Amber
2010-Jul-21 02:29 UTC
[Rd] Package RPostgreSQL_0.1-6.tar.gz has been checked and built
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, ¹ËС²¨ <guxiaobo1982@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@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, ¹ËС²¨ <guxiaobo1982@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@debian.org]
> | > Sent: Sunday, July 18, 2010 9:59 PM
> | > To: ¹ËС²¨
> | > 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, ¹ËС²¨ 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@debian.org]
> | > | Sent: Monday, June 28, 2010 11:34 PM
> | > | To: Uwe Ligges
> | > | Cc: edd@debian.org; ¨¦???¡ã??3¡é
> | > | 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@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]]
Prof Brian Ripley
2010-Jul-21 07:04 UTC
[Rd] Package RPostgreSQL_0.1-6.tar.gz has been checked and built
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 at 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