On Mar 27, 2012, at 3:44 PM, THIOULOUSE JEAN wrote:

> 
> Le 27 mars 2012 à 16:49, Simon Urbanek a écrit :
>> 
>> On Mar 27, 2012, at 10:40 AM, THIOULOUSE JEAN wrote:
>> 
>>> Hi,
>>> 
>>> Sorry to bother you about what is probably a bad configuration of my 
>>> system. I have the following error when checking a package on my Mac (Mac 
>>> Pro mid-2010 with Mac OS X Lion 10.7.3 (11D50), running R-2.14.2 from 
>>> CRAN). I have Xcode 4.3.2 and the GNU Fortran compiler from 
>>> http://r.research.att.com/. The package is prepRISA and it compiles without 
>>> problem on R-Forge.
>>> 
>>> Here is the install.out file of R CMD check prepRISA:
>>> 
>>> * installing *source* package ‘prepRISA’ ...
>>> ** libs
>>> *** arch - i386
>>> gcc -arch i386 -std=gnu99 
>>> -I/Library/Frameworks/R.framework/Resources/include 
>>> -I/Library/Frameworks/R.framework/Resources/include/i386 
>>> -I/usr/local/mysql/include -I/usr/local/include    -fPIC  -g -O2 -c 
>>> repClass.c -o repClass.o
>>> gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names 
>>> -undefined dynamic_lookup -single_module -multiply_defined suppress 
>>> -L/usr/local/lib -o prepRISA.so repClass.o -L/usr/local/mysql/lib 
>>> -lmysqlclient -lSystemStubs -F/Library/Frameworks/R.framework/.. -framework 
>>> R -Wl,-framework -Wl,CoreFoundation
>>> ld: library not found for -lSystemStubs
>>> collect2: ld returned 1 exit status
>>> make: *** [prepRISA.so] Error 1
>>> ERROR: compilation failed for package ‘prepRISA’
>>> * removing 
>>> ‘/Volumes/Macintosh-HD/Users/jthioulo/Desktop/prepRISA.Rcheck/prepRISA’
>>> 
>>> I tried to search about this SystemStubs library, but could only find that 
>>> it is deprecated in MacOS X 10.7.
>>> 
>>> Here is my sessionInfo:
>>>> sessionInfo()
>>> R version 2.14.2 (2012-02-29)
>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>> 
>>> locale:
>>> [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8
>>> 
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  tcltk     methods  
>>> [8] base     
>>> 
>>> other attached packages:
>>> [1] ade4TkGUI_0.2-5 ade4_1.4-17    
>>>> 
>>> 
>>> What can I do to get rid of this problem ?
>>> 
>> 
>> The problem seems local to your R or settings - did you perhaps override any 
>> PKG_* with bogus flags? This is what you get with released R:
>> 
>> ** libs
>> *** arch - i386
>> gcc -arch i386 -std=gnu99 
>> -I/Library/Frameworks/R.framework/Resources/include 
>> -I/Library/Frameworks/R.framework/Resources/include/i386  
>> -I/usr/local/include    -fPIC  -Wall -pedantic -g -O2 -c repClass.c -o 
>> repClass.o
>> gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names 
>> -undefined dynamic_lookup -single_module -multiply_defined suppress 
>> -L/usr/local/lib -o prepRISA.so repClass.o 
>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework 
>> -Wl,CoreFoundation
>> installing to 
>> /Library/Frameworks/R.framework/Versions/2.14/Resources/library/prepRISA/libs/i386
>> 
>> note that you have superfluous "-L/usr/local/mysql/lib -lmysqlclient 
>> -lSystemStubs" in your linking step which is *not* part of R ...
>> 
>> Cheers,
>> Simon
> 
> Thank you, this probably comes from a previous install of a mysql server 
> implementation. Is there a way to know how these flags get added to the R CMD 
> gcc command line ? I deleted all the R and mysql instances I found on my Mac 
> and re-installed R from CRAN, but the problem remains.
> 

It has nothing to do with those -- it is your user setting. It could be in your 
environment (try set | grep PKG) or any startup files (.Rprofile, .Renviron or 
any of the site-configuration files of .R/Makevars and friends ..).

Cheers,
Simon

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