[R-SIG-Mac] RMySQL and MySQL 5.0

[Christopher Fonnesbeck]

On Jan 13, 2006, at 12:22 PM, Simon Urbanek wrote:

>
> On Jan 13, 2006, at 12:14 PM, Christopher Fonnesbeck wrote:
>
>> Has anyone managed to get RMySQL working with MySQL 5.0? I have  
>> successfully built and installed the module, but run into an error  
>> when loading:
>>
>> > library(RMySQL)
>> Loading required package: DBI
>> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>> 	unable to load shared library '/Library/Frameworks/R.framework/ 
>> Resources/library/RMySQL/libs/RMySQL.so':
>>   dlopen(/Library/Frameworks/R.framework/Resources/library/RMySQL/ 
>> libs/RMySQL.so, 6): Symbol not found: _fprintf$LDBLStub
>>   Referenced from: /Library/Frameworks/R.framework/Resources/ 
>> library/RMySQL/libs/RMySQL.so
>>   Expected in: flat namespace
>> Error in library(RMySQL) : .First.lib failed for 'RMySQL'
>>
>
> I didn't test MySQL, but AFAIR this problem is caused by compiler  
> mismatch (it started with Xcode 2.2 I believe). Did you run sudo  
> gcc_select 3.3 before compiling? The real reason for the above is  
> that you're missing -lSystemStubs (which is static) when compiling  
> RMySQL. Adding that to the LIBS for the package should work.

I can confirm now that I was using gcc 3.3, but there were some  
warnings. Here is the build log:

