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getting started with R and mysql

Michael Friendly 
I have a mysql database I installed on my Ubuntu server, and I'm trying 
to figure out how to access and analyze it
from a Win XP machine running R 2.15.1.

I thought that RMySQL was the way to go. (Is there an easier way?) I 
tried to follow the instructions at
http://www.r-bloggers.com/installing-the-rmysql-package-on-windows-7/
so I installed mysql-installer-community-5.5.27.0.msi, then set the 
environment variable MYSQL_HOME,
and tried to install RMySQL within R. It failed, as shown below, but I 
can't see what is wrong.
What's missing? If I only want to read tables from the database and work 
on them in R, is there an
easier package?

 > Sys.getenv("MYSQL_HOME")
[1] "C:\\Program Files\\MySQL\\MySQL Server 5.5"
 > install.packages('RMySQL',type='source')
also installing the dependency ?DBI?

trying URL 'http://probability.ca/cran/src/contrib/DBI_0.2-5.tar.gz'
Content type 'application/x-gzip' length 308395 bytes (301 Kb)
opened URL
downloaded 301 Kb

trying URL 'http://probability.ca/cran/src/contrib/RMySQL_0.9-3.tar.gz'
Content type 'application/x-gzip' length 165363 bytes (161 Kb)
opened URL
downloaded 161 Kb

* installing *source* package 'DBI' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'summary' from package 'base' in package 
'DBI'
** help
*** installing help indices
** building package indices
** installing vignettes
'DBI.Rnw'
** testing if installed package can be loaded

* DONE (DBI)
* installing *source* package 'RMySQL' ...
** package 'RMySQL' successfully unpacked and MD5 sums checked
checking for $MYSQL_HOME... C:\Program Files\MySQL\MySQL Server 5.5
test: Files\MySQL\MySQL: unknown operand
** libs
Warning: this package has a non-empty 'configure.win' file,
so building only the main architecture

gcc -I"C:/R/R-215~1.1/include" -DNDEBUG -I"C:\Program Files\MySQL\MySQL 
Server 5.5"/include -O3 -Wall -std=gnu99 -mtune=core2 -c RS-DBI.c -o 
RS-DBI.o
RS-DBI.c:1: error: bad value (core2) for -mtune= switch
make: *** [RS-DBI.o] Error 1
ERROR: compilation failed for package 'RMySQL'
* removing 'C:/R/R-2.15.1/library/RMySQL'

The downloaded source packages are in
?C:\Documents and Settings\friendly\Local 
Settings\Temp\RtmpCU2QBs\downloaded_packages?
Warning messages:
1: running command 'C:/R/R-2.15.1/bin/i386/R CMD INSTALL -l 
"C:/R/R-2.15.1/library" 
C:\DOCUME~1\friendly\LOCALS~1\Temp\RtmpCU2QBs/downloaded_packages/RMySQL_0.9-3.tar.gz' 
had status 1
2: In install.packages("RMySQL", type = "source") :
installation of package ?RMySQL? had non-zero exit status
 >

Thread (3 messages)

Michael Friendly getting started with R and mysql Aug 8 Curt Seeliger getting started with R and mysql Aug 8 Brian Ripley getting started with R and mysql Aug 8