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 ?
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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