* Installing *source* package 'RMySQL' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for compress in -lz... yes
checking for getopt_long in -lc... yes
checking for mysql_init in -lmysqlclient... no
checking for mysql.h... no
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ 
include -I/usr/local/mysql/include -I/usr/local/include   -fno- 
common  -g -O2 -c RS-DBI.c -o RS-DBI.o
gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ 
include -I/usr/local/mysql/include -I/usr/local/include   -fno- 
common  -g -O2 -c RS-MySQL.c -o RS-MySQL.o
gcc-3.3 -bundle -flat_namespace -undefined suppress -L/usr/local/lib - 
o RMySQL.so RS-DBI.o RS-MySQL.o -L/usr/local/mysql/lib -lmysqlclient - 
lz -lcc_dynamic -F/Library/Frameworks/R.framework/.. -framework R
ld: warning multiple definitions of symbol _compress
/usr/lib/libz.dylib(compress.o) definition of _compress
/Library/Frameworks/R.framework/../R.framework/R(compress.lo)  
definition of _compress
ld: warning multiple definitions of symbol _compressBound
/usr/lib/libz.dylib(compress.o) definition of _compressBound
/Library/Frameworks/R.framework/../R.framework/R(compress.lo)  
definition of _compressBound
ld: warning multiple definitions of symbol _compress2
/usr/lib/libz.dylib(compress.o) definition of _compress2
/Library/Frameworks/R.framework/../R.framework/R(compress.lo)  
definition of _compress2
ld: warning multiple definitions of symbol _deflateEnd
/usr/lib/libz.dylib(deflate.o) definition of _deflateEnd
/Library/Frameworks/R.framework/../R.framework/R(deflate.lo)  
definition of _deflateEnd
ld: warning multiple definitions of symbol _deflate
/usr/lib/libz.dylib(deflate.o) definition of _deflate
/Library/Frameworks/R.framework/../R.framework/R(deflate.lo)  
definition of _deflate
ld: warning multiple definitions of symbol _deflateCopy
/usr/lib/libz.dylib(deflate.o) definition of _deflateCopy
/Library/Frameworks/R.framework/../R.framework/R(deflate.lo)  
definition of _deflateCopy
ld: warning multiple definitions of symbol _deflateParams
/usr/lib/libz.dylib(deflate.o) definition of _deflateParams
/Library/Frameworks/R.framework/../R.framework/R(deflate.lo)  
definition of _deflateParams
ld: warning multiple definitions of symbol _deflatePrime
/usr/lib/libz.dylib(deflate.o) definition of _deflatePrime
/Library/Frameworks/R.framework/../R.framework/R(deflate.lo)  
definition of _deflatePrime
ld: warning multiple definitions of symbol _deflateReset
/usr/lib/libz.dylib(deflate.o) definition of _deflateReset
/Library/Frameworks/R.framework/../R.framework/R(deflate.lo)  
definition of _deflateReset
ld: warning multiple definitions of symbol _deflateSetDictionary
/usr/lib/libz.dylib(deflate.o) definition of _deflateSetDictionary
/Library/Frameworks/R.framework/../R.framework/R(deflate.lo)  
definition of _deflateSetDictionary
ld: warning multiple definitions of symbol _deflateInit_
/usr/lib/libz.dylib(deflate.o) definition of _deflateInit_
/Library/Frameworks/R.framework/../R.framework/R(deflate.lo)  
definition of _deflateInit_
ld: warning multiple definitions of symbol _deflateInit2_
/usr/lib/libz.dylib(deflate.o) definition of _deflateInit2_
/Library/Frameworks/R.framework/../R.framework/R(deflate.lo)  
definition of _deflateInit2_
ld: warning multiple definitions of symbol _deflateBound
/usr/lib/libz.dylib(deflate.o) definition of _deflateBound
/Library/Frameworks/R.framework/../R.framework/R(deflate.lo)  
definition of _deflateBound
ld: warning multiple definitions of symbol _inflateSyncPoint
/usr/lib/libz.dylib(inflate.o) definition of _inflateSyncPoint
/Library/Frameworks/R.framework/../R.framework/R(inflate.lo)  
definition of _inflateSyncPoint
ld: warning multiple definitions of symbol _inflateReset
/usr/lib/libz.dylib(inflate.o) definition of _inflateReset
/Library/Frameworks/R.framework/../R.framework/R(inflate.lo)  
definition of _inflateReset
ld: warning multiple definitions of symbol _inflateCopy
/usr/lib/libz.dylib(inflate.o) definition of _inflateCopy
/Library/Frameworks/R.framework/../R.framework/R(inflate.lo)  
definition of _inflateCopy
ld: warning multiple definitions of symbol _inflate
/usr/lib/libz.dylib(inflate.o) definition of _inflate
/Library/Frameworks/R.framework/../R.framework/R(inflate.lo)  
definition of _inflate
ld: warning multiple definitions of symbol _inflateInit_
/usr/lib/libz.dylib(inflate.o) definition of _inflateInit_
/Library/Frameworks/R.framework/../R.framework/R(inflate.lo)  
definition of _inflateInit_
ld: warning multiple definitions of symbol _inflateSetDictionary
/usr/lib/libz.dylib(inflate.o) definition of _inflateSetDictionary
/Library/Frameworks/R.framework/../R.framework/R(inflate.lo)  
definition of _inflateSetDictionary
ld: warning multiple definitions of symbol _inflateSync
/usr/lib/libz.dylib(inflate.o) definition of _inflateSync
/Library/Frameworks/R.framework/../R.framework/R(inflate.lo)  
definition of _inflateSync
ld: warning multiple definitions of symbol _inflateInit2_
/usr/lib/libz.dylib(inflate.o) definition of _inflateInit2_
/Library/Frameworks/R.framework/../R.framework/R(inflate.lo)  
definition of _inflateInit2_
ld: warning multiple definitions of symbol _inflateEnd
/usr/lib/libz.dylib(inflate.o) definition of _inflateEnd
/Library/Frameworks/R.framework/../R.framework/R(inflate.lo)  
definition of _inflateEnd
ld: warning multiple definitions of symbol _uncompress
/usr/lib/libz.dylib(uncompr.o) definition of _uncompress
/Library/Frameworks/R.framework/../R.framework/R(uncompr.lo)  
definition of _uncompress
ld: warning multiple definitions of symbol _crc32
/Library/Frameworks/R.framework/../R.framework/R(crc32.lo) definition  
of _crc32
/usr/lib/libz.dylib(crc32.o) definition of _crc32
ld: warning multiple definitions of symbol _get_crc_table
/Library/Frameworks/R.framework/../R.framework/R(crc32.lo) definition  
of _get_crc_table
/usr/lib/libz.dylib(crc32.o) definition of _get_crc_table
ld: warning multiple definitions of symbol _adler32
/usr/lib/libz.dylib(adler32.o) definition of _adler32
/Library/Frameworks/R.framework/../R.framework/R(adler32.lo)  
definition of _adler32
ld: warning multiple definitions of symbol _zlibCompileFlags
/usr/lib/libz.dylib(zutil.o) definition of _zlibCompileFlags
/Library/Frameworks/R.framework/../R.framework/R(zutil.lo) definition  
of _zlibCompileFlags
ld: warning multiple definitions of symbol _zError
/usr/lib/libz.dylib(zutil.o) definition of _zError
/Library/Frameworks/R.framework/../R.framework/R(zutil.lo) definition  
of _zError
ld: warning multiple definitions of symbol _zlibVersion
/usr/lib/libz.dylib(zutil.o) definition of _zlibVersion
/Library/Frameworks/R.framework/../R.framework/R(zutil.lo) definition  
of _zlibVersion
ld: warning multiple definitions of symbol _signgam
/Library/Frameworks/R.framework/../R.framework/R(lgamma.lo)  
definition of _signgam
/usr/lib/libSystem.dylib(gamma9.o) definition of _signgam



--
Christopher J. Fonnesbeck

Population Ecologist, Marine Mammal Section
Fish & Wildlife Research Institute (FWC)
St. Petersburg, FL

Adjunct Assistant Professor
Warnell School of Forest Resources
University of Georgia
Athens, GA

T: 727.235.5570
E: chris at trichech.us


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