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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