From martin.morgan at roswellpark.org  Mon Jan 22 16:01:44 2018
From: martin.morgan at roswellpark.org (Martin Morgan)
Date: Mon, 22 Jan 2018 10:01:44 -0500
Subject: [Rd] How to address the following: CRAN packages not using
 Suggests conditionally
In-Reply-To: <3b2856da-63c6-6706-214e-84518960eb4a@bioinf.jku.at>
References: <d4a372db-e2e1-9869-b281-107fd1d500cf@bioinf.jku.at>
 <46ae6e78-6e55-77d7-6df9-d7fa6de470d3@bioinf.jku.at>
 <CALEXWq2CK-aoLuo41z2UtyJKtfGu=DC7-=A91Mc83QwXRjAMXw@mail.gmail.com>
 <CALEXWq1Sab3azEnER9baV1Y3f44U_PhQc9v0x2wt3xqz1uDE5A@mail.gmail.com>
 <3b2856da-63c6-6706-214e-84518960eb4a@bioinf.jku.at>
Message-ID: <745be8e2-5dec-b739-768d-ac26a7876b64@roswellpark.org>

On 01/22/2018 08:40 AM, Ulrich Bodenhofer wrote:
> Thanks a lot, I?aki, 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.

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'm not sure whether my comments are consistent 
with Writing R Extensions or not.

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.

Martin Morgan
Bioconductor

> 
> Best regards,
> Ulrich
> 
> 
> On 01/22/2018 10:16 AM, I?aki ?car 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, "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.
>>
>>
>> ??????? ______________________________________________
>> ??????? R-devel at r-project.org <mailto:R-devel at r-project.org> mailing list
>> ??????? https://stat.ethz.ch/mailman/listinfo/r-devel
>> ??????? <https://stat.ethz.ch/mailman/listinfo/r-devel>
>>
>>
> 
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[Rd] How to address the following: CRAN packages not using Suggests conditionally
Martin Morgan