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Question: Error loading package RdbiPgSQL / R2.12.1/ Mac OS X 10.6.6
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gravatar for Aszodi,Andras
6.8 years ago by
Aszodi,Andras30 wrote:
On Feb 23, 2011, at 8:09 PM, Dan Tenenbaum wrote: On Wed, Feb 23, 2011 at 3:07 AM, Aszodi,Andras <andras.aszodi@imp.ac.at<mailto:andras.aszodi@imp.ac.at>> wrote: Dear Mailing List, When I say:- > library("RdbiPgSQL") ...then I get the following errors:- Loading required package: Rdbi Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.12/Resources/library/RdbiP gSQL/libs/x86_64/RdbiPgSQL.so': dlopen(/Library/Frameworks/R.framework/Versions/2.12/Resources/library /RdbiPgSQL/libs/x86_64/RdbiPgSQL.so, 6): Symbol not found: _PQbackendPID Referenced from: /Library/Frameworks/R.framework/Versions/2.12/Resources/library/RdbiPg SQL/libs/x86_64/RdbiPgSQL.so Expected in: dynamic lookup Error: package/namespace load failed for 'RdbiPgSQL' I use only binary packages for R and R itself was installed as binary. But I must admit my Postgres installation (8.4.7) was compiled from source and placed into a "nonstandard" location /usr/local/pgsql/current . But the problem persists even if I put the library path /usr/local/pgsql/current/lib in the DYLD_LIBRARY_PATH variable. This happens on a Mac Pro (64-bit Intel), with OS X 10.6.6. I would be grateful for any fixes or workaround advice. Thank you very much! PS I first sent this to the R bug tracking system but Professor Ripley advised me to submit it to Bioconductor since RdbiPgSQL is a BioC contributed package. I hope this is now the right place... Hi, you don't include the output of sessionInfo(), Sorry, my bad. Here it is. I wonder if this helps though... > sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Rdbi_1.24.0 loaded via a namespace (and not attached): [1] tools_2.12.1 nor explain how you installed RdbiPgSQL in the first place I said "I use only binary packages for R", see above. So RdbiPgSQL was installed with bioClite as usual. Definitely not from source. and whether there were any errors. No, there were no errors. You might try building RdbiPgSQL from source: source("http://bioconductor.org/biocLite.R") biocLite("RdbiPgSQL",type="source") This will give you some informative messages about how to tell the build process about your PostgreSQL installation. This is a good suggestion. What bothers me though that even if I specify LD_LIBRARY_PATH or DYLD_LIBRARY_PATH it won't help. Are the shared library locations somehow hard-coded in the pre-build packages? The pre-built version expects PostgreSQL to be in a standard location. That might be the problem. However, for Postgres there is no unequivocal "standard location" under OS X. Some people put it in /usr/local, Linux-style. There are pre-built versions that put the whole thing under /Library, MacPorts uses /opt I believe... it is a mess. My reason for the not-quite-standard location is that I plan to run 8.4 and 9.0 as well. Dan Many thanks for your prompt reply and for your suggestions! AndrĂ¡s [[alternative HTML version deleted]]
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