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RSPerl and leopard (osx 10.5.3/4)

3 messages · gregory lefebvre, Simon Urbanek

Original
gregory lefebvre
# 
Hi all,

does anybody has any experience in installing RSPerl on leopard  
(10.5.3/4) ?

I am using R version 2.7.1 (2008-06-23) with the command:
sudo R CMD INSTALL -c --configure-args='--with-in-perl'  
RSPerl_0.92-2.tar.gz

First the compiler stopped after returning :
cc1: error: invalid option 'arch=nocona'

Then in the /Library/Frameworks/R.framework/Resources/etc/i386/ 
Makeconf file, I removed the "-march=nocona" entries (https://stat.ethz.ch/pipermail/r-sig-mac/2008-January/004462.html 
) and now here is the returned message :

* Installing to library '/Library/Frameworks/R.framework/Resources/ 
library'
* Installing *source* package 'RSPerl' ...
checking for perl... /usr/bin/perl
No support for any of the Perl modules from calling Perl from R.
*****************************************************

       Set PERL5LIB to /Library/Frameworks/R.framework/Resources/ 
library/RSPerl/perl

*****************************************************
Testing: -F/Library/Frameworks/R.framework/.. -framework R
Using '/usr/bin/perl' as the perl executable
Perl modules (no):
Adding R package to list of Perl modules to enable callbacks to R from  
Perl
Creating the C code for dynamically loading modules with native code  
for Perl:  R
modules:   R; linking:
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
Support R in Perl: yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating inst/scripts/RSPerl.csh
config.status: creating inst/scripts/RSPerl.bsh
config.status: creating src/RinPerlMakefile
config.status: creating src/Makefile.PL
config.status: creating cleanup
config.status: creating src/R.pm
config.status: creating R/perl5lib.R
making target all in RinPerlMakefile
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ 
Resources/include -I/Library/Frameworks/R.framework/Resources/include/ 
i386 -I.  -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -no- 
cpp-precomp -fno-strict-aliasing -Wdeclaration-after-statement -I/usr/ 
local/include  -I/System/Library/Perl/5.8.8/darwin-thread-multi-2level/ 
CORE  -DPERL_POLLUTE   -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 - 
DWITH_R_IN_PERL=1 -msse3    -fPIC  -g -O2  -c Converters.c -o  
Converters.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ 
Resources/include -I/Library/Frameworks/R.framework/Resources/include/ 
i386 -I.  -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -no- 
cpp-precomp -fno-strict-aliasing -Wdeclaration-after-statement -I/usr/ 
local/include  -I/System/Library/Perl/5.8.8/darwin-thread-multi-2level/ 
CORE  -DPERL_POLLUTE   -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 - 
DWITH_R_IN_PERL=1 -msse3    -fPIC  -g -O2  -c Reflectance.c -o  
Reflectance.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ 
Resources/include -I/Library/Frameworks/R.framework/Resources/include/ 
i386 -I.  -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -no- 
cpp-precomp -fno-strict-aliasing -Wdeclaration-after-statement -I/usr/ 
local/include  -I/System/Library/Perl/5.8.8/darwin-thread-multi-2level/ 
CORE  -DPERL_POLLUTE   -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 - 
DWITH_R_IN_PERL=1 -msse3    -fPIC  -g -O2  -c ForeignReference.c -o  
ForeignReference.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ 
Resources/include -I/Library/Frameworks/R.framework/Resources/include/ 
i386 -I.  -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -no- 
cpp-precomp -fno-strict-aliasing -Wdeclaration-after-statement -I/usr/ 
local/include  -I/System/Library/Perl/5.8.8/darwin-thread-multi-2level/ 
CORE  -DPERL_POLLUTE   -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 - 
DWITH_R_IN_PERL=1 -msse3    -fPIC  -g -O2  -c UserConverters.c -o  
UserConverters.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ 
Resources/include -I/Library/Frameworks/R.framework/Resources/include/ 
i386 -I.  -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -no- 
cpp-precomp -fno-strict-aliasing -Wdeclaration-after-statement -I/usr/ 
local/include  -I/System/Library/Perl/5.8.8/darwin-thread-multi-2level/ 
CORE  -DPERL_POLLUTE   -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 - 
DWITH_R_IN_PERL=1 -msse3    -fPIC  -g -O2  -c GeneralConverters.c -o  
GeneralConverters.o
making libPerlConverter.dylib
MACOSX_DEPLOYMENT_TARGET="10.3" gcc -dynamiclib -undefined  
dynamic_lookup -o libPerlConverter.dylib -install_name /Library/ 
Frameworks/R.framework/Resources/library/RSPerl/libs/ 
libPerlConverter.dylib Converters.o Reflectance.o ForeignReference.o  
UserConverters.o GeneralConverters.o -F/Library/Frameworks/ 
R.framework/.. -framework R
if test ! -d /Library/Frameworks/R.framework/Resources/library/RSPerl/ 
libs ; then mkdir /Library/Frameworks/R.framework/Resources/library/ 
RSPerl/libs ; fi
cp libPerlConverter.dylib /Library/Frameworks/R.framework/Resources/ 
library/RSPerl/libs
/usr/bin/perl Makefile.PL PREFIX=/Library/Frameworks/R.framework/ 
Resources/library/RSPerl LIB=/Library/Frameworks/R.framework/Resources/ 
library/RSPerl/perl
Warning: -L. changed to -L/tmp/R.INSTALL.D56cTa/RSPerl/src/.
Unrecognized argument in LIBS ignored: '-F/Library/Frameworks/ 
R.framework/..'
Unrecognized argument in LIBS ignored: '-framework'
Unrecognized argument in LIBS ignored: 'R'
Writing Makefile.perl for R
make -f Makefile.perl LD=/usr/bin/gcc
cp R.pm blib/lib/R.pm
AutoSplitting blib/lib/R.pm (blib/lib/auto/R)
cp RReferences.pm blib/lib/RReferences.pm
cc -c  -I. -I/Library/Frameworks/R.framework/Resources/include -I/ 
Library/Frameworks/R.framework/Resources/include/i386 -arch i386 -arch  
ppc -g -pipe -fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict- 
aliasing -Wdeclaration-after-statement -I/usr/local/include -O3   - 
DVERSION=\"0.01\" -DXS_VERSION=\"0.01\"  "-I/System/Library/Perl/5.8.8/ 
darwin-thread-multi-2level/CORE"  -g -D_R_=1 -DUSE_R=1 - 
DWITH_R_IN_PERL=1 R.c
Running Mkbootstrap for R ()
chmod 644 R.bs
rm -f blib/arch/auto/R/R.bundle
LD_RUN_PATH="/tmp/R.INSTALL.D56cTa/RSPerl/src" /usr/bin/gcc  -arch  
i386 -arch ppc -bundle -undefined dynamic_lookup -L/usr/local/lib R.o - 
F/Library/Frameworks/R.framework/.. -framework R -o blib/arch/auto/R/ 
R.bundle         \
           -L/tmp/R.INSTALL.D56cTa/RSPerl/src -L/Library/Frameworks/ 
R.framework/Resources/library/RSPerl/libs -lPerlConverter   \

