I have been trying to install RMySQL on Windows 7 following the procedure at: http://biostat.mc.vanderbilt.edu/wiki/Main/RMySQL I think I have properly installed RTools and created a proper Renviron.site file saying: MYSQL_HOME="C:/Program Files/MySQL/MySQL Server 5.5" When I try to install the packages from source, I get warnings that suggest I'm still not quite "with the program" yet. There are comments about POSIX paths that I don't quite grasp. Can anyone give me additional hints? There seems to be a libmysql.dll in the /lib subdirectory although the install seems to be looking in the /bin directory for a file of similar name. Is this something that has changed with recent versions of MySQL that should be fixed in the RMySQL package or is it something I can work around by hand or by properly setting some environmental variable? Thanks, Rob The errors ... > install.packages('RMySQL',type='source') trying URL 'http://cran.wustl.edu/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 'RMySQL' ... ** package 'RMySQL' successfully unpacked and MD5 sums checked 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-215~1.1/etc/x64/Makeconf Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-215~1.1/etc/x64/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 -m64 -I"C:/PROGRA~1/R/R-215~1.1/include" -DNDEBUG -I"C:/Program Files/MySQL/MySQL Server 5.5"/include -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c RS-DBI.c -o RS-DBI.o RS-DBI.c: In function 'RS_na_set': RS-DBI.c:1219:11: warning: variable 'c' set but not used [-Wunused-but-set-variable] gcc -m64 -I"C:/PROGRA~1/R/R-215~1.1/include" -DNDEBUG -I"C:/Program Files/MySQL/MySQL Server 5.5"/include -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c RS-MySQL.c -o RS-MySQL.o RS-MySQL.c: In function 'RS_MySQL_fetch': RS-MySQL.c:657:13: warning: variable 'fld_nullOk' set but not used [-Wunused-but-set-variable] RS-MySQL.c: In function 'RS_DBI_invokeBeginGroup': RS-MySQL.c:1137:30: warning: variable 'val' set but not used [-Wunused-but-set-variable] RS-MySQL.c: In function 'RS_DBI_invokeNewRecord': RS-MySQL.c:1158:20: warning: variable 'val' set but not used [-Wunused-but-set-variable] RS-MySQL.c: In function 'RS_MySQL_dbApply': RS-MySQL.c:1219:38: warning: variable 'fld_nullOk' set but not used [-Wunused-but-set-variable] gcc -m64 -shared -s -static-libgcc -o RMySQL.dll tmp.def RS-DBI.o RS-MySQL.o C:/Program Files/MySQL/MySQL Server 5.5/bin/libmySQL.dll -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-215~1.1/bin/x64 -lR gcc.exe: error: C:/Program Files/MySQL/MySQL Server 5.5/bin/libmySQL.dll: No such file or directory ERROR: compilation failed for package 'RMySQL' * removing 'C:/Program Files/R/R-2.15.1/library/RMySQL' The downloaded source packages are in ?C:\Users\rbaer\AppData\Local\Temp\Rtmps9adPQ\downloaded_packages? Warning messages: 1: running command 'C:/PROGRA~1/R/R-215~1.1/bin/x64/R CMD INSTALL -l "C:/Program Files/R/R-2.15.1/library" C:\Users\rbaer\AppData\Local\Temp\Rtmps9adPQ/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 > R.Version() $platform [1] "x86_64-pc-mingw32" $arch [1] "x86_64" $os [1] "mingw32" $system [1] "x86_64, mingw32" $status [1] "" $major [1] "2" $minor [1] "15.1" $year [1] "2012" $month [1] "06" $day [1] "22" $`svn rev` [1] "59607" $language [1] "R" $version.string [1] "R version 2.15.1 (2012-06-22)" $nickname [1] "Roasted Marshmallows"
RMySQL install on windows
4 messages · Gabor Grothendieck, Greg Snow, Robert Baer
On Tue, Oct 9, 2012 at 5:08 PM, Robert Baer <rbaer at atsu.edu> wrote:
I have been trying to install RMySQL on Windows 7 following the procedure at: http://biostat.mc.vanderbilt.edu/wiki/Main/RMySQL I think I have properly installed RTools and created a proper Renviron.site file saying: MYSQL_HOME="C:/Program Files/MySQL/MySQL Server 5.5" When I try to install the packages from source, I get warnings that suggest I'm still not quite "with the program" yet. There are comments about POSIX paths that I don't quite grasp. Can anyone give me additional hints? There seems to be a libmysql.dll in the /lib subdirectory although the install seems to be looking in the /bin directory for a file of similar name. Is this something that has changed with recent versions of MySQL that should be fixed in the RMySQL package or is it something I can work around by hand or by properly setting some environmental variable? Thanks, Rob The errors ...
