R-2.01 and RSPerl-0.6.2
The omega-help mailing list is more appropriate. (See http://www.omegahat.org/mailman/listinfo) One of the things that comes to mind is whether you built R via the --enable-R-shlib entirely from scratch or did you reconfigure and rebuild from an existing compiled source. If it is the latter, and library/stats/lib/stats.so was not linked against libR.so, then bad things happen. Run the command ldd /tools/R/current/lib/R/library/stats/libs/stats.so and see if libR.so is included in the output. If not, rebuild R with make distclean ./configure --enable-R-shlib make and try things then. If this is not the problem, you can send mail directly to me and I can try to help. D.
Zachariah Zachariah wrote:
Hi,
I am somewhat new to R and RSPerl, but I think this particular problem
has to do with RSPerl and so I am not sure if this is the right forum
to ask for help. Nevertheless I am quite sure that many of you would
have used RSPerl with R.
My hardware platform is a Sun/Solaris V440 server running Solaris 9
operating system I use the gcc-3.4.0 compiler to compile R without any
problems. My intention is to call R from Perl. So I use the
--enable-R-shlib option as the document says. My perl version is at
5.8.6. I also compiled in RSPerl for dual functionality of calling
perl from R and R from Perl. Everything seems to get installed
smoothly as a well oiled machine till I run the tests in the examples
directory.
#R CMD INSTALL -c RSPerl_0.6-2.tar.gz
#R CMD INSTALL -c --configure-args='with-in-perl' RSPerl_0.6-2.tar.gz
#cd <install directory>/lib/R/library/RSPerl/examples
# perl test.pl
1..1
ok 1
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
"/tools/R/current/lib/R/library/stats/libs/stats.so":
ld.so.1: perl: fatal: relocation error: file
/tools/R/current/lib/R/library/stats/libs/stats.so: symbol MAIN__:
referenced symbol not found
Loaded RSPerl library
objects $.PerlReference [.PerlArrayReference [.PerlHashReference
[<-.PerlArrayReference [<-.PerlHashReference addConverter
foreignReference getNumPerlConverters getPerlConverterDescriptions
getPerlHandler getPerlScript names.PerlHashReference parseEval
perlInitArgs referenceHandlerGenerator removeConverter setPerlHandler
Testing search path
installing function name search
1db114
Search path: .GlobalEnv package:RSPerl package:methods
package:graphics package:grDevices package:utils package:datasets
Autoloads package:base
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
"/tools/R/current/lib/R/library/stats/libs/stats.so":
ld.so.1: perl: fatal: relocation error: file
/tools/R/current/lib/R/library/stats/libs/stats.so: symbol MAIN__:
referenced symbol not found
In addition: Warning message:
package stats in options("defaultPackages") was not found
Error in library(package = "stats") : package/namespace load failed for 'stats'
Segmentation fault
I searched the documents for any clue and I believe that I have
followed everything specified in the documentation. I had done a
successful install of R-1.9.1 and RSPerl-0.5.7 on a similar hardware
platform that I thought had given me some confidence but not so with
this one. The documentation did not seem to suggest anything new for
the latest versions of R and RSPerl Thanks in advance for any
help/pointers/tips/etc. Here are my environment variables if that
would help.
# env
PWD=/tools/R/current/lib/R/library/RSPerl/examples
GS_FONTPATH=/usr/lib/X11/fonts/Type1Adobe
TZ=US/Pacific
ORACLE_SID=prosrv
TMPDIR=/usr/tmp
MODULEPATH=/share/init/mod
GS_LIB=/netopt/gs/6.52/lib/
PAGER=less
LOADEDMODULES=sysenv:X11/R6:gnu:sundry:news:perl/current:net:Xmisc:ncbi:gcg/10.3:metamail/current:netscape/current:motif/1.2.3p26:mail:transcript:cap/man:emacs/current:gs/current:acrobat:standard:nsr/current:oracle:R:oraclient/current
