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

[Mike]

The static library is available for linking once flowCore is installed. 
But headers comes from BH package. So you need to add BH to 'linkingTo' 
field of DESCRIPTION file and point to flowCore's compiled static 
library through 'PKG_LIBS' in your Makevars file. Use 
'flowCore:::LdFlags()' to generate the linking path automatically. See 
the example in 'flowWorkspace/src/Makevars.in'

Once Bioconductor upgrades gcc to 4.9,  all of these will be unnecessary 
. see https://github.com/RGLab/flowWorkspace/issues/160.

Mike

On 01/25/2016 04:08 AM, Morgan, Martin wrote:
> 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.
>
> A real question is, do you really need this functionality at the C level?
>
> 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.
>
> 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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