install.packages('RMySQL',type='source')
trying URL 'http://cran.wustl.edu/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 'RMySQL' ... ** package 'RMySQL' successfully unpacked and MD5 sums checked 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-215~1.1/etc/x64/Makeconf Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-215~1.1/etc/x64/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 -m64 -I"C:/PROGRA~1/R/R-215~1.1/include" -DNDEBUG -I"C:/Program Files/MySQL/MySQL Server 5.5"/include -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c RS-DBI.c -o RS-DBI.o RS-DBI.c: In function 'RS_na_set': RS-DBI.c:1219:11: warning: variable 'c' set but not used [-Wunused-but-set-variable] gcc -m64 -I"C:/PROGRA~1/R/R-215~1.1/include" -DNDEBUG -I"C:/Program Files/MySQL/MySQL Server 5.5"/include -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c RS-MySQL.c -o RS-MySQL.o RS-MySQL.c: In function 'RS_MySQL_fetch': RS-MySQL.c:657:13: warning: variable 'fld_nullOk' set but not used [-Wunused-but-set-variable] RS-MySQL.c: In function 'RS_DBI_invokeBeginGroup': RS-MySQL.c:1137:30: warning: variable 'val' set but not used [-Wunused-but-set-variable] RS-MySQL.c: In function 'RS_DBI_invokeNewRecord': RS-MySQL.c:1158:20: warning: variable 'val' set but not used [-Wunused-but-set-variable] RS-MySQL.c: In function 'RS_MySQL_dbApply': RS-MySQL.c:1219:38: warning: variable 'fld_nullOk' set but not used [-Wunused-but-set-variable] gcc -m64 -shared -s -static-libgcc -o RMySQL.dll tmp.def RS-DBI.o RS-MySQL.o C:/Program Files/MySQL/MySQL Server 5.5/bin/libmySQL.dll -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-215~1.1/bin/x64 -lR gcc.exe: error: C:/Program Files/MySQL/MySQL Server 5.5/bin/libmySQL.dll: No such file or directory ERROR: compilation failed for package 'RMySQL' * removing 'C:/Program Files/R/R-2.15.1/library/RMySQL' The downloaded source packages are in ?C:\Users\rbaer\AppData\Local\Temp\Rtmps9adPQ\downloaded_packages? Warning messages: 1: running command 'C:/PROGRA~1/R/R-215~1.1/bin/x64/R CMD INSTALL -l "C:/Program Files/R/R-2.15.1/library" C:\Users\rbaer\AppData\Local\Temp\Rtmps9adPQ/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
R.Version()
$platform [1] "x86_64-pc-mingw32" $arch [1] "x86_64" $os [1] "mingw32" $system [1] "x86_64, mingw32" $status [1] "" $major [1] "2" $minor [1] "15.1" $year [1] "2012" $month [1] "06" $day [1] "22" $`svn rev` [1] "59607" $language [1] "R" $version.string [1] "R version 2.15.1 (2012-06-22)" $nickname [1] "Roasted Marshmallows"
______________________________________________ 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.
Most people who have problems have them because they followed instructions on the internet rather than the ones that come with the package. Go to: http://cran.r-project.org/web/packages/RMySQL/index.html and click on the Installation link (or download the source and read the INSTALL file).
Statistics & Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com
I finally was able to compile/load it under windows 7. I had similar problems to what you show below. I set the MYSQL_HOME environmental variable through windows (start button > control panel > System and Security > system > Advanced System Settings > Environmental variables). I had to set it to the version of the path without spaces, in my case it was: c:\PROGRA~1\MySQL\MYSQLS~1.5 Then I opened a command prompt window, changed to the directory where I had downloaded the tar.gz file from cran and entered the command: "c:\Program Files\R\R-2.15.1\bin\x64\R" CMD INSTALL RMySQL_0.9-3.tar.gz and everything worked (it did not work if I used i386 or just the regular bin folder, possibly due to the version of MySQL I downloaded). Then I started a new instance of R and did library(MySQL) and everything loaded and I was able to connect to a local MySQL database. Hope this helps you as well.
