On Jan 8, 2010, at 9:13 AM, Massimo Pinto wrote:
Dear Simon and all list subscribers,
Happy New Year!
Back to a problem that I had at Christmas time, when I could not
install any new BioC packages in R. I ended up re-installing the
operating system from scratch, as you Simon suggested, with Xcode, but
got only partial success. R can now find gcc and several more programs
(see below). When I try to install Rgraphviz either from source or
from Mac Binary, again tar notifies me that it could not set the
default locale and cannot complete the installation.
Just to be sure, I also downloaded the Mac binary and the source
"tarball" and tried a manual installation:
:> install.packages("/Users/massimopinto/Downloads/
Rgraphviz_1.24.0.tgz",
repos=NULL, lib="/Users/massimopinto/Library/R/2.10/library",
type="mac.binary")
tar: Failed to set default locale
but to no avail. Does this provide any extra elements as to how to
proceed?
Thank you in advance,
Yours Truly
Massimo
installation log follows.
-----
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_TIME failed, using "C"
snipped
checking for whether compiler has bool... yes
configure: No --with-graphviz option was specified. Trying to find
Graphviz using other methods.
checking for pkg-config... no
checking for dotneato-config... no
configure: dotneato-config not found in PATH.
configure: Using default directory /usr/local, consider specifiying
--with-graphviz
configure: error: /usr/local/bin/dot not found. Check Graphviz
installation.
ERROR: configuration failed for package 'Rgraphviz'
It's also telling you that Graphviz was not installed. It's possible
that the error regarding locale is not the critical problem.
--
David
* removing '/Library/Frameworks/R.framework/Versions/2.10/Resources/
library/Rgraphviz'
* restoring previous
'/Library/Frameworks/R.framework/Versions/2.10/Resources/library/
Rgraphviz'
------
Massimo Pinto
Post Doctoral Research Fellow
Enrico Fermi Centre and Italian Public Health Research Institute
(ISS), Rome
http://claimid.com/massimopinto
On Tue, Dec 22, 2009 at 19:22, Simon Urbanek
<simon.urba...@r-project.org> wrote:
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.urba...@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
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Heritage Laboratories
West Hartford, CT
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