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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