On Tue, Oct 9, 2012 at 3:08 PM, Robert Baer <rbaer at atsu.edu> wrote:
I have been trying to install RMySQL on Windows 7 following the procedure at: http://biostat.mc.vanderbilt.edu/wiki/Main/RMySQL I think I have properly installed RTools and created a proper Renviron.site file saying: MYSQL_HOME="C:/Program Files/MySQL/MySQL Server 5.5" When I try to install the packages from source, I get warnings that suggest I'm still not quite "with the program" yet. There are comments about POSIX paths that I don't quite grasp. Can anyone give me additional hints? There seems to be a libmysql.dll in the /lib subdirectory although the install seems to be looking in the /bin directory for a file of similar name. Is this something that has changed with recent versions of MySQL that should be fixed in the RMySQL package or is it something I can work around by hand or by properly setting some environmental variable? Thanks, Rob The errors ...
install.packages('RMySQL',type='source')
trying URL 'http://cran.wustl.edu/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 'RMySQL' ... ** package 'RMySQL' successfully unpacked and MD5 sums checked 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-215~1.1/etc/x64/Makeconf Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-215~1.1/etc/x64/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 -m64 -I"C:/PROGRA~1/R/R-215~1.1/include" -DNDEBUG -I"C:/Program Files/MySQL/MySQL Server 5.5"/include -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c RS-DBI.c -o RS-DBI.o RS-DBI.c: In function 'RS_na_set': RS-DBI.c:1219:11: warning: variable 'c' set but not used [-Wunused-but-set-variable] gcc -m64 -I"C:/PROGRA~1/R/R-215~1.1/include" -DNDEBUG -I"C:/Program Files/MySQL/MySQL Server 5.5"/include -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c RS-MySQL.c -o RS-MySQL.o RS-MySQL.c: In function 'RS_MySQL_fetch': RS-MySQL.c:657:13: warning: variable 'fld_nullOk' set but not used [-Wunused-but-set-variable] RS-MySQL.c: In function 'RS_DBI_invokeBeginGroup': RS-MySQL.c:1137:30: warning: variable 'val' set but not used [-Wunused-but-set-variable] RS-MySQL.c: In function 'RS_DBI_invokeNewRecord': RS-MySQL.c:1158:20: warning: variable 'val' set but not used [-Wunused-but-set-variable] RS-MySQL.c: In function 'RS_MySQL_dbApply': RS-MySQL.c:1219:38: warning: variable 'fld_nullOk' set but not used [-Wunused-but-set-variable] gcc -m64 -shared -s -static-libgcc -o RMySQL.dll tmp.def RS-DBI.o RS-MySQL.o C:/Program Files/MySQL/MySQL Server 5.5/bin/libmySQL.dll -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-215~1.1/bin/x64 -lR gcc.exe: error: C:/Program Files/MySQL/MySQL Server 5.5/bin/libmySQL.dll: No such file or directory ERROR: compilation failed for package 'RMySQL' * removing 'C:/Program Files/R/R-2.15.1/library/RMySQL' The downloaded source packages are in ?C:\Users\rbaer\AppData\Local\Temp\Rtmps9adPQ\downloaded_packages? Warning messages: 1: running command 'C:/PROGRA~1/R/R-215~1.1/bin/x64/R CMD INSTALL -l "C:/Program Files/R/R-2.15.1/library" C:\Users\rbaer\AppData\Local\Temp\Rtmps9adPQ/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
R.Version()
$platform [1] "x86_64-pc-mingw32" $arch [1] "x86_64" $os [1] "mingw32" $system [1] "x86_64, mingw32" $status [1] "" $major [1] "2" $minor [1] "15.1" $year [1] "2012" $month [1] "06" $day [1] "22" $`svn rev` [1] "59607" $language [1] "R" $version.string [1] "R version 2.15.1 (2012-06-22)" $nickname [1] "Roasted Marshmallows"
______________________________________________ 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.
Gregory (Greg) L. Snow Ph.D. 538280 at gmail.com
2 days later
On 10/10/2012 12:58 PM, Greg Snow wrote:
I finally was able to compile/load it under windows 7. I had similar problems to what you show below. I set the MYSQL_HOME environmental variable through windows (start button > control panel > System and Security > system > Advanced System Settings > Environmental variables). I had to set it to the version of the path without spaces, in my case it was: c:\PROGRA~1\MySQL\MYSQLS~1.5 Then I opened a command prompt window, changed to the directory where I had downloaded the tar.gz file from cran and entered the command: "c:\Program Files\R\R-2.15.1\bin\x64\R" CMD INSTALL RMySQL_0.9-3.tar.gz and everything worked (it did not work if I used i386 or just the regular bin folder, possibly due to the version of MySQL I downloaded). Then I started a new instance of R and did library(MySQL) and everything loaded and I was able to connect to a local MySQL database. Hope this helps you as well.
Thanks, Greg. I got a couple of warnings during the build, but I can at least load the library. Now, I'll to to learn to use it<G> I had downloaded the 64-bit MySQL engine. The seemingly successful install was on R (64-bit). I guess not unexpectedly I get the from R (i386) > library(RMySQL) Error: package ?RMySQL? is not installed for 'arch=i386' Appreciate the guidance. Rob