Hi Simon,

many thanks for your answer. I'll have a try with R from source and  
contact the maintainer.
Moreover you can find the latest version of RSPerl here :
http://www.omegahat.org/RSPerl/RSPerl_0.92-2.tar.gz

Regards
Greg

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Greg Lefebvre, PhD
Bioinformatics and Biostatistics Core Facility
Federal Polytechnical School of Lausanne
Webpage
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On Jul 1, 2008, at 3:40 PM, Simon Urbanek wrote:

>
> On Jul 1, 2008, at 3:39 AM, gregory lefebvre wrote:
>
>> Hi all,
>>
>> does anybody has any experience in installing RSPerl on leopard
>> (10.5.3/4) ?
>>
>
> 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 ...
>
>
>
>> 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
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
>


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