Installing RPostgreSQL on Red Hat Linux

[Marta Cretu]

I have 

        Linux version 2.6.32-279.22.1.el6.x86_64 (mock...@c6b10.bsys.dev.centos.org) (gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC) ) #1 SMP Wed Feb 6 03:10:46 UTC 2013

  LSB Version: :core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-‌​4.0-amd64:printing-4.0-noarch

When I try in R to install.packages('RPostgreSQL'), 
it fails with unspecified errors:

     Warning message
     In install.packages("RPostgreSQL") :
     installation of package ‘RPostgreSQL’ had non-zero exit status

I'm beginner at linux, help me please, to solve this problem.

[Sean O'Riordain]

Hi Marta,

I don't use Redhat... but I suspect that there was another more relevant error above the "Warning message"... there might be dependencies? try doing install.packages('RPostgreSQL', dep=TRUE)

Sometimes the dependency chain doesn't work properly so you might have to "manually" install these missing packages.

Good luck,
Seán

Trinity College, Dublin

On 6 March 2014 07:52, Marta Cretu <mart...@gmail.com> wrote:

I have 

        Linux version 2.6.32-279.22.1.el6.x86_64 (mock...@c6b10.bsys.dev.centos.org) (gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC) ) #1 SMP Wed Feb 6 03:10:46 UTC 2013

  LSB Version: :core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch

When I try in R to install.packages('RPostgreSQL'), 

it fails with unspecified errors:

     Warning message
     In install.packages("RPostgreSQL") :
     installation of package ‘RPostgreSQL’ had non-zero exit status

I'm beginner at linux, help me please, to solve this problem.

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[Marta Cretu]

Hi Sean,

unfortunately, it still doesn' t work. More information hier:

http://gyazo.com/8010ca31fceee8e4eaf21a907abd518c

[Sean O'Riordain]

Hi Marta,
Near the top of the screenshot it says

checking for "/libpq-fe.h"... no

To me this implies that it cannot find the header files for postgresql, so I'm guessing the postgresql-devel yum package is needed.

You might also need to install the postgresql libs, so on redhat it might be something like??? I am an ubuntu user myself and I haven't use Redhat since about 1998 :-)
yum install postgresql-libs
yum install postgresql-devel

Take care,

Seán

--

[Marta Cretu]

Sean,

thank you a lot!!! It works! :)))

[NISHIYAMA Tomoaki]

Hi,

If you don't have the libraries and headers installed that doesn't work.
If you have the root privilege of the system, an easy way is

# yum install postgresql-devel postgresql-libs

General requirement is that
$ pg_config
on the command prompt shows proper information of library and header paths.

Best regards,
--
Tomoaki NISHIYAMA

Advanced Science Research Center,
Kanazawa University,
13-1 Takara-machi,
Kanazawa, 920-0934, Japan

[Nelson Jaiva]

Dear Tomoaki and other,

I have a problem similar to Martas about one year ago (see copy of terminal output below). My situation is as follows:
I have installed R-3.2.2 and PostgreSQL-9.4.4 on Linux supercomputing cluster, where I do not have root user rights. Therefore I installed postgres in a directory, where I have writing permission:

mkdir postgresql
./configure --prefix=/home/hpc/pr48co/gu28luf2/postgresql
make
make install

Now, the header '/libpq-fe.h' is in ~/postgresql/include/, but cannot be found during the installation of RPostgreSQL. I tried to add the include directory to the search path:

export PATH=$PATH:~/postgresql/include

but that did not work either. It seems that somewhere a reference to libpq-fe.h is missing, but I do not know how do fix it. Maybe the reference should be in pg_config? If yes, how would it look like?

This is the linux distribution on the cluster:
Linux version 3.0.101-0.47.55-default (geeko@buildhost) (gcc version 4.3.4 [gcc-4_3-branch revision 152973] (SUSE Linux) ) #1 SMP Thu May 28 08:25:11 UTC 2015 (dc083ee)

