[R-pkg-devel] CRAN student assistants

Duncan Murdoch murdoch@dunc@n @end|ng |rom gm@||@com
Thu May 16 21:42:44 CEST 2019

On 16/05/2019 1:10 p.m., Jennifer Bryan wrote:
> Thanks for the excellent comparable package, Hong.
> Today's rejection of gargle instructs me to use \donttest{} instead of
> \dontrun{}. Most of the affected functions create, load, and/or refresh
> service account tokens and OAuth2 credentials. I see that \dontrun{} is
> used in AzureAuth, which does seem more appropriate and is what I did. My
> impression is that \donttest{} code is still run under some circumstances.
> Perhaps this is another good topic for discussion, now that we've worked
> through cat() vs message().
> It seems like you've also got a few functions without examples at all
> (e.g., format_auth_header(), AzureR_dir()). How does this get through CRAN
> review? When is that OK and when is it not?

I haven't been involved with CRAN for a couple of years, but for the 
year when I was, one thing that really, really pissed us off was a 
question like this.  Obviously it is better if all functions have 
examples.  When package authors tried to determine the absolute least 
work they could get away with it really wasted our time trying to decide 
which side of the line a particular package fell on.  We tried to be 
consistent, but clearly that would be impossible.

So the answer to your question is:  put excellent examples in all of 
your help pages, and don't try to find the minimally publishable package.

> I would simply like to understand the standards, so that I can impose them
> on myself and go through fewer submissions. Maybe we could even automate
> some of those checks. That would reduce workload all around.

Impose higher standards on yourself than you think are necessary, and 
your packages will be better and will be published faster.

