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
--
View this message in context:
http://r.789695.n4.nabble.com/RMySQL-problem-on-Windows-7-32-bit-tp3520472p3520472.html
Sent from the R help mailing list archive at Nabble.com.
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
