[BioC] Error loading package RdbiPgSQL / R2.12.1/ Mac OS X 10.6.6

[Martin Morgan]

On 02/24/2011 05:20 AM, Dan Tenenbaum wrote:
> On Thu, Feb 24, 2011 at 1:58 AM, Aszodi,Andras <Andras.Aszodi at imp.ac.at>wrote:
> 
>>
>> On Feb 23, 2011, at 8:09 PM, Dan Tenenbaum wrote:
>>
>>
>>
>> On Wed, Feb 23, 2011 at 3:07 AM, Aszodi,Andras <Andras.Aszodi at imp.ac.at>wrote:
>>
>>> Dear Mailing List,
>>>
>>> When I say:-
>>>
>>>> library("RdbiPgSQL")

wanted to mention RPostgreSQL on CRAN as an alternative. Martin

>>>
>>> ...then I get the following errors:-
>>>
>>> Loading required package: Rdbi
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>  unable to load shared object
>>>
>>> '/Library/Frameworks/R.framework/Versions/2.12/Resources/library/RdbiPgSQL/libs/x86_64/RdbiPgSQL.so':
>>>
>>>
>>> dlopen(/Library/Frameworks/R.framework/Versions/2.12/Resources/library/RdbiPgSQL/libs/x86_64/RdbiPgSQL.so,
>>> 6): Symbol not found: _PQbackendPID
>>>  Referenced from:
>>>
>>> /Library/Frameworks/R.framework/Versions/2.12/Resources/library/RdbiPgSQL/libs/x86_64/RdbiPgSQL.so
>>>  Expected in: dynamic lookup
>>>
>>> Error: package/namespace load failed for 'RdbiPgSQL'
>>>
>>> I use only binary packages for R and R itself was installed as binary. But
>>> I
>>> must admit my Postgres installation (8.4.7) was compiled from source and
>>> placed
>>> into a "nonstandard" location /usr/local/pgsql/current . But the problem
>>> persists even if I put the library path /usr/local/pgsql/current/lib in
>>> the
>>> DYLD_LIBRARY_PATH variable. This happens on a Mac Pro (64-bit Intel), with
>>> OS X
>>> 10.6.6. I would be grateful for any fixes or workaround advice. Thank you
>>> very
>>> much!
>>>
>>> PS I first sent this to the R bug tracking system but Professor Ripley
>>> advised me to submit it to Bioconductor since RdbiPgSQL is a BioC
>>> contributed package. I hope this is now the right place...
>>>
>>>
>> Hi, you don't include the output of sessionInfo(),
>>
>>
>> Sorry, my bad. Here it is. I wonder if this helps though...
>>
>>> sessionInfo()
>> R version 2.12.1 (2010-12-16)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] Rdbi_1.24.0
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.12.1
>>
>> nor explain how you installed RdbiPgSQL in the first place
>>
>>
>> I said "I use only binary packages for R", see above. So RdbiPgSQL was
>> installed with bioClite as usual. Definitely not from source.
>>
>> and whether there were any errors.
>>
>>
>> No, there were no errors.
>>
>>
>> You might try building RdbiPgSQL from source:
>>
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("RdbiPgSQL",type="source")
>>
>> This will give you some informative messages about how to tell the build
>> process about your PostgreSQL installation.
>>
>>
>> This is a good suggestion. What bothers me though that even if I specify
>> LD_LIBRARY_PATH or DYLD_LIBRARY_PATH it won't help. Are the shared library
>> locations somehow hard-coded in the pre-build packages?
>>
>> Yes.
> 
> 
>>
>> The pre-built version expects PostgreSQL to be in a standard location.
>>
>>
>> That might be the problem. However, for Postgres there is no unequivocal
>> "standard location" under OS X. Some people put it in /usr/local,
>> Linux-style. There are pre-built versions that put the whole thing under
>> /Library, MacPorts uses /opt I believe... it is a mess. My reason for the
>> not-quite-standard location is that I plan to run 8.4 and 9.0 as well.
>>
>>
> See here for how it is built on our Mac build system:
> http://bioconductor.org/checkResults/release/bioc-LATEST/RdbiPgSQL/pelham-checksrc.html
> Note the occurrences of /usr/local/include and /usr/local/lib.
> 
>  When I add the 'type="source"' flag to biocLite("RdbiPgSQL"), I see the
> following;
> 
> I could not find your PostgreSQL client libraries!
> Use --with-pgsql-libraries=PATH; if running R's INSTALL,
> use --configure-args='--with-pgsql-libraries=PATH'; or
> set PG_LIB_DIR in your environment to the library path,
> and rerun the configure/install.
> 
> Passing these arguments by adding them to configure.args in your call to
> biocLite(), and/or setting environment variables as described, should
> probably build the package successfully for you.
> 
>> Dan
>>
>> Many thanks for your prompt reply and for your suggestions!
>> András
>>
>> Dan
> 
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> 
> 
> 
> 
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