Duncan Murdoch

> I've taken your advice to reply via email with full explanation and cc
> others at CRAN. Maybe this will also lead to speedy resolution with no fuss.
> -- Jenny
> On Wed, May 15, 2019 at 2:18 PM Hong Ooi <hongooi using microsoft.com> wrote:
>> I had a similar experience with a couple of my package updates needing
>> changes. The background is that I have a family of packages for talking to
>> Microsoft's Azure cloud service from R, and my examples are all marked
>> \dontrun because they need an Azure subscription to work. This had
>> previously been cleared with Uwe Ligges, but I guess the other CRAN
>> reviewers weren't aware of this.
>> In both cases, replying to the CRAN email and cc'ing Uwe resolved the
>> issue quickly and without fuss.
>> -----Original Message-----
>> From: R-package-devel <r-package-devel-bounces using r-project.org> On Behalf
>> Of Mark van der Loo
>> Sent: Thursday, 16 May 2019 1:50 AM
>> To: Jennifer Bryan <jenny.f.bryan using gmail.com>
>> Cc: R Package Development <r-package-devel using r-project.org>
>> Subject: Re: [R-pkg-devel] CRAN student assistants
>> For what it's worth,
>> I recently submitted a new package that was initially refused (with
>> comments) by CRAN. I updated number of them accordingly, but there were a
>> few that with good reasons I could not change. I explained this in the
>> comments when uploading a new version and it got accepted. So I don't see
>> the problem.
>> (The case here was a use of \dontrun{}. I had to switch an example off
>> because a warning was thrown which would upset R CMD check. But
>> demonstrating the warning was exactly the point of the example.)
>> All this aside. I think it is extremely unethical to publish privately
>> sent CRAN emails on GH, including personal details such as name and e-mail
>> address of the sender without their explicit consent.
>> Best,
>> Mark
>> On Wed, May 15, 2019 at 4:44 PM Jennifer Bryan <jenny.f.bryan using gmail.com>
>> wrote:
>>> Hello,
>>> Since this has turned into a worldwide code review, I will briefly
>>> address that, then reiterate the point of the original message.
>>> I am working on an initial release of a package. It reveals
>>> information to a user, sometimes in a print method-y way, sometimes in
>>> more of a verbose / debugging way that is under control of a
>>> documented option, which defaults to "off" or "quiet". For now, I have
>>> chosen to send all of this output through a single functions that,
>>> yes, uses cat(). I went this direction for an initial release to keep
>>> the package simple and accumulate some user experience. If the
>>> "debugging mode" proves to be useful, I will rework it, possibly using
>>> UI functionality that I believe our group might release in the future.
>>> Rest assured, I understand cat() vs message() and the various
>>> tradeoffs. I made mine and it is my impression that package maintainers
>> have this level of freedom.
>>> The real point is: the currenrt CRAN submission process is designed
>>> for one-way communication and there's no guarantee of continuity of
>> reviewer.
>>> If this type of implementation review is going to happen, it seems
>>> that many aspects of the process would need to change, to make sure
>>> these new standards are applied consistently to every submission and
>>> that existing package are brought up to current standards.
>>> To clarify something for Joris, I am not aware of any special channel
>>> of communication or influence between CRAN and the R Foundation (of
>>> which I am also a member). I think this is an aspect of CRAN vs R
>>> Foundation (vs R Core even) that is unclear to many. These entities
>>> operate quite independently, except for the fact that specific people
>>> belong to more than one. So RF members interact with CRAN the same way
>>> as any other of member of the community.
>>> -- Jenny
>>> On Wed, May 15, 2019 at 6:43 AM Jim Hester <james.f.hester using gmail.com>
>>> wrote:
>>>> Sorry first sentence should read
>>>> I agree that `message()` is ideally preferred, precisely because of
>>>> the reasons Martin stated, it is easily controlled by the user.
>>>> On Wed, May 15, 2019 at 9:41 AM Jim Hester
>>>> <james.f.hester using gmail.com>
>>>> wrote:
>>>>> I agree that `message()` is in an ideally preferred, precisely
>>>>> because of the reasons Martin stated, it is easily controlled by the
>> user.
>>>>> Unfortunately, in the real world, the windows R gui console and
>>>>> RStudio (which copied behavior) color messages, and anything on
>>>>> stderr in fact, in red, which confuses most users who are trained
>>>>> to treat messages in red as errors.
>>>>> This also makes using colored output (where available) more
>>>>> challenging when using `message()`.  You either have to accept the
>>>>> text as red, or unconditionally change the text color to black or
>>>>> similar, which can then be unreadable if the user is using a dark
>>>>> color theme.
>>>>> Jenny is an experienced package developer. She knew this tradeoff
>>>>> and the use of `cat()` in gargle was deliberate choice in an
>>>>> imperfect world. She did not make this decision out of ignorance
>>>>> of a better way.
>>>>> However there is no way for Jenny or any other package developers
>>>>> to have a dialog during a CRAN submission, the communication is
>>>>> only in one direction, if she resubmits explaining her rationale
>>>>> for the choice she may not even have the same reviewer the next time.
>>>>> Bioconductor seems to have a much better review process for
>>>>> submissions, with real dialog between the reviewer and package
>>>>> author, perhaps CRAN can learn from that process and improve the
>>>>> submission experience in the future.
>>>>> Jim
>>>>> On Wed, May 15, 2019 at 7:41 AM Martin Morgan
>>>>> <mtmorgan.bioc using gmail.com
>>>> wrote:
>>>>>> message() / warning() / stop() write to stderr whereas print() /
>>> cat()
>>>> write (by default) to stdout. Even without being able to suppress
>>> messages,
>>>> it is well-established practice (the story is that this is the
>>>> reason why 'stderr' was introduced into unix,
>>> https://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.
>>> jstorimer.com%2Fblogs%2Fworkingwithcode%2F7766119-when-to-use-stderr-i
>>> nstead-of-stdout&data=01%7C01%7Chongooi%40microsoft.com%7C6ab84a03
>>> dd6048a5160d08d6d94d0b70%7C72f988bf86f141af91ab2d7cd011db47%7C1&sd
>>> ata=8%2F6BhGQWQqy7OOrjw4gaDRuYfPgYIdEoLEpTl6Q4hgQ%3D&reserved=0
>>>> ) to separate diagnostic messages from program output. I agree that
>>> gargle
>>>> (in particular, and packages in general, given the theme of this
>>>> mailing
>>>> list) would be a better package if it used message() where it now
>>>> uses cat().
>>>>>> Martin
>>>>>> On 5/15/19, 5:04 AM, "R-package-devel on behalf of Joris Meys"
>>>>>> <
>>>> r-package-devel-bounces using r-project.org on behalf of
>>>> Joris.Meys using ugent.be>
>>>> wrote:
>>>>>>      2) Where cat() is used in gargle, message() is a better
>>>>>> option
>>> for
>>>> the
>>>>>>      following reason:
>>>>>>      > myfun <- function(){cat("Yes");message("No")}
>>>>>>      > suppressMessages(myfun())
>>>>>>      Yes
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