Re: [Seqan-dev] placing seqan headers into R package

[August Guang <august.guang@gmail.com>]

Thanks, I have included the license file and a notice about citations now. Will there be support for seqan/2.4 for mingw? I saw that there was on older versions. The reason I'm asking is that R packages submitted to Bioconductor/CRAN have to build and pass checks on Linux, OS and Windows, but on Windows the packages are tested with the mingw compiler and I haven't found a way around it.

If not, would I be able to get some help with writing support for it? I have been trying to address various issues specific to mingw but am not familiar with Windows specific implementations and am getting way out of my depth. So far I have added mman-win32 to replace sys/mman.h and changed some enum values to not use posix_madvise. The current error I am trying to tackle is the fact that getuid, geteuid, getgid and getegid are Unix-only. It appears I can either write my own macros for them (https://stackoverflow.com/questions/1594746/win32-equivalent-of-getuid) or install LibGW32 for them (http://gnuwin32.sourceforge.net/packages/libgw32c.htm). Is there an option that would be better and can I get some advice on how I would implement it?

thanks,

august

On Mon, Feb 26, 2018 at 7:49 AM, Hannes Hauswedell <hannes.hauswedell@fu-berlin.de> wrote:

Am Donnerstag, 22. Februar 2018, 11:05:38 schrieb August Guang:
> Hi,
>
> I would like to package the SeqAn headers for easy use in a few R packages
> I will be writing with my team, the Computational Biology Core at Brown
> University in the US. Would this be ok with you all? I am leaving the
> license as BSD 3 clause as well, and if you would like to make any
> additions to the license please let me know.
>
> You can view the current state of the repository here:
> https://github.com/compbiocore/RSeqAn
>
> Thanks,
> august

Dear August,

that's great to hear, feel very free to include it in your package. As long as
the LICENSE file is shipped with the package there is no problem. Please also
include a link to www.seqan.de in your documentation and if possible also the
following note:
"Please do not forget to cite SeqAn if you use this package in your acedemic
work, even if only in auxiliary tools or pipelines:
https://doi.org/10.1016/j.jbiotec.2017.07.017"

That would be great!

Thank you,
Hannes
--
Hannes Hauswedell

Scientific staff & PhD candidate
Freie Universität Berlin / Max Planck Institute for Molecular Genetics

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--

August Guang

HMC Class of 2012

Mathematics

Brown University

Applied Mathematics