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

David Winsemius dwinsemius at comcast.net
Fri Jan 8 16:13:18 CET 2010 

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.urbanek at 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.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
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
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David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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