From pgilbert902 at gmail.com  Mon Jun  2 17:19:39 2014
From: pgilbert902 at gmail.com (Paul Gilbert)
Date: Mon, 02 Jun 2014 11:19:39 -0400
Subject: [Rd] R CMD check for the R code from vignettes
In-Reply-To: <CADwqtCP=PJR=hDx9KSjs4HeSaqdgpdLZR-EpS0a5A2DPcW_7=Q@mail.gmail.com>
References: <CANROs4dyoXEUEzouGTsL9sHCMM8RcjYWw9584SUAEYfGntPrFg@mail.gmail.com>	<538885F3.8020807@gmail.com>	<CANROs4eect+qAvXTLEzPhM=X2Eg5R0T-DCUBO6=VDfBFVJNCuQ@mail.gmail.com>	<CADwqtCN2XixFy0H43BeFMU7R_p+sQCaOHBU5W6tXn7Ng7pP1pA@mail.gmail.com>	<CANROs4c=x7BNDWJ7ObS5pB36+NBGzVmTmN7-94t8T+dowcEA5A@mail.gmail.com>	<538A63C6.5030201@fhcrc.org>	<CANROs4cM=q0isYqUO6eg2vWjT2HieUy996u7HtS8_deydFa-8g@mail.gmail.com>	<CADwqtCNQEAz==L4fSomQt+Ayw6wSo61-uM=xN_9K26K1XRoFwQ@mail.gmail.com>	<CANROs4cuHbSTeNXgBuWFAhpHGMVdGLsAs5gFH+8s=HCq8NYiwQ@mail.gmail.com>	<CAN_1p9wgx57ZRAYz56m+-51_UMYTtm97-JmpYSKYtHSobLkOzQ@mail.gmail.com>
	<CADwqtCP=PJR=hDx9KSjs4HeSaqdgpdLZR-EpS0a5A2DPcW_7=Q@mail.gmail.com>
Message-ID: <538C960B.2040509@gmail.com>



On 06/02/2014 12:16 AM, Gabriel Becker wrote:
> Carl,
>
> I don't really have a horse in this race other than a strong feeling that
> whatever check does should be mandatory.
>
> That having been said, I think it can be argued that the fact that check
> does this means that it IS in the R package vignette specification that all
> vignettes must be such that their tangled code will run without errors.

My understanding of this is that the package maintainer can turn off 
building the vignette (--no-vignettes) but R CMD check and CRAN still 
check that the tangle code runs, and the check fails if it does not. 
Running the tangle code can be turned off, just not by the package 
maintainer. You have to make a special appeal to the CRAN maintainers, 
and give reasons they are prepared to accept. I think the intention is 
that the tangle code should run without errors. I doubt they would 
accept "it doesn't work" as an acceptable reason. But there are reasons, 
like the vignette requires access to a commercial database engine. Also, 
I think, turning this off means they just do not run it regularly, in 
the daily checks. I don't think it necessarily means the code is never 
tested. The testing may need to be done on machines with special resources.

Thus, --no-vignettes provides a mechanism to avoid running the tangle 
code twice but, without special exemption, it is still run once. Some 
package maintainers may not think of several feature of 'R CMD check' as 
'aids'. I think of it having more to do with maintaining some quality 
assurance, which I think of as an aid but not a debugging aid.

I believe the CRAN maintainers have intentionally, and successfully, 
made disabling the running of tangled code  more trouble than it is 
generally worth. Effectively, a package should have tangle code that 
runs without errors.

(Of course, I could be wrong about all this, it has happened before.)

