[Rd] R CMD check: non source files in src on (2.3.0 RC (2006-04-19 r37860))
Kasper Daniel Hansen
khansen at stat.Berkeley.EDU
Thu Apr 20 22:06:00 CEST 2006
One thing which I personally disagree with is that the procedure for
the check is different when run on a directory than on a tarball (I
am talking about the defaults here, I now know I can change it
locally). I could understand the difference if the check resulted in
an _error_ such that I would be unable to install the package if I
have eg. object files in the src directory.
I did the original checking for the package Jim (the OP) referred to,
and I did expect that since it passed R CMD check (on my svn checkout
directory), everything would be fine (this was with R-beta from
Sunday). It was a bit of a surprise for me to learn that there was
differences.
This is a case where I fail to see the advantage of the default
settings, and I do see some disadvantages. But probably not important
enough for R-2.3.0.
/Kasper
On Apr 20, 2006, at 12:40 PM, Prof Brian Ripley wrote:
> On Thu, 20 Apr 2006, Robert Gentleman wrote:
>
>> Hi,
>>
>> Well, I guess if someone thinks they know how I am going to
>> configure and
>> build the sources needed to construct appropriate dynamic
>> libraries so well
>> that they can feel free to exclude files at their whim at install
>> time,
>> perhaps they could feel just as free to exclude them at build time?
>
> The checks are different if there is a configure file:
>
> Further, the check on the @file{src} directory is only run if the
> package/bundle does not contain a @file{configure} script (which
> corresponds to the value @samp{yes-maybe}) and there is no
> @file{src/Makefile} or @file{src/Makefile.in}.
>> This makes no sense to me and certainly does not solve the size
>> problem
>> mentioned by Brian. If there is a single example of something that
>> was better
>> this way, I would be interested to hear it. I can think of several
>> things
>> that are worse.
>
> We found several examples with large and unnecessary files in the src
> directory via this check, as well as files in directories other
> than the
> ones the package author had intended.
>
> It `makes no sense to me' to discuss situations that are not as
> implemented. This was discussed some months ago, ideas trialled
> and those
> that were found worthwhile retained. And now we are in code freeze.
>
>>
>> best wishes
>> Robert
>>
>>
>> Roger Bivand wrote:
>>> On Thu, 20 Apr 2006, Robert Gentleman wrote:
>>>
>>>
>>>> I disagree, things like README files and other objects are
>>>> important and
>>>> should be included. I don't see the real advantage to such
>>>> warnings, if
>>>> someone wants them they could be turned on optionally.
>
> Well, they are turned on optionally, but as the CRAN maintainers
> want them, submitters to CRAN ought to be aware that they will be run.
>
>
>>> Isn't the point at least partly that all those files are lost on
>>> installation? If the README is to be accessible after
>>> installation, it can
>>> be placed under inst/, so that both users reading the source and
>>> installed
>>> versions can access it. So maybe the warning could be re-phrased
>>> to suggest
>>> use of the inst/ tree for files with important content?
>>>
>>> Best wishes,
>>>
>>> Roger
>>>
>>>
>>>> If size is an issue then authors should be warned that their
>>>> package is
>>>> large (in the top 1% at CRAN would be useful to some). I also
>>>> find it
>>>> helpful to know whose packages take forever to build, which we
>>>> don't do.
>>>>
>>>> Just because someone put something in TFM doesn't mean it is
>>>> either a good
>>>> idea or sensible, in my experience.
>>>>
>>>> best wishes
>>>> Robert
>>>>
>>>>
>>>> Prof Brian Ripley wrote:
>>>>
>>>>> On Wed, 19 Apr 2006, James Bullard wrote:
>>>>>
>>>>>
>>>>>
>>>>>> Hello, I am having an issue with R CMD check with the nightly
>>>>>> build of
>>>>>> RC 2.3.0 (listed in the subject.)
>>>>>
>>>>>
>>>>> This is all explained in TFM, `Writing R Extensions'.
>>>>>
>>>>>
>>>>>
>>>>>> The problem is this warning:
>>>>>>
>>>>>> * checking if this is a source package ... WARNING
>>>>>> Subdirectory 'src' contains:
>>>>>> README _Makefile
>>>>>> These are unlikely file names for src files.
>>>>>>
>>>>>> In fact, they are not source files, but I do not see any
>>>>>> reason why they
>>>>>> cannot be there, or why I need to be warned of their presence.
>>>>>> Potentially I could be informed of their presence, but that is
>>>>>> another
>>>>>> matter.
>>>>>
>>>>>
>>>>> Having unnecessary files in other people's packages just waste
>>>>> space and
>>>>> download bandwidth for each one of the users.
>>>>>
>>>>>
>>>>>
>>>>>> Now, I only get this warning when I do:
>>>>>>
>>>>>> R CMD build affxparser
>>>>>> R CMD check -l ~/R-packages/ affxparser_1.3.3.tar.gz
>>>>>>
>>>>>> If I do:
>>>>>>
>>>>>> R CMD check -l ~/R-packages affxparser
>>>>>>
>>>>>> I do not get the warning. Is this inconsistent, or is there
>>>>>> rationale
>>>>>> behind this? I think the warning is inappropriate, or at the
>>>>>> least a
>>>>>> little restrictive. It seems as if I should be able to put
>>>>>> whatever I
>>>>>> want in there, especially the _Makefile as I like to build
>>>>>> test programs
>>>>>> directly and I want to be able to build exactly what I check
>>>>>> out from
>>>>>> my source code repository without having to copy files in and
>>>>>> out.
>>>>>
>>>>>
>>>>> All described in TFM, including how to set defaults for what is
>>>>> checked.
>>>>>
>>>>>
>>>>>
>>>>>> The output from R CMD check is below. Any insight would be
>>>>>> appreciated.
>>>>>> As always thanks for your patience.
>>>>>
>>>>>
>>>>> [...]
>>>>>
>>>>>
>>>>
>>>>
>>>
>>
>>
>
> --
> Brian D. Ripley, ripley at stats.ox.ac.uk
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UK Fax: +44 1865 272595
>
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