <mailto:bodenhofer at bioinf.jku.at>> escribi?:

        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>

    I?aki


        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.