[BioC] How to get the relative path with list.celfiles() from the oligo package?

[Henrik Bengtsson]

On Fri, Aug 21, 2009 at 3:59 AM, Peng Yu<pengyu.ut at gmail.com> wrote:
> According the previous messages in this thread, list.celfiles()
> forwards the arguments to list.files(). So all the arguments that
> accepted by list.files() should be documented in list.celfiles().

A common strategy among package developers is to *minimize the
redundancy* of code and documentation in order to improve quality and
ease maintenance.  By passing down arguments to internal/support
functions via '...', and not replicating the argument names and pass
then explicitly (e.g. full.names=full.names), you will always get
access to the most up-to-date features *and* documentation of the
internal function (here list.files()) in case that is updated.  Vice
versa, if list.files() is updated with, say, new arguments the
list.celfiles() and oligo does not have to be updated.  This means
that you as a user don't have to wait for a package to be updated and
the package developer don't have to keep track of all updates
occurring in all other packages. Maintaining package code and
documentation is already time consuming as it is.

So, if I was the developer of oligo, I would (for my and the user's
sake) *not* document list.files() argument explicitly in
list.celfiles() beyond "{...}{Additional arguments passed to
list.files().}.

My $.02

/Henrik


>
> Regards,
> Peng
>
> On Thu, Aug 20, 2009 at 8:27 PM, Benilton Carvalho<bcarvalh at jhsph.edu> wrote:
>> Documentation is on the works, Peng. Thanks for the reminder.
>>
>> About list.celfiles() specifically, what is your recommendation to improve
>> the documentation?
>>
>> b
>>
>> On Aug 20, 2009, at 10:13 PM, Peng Yu wrote:
>>
>>> On Thu, Aug 20, 2009 at 7:57 PM, Sean Davis<seandavi at gmail.com> wrote:
>>>>
>>>>
>>>> On Thu, Aug 20, 2009 at 7:43 PM, Peng Yu <pengyu.ut at gmail.com> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> So in summary, you use an older version of R than mine, but you get a
>>>>> newer version of help page. This is really strange. Can somebody help
>>>>> me figure out what the problem is with my R installation?
>>>>
>>>> Hi, Peng.  You'll want to look at the section called "Arguments" in the
>>>> help
>>>> file.  That is where the suggestion to look at list.files() comes.  I do
>>>> not
>>>> think there is a problem with your installation, at least not
>>>> contributing
>>>> to the current problem.
>>>
>>> I misunderstood the previous messages. Thank you for reminding me. But
>>> I think the document for list.celfiles should definitely be improved
>>> in future release of oligo.
>>>
>>> Regards,
>>> Peng
>>>
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>>
>>
>
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