Question: Error loading package RdbiPgSQL / R2.12.1/ Mac OS X 10.6.6
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gravatar for Dan Tenenbaum
8.7 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
On Thu, Feb 24, 2011 at 1:58 AM, Aszodi,Andras <andras.aszodi@imp.ac.at>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>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/Rd biPgSQL/libs/x86_64/RdbiPgSQL.so': >> >> >> dlopen(/Library/Frameworks/R.framework/Versions/2.12/Resources/libr ary/RdbiPgSQL/libs/x86_64/RdbiPgSQL.so, >> 6): Symbol not found: _PQbackendPID >> Referenced from: >> >> /Library/Frameworks/R.framework/Versions/2.12/Resources/library/Rdb iPgSQL/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? > > Yes. > > 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. > > See here for how it is built on our Mac build system: http://bioconductor.org/checkResults/release/bioc-LATEST/RdbiPgSQL /pelham-checksrc.html Note the occurrences of /usr/local/include and /usr/local/lib. When I add the 'type="source"' flag to biocLite("RdbiPgSQL"), I see the following; I could not find your PostgreSQL client libraries! Use --with-pgsql-libraries=PATH; if running R's INSTALL, use --configure-args='--with-pgsql-libraries=PATH'; or set PG_LIB_DIR in your environment to the library path, and rerun the configure/install. Passing these arguments by adding them to configure.args in your call to biocLite(), and/or setting environment variables as described, should probably build the package successfully for you. > Dan > > Many thanks for your prompt reply and for your suggestions! > AndrĂ¡s > > Dan [[alternative HTML version deleted]]
rdbipgsql process • 482 views
ADD COMMENTlink written 8.7 years ago by Dan Tenenbaum8.2k
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