[R-SIG-Mac] unprecedented errors at start-up

[Simon Urbanek]

On Dec 22, 2009, at 1:07 PM, Massimo Pinto wrote:

> Thank you Simon. I have tried the changing locale option but got no
> result. When you allude to restoring permissions, what are the files
> that you have in mind?

I meant fix permissions using Disk Utility - the usual step to take on a OS that acts funny, but I suspect you may have to re-install OS X in the end (the issue is not R-specific pretty much everything will fail on the locales as you can see from tar ...)

(BTW: you don't have Xcode installed so the failed source installation is due to that which is unrelated to the locales...).

Cheers,
Simon


> Cheers
> Massimo
> 
> 
> On Tue, Dec 22, 2009 at 16:44, Simon Urbanek
> <simon.urbanek at r-project.org> wrote:
>> 
>> On Dec 22, 2009, at 9:34 , Massimo Pinto wrote:
>> 
>>> Greetings all
>>> 
>>> I have left R aside for about a week and upon going back to it I have
>>> found errors which I had not encountered before. I have upgraded to
>>> OSX 10.6 recently and these errors may be a consequence of such
>>> upgrade.
>>> 
>> 
>> Seems like it. Your system locales seem to be completely messed up. Seems
>> like Archive&Install is probably what you want to do ... I have never seen
>> this before so I don't know why your OS broke so badly. You may try the
>> usual restore permissions, change locale, re-install OS X etc.
>> 
>> Cheers,
>> Simon
>> 
>> 
>>> A first error encountered at start-up refers to the use of my locale:
>>> 
>>> ========
>>> 
>>> During startup - Warning messages:
>>> 1: Setting LC_CTYPE failed, using "C"
>>> 2: Setting LC_COLLATE failed, using "C"
>>> 3: Setting LC_TIME failed, using "C"
>>> 4: Setting LC_MESSAGES failed, using "C"
>>> [R.app GUI 1.31 (5537) i386-apple-darwin9.8.0]
>>> 
>>> WARNING: You're using a non-UTF8 locale, therefore only ASCII
>>> characters will work.
>>> Please read R for Mac OS X FAQ (see Help) section 9 and adjust your
>>> system preferences accordingly.
>>> 
>>> ============
>>> 
>>> when trying to install a binary package from BioConductor, using the R
>>> GUI, I get:
>>> 
>>> =-===========
>>> The downloaded packages are in
>>> 
>>>  ‘/private/var/folders/vM/vMSy+Iu8HwS2jf2eaEcYFU+++TI/-Tmp-/RtmpipsYIY/downloaded_packages’
>>> trying URL
>>> 'http://www.bioconductor.org/packages/2.5/bioc/bin/macosx/leopard/contrib/2.10/Rgraphviz_1.24.0.tgz'
>>> Content type 'application/x-gzip' length 800621 bytes (781 Kb)
>>> opened URL
>>> 
>>> downloaded 781 Kb
>>> 
>>> tar: Failed to set default locale
>>> ===============================================
>>> 
>>> similarly, when trying a source package:
>>> 
>>> =========
>>> trying URL
>>> 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/Rgraphviz_1.24.0.tar.gz'
>>> Content type 'application/x-gzip' length 571761 bytes (558 Kb)
>>> opened URL
>>> ==================================================
>>> downloaded 558 Kb
>>> 
>>> During startup - Warning messages:
>>> 1: Setting LC_CTYPE failed, using "C"
>>> 2: Setting LC_TIME failed, using "C"
>>> 3: Setting LC_MESSAGES failed, using "C"
>>> tar: Failed to set default locale
>>> * installing *source* package 'Rgraphviz' ...
>>> checking for gcc... no
>>> checking for cc... no
>>> checking for cl.exe... no
>>> configure: error: no acceptable C compiler found in $PATH
>>> See `config.log' for more details.
>>> ERROR: configuration failed for package 'Rgraphviz'
>>> * removing
>>> '/Library/Frameworks/R.framework/Versions/2.10/Resources/library/Rgraphviz'
>>> * restoring previous
>>> 
>>> '/Library/Frameworks/R.framework/Versions/2.10/Resources/library/Rgraphviz'
>>> ============================
>>> 
>>> This situation won't change if I set the locale to
>>> 
>>>> Sys.setlocale("LC_ALL", "en_GB.UTF-8")
>>> 
>>> Has anyone experienced this before?
>>> Thank you in advance
>>> Massimo
>>> 
>>>> sessionInfo()
>>> 
>>> R version 2.10.1 (2009-12-14)
>>> i386-apple-darwin9.8.0
>>> 
>>> locale:
>>> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>>> 
>>> attached base packages:
>>> [1] grid      stats     graphics  grDevices utils     datasets
>>> methods   base
>>> 
>>> other attached packages:
>>> [1] graph_1.22.2
>>> 
>>> loaded via a namespace (and not attached):
>>> [1] tools_2.10.1
>>> 
>>> Massimo Pinto
>>> Post Doctoral Research Fellow
>>> Enrico Fermi Centre and Italian Public Health Research Institute (ISS),
>>> Rome
>>> http://claimid.com/massimopinto
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>>> 
>> 
>> 
> 
>