[R] RMySQL problem on Windows 7 32 bit

[Uwe Ligges]

On 13.05.2011 17:06, byzin wrote:
> I am attempting to analyze Affymetrix exonchip data using the exon map
> package.  I have installed this package but have had problems installing the
> associated programs, specifically RMySQL since no windows binary exists.
>
> I have followed the directions for compiling the package as found on -
> http://biostat.mc.vanderbilt.edu/wiki/Main/RMySQL - but still have an error
> when executing the install.package command.
>
> RTools, and MSQL 5.5 have been installed on my computer. Path environment
> altered to include RTools and R, verified to be working.
>
> Thanks in advance,
>
> Mike
>
> o ‘C:\Users\Mike\Documents/R/win-library/2.12’
> (as ‘lib’ is unspecified)
> trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/RMySQL_0.7-5.tar.gz'
> Content type 'application/x-gzip' length 160769 bytes (157 Kb)
> opened URL
> downloaded 157 Kb
>
> * installing *source* package 'RMySQL' ...
> checking for $MYSQL_HOME... C:/Program Files/MySQL/MySQL Server 5.5
> cygwin warning:
>    MS-DOS style path detected: C:/Program
>    Preferred POSIX equivalent is: /cygdrive/c/Program
>    CYGWIN environment variable option "nodosfilewarning" turns off this
> warning.
>    Consult the user's guide for more details about POSIX paths:
>      http://cygwin.com/cygwin-ug-net/using.html#using-pathnames

I think yoiu should do the above to make your output more readable (omit 
those cygwin warnings).


> test: Files/MySQL/MySQL: unknown operand

Do you have a space in your pathname. Maybe it is sufficient to quote it 
appropriately when setting the environment variables?

Uwe Ligges


> ** libs
> Warning: this package has a non-empty 'configure.win' file,
> so building only the main architecture
>
> cygwin warning:
>    MS-DOS style path detected: C:/PROGRA~1/R/R-212~1.1/etc/i386/Makeconf
>    Preferred POSIX equivalent is:
> /cygdrive/c/PROGRA~1/R/R-212~1.1/etc/i386/Makeconf
>    CYGWIN environment variable option "nodosfilewarning" turns off this
> warning.
>    Consult the user's guide for more details about POSIX paths:
>      http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
> gcc -I"C:/PROGRA~1/R/R-212~1.1/include" -I"C:/Program Files/MySQL/MySQL
> Server 5.5"/include        -O3 -Wall  -std=gnu99 -c RS-DBI.c -o RS-DBI.o
> gcc -I"C:/PROGRA~1/R/R-212~1.1/include" -I"C:/Program Files/MySQL/MySQL
> Server 5.5"/include        -O3 -Wall  -std=gnu99 -c RS-MySQL.c -o RS-MySQL.o
> gcc -shared -s -static-libgcc -o RMySQL.dll tmp.def RS-DBI.o RS-MySQL.o
> C:/Program Files/MySQL/MySQL Server 5.5/lib/opt/libmysql.lib
> -LC:/PROGRA~1/R/R-212~1.1/bin/i386 -lR
> gcc.exe: C:/Program Files/MySQL/MySQL Server 5.5/lib/opt/libmysql.lib: No
> such file or directory
> ERROR: compilation failed for package 'RMySQL'
> * removing 'C:/Users/Mike/Documents/R/win-library/2.12/RMySQL'
> * restoring previous 'C:/Users/Mike /Documents/R/win-library/2.12/RMySQL'
>
> The downloaded packages are in
>          ‘C:\Users\Mike \AppData\Local\Temp\Rtmp56pouO\downloaded_packages’
> Warning messages:
> 1: running command 'C:\PROGRA~1\R\R-212~1.1/bin/i386/R CMD INSTALL -l
> "C:\Users\Mike \Documents/R/win-library/2.12"
> C:\Users\MIKEBY~1\AppData\Local\Temp\Rtmp56pouO/downloaded_packages/RMySQL_0.7-5.tar.gz'
> had status 1
> 2: In install.packages("RMySQL", type = "source") :
>    installation of package 'RMySQL' had non-zero exit status
>> sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.12.1
>>
>
>
>
>
> --
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>
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