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

[Simon Urbanek]

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
>
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