pg.ddx.io pgsql-interfaces@postgresql.org mailing list archive
help / color / mirror / Atom feedConnecting R to PostgreSQL
4+ messages / 3 participants
[nested] [flat]
* Connecting R to PostgreSQL
@ 2002-09-14 14:29 Adam Witney <awitney@sghms.ac.uk>
0 siblings, 2 replies; 4+ messages in thread
From: Adam Witney @ 2002-09-14 14:29 UTC (permalink / raw)
To: pgsql-interfaces
Hi,
I am not sure if the problem here relates to PostgreSQL or elsewhere, but I
am trying to connect the R statistical package to my PostgreSQL database
using the Rdbi.PgSQL driver.
The driver installs ok, however when I try to load it in R I get the
following error
> library(Rdbi.PgSQL)
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library "/Users/adam/Projects/R
stuff/rlibs/Rdbi.PgSQL/libs/Rdbi.PgSQL.so":
dlcompat: dyld: /sw/lib/R/bin/R.bin Undefined symbols:
_ERR_get_error
_ERR_reason_error_string
_SSL_CTX_new
_SSL_connect
_SSL_free
_SSL_library_init
_SSL_load_error_strings
_SSL_new
_SSL_read
_SSL_set_fd
_SSL_write
_SSLv23_method
Error in library(Rdbi.PgSQL) : .First.lib failed
Looking through the source code the driver includes <libpq-fe.h> which
subsequently includes openssl/ssl.h
I don't know if this is where the problem lies?
My system is Mac OSX 10.2
Any ideas or pointers to further information would be greatly appreciated.
Thanks
Adam
--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.
^ permalink raw reply [nested|flat] 4+ messages in thread
* Re: Connecting R to PostgreSQL
@ 2002-09-14 18:30 Tom Lane <tgl@sss.pgh.pa.us>
parent: Adam Witney <awitney@sghms.ac.uk>
1 sibling, 1 reply; 4+ messages in thread
From: Tom Lane @ 2002-09-14 18:30 UTC (permalink / raw)
To: Adam Witney <awitney@sghms.ac.uk>; +Cc: pgsql-interfaces
Adam Witney <awitney@sghms.ac.uk> writes:
> The driver installs ok, however when I try to load it in R I get the
> following error
>> library(Rdbi.PgSQL)
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
> unable to load shared library "/Users/adam/Projects/R
> stuff/rlibs/Rdbi.PgSQL/libs/Rdbi.PgSQL.so":
> dlcompat: dyld: /sw/lib/R/bin/R.bin Undefined symbols:
> _ERR_get_error
> _ERR_reason_error_string
> _SSL_CTX_new
> _SSL_connect
> _SSL_free
> _SSL_library_init
It looks like the dynamic loader is failing to find the SSL library
(libssl.so), which is required by your PG client library. I don't know
enough about OSX to know how library searching is handled, but on other
Unixen you'd need to mess with ldconfig or LD_LIBRARY_PATH ... or
perhaps easier, put libssl.so into a more standard location than
wherever it is now.
Alternatively, you could rebuild PG omitting SSL support.
regards, tom lane
^ permalink raw reply [nested|flat] 4+ messages in thread
* Re: Connecting R to PostgreSQL
@ 2002-09-14 23:36 Steven O'Toole <lists@o2l.com>
parent: Adam Witney <awitney@sghms.ac.uk>
1 sibling, 0 replies; 4+ messages in thread
From: Steven O'Toole @ 2002-09-14 23:36 UTC (permalink / raw)
To: Adam Witney <awitney@sghms.ac.uk>; +Cc: pgsql-interfaces
On Saturday, September 14, 2002, at 07:29 AM, Adam Witney wrote:
> dlcompat: dyld: /sw/lib/R/bin/R.bin Undefined symbols:
> _ERR_get_error
> _ERR_reason_error_string
> _SSL_CTX_new
I don't know if this is helpful to you since I am a novice and don't
know R. But I am connecting to libpq on OSX and ran into similar
errors. I solved them (assuming you're using ProjectBuilder in 10.2)
in the Target/Linker Settings area. Under the field titled Other Mach
-O Linker Flags I entered:
-lcrypto -lssl
I still get a warning about a duplicate definition of _crypto that I
haven't figured out. But the interface to PostgreSQL works great.
^ permalink raw reply [nested|flat] 4+ messages in thread
* Re: Connecting R to PostgreSQL
@ 2002-09-20 13:18 Adam Witney <awitney@sghms.ac.uk>
parent: Tom Lane <tgl@sss.pgh.pa.us>
0 siblings, 0 replies; 4+ messages in thread
From: Adam Witney @ 2002-09-20 13:18 UTC (permalink / raw)
To: Tom Lane <tgl@sss.pgh.pa.us>; Adam Witney <awitney@sghms.ac.uk>; +Cc: pgsql-interfaces
On 14/9/02 7:30 pm, "Tom Lane" <tgl@sss.pgh.pa.us> wrote:
> Adam Witney <awitney@sghms.ac.uk> writes:
>> The driver installs ok, however when I try to load it in R I get the
>> following error
>
>>> library(Rdbi.PgSQL)
>> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>> unable to load shared library "/Users/adam/Projects/R
>> stuff/rlibs/Rdbi.PgSQL/libs/Rdbi.PgSQL.so":
>> dlcompat: dyld: /sw/lib/R/bin/R.bin Undefined symbols:
>> _ERR_get_error
>> _ERR_reason_error_string
>> _SSL_CTX_new
>> _SSL_connect
>> _SSL_free
>> _SSL_library_init
>
> It looks like the dynamic loader is failing to find the SSL library
> (libssl.so), which is required by your PG client library. I don't know
> enough about OSX to know how library searching is handled, but on other
> Unixen you'd need to mess with ldconfig or LD_LIBRARY_PATH ... or
> perhaps easier, put libssl.so into a more standard location than
> wherever it is now.
>
> Alternatively, you could rebuild PG omitting SSL support.
Hmm, I downloaded the non ssl version of postgresql from fink. Again fink
does all the compiling so I am not sure how it did it. Is there a way of
testing for sure if the ssl was or not compiled in?
Thanks
adam
^ permalink raw reply [nested|flat] 4+ messages in thread
end of thread, other threads:[~2002-09-20 13:18 UTC | newest]
Thread overview: 4+ messages (download: mbox mbox.gz follow: Atom feed)
-- links below jump to the message on this page --
2002-09-14 14:29 Connecting R to PostgreSQL Adam Witney <awitney@sghms.ac.uk>
2002-09-14 18:30 ` Tom Lane <tgl@sss.pgh.pa.us>
2002-09-20 13:18 ` Adam Witney <awitney@sghms.ac.uk>
2002-09-14 23:36 ` Steven O'Toole <lists@o2l.com>
This inbox is served by DDX for PostgreSQL; see mirroring instructions
for how to clone and mirror all data and code used for this inbox