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12.6 years ago by
I am running R 2.4.1 (not Bioconductor) on a RedHat Linux system. I have successfully built and installed (independently) versions 1.8 and 1.10 of Rdbi and RdbiPgSQL. Rdbi loads without problems for both versions. However, when I attempt to load RdbiPgSQL, I get the following error: > library(RdbiPgSQL) Loading required package: Rdbi Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so' : /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so: undefined symbol: PQfsize Error: package/namespace load failed for 'RdbiPgSQL' The library /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so does exist. Any suggestions? Regards, Tom -- Thomas E Adams National Weather Service Ohio River Forecast Center 1901 South State Route 134 Wilmington, OH 45177 EMAIL: thomas.adams at noaa.gov VOICE: 937-383-0528 FAX: 937-383-0033
rdbi rdbipgsql • 547 views
modified 12.6 years ago by Seth Falcon7.4k • written 12.6 years ago by Thomas Adams60
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12.6 years ago by
I am running R 2.4.1 (not Bioconductor) on a RedHat Linux system. I have successfully built and installed (independently) versions 1.8 and 1.10 of Rdbi and RdbiPgSQL. Rdbi loads without problems for both versions. However, when I attempt to load RdbiPgSQL, I get the following error: > library(RdbiPgSQL) Loading required package: Rdbi Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so' : /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so: undefined symbol: PQfsize Error: package/namespace load failed for 'RdbiPgSQL' The library /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so does exist. Any suggestions? Regards, Tom -- Thomas E Adams National Weather Service Ohio River Forecast Center 1901 South State Route 134 Wilmington, OH 45177 EMAIL: thomas.adams at noaa.gov VOICE: 937-383-0528 FAX: 937-383-0033
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12.6 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Thomas Adams <thomas.adams at="" noaa.gov=""> writes: > I am running R 2.4.1 (not Bioconductor) on a RedHat Linux system. I have > successfully built and installed (independently) versions 1.8 and 1.10 > of Rdbi and RdbiPgSQL. Rdbi loads without problems for both versions. > However, when I attempt to load RdbiPgSQL, I get the following error: > > > library(RdbiPgSQL) > Loading required package: Rdbi > Error in dyn.load(x, as.logical(local), as.logical(now)) : > unable to load shared library > '/awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.s o': > /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so: > undefined symbol: PQfsize > Error: package/namespace load failed for 'RdbiPgSQL' > > The library > /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so > does exist. > > Any suggestions? Did you try using biocLite? Details in just about every other post on this list and on the BioC website. Anyhow, version 1.8.0 for Rdbi and RdbiPgSQL are the ones to use with R 2.4.1. What version of PostgreSQL are you using? We have tested against 8.1.4. If you have a different version, you might want to verify that PQfsize is indeed gone. I did: pg_config --version grep PQfsize pg_config --includedir/*.h + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
Seth, Thanks for your help and suggestions. Well, we have PostgreSQL 7.4.8 installed and your grep command reveals that PQfsize is in the libpq-fe.h file located in /usr/include. In fact, when I install RdbiPgSQL from source, it's easy to see that the build process explicitly looks for the availability of libpq-fe.h. I do not have any control over what version of PostgreSQL we have installed, so migrating to version 8.1.4 (or whatever) is not possible at this time. Can anyone suggest an alternative way to install RdbiPgSQL that circumvents this problem? Is there a Linux binary available that I can install ? will this even work? Regards, Tom Seth Falcon wrote: > Thomas Adams <thomas.adams at="" noaa.gov=""> writes: > > >> I am running R 2.4.1 (not Bioconductor) on a RedHat Linux system. I have >> successfully built and installed (independently) versions 1.8 and 1.10 >> of Rdbi and RdbiPgSQL. Rdbi loads without problems for both versions. >> However, when I attempt to load RdbiPgSQL, I get the following error: >> >> > library(RdbiPgSQL) >> Loading required package: Rdbi >> Error in dyn.load(x, as.logical(local), as.logical(now)) : >> unable to load shared library >> '/awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL. so': >> /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so: >> undefined symbol: PQfsize >> Error: package/namespace load failed for 'RdbiPgSQL' >> >> The library >> /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so >> does exist. >> >> Any suggestions? >> > > Did you try using biocLite? Details in just about every other > post on this list and on the BioC website. Anyhow, version 1.8.0 for > Rdbi and RdbiPgSQL are the ones to use with R 2.4.1. > > What version of PostgreSQL are you using? We have tested against > 8.1.4. If you have a different version, you might want to verify that > PQfsize is indeed gone. I did: > > pg_config --version > grep PQfsize pg_config --includedir/*.h > > + seth > > -- Thomas E Adams National Weather Service Ohio River Forecast Center 1901 South State Route 134 Wilmington, OH 45177 EMAIL: thomas.adams at noaa.gov VOICE: 937-383-0528 FAX: 937-383-0033
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12.6 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Thomas Adams <thomas.adams at="" noaa.gov=""> writes: > Seth, > > Thanks for your help and suggestions. Well, we have PostgreSQL 7.4.8 > installed and your grep command reveals that PQfsize is in the > libpq-fe.h file located in /usr/include. In fact, when I install > RdbiPgSQL from source, it's easy to see that the build process > explicitly looks for the availability of libpq-fe.h. That's good. I expect RdbiPgSQL will work with 7.4.8 (not sure, but I think your problem lies elsewhere). > I do not have any control over what version of PostgreSQL we have > installed, so migrating to version 8.1.4 (or whatever) is not possible > at this time. Can anyone suggest an alternative way to install > RdbiPgSQL that circumvents this problem? Is there a Linux binary > available that I can install ? will this even work? Did you try via biocLite? It might fail, but that failure might give us some clues. Can you look at the output of "ldd /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so" both from the command line where you successfully built/installed RdbiPgSQL and from inside R using the system() command? + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
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12.6 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
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12.6 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Thomas Adams <thomas.adams at="" noaa.gov=""> writes: > Sean & Seth, > > Thanks so much for your help and good suggestions. Unfortunately, none > worked. I even went so far as to install R 2.5.0 and PostgreSQL 8.2.4 > (into a local directory)? > > One interesting point, is that when I install RdbiPgSQL 1.8, the > install script is still looking for the include file libpq-fe.h in > /usr/include even though I have specified the PostgreSQL 8.2.4 > libraries & includes elsewhere using: Another strange point is that somehow the install process doesn't seem to be linking against libpq. I'm baffled at the extent of your difficulties. I'm sure you are quite frustrated. It seems that you've been trying many things and I wonder if the state of the system is what you think it is. For example, did you edit the RdbiPgSQL package at any point? How many PostgreSQL installs do you have now? And so on. You need to figure out how to get RdbiPgSQL.so to link against libpq. This has to happen at compile time _and_ the libpq library needs to be resolvable at load time -- you may need to modify your LD_LIBRARY_PATH, for example, to get this to work. Good Luck. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org