[BioC] rTANDEM package -- An R encapsulation of the X!Tandem algorithm

[Steve Lianoglou]

Ahh, yes.

Frederic also emailed me offlist indicating that it was used to get
around some warning (notice(?)) in R CMD CHECK, which is why I've
never seen it:

I don't submit packages often, but when I do ... I don't test them.

Sincerely,
The most interesting programmer in the world.

;-)


On Wed, Dec 19, 2012 at 7:37 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 12/19/2012 08:32 AM, Steve Lianoglou wrote:
>>
>> Hi Frederic,
>>
>> On Wed, Dec 19, 2012 at 10:36 AM, Frederic Fournier
>> <frederic.bioinfo at gmail.com> wrote:
>>>
>>> Dear Bioconductor users,
>>>
>>> I would like to announce the release of the new package rTANDEM on
>>> bioconductor.
>>> This package encapsulates the mass spectrometry indentification algorithm
>>> X!Tandem in R, making it possible to conduct a full ms-ms analysis in R
>>> and
>>> to use R datamining capacities to search the results. We hope that
>>> rTANDEM
>>> can become the center of a viable pipeline for ms-ms proteomics in R.
>>>
>>> Questions, suggestions, bug-reports, and feedback of any kind is more
>>> than
>>> welcome.
>>
>>
>> Really cool!
>>
>> Thanks for putting this together ... I checked out the source code to
>> skim the package and notice that you use data.table (good choice :-) I
>> see, however, that you felt that you needed to resort to some hacks to
>> get it to work correctly, for instance in `GetPeptides`, you have:
>>
>>    ## Dummy declaration to prevent "no visible binding" note when using
>> data.table subset:
>>    pep.id=prot.uid=uid=NULL
>>    rm(pep.id, prot.uid, uid)
>>    ...
>>
>> But this shouldn't be necessary, so if there's a problem in data.table
>> I'd like to fix it.
>>
>> I'm curious if you list data.table in your "Imports" field in your
>> DESCRIPTION file, then `import(data.table)` in your NAMESPACE, is this
>> still necessary?
>>
>> I don't think I've run into this problem before, so I'm hoping these
>> small changes should do the trick.
>
>
> I'm not sure, but I think this cannot be solved by import'ing data.table.
> Here
>
>   df <- data.frame(xx=1:5)
>   subset(df, xx > 2)
>
> would trigger the same kind of warning about "no visible binding for global
> variable ‘xx’" because codetools (used by R CMD check) doesn't know about
> the local environment in which subset is being evaluated and xx is to be
> found, as illustrated with
>
>> library(codetools)
>> f = function() { df = data.frame(xx=1:5); subset(df, xx > 2) }
>> f()
>   xx
> 3  3
> 4  4
> 5  5
>> findGlobals(f)
> [1] "="          ">"          ":"          "{"          "data.frame"
> [6] "subset"     "xx"
>
> utils::globalVariables is another solution to this problem, but in some ways
> not very satisfactory (it excludes named variables from the warning, but at
> package-level scope instead of the function in which the variable is being
> used).
>
> Martin
>
>
>>
>> HTH,
>> -steve
>>
>
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
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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