On 8/30/2006 2:13 PM, Paul Gilbert wrote:
>
> Duncan Murdoch wrote:
>> On 8/30/2006 12:28 PM, Paul Gilbert wrote:
>>> Duncan Murdoch wrote:
>>>> On 8/30/2006 4:44 AM, Martin Maechler wrote:
>>>>>>>>>> "FrL" == friedrich leisch <[EMAIL PROTECTED]>
>>>>>>>>>> on Wed, 30 Aug 2006 09:34:13 +0200 (MEST) writes:
>>>>> >> Duncan Murdoch <[EMAIL PROTECTED]> writes:
>>>>> >>> I think we need an option to R CMD check rather than a new
>>>>> field in the
>>>>> >>> DESCRIPTION. Currently a package could be mentioned for any
>>>>> of these
>>>>> >>> reasons:
>>>>> >>> >>> 1. To make functions, examples or vignettes work
>>>>> >>> 2. To allow optional functionality in functions, examples
>>>>> or vignettes.
>>>>> >>> 3. Because it contains complementary functions.
>>>>> >>> >>> I don't think we really need to worry about 3: it
>>>>> should be contained
>>>>> >>> in 1 or 2, if reasonably complete examples are given.
>>>>> >>> >>> Case 1 is handled by Depends.
>>>>> >> >> I think there is an important distinction between a
>>>>> dependency needed
>>>>> >> for the package to function and a dependency needed to
>>>>> demonstrate
>>>>> >> said functionality via an example or vignette. The former is
>>>>> what
>>>>> >> Depends is about, the latter is something else (Suggests).
>>>>>
>>>>> FrL> Sorry to join in late, I am at the Compstat conference and
>>>>> have limited
>>>>> FrL> email access. What Seth describes in the above paragraph is
>>>>> exactly what I
>>>>> FrL> had in mind when splitting the single Depends field we had
>>>>> into Depends
>>>>> FrL> and Suggests: Depends are a necessity to run the package,
>>>>> Suggests is nice
>>>>> FrL> to have but not necessary. If you know how to use a package
>>>>> you may the
>>>>> FrL> decide not to install a package that is only suggested, but
>>>>>
>>>>> FrL> * may not be interested to execute the examples,
>>>>> FrL> * know that you never need the extra functionality
>>>>> FrL> * ...
>>>>>
>>>>> FrL> so it should not be auto-installed unless you ask for
>>>>> FrL> it (the default could also be the other way round, the
>>>>> FrL> point is that it should be possible to have package foo
>>>>> FrL> but not the packages it only suggests). On CRAN we
>>>>> FrL> check with all suggestions to test all bits and pieces,
>>>>> FrL> having an option in R CMD check to test only with
>>>>> FrL> suggests may be nice, if there is use for it.
>>>>>
>>>>> Yes.
>>>>> However, I see two (related) problems with the current 'Suggests'
>>>>> and that's why I opened this thread proposing to have a (what I now
>>>>> would want to simply call) 'canUse' :
>>>>>
>>>>> 1) For 'R CMD check' (and hence CRAN checking),
>>>>> Packages in 'Suggests' must be require()able, and
>>>>> hence all testing only happens *with* the suggested packages
>>>>> being there, and not without.
>>>>>
>>>>> 2) "Suggests" suggests to the human reader of DESCRIPTION that
>>>>> the package authors suggest to also install the packages listed
>>>>> there.
>>>>> Now there are cases, I (as package author) want to show some
>>>>> stuff, or even provide compatibility functionality for some
>>>>> packages that are related to mine, but which I really do not
>>>>> ``suggest''
>>>>> to also be installed, e.g., because the other packages do
>>>>> similar stuff as mine, but I believe my package to be
>>>>> superior. In such a case, I may, e.g., want to provide
>>>>> functions for porting the other package classes to my package's.
>>>>>
>>>>> Duncan Murdoch has proposed to take care of "1)" by
>>>>> still only use 'Suggests' but adding another option to 'R CMD
>>>>> check', let's say --no-suggests which would run all the
>>>>> checks without having the suggested packages available ---
>>>>> something not quite easy to implement, BTW:
>>>>> Imagine the typical windows users who (AFAICS) always only use
>>>>> one library into which they install all packages.
