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 <[email protected]> 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" < > [email protected] on behalf of [email protected]> > 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 <[email protected]> > Sent: Saturday, November 7, 2020 3:30 PM > To: Alexandru Voda <[email protected]>; > [email protected] <[email protected]> > 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" < > [email protected] on behalf of [email protected]> > 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 > > [[alternative HTML version deleted]] > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > [[alternative HTML version deleted]] > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Best, Kasper [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
