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-boun...@r-project.org> on behalf of Jiří Hon
<xhonj...@stud.fit.vutbr.cz> Sent: Monday, January 25, 2016 4:33 AM
To: Charles Determan Cc: bioc-devel@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
<xhonj...@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
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