[Rd] Mac and Windows binaries of rJava broken for R-devel?

Hervé Pagès hpages at fhcrc.org
Fri Oct 19 07:52:29 CEST 2012


Here is a problem we see with the Mac and Windows binaries of
rJava (0.9-3) currently available on CRAN for R-devel (i.e. under
bin/macosx/leopard/contrib/2.16/ and bin/windows/contrib/2.16/):

   > library(rJava)
   > .jinit("gaggle/inst/jars/gaggleRShell.jar")
   Error in .Call("R_do_new_object", ClassDef, PACKAGE = "base") :
     "R_do_new_object" not available for .Call() for package "base"

The same code works fine with R-devel on Linux and the same version
of rJava, or with R-2.15 on all platforms and the same version of
rJava (Mac or Windows binaries installed from CRAN).

The binaries currently available on CRAN for R-devel seem to predate
some important changes in R-devel with respect to the exposure of
some .Call entry points. Could it be that those binaries just need
to be rebuilt with a more recent version of R-devel?

FWIW, we have a few packages in the development version of Bioconductor
that are affected by this issue.

Thanks in advance,

 > sessionInfo()
R Under development (unstable) (2012-10-17 r60955)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

[1] en_US/en_US/en_US/C/en_US/en_US

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] rJava_0.9-3

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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