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"
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