[R-SIG-Mac] Problem with R 3.0.1

[Marc Schwartz]

Are you running R from the terminal or via any GUIs?

If the latter, try running from the terminal to see if you can replicate the behavior. If it runs fine, it may suggest that you have a GUI app conflict.

You can try running "R --vanilla" from the CLI to see if that resolves any issues. If it does, you might also check for a ~/.Rprofile file that contains any settings/options that may be problematic. Also remove any ~/.RData files for similar reasons.

If none of the above help, I would be sure that before installing 3.0.1 again, that you completely remove the R installation directory tree, which is typically:

  /Library/Frameworks/R.framework

as well as any R related GUI's that are in:

  /Applications

just to be sure that you are starting with a clean install.

Is the program that you are running small enough to post here to be able to try it on another system? If not, can you distill the program down to the smallest possible set of lines that causes the segfault?

Regards,

Marc


On Jun 27, 2013, at 12:42 PM, Gang Chen <gangchen at mail.nih.gov> wrote:

> Thanks for the suggestion! The hash value for my download does match the one listed on the webpage. 
> 
> A further complication for R 3.0 is that a program I wrote before works fine with R 3.0 on Mac 10.6, but gives me "Segmentation fault" error with R 3.0 on Mac 10.8: 
> 
> *** caught segfault ***
> address 0x0, cause 'memory not mapped'
> 
> And the program works properly with R 2.15 on both 10.6 and 10.8.
> 
> Gang
> 
> 
> On Jun 27, 2013, at 1:00 PM, Marc Schwartz wrote:
> 
>> 
>> On Jun 27, 2013, at 11:44 AM, "Chen, Gang (NIH/NIMH) [C]" <gangchen at mail.nih.gov> wrote:
>> 
>>> R 3.0.1 does not seem to work properly on two of my Mac notebooks, one with 10.8.2 and the other 10.6.8. When I start R on the terminal, I get the following:
>>> 
>>> Error in .Call("R_isMethodsDispatchOn", onOff, PACKAGE = "base") :
>>> "R_isMethodsDispatchOn" not available for .Call() for package "base"
>>> 
>>> R version 3.0.1 (2013-05-16) -- "Good Sport"
>>> ...
>>> 
>>> Even the following does not work:
>>> 
>>>> citation()
>>> Error: could not find function "citation"
>>> 
>>> However, once I downgraded R from 3.0.1 to 3.0, everything works fine. What could be the source of the problem?
>>> 
>>> Thanks!
>>> 
>>> Gang
>> 
>> 
>> I would try to download 3.0.1 from a different CRAN mirror. My first guess is that your download was corrupted and/or did not install correctly or fully.
>> 
>> You could try to test the MD5 hash for the downloaded file. The correct hash value is listed on the download page for OSX:
>> 
>> In a terminal:
>> 
>> md5 R-3.0.1.pkg
>> MD5 (R-3.0.1.pkg) = c0e6e702742f17cd9b2f2e4cb1c5dcad
>> 
>> 
>> Regards,
>> 
>> Marc Schwartz
>> 
>> P.S. to Simon. Should there be a consideration for replacing MD5 with SHA, given the issues with the former?
>> 
>