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.soExpected 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 ** libsgcc-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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