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

Jiří Hon xhonji01 at stud.fit.vutbr.cz
Mon Jan 25 18:40:56 CET 2016

Hi Martin

Dne 25.1.2016 v 13:08 Morgan, Martin napsal(a):
> There is discussion at
> http://stackoverflow.com/questions/23556205/using-boost-regex-with-rcpp
>pointing to
> http://gallery.rcpp.org/articles/boost-regular-expressions/
> There is a Bioconductor example in that bundles the regex library at
>  flowCore/src/
> https://github.com/Bioconductor-mirror/flowCore
> A second example is in the mzR package.

Thank you for pointing me to the flowCore and mzR packages, these
examples are really helpful.

> A real question is, do you really need this functionality at the C
> level?

I think it's unavoidable in my case for performance reasons. I'am trying
to dedect all possible overlapping motifs in DNA compounded from
elements matching some regular expression.

> A secondary question is that if several packages are using this
> functionality, then perhaps the library could be bundled separately
> and made available just once; zlibbioc does something like this (sort
> of; zlib is only needed on Windows). The flowCore and mzR maintainers
> (cc'd) might be a valuable resource in this regard.

Efficient regexp algorithms seems useful to me for solving many
bioinformatic problems. So it would be natural to have package with C
API to the most efficient regexp libraries.

> Martin
> ________________________________________ From: Bioc-devel
> <bioc-devel-bounces at r-project.org> on behalf of Jiří Hon
> <xhonji01 at stud.fit.vutbr.cz> Sent: Monday, January 25, 2016 4:33 AM
> To: Charles Determan Cc: bioc-devel at r-project.org Subject: Re:
> [Bioc-devel] C library or C package API for regular expressions
> Hi Charles,
> thank you a lot for your helpful hint. There is still a thing that
> I'm not sure about - Boost manual says that Boost.Regex is not header
> only [1]. So as BH package contains only headers, I will have to
> bundle the Boost.Regex library into the package code anyway. Am I
> right?
> Jiri
> [1]
> http://www.boost.org/doc/libs/1_60_0/more/getting_started/unix-variants.html#header-only-libraries
Dne 23.1.2016 v 13:35 Charles Determan napsal(a):
>> Hi Jiri,
>> I believe you can use the BH package. It contains most of the
>> Boost
> headers.
>> Regards, Charles
>> On Saturday, January 23, 2016, Jiří Hon
>> <xhonji01 at stud.fit.vutbr.cz>
> wrote:
>>> 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
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