Best,
Nelson Jaiva


APPENDIX: error when trying to install RPostgreSQL

gu28luf2@lxa191:~> ~/r/R-3.2.2/bin/R CMD INSTALL $PKG
* installing to library ‘/home/hpc/pr48co/gu28luf2/r/R-3.2.2/library’
* installing *source* package ‘RPostgreSQL’ ...
** package ‘RPostgreSQL’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for pg_config... no
configure: checking for PostgreSQL header files
configure: Checking include /usr/include.
configure: Checking include /usr/include/pgsql.
configure: Checking include /usr/include/postgresql.
configure: Checking include /usr/local/include.
configure: Checking include /usr/local/include/pgsql.
configure: Checking include /usr/local/include/postgresql.
configure: Checking include /usr/local/pgsql/include.
configure: Checking include /usr/local/postgresql/include.
configure: Checking include /opt/include.
configure: Checking include /opt/include/pgsql.
configure: Checking include /opt/include/postgresql.
configure: Checking include /opt/local/include.
configure: Checking include /opt/local/include/postgresql.
configure: Checking include /opt/local/include/postgresql84.
configure: Checking include /sw/opt/postgresql-8.4/include.
configure: Checking include /Library/PostgresPlus/8.4SS/include.
configure: Checking include /sw/include/postgresql.
configure: Checking lib /usr/lib.
configure: Checking lib /usr/lib/pgsql.
configure: Checking lib /usr/lib/postgresql.
configure: Checking lib /usr/local/lib.
configure: Checking lib /usr/local/lib/pgsql.
configure: Checking lib /usr/local/lib/postgresql.
configure: Checking lib /usr/local/pgsql/lib.
configure: Checking lib /usr/local/postgresql/lib.
configure: Checking lib /opt/lib.
configure: Checking lib /opt/lib/pgsql.
configure: Checking lib /opt/lib/postgresql.
configure: Checking lib /opt/local/lib.
configure: Checking lib /opt/local/lib/postgresql.
configure: Checking lib /opt/local/lib/postgresql84.
configure: Checking lib /sw/opt/postgresql-8.4/lib.
configure: Checking lib /Library/PostgresPlus/8.4SS/lib.
configure: Checking lib /sw/lib.

checking for "/libpq-fe.h"... no

configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/hpc/pr48co/gu28luf2/r/R-3.2.2/include -DNDEBUG -I -I/usr/local/include    -fpic  -g -O2  -c RS-DBI.c -o RS-DBI.o
gcc -std=gnu99 -I/home/hpc/pr48co/gu28luf2/r/R-3.2.2/include -DNDEBUG -I -I/usr/local/include    -fpic  -g -O2  -c RS-PQescape.c -o RS-PQescape.o
In file included from RS-PQescape.c:7:
RS-PostgreSQL.h:23:26: error: libpq-fe.h: No such file or directory
RS-PQescape.c: In function ‘RS_PostgreSQL_escape’:
RS-PQescape.c:21: error: ‘PGconn’ undeclared (first use in this function)
RS-PQescape.c:21: error: (Each undeclared identifier is reported only once
RS-PQescape.c:21: error: for each function it appears in.)
RS-PQescape.c:21: error: ‘my_connection’ undeclared (first use in this function)
RS-PQescape.c:28: error: expected expression before ‘)’ token
RS-PQescape.c:32: warning: implicit declaration of function ‘PQescapeStringConn’
make: *** [RS-PQescape.o] Error 1
ERROR: compilation failed for package ‘RPostgreSQL’
* removing ‘/home/hpc/pr48co/gu28luf2/r/R-3.2.2/library/RPostgreSQL’
gu28luf2@lxa191:~>

[Joe Conway]

On 09/10/2015 07:35 AM, Nelson Jaiva wrote:
> mkdir postgresql
> ./configure --prefix=/home/hpc/pr48co/gu28luf2/postgresql
> make
> make install
>
> Now, the header '/libpq-fe.h' is in ~/postgresql/include/, but cannot be
> found during the installation of RPostgreSQL. I tried to add the include
> directory to the search path:
>
> export PATH=$PATH:~/postgresql/include

PATH is for executables, not includes. Looks like C_INCLUDE_PATH might
work -- see:

http://www.network-theory.co.uk/docs/gccintro/gccintro_23.html

You might need to set LD_LIBRARY_PATH too.

> but that did not work either. It seems that somewhere a reference to
> libpq-fe.h is missing, but I do not know how do fix it. Maybe the
> reference should be in pg_config? If yes, how would it look like?

pg_config can get those locations for you, e.g. something like:

export C_INCLUDE_PATH=$(pg_config --includedir):${C_INCLUDE_PATH}
export LD_LIBRARY_PATH=$(pg_config --libdir):${LD_LIBRARY_PATH}

HTH,

Joe

--
Crunchy Data - http://crunchydata.com
PostgreSQL Support for Secure Enterprises
Consulting, Training, & Open Source Development

[Nelson Jaiva]

Dear Joe,

excellent - that worked.

Thank's a lot your help and thank's also for the reference: That book is something I was looking for.
Nelson