Hi all,
I’m wondering if someone an offer advice on a problem I’m facing in developing
a package.
My package essentially generates code and formats data for one of two MCMC
sampling engines, JAGS accessed via rjags or nimble (a native R package), calls
the engines, and then provides functions to access the results. Since only one
of the engines is needed I would like to include rjags and nimble in Suggests
in the DESCRIPTION and use requireNamespace() to load the appropriate package
when its functionality is needed.
Unfortunately, nimble will not work with this mechanism. It relies on a complex
mechanism to compile C++ code to run the sampler, and some of the functions
cannot be found when the package is loaded in this way. I’ve been in touch with
the maintainers and they are aware of the issue but the current fix is to
include the package under Depends. However, this forces a user to install
nimble (which itself requires compiling lengthy C++ code) even if the user
intends to run the sampler in JAGS.
I thought I’d solved the problem by including nimble in Suggests and then
loading it via library() so that all of its functions are attached. This works,
but produces a note during the check:
❯ checking dependencies in R code ... NOTE
'library' or 'require' call to ‘nimble’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual
What is the recommendation?
I see two options:
1. Include nimble in Depends and force user to install it.
2. Ignore the note and explain the problem when I resubmit to CRAN.
Am I missing anything?
Thanks in advance!
Simon
Simon Bonner
Assistant Professor of Environmetrics
Department of Statistical and Actuarial Sciences
University of Western Ontario
Office: Western Science Centre rm 276
Email: sbonn...@uwo.ca<mailto:sbonn...@uwo.ca> | Telephone: 519-661-2111 x88205
| Fax: 519-661-3813
Twitter: @bonnerstatslab | Website: http://simon.bonners.ca/bonner-lab/wpblog/
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