ld: warning, duplicate dylib /usr/local/lib/libgcc_s.1.dylib
ld: warning, duplicate dylib /usr/local/lib/libgcc_s.1.dylib
ld: warning in /tmp/R.INSTALL.D56cTa/RSPerl/src/ 
libPerlConverter.dylib, file is not of required architecture
ld: warning, duplicate dylib /usr/local/lib/libgcc_s.1.dylib
ld: warning, duplicate dylib /usr/local/lib/libgcc_s.1.dylib
chmod 755 blib/arch/auto/R/R.bundle
cp R.bs blib/arch/auto/R/R.bs
chmod 644 blib/arch/auto/R/R.bs
Manifying blib/man3/R.3pm
Manifying blib/man3/RReferences.3pm
calling make -f Makefile.perl install
Manifying blib/man3/R.3pm
Manifying blib/man3/RReferences.3pm
Installing /Library/Frameworks/R.framework/Resources/library/RSPerl/ 
perl/darwin-thread-multi-2level/auto/R/R.bs
Installing /Library/Frameworks/R.framework/Resources/library/RSPerl/ 
perl/darwin-thread-multi-2level/auto/R/R.bundle
Files found in blib/arch: installing files in blib/lib into  
architecture dependent library tree
Installing /Library/Frameworks/R.framework/Resources/library/RSPerl/ 
perl/darwin-thread-multi-2level/R.pm
Installing /Library/Frameworks/R.framework/Resources/library/RSPerl/ 
perl/darwin-thread-multi-2level/RReferences.pm
Installing /Library/Frameworks/R.framework/Resources/library/RSPerl/ 
perl/darwin-thread-multi-2level/auto/R/autosplit.ix
Installing /Library/Frameworks/R.framework/Resources/library/RSPerl/ 
share/man/man3/R.3pm
Installing /Library/Frameworks/R.framework/Resources/library/RSPerl/ 
share/man/man3/RReferences.3pm
Writing /Library/Frameworks/R.framework/Resources/library/RSPerl/perl/ 
darwin-thread-multi-2level/auto/R/.packlist
Appending installation info to /Library/Frameworks/R.framework/ 
Resources/library/RSPerl/perl/darwin-thread-multi-2level/perllocal.pod
Finished configuration
** libs
** arch - i386
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ 
Resources/include -I/Library/Frameworks/R.framework/Resources/include/ 
i386 -I.  -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -no- 
cpp-precomp -fno-strict-aliasing -Wdeclaration-after-statement -I/usr/ 
local/include  -I/System/Library/Perl/5.8.8/darwin-thread-multi-2level/ 
CORE  -DPERL_POLLUTE   -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 - 
DWITH_R_IN_PERL=1 -msse3    -fPIC  -g -O2  -c RPerlElements.c -o  
RPerlElements.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ 
Resources/include -I/Library/Frameworks/R.framework/Resources/include/ 
i386 -I.  -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -no- 
cpp-precomp -fno-strict-aliasing -Wdeclaration-after-statement -I/usr/ 
local/include  -I/System/Library/Perl/5.8.8/darwin-thread-multi-2level/ 
CORE  -DPERL_POLLUTE   -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 - 
DWITH_R_IN_PERL=1 -msse3    -fPIC  -g -O2  -c RPerlEval.c -o RPerlEval.o
RPerlEval.c: In function 'RS_PerlEvalString':
RPerlEval.c:20: warning: ISO C90 forbids mixed declarations and code
RPerlEval.c: In function 'RS_PerlEvalString':
RPerlEval.c:20: warning: ISO C90 forbids mixed declarations and code
RPerlEval.c: In function 'RS_PerlGet':
RPerlEval.c:128: warning: ISO C90 forbids mixed declarations and code
RPerlEval.c: In function 'RS_PerlCallModified':
RPerlEval.c:208: warning: ISO C90 forbids mixed declarations and code
RPerlEval.c: In function 'RS_PerlGet':
RPerlEval.c:128: warning: ISO C90 forbids mixed declarations and code
RPerlEval.c: In function 'RS_PerlCallModified':
RPerlEval.c:208: warning: ISO C90 forbids mixed declarations and code
RPerlEval.c: In function 'RS_PerlCall':
RPerlEval.c:377: warning: ISO C90 forbids mixed declarations and code
RPerlEval.c: In function 'RS_PerlCall':
RPerlEval.c:377: warning: ISO C90 forbids mixed declarations and code
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ 
Resources/include -I/Library/Frameworks/R.framework/Resources/include/ 
i386 -I.  -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -no- 
cpp-precomp -fno-strict-aliasing -Wdeclaration-after-statement -I/usr/ 
