Re: [R] Error installing RSPerl.
Hi List, Just to close this thread. It seems my problem was of a more haste less speed nature, i.e. a typo, which Duncan helpfully pointed out. I was installing RSPerl with the command: R CMD INSTALL -c --configure-args=--with-modules='IO Fcntl Socket Storable XML::Parser::Expat DB_File::Glob GDBM_File SDBM_File POSIX' RSPerl I specified: DB_File::Glob Instead of (the correct) DB_File File::Glob As Duncan pointed out: Specifying DB_File::Glob will cause the package to have a boot entry named D_File__Glob precisely what it is complaining about. So it looks like this is a simple typo. The package does not verify that the modules are there if you explicitly specify them. Suitably embarrassed, Grainne. On Thu, Oct 29, 2009 at 3:37 PM, Duncan Temple Lang dun...@wald.ucdavis.edu wrote: Hi Grainne There is one likely cause. But before getting into the explanation, can you send me the output from when you installed the package, e.g. the output from R CMD INSTALL RSPerl and any configuration arguments you specified. You can send this to me off-list and we can summarize at the end. Thanks, D. Grainne Kerr wrote: Dear list, I have updated to version R-2.10.0. When I try to load the RSPerl library I get the following error: library(RSPerl) Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/usr/local/lib/R/library/RSPerl/libs/RSPerl.so': /usr/local/lib/R/library/RSPerl/libs/RSPerl.so: undefined symbol: boot_DB_File__Glob Error: package/namespace load failed for 'RSPerl' I do not know how to fix this. Can anyone please help? I'm runninn R on Ubuntu 9.04 Many thanks, Grainne. sessionInfo() R version 2.10.0 (2009-10-26) i686-pc-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Error installing RSPerl.
Dear list, I have updated to version R-2.10.0. When I try to load the RSPerl library I get the following error: library(RSPerl) Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/usr/local/lib/R/library/RSPerl/libs/RSPerl.so': /usr/local/lib/R/library/RSPerl/libs/RSPerl.so: undefined symbol: boot_DB_File__Glob Error: package/namespace load failed for 'RSPerl' I do not know how to fix this. Can anyone please help? I'm runninn R on Ubuntu 9.04 Many thanks, Grainne. sessionInfo() R version 2.10.0 (2009-10-26) i686-pc-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Perl error - Can't locate R/Rdconv.pm in @INC
Dear list, I've a package, myPkg, which was developed on R v 2.6.1. I have installed R v2.9.2 from source, with a shared library and tcktk support. The package, myPkg, depends on RSPerl, and imports it in its NAMESPACE. I've downloaded and installed RSPerl using command: R CMD INSTALL -c --configure-args=--with-modules='IO \ Fcntl Socket Storable XML::Parser::Expat DB_File File::Glob \ GDBM_File SDBM_File POSIX' RSPerl When installing myPkg, I use the following command: R CMD INSTALL myPkg * Installing to library ‘/usr/local/lib/R/library’ * Installing *source* package ‘myPkg’ ... ** R ** inst ** preparing package for lazy loading Warning: 'Sys.putenv' is deprecated. Use 'Sys.setenv' instead. See help(Deprecated) ** help *** installing help indices Can't locate R/Rdconv.pm in @INC (@INC contains: /usr/local/lib/R/library/ RSPerl/perl/i486-linux-gnu-thread-multi /usr/local/lib/R/library/RSPerl/perl /etc/perl /usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at /usr/local/lib/R/share/perl/build-help.pl line 21. BEGIN failed--compilation aborted at /usr/local/lib/R/share/perl/build-help.pl line 21. ERROR: building help failed for package ‘myPkg’ So - its can't find the perl module, Rdconv.pm, to build the help modules in the perl path. Doing a quick search for this module - its found at the location below (a location not in the perl path). find / -name Rdconv.pm /usr/local/lib/R/share/perl/R/Rdconv.pm I changed the NAMESPACE file in my myPkg package, so as not to import RSPerl. I altered the build-help.pl in R to print out the perl path. Path when RSPerl not imported: /usr/local/lib/R/share/perl /usr/local/lib/R/share/perl /etc/perl /usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl (Also, the perl path when installing RSPerl (i.e. before installing myPkg) /usr/local/lib/R/share/perl /usr/local/lib/R/share/perl /etc/perl /usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl) Obviously, if I run R CMD INSTALL --no-docs myPkg it installs fine. It also installs with older versions of R. I'm running Ubuntu 9.04. I have already posted (probably erroneously) this help plea of the r-devel mailing list - I apologise for cross-posting. Any ideas what should I look for in the code in order to fix this? Any pointers in the right direction or what to look for would be very much appreciated. Thanks in advance! Grainne. R sessionInfo() R version 2.9.2 (2009-08-24) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
