Thread: Connecting R to PostgreSQL
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.
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
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.
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