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

Shraddha Pai @hr@ddh@@p@| @end|ng |rom utoronto@c@
Thu Oct 21 15:21:59 CEST 2021

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.



*Shraddha Pai, PhD*
Principal Investigator, OICR
Assistant Professor, Department of Medical Biophysics, University of Toronto
shraddhapai.com; @spaiglass on Twitter

*Ontario Institute for Cancer Research*
MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G
*@OICR_news* <https://twitter.com/oicr_news> | *www.oicr.on.ca*

*Collaborate. Translate. Change lives.*

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