CLASSPATH=/netopt/netscape/4.78/java/classes/java40.jar
MANPATH=/tools/perl/current/man:/usr/local/man:/usr/man:/usr/java/man:/netopt/man:/netopt/gnu/man:/tools/X11/R6/man:/tools/gnu/man:/local/links/man:/tools/sundry/man:/tools/news/man:/tools/net/man:/tools/Xmisc/man:/tools/metamail/2.6/man:/netopt/netscape/4.78/man:/tools/motif/1.2.3p26/man:/tools/mail/man:/netopt/emacs/21.3/man:/netopt/gs/6.52/man:/tools/R/current/man
SYS=sparc-sol
XLOCALEDIR=/tools/X11/R6/lib/X11/locale
MODULESHOME=/tools/Modules/2.2
NNTPSERVER=nntp
USER=root
MACHTYPE=sparc
CVS_SERVER=/tools/gnu/bin/cvs
SSH2_SFTP_LOG_FACILITY=-1
XFILESEARCHPATH=/share/init/%T/%N%S:/tools/X11/R6/lib/X11/%T/%N%C%S:/tools/X11/R6/lib/X11/%T/%N%S:/tools/Xmisc/lib/%T/%N%S:/tools/motif/1.2.3p26/lib/X11/%T/%N%C%S:/tools/motif/1.2.3p26/lib/X11/%T/%N%S
LPDEST=NULL
ORACLE_HOME=/share/ora-homes/9.2.0
INFOPATH=/tools/gnu/info:/netopt/emacs/local-info:/netopt/emacs/21.3/info
DISPLAY=sitar:11.0
NPX_PLUGIN_PATH=/usr/j2se/jre/plugin/sparc/ns4
LOGNAME=root
SHLVL=2
_LMFILES_=/share/init/mod/sysenv:/share/init/mod/X11/R6:/share/init/mod/gnu:/share/init/mod/sundry:/share/init/mod/news:/share/init/mod/perl/current:/share/init/mod/net:/share/init/mod/Xmisc:
/share/init/mod/ncbi:/share/init/mod/gcg/10.3:/share/init/mod/metamail/current:/share/init/mod/netscape/current:/share/init/mod/motif/1.2.3p26:/share/init/mod/mail:/share/init/mod/transcript:
/share/init/mod/cap/man:/share/init/mod/emacs/current:/share/init/mod/gs/current:/share/init/mod/acrobat:/share/init/mod/standard:/share/init/mod/nsr/current:/share/init/mod/oracle:/share/init/mod/R:
/share/init/mod/oraclient/current
ORAENV_ASK=NO
SHELL=/bin/bash
UIDPATH=/tools/Xmisc/lib/uid/%U:/tools/motif/1.2.3p26/lib/X11/uid/%U
PRINTER=NULL
HOSTTYPE=sun4
MYWM=twm
OSTYPE=solaris
TERM=xterm
RAD_LOG_FACILITY=LOG_LOCAL0
_=/netopt/bin/sudo
SUDO_COMMAND=/usr/bin/tcsh
LD_LIBRARY_PATH=/share/guitar/ora-homes/9.2.0/lib32:/usr/local/lib:/tools/X11/R6/lib:/tools/gnu/lib:/tools/Xmisc/lib:/usr/lib:/lib:/usr/local/lib:/netopt/lib:/netopt/gnu/lib:/tools/R/current/lib/R/lib:
/tools/R/current/lib/R/bin:/tools/R/current/lib/R/library/RSPerl/libs:/tools/R/current/lib/R/library/tools/libs:/tools/R/current/lib/R/library/stats/libs:/tools/R/current/lib/R/library/methods/libs:
/tools/R/current/lib/R/library/grid/libs:/tools/R/current/lib/R/library/splines/libs:/tools/R/current/lib/R/library/tcltk/libs:/tools/R/current/lib/R/library/MASS/libs:/tools/R/current/lib/R/library/class/libs:
/tools/R/current/lib/R/library/nnet/libs:/tools/R/current/lib/R/library/spatial/libs:/tools/R/current/lib/R/library/cluster/libs:/tools/R/current/lib/R/library/foreign/libs:/tools/R/current/lib/R/library/KernSmooth/libs:
/tools/R/current/lib/R/library/lattice/libs:/tools/R/current/lib/R/library/nlme/libs:/tools/R/current/lib/R/library/mgcv/libs:/tools/R/current/lib/R/library/rpart/libs:/tools/R/current/lib/R/library/survival/libs:/tools/R/current/lib/R/library/RSPerl/libs
MAKE=gmake
PATH=/share/guitar/ora-homes/9.2.0/bin:/tools/perl/current/bin:/usr/bin:/usr/ucb/bin:/usr/ccs/bin:/usr/local/bin:/tools/gnu/bin:/tools/R/current/bin
PERLLIB=/tools/R/current/lib/R/library/RSPerl/share/blib/arch:/tools/R/current/lib/R/library/RSPerl/share/blib/lib:/tools/R/current/lib/R/library/RSPerl/scripts
R_HOME=/tools/R/current/lib/R
LD_LIBRARY_PATH_64=/share/guitar/ora-homes/9.2.0/lib
--Zachariah
Systems Administrator
Stanford University
______________________________________________ R-help at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Duncan Temple Lang duncan at wald.ucdavis.edu Department of Statistics work: (530) 752-4782 371 Kerr Hall fax: (530) 752-7099 One Shields Ave. University of California at Davis Davis, CA 95616, USA