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
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