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.
Cheers,
H.
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
*@OICR_news* <https://twitter.com/oicr_news> | *www.oicr.on.ca*
<http://www.oicr.on.ca/>
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