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.uca...@gmail.com
<mailto:i.uca...@gmail.com>> escribió:
El 22 ene. 2018 8:12, "Ulrich Bodenhofer"
<bodenho...@bioinf.jku.at <mailto:bodenho...@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 <bodenho...@bioinf.jku.at
<mailto:bodenho...@bioinf.jku.at>>
To: Prof Brian Ripley <rip...@stats.ox.ac.uk
<mailto:rip...@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.
