[Bioc-devel] How to simplify install when package dependency requires compilation from source

Hervé Pagès hp@ge@@on@g|thub @end|ng |rom gm@||@com
Thu Oct 21 22:22:14 CEST 2021

Hi Shraddha,

I don't think you want to start the business of building and 
distributing Mac binary packages from other people to your users. Even 
if you were doing this, BiocManager::install() would not know about 
these binaries, and I'm not sure that there would be a simple way to 
make your users aware that they can get these binaries from a repository 
that you host and manage.

Also that would mean that you would need to rebuild all the binaries 
that netDx depends on each time they get updated. Would you be able to 
commit to that?

There is no Mac binary for clusterExperiment because the package has a 
TIMEOUT on this platform. The maintainer was contacted recently and is 
working on it.

Thanks for your patience.


On 21/10/2021 06:21, Shraddha Pai wrote:
> Hi all,
> How do I simplify install when a dependency is available only in source
> form and requires compilation using C/C++/Fortran?
> My package netDx has "clusterExperiment" as a dependency (Suggests).
> When I run BiocManager::install("netDx",dependencies=TRUE), I get:
> "Package which is only available in source form, and may need compilation of
>    C/C++/Fortran: ‘clusterExperiment’
> Do you want to attempt to install these from sources? (Yes/no/cancel)"
> If I say yes, it fails because the laptop doesn't have gcc installed, and
> then I have to go run "brew install gcc" (this is OS X). This is getting
> too complicated for your average user.
> Is there a way I could precompile needed packages and just make them
> available to my users? Are there instructions for how to do this somewhere?
> I can host the compiled version on a lab server.
> Thanks,
> Shraddha
> --
> *Shraddha Pai, PhD*
> Principal Investigator, OICR
> Assistant Professor, Department of Medical Biophysics, University of Toronto
> shraddhapai.com; @spaiglass on Twitter
> https://pailab.oicr.on.ca
> *Ontario Institute for Cancer Research*
> MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G
> 0A3
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