Consider this script (with h5 installed):
$ cat test.R
library(h5)
name <- tempfile()
f <- h5file(name)
file.remove(name)
$ Rscript test.R
Error in initialize(value, ...) :
cannot use object of class "character" in new(): class "H5File" does not
extend that class
Calls: h5file -> new -> initialize -> initialize
Execution halted
$ /usr/lib64/R/bin/R --slave --no-restore --file=test.R
[1] TRUE
$ R_DEFAULT_PACKAGES= Rscript test.R
[1] TRUE
$ R
> source('test.R')
>
$ R_DEFAULT_PACKAGES='datasets,utils,grDevices,graphics,stats' R
> source('test.R')
Error in initialize(value, ...) :
cannot use object of class "character" in new(): class "H5File" does not
extend that class
>
After looking into C source code, I found that Rscript by default fills
environment variable R_DEFAULT_PACKAGES with
"datasets,utils,grDevices,graphics,stats", and it somehow fails some
package like h5.
The problem here is, not setting R_DEFAULT_PACKAGES is equivalent to
setting it to a magic value, it's really confusing. I suggest remove this
feature.
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