Hello,
I am having errors when I try to install RSPerl-0.92 under fedora 14.
I have the following rpms installed:
R-devel-2.13.0-1.fc14.x86_64
R-core-2.13.0-1.fc14.x86_64
perl-5.12.3-143.fc14.x86_64
perl-devel-5.12.3-143.fc14.x86_64
perl-ExtUtils-* (all of them from yum)
Now I get the following errors:
# R CMD INSTALL RSPerl_0.92-1.tar.gz
* installing to library /usr/lib64/R/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 /usr/lib64/R/library/RSPerl/perl
*****************************************************
Testing: -L/usr/lib64/R/lib -lR
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 -m64 -std=gnu99 -I/usr/include/R -I. -D_REENTRANT -D_GNU_SOURCE
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE
-DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-c Converters.c -o Converters.o
Converters.c: In function 'makeForeignPerlReference':
Converters.c:568:8: warning: unused variable 'key'
Converters.c:566:6: warning: unused variable 'n'
Converters.c: In function 'RS_discardPerlForeignReference':
Converters.c:675:14: warning: unused variable 'key'
Converters.c: In function 'PerlAddHomogeneousElement':
Converters.c:1056:7: error: duplicate case value
Converters.c:1041:7: error: previously used here
make: *** [Converters.o] Error 1
calling make -f Makefile.perl install
make: Makefile.perl: No such file or directory
make: *** No rule to make target `Makefile.perl'. Stop.
chmod: cannot access `blib/lib/R.pm': No such file or directory
Finished configuration
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -I. -D_REENTRANT -D_GNU_SOURCE
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE
-DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-c Converters.c -o Converters.o
Converters.c: In function makeForeignPerlReference:
Converters.c:568:8: warning: unused variable key
Converters.c:566:6: warning: unused variable n
Converters.c: In function RS_discardPerlForeignReference:
Converters.c:675:14: warning: unused variable key
Converters.c: In function PerlAddHomogeneousElement:
Converters.c:1056:7: error: duplicate case value
Converters.c:1041:7: error: previously used here
make: *** [Converters.o] Error 1
ERROR: compilation failed for package RSPerl
* removing /usr/lib64/R/library/RSPerl
The errors involve the use of C constants SVt_IV (perl integer) and SVt_RV
(perl reference).
As of perl 5.12, SVt_RV is synonymous with SVt_IV.
So the switch statements containing both throw a duplicate value error.
Well, I reasoned that the integer interpretation may only be needed now and
commented out the SVt_IV entries in Converters.c and Reflections.c switch
statements.
I know I am treading on dangerous ground here.
But it got RSPerl to compile to the following stage:
# R CMD INSTALL RSPerl_0.92-1_modified.tar.gz
* installing to library /usr/lib64/R/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 /usr/lib64/R/library/RSPerl/perl
*****************************************************
Testing: -L/usr/lib64/R/lib -lR
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 -m64 -std=gnu99 -I/usr/include/R -I. -D_REENTRANT -D_GNU_SOURCE
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE
-DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-c Converters.c -o Converters.o
Converters.c: In function 'makeForeignPerlReference':
Converters.c:568:8: warning: unused variable 'key'
Converters.c:566:6: warning: unused variable 'n'
Converters.c: In function 'RS_discardPerlForeignReference':
Converters.c:675:14: warning: unused variable 'key'
Converters.c: In function 'RS_GetPerlReferenceObjects':
Converters.c:637:16: warning: 'ans' may be used uninitialized in this
function
gcc -m64 -std=gnu99 -I/usr/include/R -I. -D_REENTRANT -D_GNU_SOURCE
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE
-DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-c Reflectance.c -o Reflectance.o
Reflectance.c: In function 'computeRSPerlClassVector':
Reflectance.c:427:11: warning: unused variable 'tt'
Reflectance.c:445:10: warning: operation on 'classes' may be undefined
Reflectance.c: In function 'isHomogeneous':
Reflectance.c:541:7: warning: enumeration value 'SVt_NULL' not handled in
switch
Reflectance.c:541:7: warning: enumeration value 'SVt_BIND' not handled in
switch
Reflectance.c:541:7: warning: enumeration value 'SVt_IV' not handled in
switch
Reflectance.c:541:7: warning: enumeration value 'SVt_NV' not handled in
switch
Reflectance.c:541:7: warning: enumeration value 'SVt_PV' not handled in
switch
Reflectance.c:541:7: warning: enumeration value 'SVt_PVIV' not handled in
switch
Reflectance.c:541:7: warning: enumeration value 'SVt_PVNV' not handled in
switch
Reflectance.c:541:7: warning: enumeration value 'SVt_PVMG' not handled in
switch
Reflectance.c:541:7: warning: enumeration value 'SVt_REGEXP' not handled in
switch
Reflectance.c:541:7: warning: enumeration value 'SVt_PVGV' not handled in
switch
Reflectance.c:541:7: warning: enumeration value 'SVt_PVLV' not handled in
switch
Reflectance.c:541:7: warning: enumeration value 'SVt_PVCV' not handled in
switch
Reflectance.c:541:7: warning: enumeration value 'SVt_PVFM' not handled in
switch
Reflectance.c:541:7: warning: enumeration value 'SVt_PVIO' not handled in
switch
Reflectance.c:541:7: warning: enumeration value 'SVt_LAST' not handled in
switch
Reflectance.c: In function 'RS_getPerlType':
Reflectance.c:139:6: warning: 'el' may be used uninitialized in this
function
Reflectance.c: In function 'isHomogeneous':
Reflectance.c:516:12: warning: 'el' may be used uninitialized in this
function
gcc -m64 -std=gnu99 -I/usr/include/R -I. -D_REENTRANT -D_GNU_SOURCE
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE
-DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-c ForeignReference.c -o ForeignReference.o
ForeignReference.c: In function 'RPerl_createRProxy':
ForeignReference.c:212:8: warning: value computed is not used
gcc -m64 -std=gnu99 -I/usr/include/R -I. -D_REENTRANT -D_GNU_SOURCE
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE
-DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-c UserConverters.c -o UserConverters.o
UserConverters.c: In function 'RPerl_addConverter':
UserConverters.c:264:32: warning: 'className' may be used uninitialized in
this function
gcc -m64 -std=gnu99 -I/usr/include/R -I. -D_REENTRANT -D_GNU_SOURCE
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE
-DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-c GeneralConverters.c -o GeneralConverters.o
making libPerlConverter.so
/usr/lib64/R/bin/R CMD SHLIB -o libPerlConverter.so Converters.c
Reflectance.c ForeignReference.c UserConverters.o GeneralConverters.o
make[1]: Entering directory `/tmp/RtmpHyWOHo/R.INSTALL281f2591/RSPerl/src'
gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o libPerlConverter.so
Converters.o Reflectance.o ForeignReference.o UserConverters.o
GeneralConverters.o -Wl,--enable-new-dtags -Wl,-rpath,/usr/lib64/perl5/CORE
-fstack-protector -L/usr/lib64/perl5/CORE -lperl -lresolv -lnsl -ldl -lm
-lcrypt -lutil -lpthread -lc -L/usr/lib64/R/lib -lR
make[1]: Leaving directory `/tmp/RtmpHyWOHo/R.INSTALL281f2591/RSPerl/src'
if test ! -d /usr/lib64/R/library/RSPerl/libs ; then mkdir
/usr/lib64/R/library/RSPerl/libs ; fi
cp libPerlConverter.so /usr/lib64/R/library/RSPerl/libs
Makefile.PL PREFIX=/usr/lib64/R/library/RSPerl
LIB=/usr/lib64/R/library/RSPerl/perl
make: Makefile.PL: Command not found
make: *** [Makefile.perl] Error 127
calling make -f Makefile.perl install
make: Makefile.perl: No such file or directory
make: *** No rule to make target `Makefile.perl'. Stop.
