Re: [Rd] Package RPostgreSQL_0.1-6.tar.gz has been checked and built

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Wed, 21 Jul 2010 08:04:27 +0100 (BST)

AFAIK, you simply need to put the path to the correct pg_config first in your path -- depending how the PostgreSQL installation was done you may also need to ensure that its libraries are in your LD_LIBRARY_PATH. Given that this is the third query you have sent to the R lists about contributed packages, I think you should consider if you really need 64-bit R. 32-bit R is simpler to get working on most platforms, including Solaris, especially with external software. I am presuming (from the 'bin/amd64') that this is an Opteron/Xeon system, and there 64-bit software is problematic simply because gcc does not seem to work well. (Most often the 'particular errors' are not with Solaris but with non-standard conformant code written assuming gcc extensions or laxities -- for which the fix is often to use gcc.)

And BTW, you keep on saying 'Solaris 10u7 X64' and I've no idea what that is. The 'at a minimum' information asked for in the posting guide will give a correct description. Solaris has come for many years as a 32/64-bit OS, and there is i386 Solaris and Sparc Solaris.

On Wed, 21 Jul 2010, Amber wrote:

> Hi Dirk
> I think there are problems with pg_config, the configure script of
> RPostgreSQL checks for pg_config and got ??checking for pg_config...
> /usr/bin/pg_config??. In Solaris 10u7 X64, three versions of PostgreSQL are
> installed, there are in /usr/postgres/8.2(8.2.9) and
> /usr/postgres/8.3(8.3.3), the corresponding bin files are in
> /usr/postgres/<version>/bin and /usr/postgres/<version>/bin/amd64, and the
> libraries in /usr/bin is 8.1.11 and it seems a 32bit one, and I can??t find
> the 64bit version bins for 8.1.11.
> I'll try uninstall 8.1.11 and install 8.2.9, and my question is how to let
> RPostgreSQL configure script find the 64bit pg_config.
>
>
> Xiaobo Gu
>
> On Tue, Jul 20, 2010 at 10:32 PM, ?????? <guxiaobo1982_at_gmail.com> wrote:
>
>> Hi Dirk,
>>
>> I think this discussion should help :
>> http://stackoverflow.com/questions/1836333/how-can-i-compile-64-bit-postgres-bindings-for-perl-on-solaris,
>> are there environment variables I can set to point to 64bit libraries, or I
>> can set the 64bit libraries path /usr/local/psql/lib before /usr/lib, I'll
>> let you know the results tomorrow.
>>
>>
>>
>>
>>
>> Xiaobo.Gu
>>
>> -----Original Message-----
>> From: Dirk Eddelbuettel [mailto:edd_at_debian.org]
>> Sent: Tuesday, July 20, 2010 7:11 PM
>> To: Amber
>> Cc: Dirk Eddelbuettel; Uwe Ligges
>> Subject: Re: Package RPostgreSQL_0.1-6.tar.gz has been checked and built
>>
>>
>> Hi Amber,
>>
>> I'm at the useR conference with imperfect connectivity adn can't help much.
>> I
>> also noticed that Solaris often comes up with particular errors -- see Prof
>> Ripley's response to your Rattle query.
>>
>> RPostgresql may be easy to get built, but you may have to adapt
>> configure.in.
>>
>> On 20 July 2010 at 14:08, Amber wrote:
>> | Hi Dirk,
>> | There are problems building RPostgreSQL on 64bit solaris,
>> | The server has preinstalled PostgreSQL 8.1 client and server binaries ,
>> and
>> | we also installed Greenplum SNE 3.3.5.0 server and client installed, but
>> the
>> | postgres user, which I used to build R and RPostgreSQL can't see
>> Greenplum
>> | binaries, the error messages are:
>> |
>> | -bash-3.00$ R CMD INSTALL RPostgreSQL
>> | * installing to library '/opt/R/R2-11-1/lib/R/library'
>> | * installing *source* package 'RPostgreSQL' ...
>> | checking for gcc... /opt/sunstudio12.1/bin/cc -m64
>> | 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... no
>> | checking whether /opt/sunstudio12.1/bin/cc -m64 accepts -g... yes
>> | checking for /opt/sunstudio12.1/bin/cc -m64 option to accept ISO C89...
>> none
>> | needed
>> | checking for pg_config... /usr/bin/pg_config
>> | checking for "/usr/include/pgsql/libpq-fe.h"... yes
>>
>> Good!
>>
>> | configure: creating ./config.status
>> | config.status: creating src/Makevars
>> | ** libs
>> | /opt/sunstudio12.1/bin/cc -m64 -xc99=all -G -L/opt/R/R2-11-1/lib
>> | -L/usr/sfw/lib/amd64 -L/usr/lib/amd64 -L/opt/sfw/lib -o RPostgreSQL.so
>> | RS-DBI.o RS-PostgreSQL.o -L/usr/lib -lpq
>> | ld: fatal: file /usr/lib/libpq.so: wrong ELF class: ELFCLASS32
>> | ld: fatal: File processing errors. No output written to RPostgreSQL.so
>>
>> The linker complained about bad objkect files. Looks like you have a wrong
>> or
>> mismatched Pg library. We'd have to fix that first before RPostgreSQL can
>> be
>> built.
>>
>> Also ask Greenplum if they can help. At least they get paid for this :)
