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

[blatny@biomed.cas.cz]

Thank you very much Šimone,
I did set the locale with the "defaults" command. And do you have any
comments to the warning # 3? It seems to be a problem with permissions.

warning 3:

chmod: /Library/Frameworks/R.framework/Versions/2.2/Resources/library/R.css:
Operation not permitted

Anyway, thank you very much for your work on the OS X version of R and
good luck in the development!

With regards, Radek Blatny


> 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 "ÄŒeĹĄtina" 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,
> Ĺ imon
>
> * - 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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