[Rd] Rscript fails with some packages (for example, h5)
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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Re: [Rd] Rscript fails with some packages (for example, h5)
On 26 December 2017 at 15:24, Sun Yijiang wrote: | 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. The more confusing part is that "methods" is missing 'by design' (as loading methods is marginally more expensive that other packages). Ie for your script edd@bud:/tmp$ cat h5ex.R library(methods) library(h5) name <- tempfile() f <- h5file(name) file.remove(name) edd@bud:/tmp$ Rscript h5ex.R [1] TRUE edd@bud:/tmp$ it all works if you just add `library(methods)` as seen in the first line. For what it is worth, littler's r does not need that as it loads methods just like R itself does avoiding the confusion: edd@bud:/tmp$ cat h5ex2.R library(h5) name <- tempfile() f <- h5file(name) file.remove(name) edd@bud:/tmp$ r h5ex2.R edd@bud:/tmp$ Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rscript fails with some packages (for example, h5)
On 26 December 2017 at 22:14, Sun Yijiang wrote: | Thanks for the solution. Now I know the work-arounds, but still don't | quite get it. Why does R_DEFAULT_PACKAGES has anything to do with | library(methods)? Because it governs which packages are loaded by default. And while R also loads 'methods', Rscript does not. Source of endless confusion. | If library(h5) works, it should just work, not depend on an environment variable. Every package using S4 will fail under Rscript unless 'methods' explicitly. | Rscript is not consistent with R, that's my confusion. Indeed. And you are not the first person confused by it. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rscript fails with some packages (for example, h5)
Hi Dirk, Thanks for the solution. Now I know the work-arounds, but still don't quite get it. Why does R_DEFAULT_PACKAGES has anything to do with library(methods)? If library(h5) works, it should just work, not depend on an environment variable. Rscript is not consistent with R, that's my confusion. Steve 2017-12-26 20:46 GMT+08:00 Dirk Eddelbuettel : > > On 26 December 2017 at 15:24, Sun Yijiang wrote: > | 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. > > The more confusing part is that "methods" is missing 'by design' (as > loading > methods is marginally more expensive that other packages). Ie for your > script > >edd@bud:/tmp$ cat h5ex.R >library(methods) >library(h5) >name <- tempfile() >f <- h5file(name) >file.remove(name) >edd@bud:/tmp$ Rscript h5ex.R >[1] TRUE >edd@bud:/tmp$ > > it all works if you just add `library(methods)` as seen in the first line. > > For what it is worth, littler's r does not need that as it loads methods > just > like R itself does avoiding the confusion: > >edd@bud:/tmp$ cat h5ex2.R >library(h5) >name <- tempfile() >f <- h5file(name) >file.remove(name) >edd@bud:/tmp$ r h5ex2.R >edd@bud:/tmp$ > > Dirk > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
