[R] RMySQL install

[Peter Dalgaard]

Michaell Taylor <Michaell.Taylor at boxwoodmeans.com> writes:

> I am having trouble installing RMySQL on a clean install of Fedora Core 4 64 
> bit on a dual dual core machine (that is, two dual core processors).  Seems 
> like the LD_LIBRARY_PATH is incorrect, but I don't seem to have it quite 
> right yet. 
> 
> There are a few mentions of this problem in google, but thus far none of the 
> "fixes" and fixed my problem.  I've tried defining the LD_LIBRARY_PATH 
> environment variable, and setting the PKG_CPPFLAGS, and  PKG_LIBS environment 
> variables as well.  No luck so far.
> 
> (initially would not compile, but specification of the PKG_CPPFLAGS, and  
> PKG_LIBS got the compile to complete without errors).  I still cannot load 
> the library.  My error message is:
> 
> > library(RMySQL)
> Loading required package: DBI
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>         unable to load shared library 
> '/usr/lib64/R/library/RMySQL/libs/RMySQL.so':
>   /usr/lib64/R/library/RMySQL/libs/RMySQL.so: undefined symbol: 
> mysql_field_count

Hmm. You seem to have pressed most of the buttons that I'd try.


If it keeps acting up, the RODBC package seems to install nicely on
FC4, once you have installed unixODBC and -devel.

> Error in library(RMySQL) : .First.lib failed for 'RMySQL'
> >
> 
> Trying to install the newest RMySQL on the newest R.
> 
> > version
>          _
> platform x86_64-redhat-linux-gnu
> arch     x86_64
> os       linux-gnu
> system   x86_64, linux-gnu
> status
> major    2
> minor    2.1
> year     2005
> month    12
> day      20
> svn rev  36812
> language R
> 
> *********************
> I find libmysqlclient.so in the following location(s).
> 
> [root at BX mtaylor]# locate libmysqlclient.so
> /usr/lib/mysql/libmysqlclient.so.14.0.0
> /usr/lib/mysql/libmysqlclient.so.14
> /usr/lib64/mysql/libmysqlclient.so.10.0.0
> /usr/lib64/mysql/libmysqlclient.so.10
> /usr/lib64/mysql/libmysqlclient.so.14.0.0
> /usr/lib64/mysql/libmysqlclient.so.14
> /usr/lib64/mysql/libmysqlclient.so
> /usr/lib64/mysql3/mysql/libmysqlclient.so.10.0.0
> /usr/lib64/mysql3/mysql/libmysqlclient.so.10
> /usr/lib64/mysql3/mysql/libmysqlclient.so
> 
> **********************
> 
> I set the LD_LIBRARY_PATH according to these results, then double checked that 
> it was set.  (I also set it to /usr/lib64/mysql3/mysql as another iteration)
> 
> [root at BX mtaylor]# printenv LD_LIBRARY_PATH
> /usr/lib64/mysql3/
> 
> Just to be sure...
> 
> [root at BX mtaylor]# printenv PKG_CPPFLAGS
> -I/usr/include/mysql
> 
> [root at BX mtaylor]# printenv PKG_LIBS
> -L/usr/lib64/mysql
> 
> (also tried PKG_LIBS=-L/usr/lib64/mysql3/mysql and PKG_LIBS=-L/usr/lib/mysql)
> 
> I recompiled the package each time with R CMD INSTALL RMySQL_0.5-7.tar.gz, but 
> I always get the same error message.  
> 
> ******************
> appears to install ....
> 
> [root at BX mtaylor]# R CMD INSTALL RMySQL_0.5-7.tar.gz
> * 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 -I/usr/lib64/R/include -I/usr/include/mysql -I/usr/local/include   -fPIC  
> -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m64 -mtune=nocona -c 
> RS-DBI.c -o RS-DBI.o
> gcc -I/usr/lib64/R/include -I/usr/include/mysql -I/usr/local/include   -fPIC  
> -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m64 -mtune=nocona -c 
> RS-MySQL.c -o RS-MySQL.o
> gcc -shared -L/usr/local/lib64 -o RMySQL.so RS-DBI.o RS-MySQL.o 
> -L/usr/lib/mysql -lz  -L/usr/lib64/R/lib -lR
> ** R
> ** inst
> ** save image
> .
> snip
> .
> ** building package indices ...
> * DONE (RMySQL)
> 
> 
> [root at BX mtaylor]# /sbin/ldconfig -v | grep mysql
> /usr/lib/mysql:
>         libmysqlclient.so.14 -> libmysqlclient.so.14.0.0
>         libmysqlclient_r.so.14 -> libmysqlclient_r.so.14.0.0
> /usr/lib64/mysql:
>         libmysqlclient_r.so.10 -> libmysqlclient_r.so.10.0.0
>         libmysqlclient.so.14 -> libmysqlclient.so.14.0.0
>         libmysqlclient_r.so.14 -> libmysqlclient_r.so.14.0.0
>         libmysqlclient.so.10 -> libmysqlclient.so.10.0.0
> 
> just to make sure the headers are actually in the specified location...
> 
> [root at BX mtaylor]# ls /usr/include/mysql
> chardefs.h  m_ctype.h    my_dir.h     my_no_pthread.h  mysql_embed.h    
> my_xml.h     rlshell.h      sslopt-longopts.h
> errmsg.h    m_string.h   my_getopt.h  my_pthread.h     mysql.h          raid.h       
> rltypedefs.h   sslopt-vars.h
> history.h   my_alloc.h   my_global.h  my_semaphore.h   mysql_time.h     
> readline.h   sql_common.h   tilde.h
> keycache.h  my_config.h  my_list.h    mysql_com.h      mysql_version.h  
> rlmbutil.h   sql_state.h    typelib.h
> keymaps.h   my_dbug.h    my_net.h     mysqld_error.h   my_sys.h         
> rlprivate.h  sslopt-case.h  xmalloc.h
> 
> 
> There is a dial in here somewhere that I think I am turning the wrong 
> direction - just can't see it.  Any experience with this one?
> 
> 
> -- 
> =======================================
> Michaell Taylor, PhD.
> Principal
> Boxwood Means, Inc.
> 203.653.4100
> 
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> 

-- 
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907