local/include  -I/System/Library/Perl/5.8.8/darwin-thread-multi-2level/ 
CORE  -DPERL_POLLUTE   -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 - 
DWITH_R_IN_PERL=1 -msse3    -fPIC  -g -O2  -c RPerlInit.c -o RPerlInit.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ 
Resources/include -I/Library/Frameworks/R.framework/Resources/include/ 
i386 -I.  -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -no- 
cpp-precomp -fno-strict-aliasing -Wdeclaration-after-statement -I/usr/ 
local/include  -I/System/Library/Perl/5.8.8/darwin-thread-multi-2level/ 
CORE  -DPERL_POLLUTE   -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 - 
DWITH_R_IN_PERL=1 -msse3    -fPIC  -g -O2  -c RPerlNew.c -o RPerlNew.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ 
Resources/include -I/Library/Frameworks/R.framework/Resources/include/ 
i386 -I.  -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -no- 
cpp-precomp -fno-strict-aliasing -Wdeclaration-after-statement -I/usr/ 
local/include  -I/System/Library/Perl/5.8.8/darwin-thread-multi-2level/ 
CORE  -DPERL_POLLUTE   -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 - 
DWITH_R_IN_PERL=1 -msse3    -fPIC  -g -O2  -c RPerlReference.c -o  
RPerlReference.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ 
Resources/include -I/Library/Frameworks/R.framework/Resources/include/ 
i386 -I.  -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -no- 
cpp-precomp -fno-strict-aliasing -Wdeclaration-after-statement -I/usr/ 
local/include  -I/System/Library/Perl/5.8.8/darwin-thread-multi-2level/ 
CORE  -DPERL_POLLUTE   -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 - 
DWITH_R_IN_PERL=1 -msse3    -fPIC  -g -O2  -c RPerlVars.c -o RPerlVars.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ 
Resources/include -I/Library/Frameworks/R.framework/Resources/include/ 
i386 -I.  -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -no- 
cpp-precomp -fno-strict-aliasing -Wdeclaration-after-statement -I/usr/ 
local/include  -I/System/Library/Perl/5.8.8/darwin-thread-multi-2level/ 
CORE  -DPERL_POLLUTE   -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 - 
DWITH_R_IN_PERL=1 -msse3    -fPIC  -g -O2  -c Utils.c -o Utils.o
Utils.c: In function 'characterVectorToNullTerminatedArray':
Utils.c:35: warning: assignment discards qualifiers from pointer  
target type
Utils.c: In function 'characterVectorToArray':
Utils.c:78: warning: assignment discards qualifiers from pointer  
target type
Utils.c: In function 'characterVectorToNullTerminatedArray':
Utils.c:35: warning: assignment discards qualifiers from pointer  
target type
Utils.c: In function 'characterVectorToArray':
Utils.c:78: warning: assignment discards qualifiers from pointer  
target type
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ 
Resources/include -I/Library/Frameworks/R.framework/Resources/include/ 
i386 -I.  -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -no- 
cpp-precomp -fno-strict-aliasing -Wdeclaration-after-statement -I/usr/ 
local/include  -I/System/Library/Perl/5.8.8/darwin-thread-multi-2level/ 
CORE  -DPERL_POLLUTE   -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 - 
DWITH_R_IN_PERL=1 -msse3    -fPIC  -g -O2  -c xsinit.c -o xsinit.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -std=gnu99 -dynamiclib -Wl,- 
headerpad_max_install_names -mmacosx-version-min=10.4 -undefined  
dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/ 
lib -o RSPerl.so Converters.o ForeignReference.o GeneralConverters.o  
R.o RPerlElements.o RPerlEval.o RPerlInit.o RPerlNew.o  
RPerlReference.o RPerlVars.o Reflectance.o UserConverters.o Utils.o  
xsinit.o   -arch i386 -arch ppc -L/usr/local/lib /System/Library/Perl/ 
5.8.8/darwin-thread-multi-2level/auto/DynaLoader/DynaLoader.a -L/ 
System/Library/Perl/5.8.8/darwin-thread-multi-2level/CORE -lperl -ldl - 
lm -lutil -lc   -F/Library/Frameworks/R.framework/.. -framework R -Wl,- 
framework -Wl,CoreFoundation
ldld::  librarylibrary  notnot  foundfound  forfor  --lutillutil

