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SYNR-1260 #147

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merged 2 commits into from Apr 11, 2018
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SYNR-1260 #147

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SYNR-1260
kimyen Apr 5, 2018
1348694
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kimyen Apr 5, 2018
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Expand Up @@ -11,8 +11,8 @@ Maintainer: Bruce Hoff <bruce.hoff@sageabse.org>
BugReports: https://github.com/Sage-Bionetworks/synapser/issues
Description: Provides R language bindings for Synapse RESTful web services.
License: Apache License 2.0
Imports: PythonEmbedInR
Depends: PythonEmbedInR(>= 0.2), R(>= 3.3), methods
Imports: PythonEmbedInR(>= 0.2)
Depends: R(>= 3.3), methods
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should 'methods' be on the Depends line or the Imports line?

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I think it should be in Imports

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Though practically it probably does not matter too much since methods is one of the base packages that is usually attached on startup anyway.

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package "methods" is on Depends: line because of https://sagebionetworks.jira.com/browse/SYNR-1148
This is because we use setGeneric in .onload. When running an R script containing the following code:

try(remove.packages('PythonEmbedInR'), silent=T)
try(remove.packages('synapser'), silent=T)
install.packages('synapser', repos=c("https://cran.cnr.berkeley.edu/", Sys.getenv('RAN')))
library('synapser')

Rscript does not load methods automatically.

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I think we should call setGeneric() with its package prefix, i.e. methods::setGeneric(). All functions from other packages that aren’t imported into the synapser namespace need to be called in this way for R CMD check to pass anyway.

Suggests: testthat, knitr, rmarkdown
URL: https://www.sagebase.org
VignetteBuilder: knitr
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