Paul

>
> ~G
>
>
> On Sun, Jun 1, 2014 at 8:43 PM, Carl Boettiger <cboettig at gmail.com> wrote:
>
>> Yihui, list,
>>
>> Focusing the behavior of R CMD check, the only reason I have seen put
>> forward in the discussion for having check tangle and then source as well
>> as knit/weave the very same vignette is to assist the package maintainer in
>> debugging R errors vs pdflatex errors.  As tangle (and many other tools)
>> are already available to an author needing extra help debugging, and as the
>> error messages are usually clear on whether errors come from the R code or
>> whatever format compiling (pdflatex, markdown html, etc), this seems like a
>> poor reason for R CMD check to be wasting time doing two versions of almost
>> (but not literally) the same check.
>>
>> As has already been discussed, it is possible to write vignettes that can
>> be Sweave'd but not source'd, due to the different treatments of inline
>> chunks.  While I see the advantages of this property, I don't see why R CMD
>> check should be enforcing it through the arbitrary mechanism of running
>> both Sweave and tangle+source. If that is the desired behavior for all
>> Sweave documents it should be in part of the Sweave specification not to be
>> able to write/change values in inline expressions, or part of the tangle
>> definition to include inline chunks.  I any event I don't see any reason
>> for R CMD check doing both.  Perhaps someone can fill in whatever I've
>> overlooked?
>>
>> Carl
>>
>>
>> On Sat, May 31, 2014 at 8:17 PM, Yihui Xie <xie at yihui.name> wrote:
>>
>>> 1. The starting point of this discussion is package vignettes, instead
>>> of R scripts. I'm not saying we should abandon R scripts, or all
>>> people should write R code to generate reports. Starting from a
>>> package vignette, you can evaluate it using a weave function, or
>>> evaluate its derivative, namely an R script. I was saying the former
>>> might not be a bad idea, although the latter sounds more familiar to
>>> most R users. For a package vignette, within the context of R CMD
>>> check, is it necessary to do tangle + evaluate _besides_ weave?
>>>
>>> 2. If you are comfortable with reading pure code without narratives,
>>> I'm totally fine with that. I guess there is nothing to argue on this
>>> point, since it is pretty much personal taste.
>>>
>>> 3. Yes, you are absolutely correct -- Sweave()/knit() does more than
>>> source(), but let me repeat the issue to be discussed: what harm does
>>> it bring if we disable tangle for R package vignettes?
>>>
>>> Sorry if I did not make it clear enough, my priority of this
>>> discussion is the necessity of tangle for package vignettes. After we
>>> finish this issue, I'll be happy to extend the discussion towards
>>> tangle in general.
>>>
>>> Regards,
>>> Yihui
>>> --
>>> Yihui Xie <xieyihui at gmail.com>
>>> Web: http://yihui.name
>>>
>>>
>>> On Sat, May 31, 2014 at 9:20 PM, Gabriel Becker <gmbecker at ucdavis.edu>
>>> wrote:
>>>>
>>>>
>>>>
>>>> On Sat, May 31, 2014 at 6:54 PM, Yihui Xie <xie at yihui.name> wrote:
>>>>
>>>>> I agree that fully evaluating the code is valuable, but
>>>>> it is not a problem since the weave functions do fully evaluate the
>>>>> code. If there is a reason for why source() an R script is preferred,
>>>>>
>>>>> I guess it is users' familiarity with .R instead of .Rnw/.Rmd/...,
>>>>
>>>>
>>>> It's because .Rnw and Rmd require more from the user than .R. Also, this
>>>> started with vignettes but you seem to be talking more generally. If
>>> so, I
>>>> would point out that not all R code is intended to generate reports, and
>>>> writing pure R code that isn't going to generate a report in an
>>> .Rnw/.Rmd
>>>> file would be very strange to say the least.
>>>>
>>>>
>>>>>
>>>>> however, I guess it would be painful to read the pure R script tangled
>>>>> from the source document without the original narratives.
>>>>
>>>>
>>>> That depends a lot on what you want. Reading an woven article/report
>>> that
>>>> includes code and reading code are different and equally valid
>>> activities.
>>>> Sometimes I really just want to know what the author actually told the
>>>> computer to do.
>>>>
>>>>>
>>>>>
>>>>> So what do we really lose if we turn off tangle? We lose an R script
>>>>> as a derivative from the source document, but we do not lose the code
>>>>> evaluation.
>>>>
>>>>
>>>> We lose *isolated* code evaluation. Sweave/knit have a lot more moving
>>>> pieces than source/eval do. Many of which are  for the purpose of
>>> displaying
>>>> output, rather than running code.
>>>>
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>
>>
>>
>> --
>> Carl Boettiger
>> UC Santa Cruz
>> http://carlboettiger.info/
>>
>
>
>



[Rd] R CMD check for the R code from vignettes
Paul Gilbert