[R-SIG-Mac] warnings when installing "qtl" package

[Simon Urbanek]

Radku,

warning 1 is ok, R re-defines the signgam function that is also  
provided by the system library

warning 2 comes from the fact that you are using an unusual  
combination of settings that generates an invalid locale not  
supported by the system (english language with czech locale)*.

You can select czech language in the "System Preferences"- 
 >"International"->"Language" (you will have to click on "Edit  
List.." to make "Čeština" visible in the list) - that will lead to  
cs_CZ.UTF-8 locale which is valid.

Another alternative is to force the R GUI to select other locale  
independently of your system settings, so you could use for example

defaults write org.R-project.R force.LANG en_US.UTF-8
or
defaults write org.R-project.R force.LANG cs_CZ.UTF-8

or any other valid locale (make sure it's UTF-8, though).

Cheers,
Šimon

* - in a sense this is R GUI's fault, but there is no canonical  
locale defined in OS X, so all we can do is guess and we're combining  
the language and locale settings to create one canonical locale. This  
won't work for combinations like yours, because then we need separate  
LC_ALL and LANG. This is why we recommend manual override with  
force.LANG in the defaults in such cases. We have to specify a  
locale, because R GUI can only handle UTF-8 encoding.

On Feb 23, 2006, at 6:29 AM, Radek Blatny wrote:

>> Hello,
>> I have R for Mac OS X Aqua GUI Version 1.14 with R 2.2.0 Framework. I
>> got following warnings when installing "qtl" package 1.01-9 from CRAN
>> (sources) on the austrian mirror:
>>
>> warning 1:
>>
>> ld: warning multiple definitions of symbol _signgam
>> /Library/Frameworks/R.framework/../R.framework/R(lgamma.lo)
>> definition of _signgam
>> /usr/lib/libSystem.dylib(gamma9.o) definition of _signgam
>>
>> warning 2:
>>
>> perl: warning: Setting locale failed.
>> perl: warning: Please check that your locale settings:
>> 	LC_ALL = (unset),
>> 	LANG = "en_CZ.UTF-8"
>>     are supported and installed on your system.
>> perl: warning: Falling back to the standard locale ("C").
>>
>> warning 3:
>>
>> chmod: /Library/Frameworks/R.framework/Versions/2.2/Resources/ 
>> library/
>> R.css: Operation not permitted
>>
>> Two of them - warnings 2 and 3 - I get quite often, also with other
>> packages. Is this a real problem, packages seem to work otherwise?
>> Thank
>> you much.
>>
>> Regards, Radek
>>
>> Radek Blatny, MSc.
>> Institute of Molecular Genetics
>> Department of Mouse Molecular Genetics (Jiri Forejt unit)
>> Czech Academy of Sciences
>> Videnska 1083
>> 142 20, Prague
>> Czech Republic
>> Tel. (+420) 241 062 256
>> Fax (+420) 241 062 154
>> http://www.img.cas.cz/mmg
>> email: blatny at biomed.cas.cz
>> Skype name: blatny
>
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