collect2: ld returned 1 exit status
collect2: ld returned 1 exit status
lipo: can't open input file: /var/tmp//cc3Fb354.out (No such file or  
directory)
make: *** [RSPerl.so] Error 1
chmod: /Library/Frameworks/R.framework/Resources/library/RSPerl/libs/ 
i386/*: No such file or directory
ERROR: compilation failed for package 'RSPerl'
** Removing '/Library/Frameworks/R.framework/Resources/library/RSPerl'

I don't have any clue for resolving this issue.
Any idea would be really appreciated.
In advance many thanks.
Greg
Simon Urbanek
#
On Jul 1, 2008, at 3:39 AM, gregory lefebvre wrote:

            

      
      
      
    

        
The way RSPerl attempts to build the code simply doesn't work in this  
setup. The main problem is mismatch between what R sees and what Perl  
sees. Simply pasting their compiler flags doesn't work, because R uses  
10.4u SDK whereas Perl uses 10.5 system libraries directly. The error  
you get is due to that fact - libutil is only present in 10.5 and not  
in 10.4, but RSPerl attempts to link it using the 10.4 setup. I  
suspect that for this to work RSPerl would need to be designed more  
carefully to use the separate compiler and flags for each part of the  
interface.

You can get past that error if you use R compiled specifically for  
10.5 (thus without the 10.4u SDK), but still RSPerl doesn't work for  
me in that setup because of this error:
 > library(RSPerl)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
   unable to load shared library '/Users/urbanek/Library/R/2.8/library/ 
RSPerl/libs/i386/RSPerl.so':
   dlopen(/Users/urbanek/Library/R/2.8/library/RSPerl/libs/i386/ 
RSPerl.so, 6): Symbol not found: _boot_R
   Referenced from: /Users/urbanek/Library/R/2.8/library/RSPerl/libs/ 
i386/RSPerl.so
   Expected in: dynamic lookup

I didn't dig deeper, but I suspect here are even more problems with  
RSPerl. You may want to contact the maintainer for help.

Cheers,
Simon

PS: I could only find RSPerl_0.92-1.tar.gz on the omegahat webpage, so  
I'm wondering where you got 0.92-2 ...