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,
> Jean
> 
> 
> --
> Jean Thioulouse - Labo Biometrie et Biologie Evolutive,  UMR CNRS 5558
> Universite Lyon 1, Batiment Mendel,  69622 Villeurbanne Cedex - France
> Tel : (33)(0)472432756  Fax : (33)(0)472431388  Cel : (33)(0)675122302
> 
>              http://pbil.univ-lyon1.fr/JTHome/Biblio/                
> 
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> 

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