[R-sig-DB] RPostgreSQL installation Error - RPostgreSQL.so: undefined symbol: PQpass

[Dirk Eddelbuettel]

On 30 May 2014 at 22:39, Manoj G wrote:
| Hi All,
| 
| Thank you for your responses. It really helped. :)
| 
| The package RPostgreSQL checks for PostgreSQL libraries only in the
| following directory paths,
| 
|     /usr/lib /usr/lib/pgsql /usr/lib/postgresql /usr/local/lib
| /usr/local/lib/pgsql /usr/local/lib/postgresql /usr/local/pgsql/lib
| /usr/local/postgresql/lib /opt/lib /opt/lib/pgsql /opt/lib/postgresql
| /opt/local/lib /opt/local/lib/postgresql /opt/local/lib/postgresql84
| /sw/opt/postgresql-8.4/lib /Library/PostgresPlus/8.4SS/lib /sw/lib
| 
| It does not check for the directories either in LD_LIBRARY_PATH or in
| /etc/ld.so.conf.

It does use  pg_config --libdir    if the pg_config is found.

We could generalise this by also using   pkg-config  

   edd using max:~$ pkg-config --cflags libpq
   -I/usr/include/postgresql  
   edd using max:~$ pkg-config --libs libpq
   -lpq  
   edd using max:~$ 

but neither will help in cases where the installation is unusual in other ways.
 
| So RPostgreSQL installation will be successful only if the PostgreSQL
| libraries exist in any of the above directories.
| 
| When I copied the libraries from /usr/lib64/pgsql to /usr/lib/pgsql and
| tried installing the package. It worked. :)

We could add /usr/lib64 to the list, doubling from what /usr/lib does.

Thoughts?

Dirk

| 
| 
| 
| Regards,
| 
| Manoj G
| 
| 
| On Fri, May 23, 2014 at 6:48 PM, NISHIYAMA Tomoaki <
| tomoakin using staff.kanazawa-u.ac.jp> wrote:
| 
| > Hi,
| >
| > Because Manoj G wrote:
| >
| > >>> ERROR: loading failed
| > >>>
| > >>> * removing ‘/usr/lib64/R/library/RPostgreSQL’
| >
| > there may be no /usr/lib64/R/library/RPostgreSQL/libs/RPostgreSQL.so
| > left there.
| >
| > $ svn checkout http://rpostgresql.googlecode.com/svn/trunk/
| > rpostgresql-read-only
| > $ cd rpostgresql-read-only
| > $ R CMD INSTALL RPostgreSQL
| > $ R CMD ldd RPostgreSQL/src/RPostgreSQL.so
| >
| > or
| >
| > $ tar zxvf  RPostgreSQL_0.4.tar.gz
| > $ R CMD INSTALL RPostgreSQL
| > $ R CMD ldd RPostgreSQL/src/RPostgreSQL.so
| >
| > would be necessary to investigate which library is used.
| > In addition, I would see
| > whether psql works fine,
| > response of
| > $ pg_config
| > and
| > $ ldd `which psql`
| >
| > best regards.
| > Tomoaki
| >
| > On 2014/05/23, at 20:32, Prof Brian Ripley wrote:
| >
| > > On 23/05/2014 10:41, NISHIYAMA Tomoaki wrote:
| > >> Hi,
| > >>
| > >>>  All the library files are in the directory
| > >>> /usr/lib64/pgsql/
| > >>
| > >>
| > >> Is this directory specified in LD_LIBRARY_PATH or /etc/ld.so.conf?
| > >
| > > That is not the message I would expect if the library was not being
| > > found.  Try
| > >
| > > R CMD ldd /usr/lib64/R/library/RPostgreSQL/libs/RPostgreSQL.so
| > >
| > > to see which library is being found.
| > >
| > >>
| > >>
| > >>
| > >> On 2014/05/23, at 18:16, Manoj G wrote:
| > >>
| > >>> Hi,
| > >>>
| > >>> I am trying to install R-Package RPostgreSQL, but getting the following
| > >>> error,
| > >>>
| > >>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
| > >>>
| > >>> unable to load shared object
| > >>> '/usr/lib64/R/library/RPostgreSQL/libs/RPostgreSQL.so':
| > >>>
| > >>> /usr/lib64/R/library/RPostgreSQL/libs/RPostgreSQL.so: undefined symbol:
| > >>> PQpass
| > >>>
| > >>> Error: loading failed
| > >>>
| > >>> Execution halted
| > >>>
| > >>> ERROR: loading failed
| > >>>
| > >>> * removing ‘/usr/lib64/R/library/RPostgreSQL’
| > >>>
| > >>> I have libpq and postgresql-dev installed. All the library files are
| > in the
| > >>> directory
| > >>>
| > >>> /usr/lib64/pgsql/ and all header files are in the directory
| > >>>
| > >>> /usr/include/pgsql/
| > >>>
| > >>> Postgre Version - 9.3.4 R Version - 3.0.2 Operating System - CentOS-6.4
| > >>>
| > >>> I am missing some small thing, but unable to find out why this is
| > happening.
| > >>>
| > >>> What am I doing wrong? How to correct this?
| > >>>
| > >>>
| > >>>
| > >>> Thanks and Regards,
| > >>>
| > >>> Manoj G
| > >>>
| > >>>     [[alternative HTML version deleted]]
| > >>>
| > >>> _______________________________________________
| > >>> R-sig-DB mailing list -- R Special Interest Group
| > >>> R-sig-DB using r-project.org
| > >>> https://stat.ethz.ch/mailman/listinfo/r-sig-db
| > >>
| > >> _______________________________________________
| > >> R-sig-DB mailing list -- R Special Interest Group
| > >> R-sig-DB using r-project.org
| > >> https://stat.ethz.ch/mailman/listinfo/r-sig-db
| > >>
| > >
| > >
| > > --
| > > Brian D. Ripley,                  ripley using stats.ox.ac.uk
| > > Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
| > > University of Oxford,             Tel:  +44 1865 272861 (self)
| > > 1 South Parks Road,                     +44 1865 272866 (PA)
| > > Oxford OX1 3TG, UK                Fax:  +44 1865 272595
| >
| >
| 
| 	[[alternative HTML version deleted]]
| 
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-- 
Dirk Eddelbuettel | edd using debian.org | http://dirk.eddelbuettel.com