chmod: cannot access `blib/lib/R.pm': No such file or directory
Finished configuration
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -I. -D_REENTRANT -D_GNU_SOURCE
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE
-DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-c RPerlElements.c -o RPerlElements.o
RPerlElements.c: In function RS_PerlSetHashElements:
RPerlElements.c:165:6: warning: value computed is not used
RPerlElements.c: In function RS_PerlArrayElement:
RPerlElements.c:11:15: warning: depth may be used uninitialized in this
function
RPerlElements.c: In function RS_PerlHashElement:
RPerlElements.c:56:15: warning: depth may be used uninitialized in this
function
gcc -m64 -std=gnu99 -I/usr/include/R -I. -D_REENTRANT -D_GNU_SOURCE
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE
-DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-c RPerlEval.c -o RPerlEval.o
RPerlEval.c: In function RS_PerlCallModified:
RPerlEval.c:301:4: warning: value computed is not used
gcc -m64 -std=gnu99 -I/usr/include/R -I. -D_REENTRANT -D_GNU_SOURCE
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE
-DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-c RPerlInit.c -o RPerlInit.o
gcc -m64 -std=gnu99 -I/usr/include/R -I. -D_REENTRANT -D_GNU_SOURCE
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE
-DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-c RPerlNew.c -o RPerlNew.o
RPerlNew.c: In function toPerlTable:
RPerlNew.c:54:6: warning: value computed is not used
gcc -m64 -std=gnu99 -I/usr/include/R -I. -D_REENTRANT -D_GNU_SOURCE
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE
-DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-c RPerlReference.c -o RPerlReference.o
gcc -m64 -std=gnu99 -I/usr/include/R -I. -D_REENTRANT -D_GNU_SOURCE
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE
-DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-c RPerlVars.c -o RPerlVars.o
RPerlVars.c: In function RS_remove:
RPerlVars.c:76:6: warning: value computed is not used
RPerlVars.c: In function PerlAssign:
RPerlVars.c:121:4: warning: value computed is not used
gcc -m64 -std=gnu99 -I/usr/include/R -I. -D_REENTRANT -D_GNU_SOURCE
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE
-DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-c Utils.c -o Utils.o
Utils.c: In function characterVectorToNullTerminatedArray:
Utils.c:35:14: warning: assignment discards qualifiers from pointer target
type
Utils.c: In function characterVectorToArray:
Utils.c:78:14: warning: assignment discards qualifiers from pointer target
type
gcc -m64 -std=gnu99 -I/usr/include/R -I. -D_REENTRANT -D_GNU_SOURCE
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE
-DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-c xsinit.c -o xsinit.o
gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o RSPerl.so Converters.o
ForeignReference.o GeneralConverters.o RPerlElements.o RPerlEval.o
RPerlInit.o RPerlNew.o RPerlReference.o RPerlVars.o Reflectance.o
UserConverters.o Utils.o xsinit.o -Wl,--enable-new-dtags
-Wl,-rpath,/usr/lib64/perl5/CORE -fstack-protector -L/usr/lib64/perl5/CORE
-lperl -lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
-L/usr/lib64/R/lib -lR
installing to /usr/lib64/R/library/RSPerl/libs
** R
** inst
** preparing package for lazy loading
** help
Warning:
/tmp/RtmpHyWOHo/R.INSTALL281f2591/RSPerl/man/PerlReferenceObjects.Rd:32:
unknown macro '\textit'
*** installing help indices
converting help for package RSPerl
finding HTML links ... done
Perl html
PerlClear html
PerlDiscard html
PerlExists html
PerlExpr html
PerlFile html
PerlGetArray html
PerlGetCode html
PerlInit html
PerlInterpreter html
PerlLength html
PerlNames html
PerlNew html
PerlNewArray html
PerlPackage html
PerlReferenceDollar html
PerlReferenceObjects html
PerlReferenceSubset html
PerlSetHash html
PerlStashInfo html
PerlTerminate html
PerlType html
PerlTypes html
PerlUndef html
addConverter html
foreignReference html
getNumPerlConverters html
getPerlClasses html
getPerlDynModules html
getPerlScript html
mkRef html
parseEval html
perlInitArgs html
perlModuleLoaded html
referenceHandlerGenerator html
setPerlHandler html
** building package indices ...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/lib64/R/library/RSPerl/libs/RSPerl.so':
/usr/lib64/R/library/RSPerl/libs/RSPerl.so: undefined symbol: boot_R
Error: loading failed
Execution halted
ERROR: loading failed
* removing /usr/lib64/R/library/RSPerl
Now, I do not know where the boot_R symbol is coming from and google is not
helping.
So I am stuck.
Why won't boot_R resolve?
Is this a problem due to new versions of R?
Is my hack of commenting out of SVt_RV switch entries not going to work
anyway?
Also, I see errors in the installation related to Makefile.PL and
makefile.perl
Any help on these issues would be most helpful.
In the end, I am trying to get to statistical analyses in R that Perl does
not have.
In particular, I need a good test of normality on a set of residuals.
Hunter
--
Hunter Moseley, Ph.D. -- Univ. of Louisville
Assistant Professor, Dept. of Chemistry
Not just a scientist, but a fencer as well.
My foil is sharp, but my mind sharper still.
---------------------------------------------------------------
Email: hunter.mose...@louisville.edu (work)
hunter.mose...@gmail.com(personal)
Phone: 502-852-3168 (office) 502-852-7598 (lab) 502-852-8149 (fax)
Address: Department of Chemistry, University of Louisville
2320 South Brook Street, Louisville, KY 40292
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