[Bioc-devel] Compiling a cpp source code while installing package

[Kasper Daniel Hansen]

Alexandra,

What you're proposing is possible, but it is definitely a non-trivial task,
because you (as the package author) are now responsible for getting MAGMA
compiled on Linux / Windows and OS X. If MAGMA is not designed as a
library, that might be hard. Not impossible but hard.

Best,
Kasper

On Sun, Nov 8, 2020 at 2:33 PM Martin Morgan <mtmorgan.bioc using gmail.com>
wrote:

> At the link
>
>   https://ctg.cncr.nl/software/magma
>
> it says " The MAGMA source code can also be downloaded below, which can be
> used to compile the program on the target system if this is not supported
> by the provided binaries (note that standard copyright applies; the MAGMA
> binaries and source code may not be distributed or modified)."
>
> So it sounds like you are not able to do what you want anyway?
>
> Generally, I do not think bundling large software projects that are not
> specifically designed as libraries is a good strategy for R / Bioconductor.
> And while you might ask us to install the software on our build systems so
> that your package can use the program, I'd offer up the cost of doing that,
> both for us and for your potential users --  perhaps a better strategy is
> simply to offer your package to the MAGMA maintainers as an improvement to
> the R scripts they already provide and distribute from the link above?
>
> Martin
>
> On 11/8/20, 7:40 AM, "Bioc-devel on behalf of Alexandru Voda" <
> bioc-devel-bounces using r-project.org on behalf of alexandru.voda using seh.ox.ac.uk>
> wrote:
>
>     Thanks for the reply, Martin!
>
>     Unfortunately, the C++ software is large (
> https://ctg.cncr.nl/software/magma), not just some feature that can be
> used from R base, CRAN or Bioconductor.
>
>     Also, I wouldn't make a separate library for the C++ software because
> the *main* purpose of my package is to wrap them up for R. Other functions
> are just a secondary aim of the package.
>
>     Thank you for the recommended packages! I was wondering if there's any
> standard guidance/vignette for how Rhtslib & Rhdf5lib approached this?
> There are numerous Rcpp vignettes that I could find, but couldn't find for
> pure C compiled by R?
>     ________________________________
>     From: Martin Morgan <mtmorgan.bioc using gmail.com>
>     Sent: Saturday, November 7, 2020 3:30 PM
>     To: Alexandru Voda <alexandru.voda using seh.ox.ac.uk>;
> bioc-devel using r-project.org <bioc-devel using r-project.org>
>     Subject: Re: [Bioc-devel] Compiling a cpp source code while installing
> package
>
>     It would probably help to provide additional detail here; there are
> several examples of packages that build C / C++ libraries from source, a
> common pattern is to have a package dedicated to providing the library,
> e.g., Rhtslib or Rhdf5lib, or of building the library as part of the
> software package itself.
>
>     It's worth assessing whether the functionality is worth it (e.g., why
> use a random number generator from another package, when one can use the R
> random number generator) or already implemented (e.g., linear algebra in
> RcppArmadillo).
>
>     Martin
>
>     On 11/7/20, 10:25 AM, "Bioc-devel on behalf of Alexandru Voda" <
> bioc-devel-bounces using r-project.org on behalf of alexandru.voda using seh.ox.ac.uk>
> wrote:
>
>         Hi! I tried to look this up in the FAQ & best practices but
> couldn't find it.
>
>         My in-the-works package needs to call a legacy C++ software from
> time to time.
>
>         Since that C++ software is open-source, is there a way to make my
> package compile the source (during R package installation) I'm going to
> include? That'd make my package's dependency localized and well-controlled,
> but any other alternative is welcome (except Rcpp, which would take too
> many months to rewrite into the legacy C++ software).
>
>         Best wishes,
>         Alexandru
>
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-- 
Best,
Kasper

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