From bodenhofer at bioinf.jku.at  Mon Jan 22 08:12:24 2018
From: bodenhofer at bioinf.jku.at (Ulrich Bodenhofer)
Date: Mon, 22 Jan 2018 08:12:24 +0100
Subject: [Rd] How to address the following: CRAN packages not using Suggests
 conditionally
In-Reply-To: <d4a372db-e2e1-9869-b281-107fd1d500cf@bioinf.jku.at>
References: <d4a372db-e2e1-9869-b281-107fd1d500cf@bioinf.jku.at>
Message-ID: <46ae6e78-6e55-77d7-6df9-d7fa6de470d3@bioinf.jku.at>

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.

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.
>



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