[Bioc-devel] C library or C package API for regular expressions

[Gabe Becker]

Jirka,

Do you mean with millions of different patterns (motifs)? If not, the
R-level regular expression functions are vectorized, and so the looping
will already happen for you in C.

Also, have you confirmed that the R evaluation overhead will actually
dominate the pattern matching here if you just do it in R? That very well
may be, but it's not obvious to me that it would depending on details about
what you're doing that I'm not privy to.

Best,
~G

On Tue, Jan 26, 2016 at 3:25 AM, Jiří Hon <xhonji01 at stud.fit.vutbr.cz>
wrote:

> Hi Dan,
>
> nice to hear, I didn't notice. The only problem could be missing header
> files, but its bundling would solve it I hope.
>
> Jirka
>
> Dne 25.1.2016 v 23:38 Dan Tenenbaum napsal(a):
>
> R requires PCRE to build, therefore perhaps it is available for use within
>> packages?
>> Dan
>>
>>
>> ----- Original Message -----
>>
>>> From: "Jiří Hon" <xhonji01 at stud.fit.vutbr.cz>
>>> To: "bioc-devel" <bioc-devel at r-project.org>
>>> Sent: Saturday, January 23, 2016 1:56:52 AM
>>> Subject: [Bioc-devel] C library or C package API for regular expressions
>>>
>>
>> Dear package developers,
>>>
>>> I would like to ask you for advice. Please, what is the most seamless
>>> way to use regular expressions in C/C++ code of R/Bioconductor package?
>>> Is it allowed to bundle some C/C++ library for that (like PCRE or
>>> Boost.Regex)? Or is there existing C API of some package I can depend on
>>> and import?
>>>
>>> Thank you a lot for your attention and please have a nice day :)
>>>
>>> Jiri Hon
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Gabriel Becker, Ph.D
Associate Scientist
Bioinformatics and Computational Biology
Genentech Research

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