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
test: Files/MySQL/MySQL: unknown operand
** 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.
It looks like your MySQL is missing the libmysql.lib file. Download it from MySQL then put it in the following location: C:/Program Files/MySQL/MySQL Server 5.5/lib/opt/libmysql.lib If you are still having problems, you could try using RODBC instead.
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-pathnamesI think yoiu should do the above to make your output more readable (omit those cygwin warnings).> test: Files/MySQL/MySQL: unknown operandDo 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 at 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.
On Fri, May 13, 2011 at 11:06 AM, byzin <mbyzon at gmail.com> 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. >1. Be sure to read the INSTALL file in the RMySQL*.tar.gz in the inst directory. 2. You may not have installed mysql completely. Be sure to install it from the mysql site. Distributions such as xampp won't work out of the box. 3. After installing mysql, download Rcmd.bat from the batchfiles distribution here: http://batchfiles.googlecode.com/svn/trunk/Rcmd.bat and run this (replacing whatever): Rcmd.bat INSTALL RMySQL.whatever.tar.gz If you have put MySQL in the standard place then Rcmd.bat will temporarily set MYSQL_HOME. It will also temporarily add rtools to the path, turn off cygwin warnings and do a number of other things for you so that basically the one line above is all you need to do (after installing r, rtools, miktex and mysql). Also, Rgui.bat (same file - just rename Rcmd.bat to Rgui.bat) will start up R with those defined. -- Statistics & Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com