>>
>> Dirk
>>
>> | *** Error code 1
>> | The following command caused the error:
>> | if test "zRS-DBI.o RS-PostgreSQL.o" != "z"; then \
>> | echo /opt/sunstudio12.1/bin/cc -m64 -xc99=all -G -L/opt/R/R2-11-1/lib
>> | -L/usr/sfw/lib/amd64 -L/usr/lib/amd64 -L/opt/sfw/lib -o RPostgreSQL.so
>> | RS-DBI.o RS-PostgreSQL.o -L/usr/lib -lpq ; \
>> | /opt/sunstudio12.1/bin/cc -m64 -xc99=all -G -L/opt/R/R2-11-1/lib
>> | -L/usr/sfw/lib/amd64 -L/usr/lib/amd64 -L/opt/sfw/lib -o RPostgreSQL.so
>> | RS-DBI.o RS-PostgreSQL.o -L/usr/lib -lpq ; \
>> | fi
>> | make: Fatal error: Command failed for target `RPostgreSQL.so'
>> | ERROR: compilation failed for package 'RPostgreSQL'
>> | * removing '/opt/R/R2-11-1/lib/R/library/RPostgreSQL
>> |
>> | On Sun, Jul 18, 2010 at 10:50 PM, ?????? <guxiaobo1982_at_gmail.com> wrote:
>> |
>> | > Hi,
>> | > I have successfully built and installed DBI and RPostgreSQL on
>> 32bit
>> | > Solaris, and will repeat in on our 64bit production server tomorrow,
>> I'll
>> | > let you know the results.
>> | >
>> | > We still waiting for the building toolset for win64 to mature.
>> | >
>> | > Xiaobo.Gu
>> | >
>> | >
>> | > -----Original Message-----
>> | > From: Dirk Eddelbuettel [mailto:edd_at_debian.org]
>> | > Sent: Sunday, July 18, 2010 9:59 PM
>> | > To: ??????
>> | > Cc: 'Dirk Eddelbuettel'; 'Uwe Ligges'
>> | > Subject: RE: Package RPostgreSQL_0.1-6.tar.gz has been checked and
>> built
>> | >
>> | >
>> | > Hi again,
>> | >
>> | > On 18 July 2010 at 21:41, ?????? wrote:
>> | > | Hi Dirk,
>> | > | We have tested RPostgreSQL against 64bit RODBC both on the same
>> | > 64bit Windows Server.
>> | > |
>> | > | The Environments are as following:
>> | > |
>> | > | Case 1: 32bit R 2.11.1, 32bit RPostgreSQL,
>> | > | data <- dbGetQuery(con, "select * from optest.colana limit 50000")
>> | > | It takes about 1.5 minute to run
>> | > |
>> | > | Case2: 64bit R 2.11.1, 64bit RODBC, and 64bit DataDirect ODBC to
>> | > Greenplum
>> | > | data <- sqlQuery(con, "select * from optest.colana limit 50000")
>> | > | It runs for at least 10 minutes and still running when I kill the
>> whole R
>> | > process
>> | >
>> | > That's pretty shocking!
>> | >
>> | > | It yields out that RPostgres have great performance advantages, we
>> will
>> | > try to build RPostgreSQL on 64bit Solaris 10 u7 platform next.
>> | >
>> | > Keeping the comparison 'apples to apples' could you build Postgresql on
>> | > Windows 64, so that you could build RPostgreSQL against it?
>> | >
>> | > Dirk
>> | >
>> | > | Xiaobo.Gu
>> | > |
>> | > | -----Original Message-----
>> | > | From: Dirk Eddelbuettel [mailto:edd_at_debian.org]
>> | > | Sent: Monday, June 28, 2010 11:34 PM
>> | > | To: Uwe Ligges
>> | > | Cc: edd_at_debian.org; ?????????3??
>> | > | Subject: Re: Package RPostgreSQL_0.1-6.tar.gz has been checked and
>> built
>> | > |
>> | > |
>> | > | Uwe,
>> | > |
>> | > | On 28 June 2010 at 16:57, Uwe Ligges wrote:
>> | > | | Dirk,
>> | > | |
>> | > | | da ist derzeit kein 64-bit PostgreSQL auf winbuilder.
>> | > |
>> | > | I know that -- but it wasn't me but someone who really badly wants
>> this
>> | > on
>> | > | Windows and is seemingly in several threads on the R lists as well as
>> in
>> | > my
>> | > | inbox and who didn't edit the DESCRIPTION file before uploading this.
>> | > |
>> | > | Tschoe, Dirk
>> | > |
>> | > | |
>> | > | | Gruss,
>> | > | | Uwe
>> | > | |
>> | > | |
>> | > | |
>> | > | | On 28.06.2010 16:36, Uwe.Ligges_at_R-Project.org wrote:
>> | > | | > Dear package maintainer,
>> | > | | >
>> | > | | > this notification has been generated automatically.
>> | > | | > Your package RPostgreSQL_0.1-6.tar.gz has been built (if working)
>> and
>> | > checked for Windows.
>> | > | | > Please check the log files and (if working) the binary package
>> at:
>> | > | | > http://win-builder.r-project.org/HLQti73j3Y90
>> | > | | > The files will be removed after roughly 72 hours.
>> | > | | > Installation time in seconds: 2
>> | > | | > Check time in seconds: 43
>> | > | | > Check result: ERROR
>> | > | | > R version 2.11.1 (2010-05-31) (64-bit)
>> | > | | >
>> | > | | > All the best,
>> | > | | > Uwe Ligges
>> | > | | > (CRAN maintainer of binary packages for Windows)
>> | > | | >
>> | > |
>> | > | --
>> | > | Regards, Dirk
>> | > |
>> | >
>> | > --
>> | > Regards, Dirk
>> | >
>> | >
>>
>> --
>> Dirk Eddelbuettel | edd@debian.org | http://dirk.eddelbuettel.com
>>
>>
>
> [[alternative HTML version deleted]]
>
>

-- 
Brian D. Ripley,                  ripley_at_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

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