[datatable-help] Playing nice(r) with S4?

[Steve Lianoglou]

Ok,

The "strange" warnings had to be fixed, I just needed to
`import(methods)` in the NAMESPACE file.

These are the changes made:

DESCRIPTION (added Imports and bumped version to 1.5.2):
https://github.com/lianos/datatable/blob/master/pkg/DESCRIPTION

NAMESPACE (see the S4-ization block up top):
https://github.com/lianos/datatable/blob/master/pkg/NAMESPACE

R/AllS4.R
https://github.com/lianos/datatable/blob/master/pkg/R/AllS4.R

test.data.table.R (tests 226-228)
https://github.com/lianos/datatable/blob/master/pkg/R/test.data.table.R

Problems:
I can't get my test 228 to work when it is run through `R CMD check`.
I keep getting the following problem:

Test 228 ran without errors but failed check:
[1] FALSE

But if I load the new data.table library into an R session, then
source() the test.data.table.R file, and run the test.data.table()
function, everything works as expected.

Not quite sure what's going on -- somehow the `x` in `if (x) return()`
isn't evaluating to TRUE when it's run from the command line.

Anyway, I'm going to see if this plays nice with the package I'm
dev'ing that actually uses the S4-iztion of data.table to see if
anything breaks further ...

Thanks,
-steve
On Wed, Nov 24, 2010 at 11:51 AM, Matthew Dowle <mdowle at mdowle.plus.com> wrote:
> Additions sound fine to me.
>
> Feel free to post the strange warnings. It's the least we can
> do to help you contribute !
>
> Matthew
>
> "Steve Lianoglou" <mailinglist.honeypot at gmail.com> wrote in message
> news:AANLkTimCy6zFcL3SXCVWewsCtrZL8OJkC79Eru8XBG-Y at mail.gmail.com...
> Hi,
>
> Just an update: I'm working on adding this to package.
>
> When it's all said an done, I think we might actually have to add an
> `Imports: methods` clause to the DESCRIPTION file, as well as an
> `exportClass(data.table)` to the NAMESPACE.
>
> Would that be OK?
>
> I'm getting some strange warnings with R CMD check, so will sort that
> out over the next few days when I can find the time.
>
> Thanks,
> -steve
>
>
> On Tue, Nov 23, 2010 at 11:35 AM, Matthew Dowle <mdowle at mdowle.plus.com>
> wrote:
>>
>> Hi Steve,
>>
>> I don't know much about S4 but seems like a good idea, no objections from
>> me either.
>>
>> Please click 'request to join' button on R-Forge project page for
>> data.table, add some tests to the end of test.data.table.R, add something
>> to the NEWS file, run 'R CMD build' and 'R CMD check', and (if ok) commit.
>>
>> Matthew
>>
>>
>>> Hi Tom,
>>>
>>> On Tue, Nov 23, 2010 at 10:53 AM, Tom Short <tshort.rlists at gmail.com>
>>> wrote:
>>>> On Tue, Nov 23, 2010 at 10:33 AM, Steve Lianoglou
>>>> <mailinglist.honeypot at gmail.com> wrote:
>>>>> Hi all,
>>>>>
>>>>> Can we include some functions/declarations so that data.table objects
>>>>> can be used in S4 classes?
>>>>
>>>> Steve, S4 has always scared me off, but if we can do something easy
>>>> like that to help users, we probably should.
>>>
>>> At the start, it did for me as well, but I think I (largely) have the
>>> hang of it ... I wouldn't say I'm an expert, though.
>>>
>>>> Do we have to require any other packages?
>>>
>>> Not as far as I know. Usually a package that defines S4 classes and
>>> such is required to import the 'methods' package, but I'm not sure if
>>> it's necessary here.
>>>
>>> I simply just `svn up`d my data.table repo and added the AllS4.R as
>>> written above, then `R CMD INSTALL`ed it, and everything was kosher --
>>> no warnings or anything and it works as expected.
>>>
>>>> My only comment is related to the data.table(from) in the setAs
>>>> function. Do you want that to be as.data.table(from)? The latter is
>>>> probably faster but does less error checking and auto-conversions of
>>>> columns.
>>>
>>> Sure -- I'm largely indifferent on that, so whatever is more idiomatic
>>> for the data.table devs probably will make the most sense.
>>>
>>> Maybe for consistency sake, one would add:
>>>
>>> setAs("data.table", "data.frame"), function(from) {
>>> as.data.frame(from) ## or whatever
>>> })
>>>
>>> So we can go back the other way and convert a data.table back to a
>>> data.frame via `as(dt, "data.frame")`
>>>
>>> -steve
>>>
>>> --
>>> Steve Lianoglou
>>> Graduate Student: Computational Systems Biology
>>> | Memorial Sloan-Kettering Cancer Center
>>> | Weill Medical College of Cornell University
>>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>>> _______________________________________________
>>> datatable-help mailing list
>>> datatable-help at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help
>>>
>>
>>
>>
>
>
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
> | Memorial Sloan-Kettering Cancer Center
> | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
>
>
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>



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact