R devel - Oct 2012 - Mac and Windows binaries of rJava broken for R-devel?

Hi,

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,
H.

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

locale:
[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

-- 
Herv? Pag?s

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

Thanks for letting me know.
Currently the ./2.16 Window binary tree on CRAN is still a link to 
./2.15. We will work to get binaries up within a week.

Uwe Ligges





On 19.10.2012 07:52, Herv? Pag?s wrote:
> Hi,
>
> 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,
> H.
>
>  > sessionInfo()
> R Under development (unstable) (2012-10-17 r60955)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [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
>

On 10/19/2012 10:02 AM, Uwe Ligges wrote:
> Thanks for letting me know.
> Currently the ./2.16 Window binary tree on CRAN is still a link to
> ./2.15. We will work to get binaries up within a week.
Sounds good. Thanks!  H.
>
> Uwe Ligges
>
>
>
>
>
> On 19.10.2012 07:52, Herv? Pag?s wrote:
>> Hi,
>>
>> 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,
>> H.
>>
>>  > sessionInfo()
>> R Under development (unstable) (2012-10-17 r60955)
>> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>>
>> locale:
>> [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
>>
-- 
Herv? Pag?s

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