>>>>> How do you want the if( require(<my_suggested_package>) ) {
>>>>> ...
>>>>> }
>>>>> clause *not* to be triggered in such a case ?
>>>>
>>>> I would expect require to return FALSE. This could be done by check
>>>> installing a new version of require() (as it installs new T and F),
>>>> or by the standard require() being modified to check a stop list
>>>> before acting (I'd prefer this, because it would make it easier for
>>>> developers to experiment with functions in different environments),
>>>> or by playing around with the names of things in the library
>>>> (probably not workable on Windows), etc.
>>>>
>>>> I think the default check behaviour on CRAN should be my middle case:
>>>> test based on what is currently installed, don't require packages
>>>> listed in Suggests to be installed. I'm not sure if that should be
>>>> the default behaviour for R CMD check at the command line: as Kurt
>>>> said, usually a developer wants to check all of the code.
>>>>
>>>>> I do agree quite a bit that such a '--no-suggests' option would
>>>>> be very useful for 'R CMD check' -- in addition to my proposal.
>>>>
>>>> I think the other extreme (which I think is there now as
>>>> _R_CHECK_FORCE_SUGGESTS_) is also important.
>>>>
>>>>> Further, I think "2)" above is not taken care of anyway.
>>>>> After all the interesting statements and alternative proposals,
>>>>> I'm still proposing to introduce a 'canUse' field for DESCRIPTION
>>>>> which
>>>>> a) has a "human-readable intent" of being weaker than 'Suggests'
>>>>> b) will not require its packages to be available for R CMD check
>>>>> c) conveys extra information about the package's context, to
>>>>> humans, and
>>>>> d) will potentially be used in automated or semi-manual ``R
>>>>> package database management''
>>>>
>>>> I think d) is important, but I think there are too many variations on
>>>> a) and c) to hope that this would be used consistently. As Fritz
>>>> said, the thing he can remember (and what I would remember) is
>>>> whether a package is mandatory or optional. Fine variations within
>>>> "optional" are just too hard to define clearly in a two-level
>>>> classification.
>>>>
>>>> On the other hand, they are relatively easy to convey in clearly
>>>> written documentation. So I'd still recommend that we stay with just
>>>> Depends and Suggests, but encourage authors to document what they
>>>> mean by "Suggests".
>>>
>>> The problem I see here is that this is a change from the status quo,
>>> which is likely to make a real mess for some time.
>>
>> I'm not sure what your "this" refers to. Was it my suggestion or
>> Martin's? Must be his, I never make a real mess :-)
>
> I was referring to 'but encourage authors to document what they mean by
> "Suggests"', which to me implies that every developer gets to define
> what Suggests means to them. Thus, I would get to make a real mess,
> which I usually manage to do even without it being a legitimate option.:-)
Suggests has some meaning to R, basically corresponding to "is optional
but possibly useful". Developers should explain why they chose to label
a package that way within R. I don't see how they could mess this up.
Duncan Murdoch
>
>>
>> Duncan Murdoch
>>
>> > The status quo is
>>> that packages in Depends and Suggests are needed to check examples and
>>> vignettes. I would not change this without a very good reason. It
>>> would be best to put other suggestions of extensions, that some users
>>> may want to use, somewhere else. The current situation is that these
>>> suggestions are sprinkled in Rd files, vignettes, web pages, etc. This
>>> situation is not too bad, but it might be nice to have some place
>>> users would expect to find this information. However, changing the
>>> meaning of Suggests to be developer defined does not strike me as an
>>> improvement.
>>>
>>> Paul Gilbert
>>>>
>>>> Duncan Murdoch
>>>>
>>>>> Martin
>>>>>
>>>>> FrL> Ad the wording in the manual: obviously that is not
>>>>> FrL> optimal (otherwise no need for parts of this email
>>>>> FrL> thread), perhaps somebody else than the original author
>>>>> FrL> (=me) could try to improve it for 2.4 after this
>>>>> FrL> clarifications? Otherwise I will give it a shot next
>>>>> FrL> week after I return from Rome.
>>>>>
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