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. ______________________________________________ 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.
