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$LDBLStub Referenced from: /Library/Frameworks/R.framework/Resources/library/ RMySQL/libs/RMySQL.so Expected in: flat namespace Error in library(RMySQL) : .First.lib failed for 'RMySQL' -- Christopher J. Fonnesbeck Population Ecologist, Marine Mammal Section Fish & Wildlife Research Institute (FWC) St. Petersburg, FL Adjunct Assistant Professor Warnell School of Forest Resources University of Georgia Athens, GA T: 727.235.5570 E: chris at trichech.us -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 2417 bytes Desc: not available Url : https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20060113/d9a1c78b/smime.bin
RMySQL and MySQL 5.0
4 messages · Christopher Fonnesbeck, Simon Urbanek
On Jan 13, 2006, at 12:14 PM, Christopher Fonnesbeck wrote:
Has anyone managed to get RMySQL working with MySQL 5.0? I have successfully built and installed the module, but run into an error when loading:
library(RMySQL)
Loading required package: DBI Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/Library/Frameworks/R.framework/ Resources/library/RMySQL/libs/RMySQL.so': dlopen(/Library/Frameworks/R.framework/Resources/library/RMySQL/ libs/RMySQL.so, 6): Symbol not found: _fprintf$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. Cheers, Simon
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 -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 2417 bytes Desc: not available Url : https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20060113/7c18788e/smime.bin
1 day later
On Jan 13, 2006, at 12:30 PM, Christopher Fonnesbeck wrote:
On Jan 13, 2006, at 12:22 PM, Simon Urbanek wrote:
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:
I'm sorry that I probably didn't make myself clear - as I was trying to say the problem is (and your build log confirms it) that you have Xcode 2.2 and you didn't add -lSystemStubs. You need to do so, because R was configured with a different compiler. I just checked and the following worked for me with the latest MySQL (5.0.18) and latest Xcode (2.2.1): PKG_CPPFLAGS=-I/usr/local/mysql/include PKG_LIBS='-L/usr/local/mysql/ lib -lmysqlclient -lSystemStubs' R CMD INSTALL RMySQL Cheers, Simon