[Rd] R Tools & Vista_x64: Problem compiling RMySQL?
Hello: What do I need to do to compile R packages (especially RMySQL) for the 64-bit version of R 2.12.0 under Vista_x64? I upgraded to "Rtools212.exe" yesterday but immediately got errors from "R CMD check RMySQL_0.7-5.tar.gz". After the first error, I installed it a second time, then got "undefined reference to" roughly 50 different names beginning "mysql_"; copied below. I see two possible sources for this problem: (1) RTools212 may not be installed properly. (2) RMySQL may be incompatible with R x64 2.12.0, especially with a 32-bit version of MySQL. NOTE: RMySQL worked with R2.11.1 (and MySQL 5.1.50-community server) before I installed R2.12.0. I'm reasonably sure that my local installation of MySQL is only 32-bit. What do you suggest? I use the 32-bit version of R2.12.0? Thanks, Spencer # * installing *source* package 'RMySQL' ... checking for $MYSQL_HOME... C:/PROGRA~2/MySQL/MYSQLS~1.1/ cygwin warning: MS-DOS style path detected: C:/PROGRA~2/MySQL/MYSQLS~1.1/ Preferred POSIX equivalent is: /cygdrive/c/PROGRA~2/MySQL/MYSQLS~1.1/ 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 ** 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:/Users/sgraves/R/R-212~1.0/etc/x64/Makeconf Preferred POSIX equivalent is: /cygdrive/c/Users/sgraves/R/R-212~1.0/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 x86_64-w64-mingw32-gcc -I"C:/Users/sgraves/R/R-212~1.0/include" -I"C:/PROGRA~2/MySQL/MYSQLS~1.1/"/include-O2 -Wall -std=gnu99 -c RS-DBI.c -o RS-DBI.o x86_64-w64-mingw32-gcc -I"C:/Users/sgraves/R/R-212~1.0/include" -I"C:/PROGRA~2/MySQL/MYSQLS~1.1/"/include-O2 -Wall -std=gnu99 -c RS-MySQL.c -o RS-MySQL.o x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o RMySQL.dll tmp.def RS-DBI.o RS-MySQL.o C:/PROGRA~2/MySQL/MYSQLS~1.1//bin/libmySQL.dll -LC:/Users/sgraves/R/R-212~1.0/bin/x64 -lR RS-MySQL.o:RS-MySQL.c:(.text+0xb0): undefined reference to `mysql_more_results' RS-MySQL.o:RS-MySQL.c:(.text+0x2c6): undefined reference to `mysql_init' RS-MySQL.o:RS-MySQL.c:(.text+0x2d9): undefined reference to `mysql_options' RS-MySQL.o:RS-MySQL.c:(.text+0x2ef): undefined reference to `mysql_options' RS-MySQL.o:RS-MySQL.c:(.text+0x305): undefined reference to `mysql_options' RS-MySQL.o:RS-MySQL.c:(.text+0x338): undefined reference to `mysql_real_connect' RS-MySQL.o:RS-MySQL.c:(.text+0x399): undefined reference to `mysql_close' RS-MySQL.o:RS-MySQL.c:(.text+0x3d1): undefined reference to `mysql_error' RS-MySQL.o:RS-MySQL.c:(.text+0x7a2): undefined reference to `mysql_close' RS-MySQL.o:RS-MySQL.c:(.text+0x80f): undefined reference to `mysql_fetch_fields' RS-MySQL.o:RS-MySQL.c:(.text+0x823): undefined reference to `mysql_field_count' RS-MySQL.o:RS-MySQL.c:(.text+0xae7): undefined reference to `mysql_next_result' RS-MySQL.o:RS-MySQL.c:(.text+0xb0b): undefined reference to `mysql_use_result' RS-MySQL.o:RS-MySQL.c:(.text+0xb16): undefined reference to `mysql_field_count' RS-MySQL.o:RS-MySQL.c:(.text+0xbff): undefined reference to `mysql_affected_rows' RS-MySQL.o:RS-MySQL.c:(.text+0xd27): undefined reference to `mysql_fetch_row' RS-MySQL.o:RS-MySQL.c:(.text+0xd3d): undefined reference to `mysql_fetch_lengths' RS-MySQL.o:RS-MySQL.c:(.text+0xf2e): undefined reference to `mysql_errno' RS-MySQL.o:RS-MySQL.c:(.text+0x1093): undefined reference to `mysql_errno' RS-MySQL.o:RS-MySQL.c:(.text+0x109e): undefined reference to `mysql_error' RS-MySQL.o:RS-MySQL.c:(.text+0x1114): undefined reference to `mysql_fetch_row' RS-MySQL.o:RS-MySQL.c:(.text+0x1121): undefined reference to `mysql_free_result' RS-MySQL.o:RS-MySQL.c:(.text+0x11f0): undefined reference to `mysql_query' RS-MySQL.o:RS-MySQL.c:(.text+0x1200): undefined reference to `mysql_use_result' RS-MySQL.o:RS-MySQL.c:(.text+0x120b): undefined reference to `mysql_field_count' RS-MySQL.o:RS-MySQL.c:(.text+0x128f): undefined reference to `mysql_query' RS-MySQL.o:RS-MySQL.c:(.text+0x12ac): undefined reference to `mysql_error' RS-MySQL.o:RS-MySQL.c:(.text+0x133c): undefined reference to `mysql_affected_rows' RS-MySQL.o:RS-MySQL.c:(.text+0x1539): undefined reference to `mysql_get_client_info' RS-MySQL.o:RS-MySQL.c:(.text+0x172d): undefined reference to `mysql_get_host_info' RS-MySQL.o:RS-MySQL.c:(.text+0x174b): undefined reference to `mysql_get_server_info' RS-MySQL.o:RS-MySQL.c:(.text+0x176d): undefined reference to `mysql_get_proto_info' RS-MySQL.o:RS-MySQL.c:(.text+0x177c): undefined reference
Re: [Rd] R Tools & Vista_x64: Problem compiling RMySQL?
On 26/11/2010 1:06 PM, Spencer Graves wrote: Hello: What do I need to do to compile R packages (especially RMySQL) for the 64-bit version of R 2.12.0 under Vista_x64? The symptoms you're seeing are because the linker can't functions in libmySQL.dll which it is looking for in the somewhat strange path C:/PROGRA~2/MySQL/MYSQLS~1.1//bin/libmySQL.dll Does that file exist? Is it a 64 bit dll, compatible with MinGW? Is it compiled under the same convention as R, where no underscores are used in external names? (The latter two questions can probably be answered by looking at "objdump -x libmySQL.dll". objdump.exe is distributed as part of the MinGW distribution in Rtools.) Duncan Murdoch I upgraded to "Rtools212.exe" yesterday but immediately got errors from "R CMD check RMySQL_0.7-5.tar.gz". After the first error, I installed it a second time, then got "undefined reference to" roughly 50 different names beginning "mysql_"; copied below. I see two possible sources for this problem: (1) RTools212 may not be installed properly. (2) RMySQL may be incompatible with R x64 2.12.0, especially with a 32-bit version of MySQL. NOTE: RMySQL worked with R2.11.1 (and MySQL 5.1.50-community server) before I installed R2.12.0. I'm reasonably sure that my local installation of MySQL is only 32-bit. What do you suggest? I use the 32-bit version of R2.12.0? Thanks, Spencer # * installing *source* package 'RMySQL' ... checking for $MYSQL_HOME... C:/PROGRA~2/MySQL/MYSQLS~1.1/ cygwin warning: MS-DOS style path detected: C:/PROGRA~2/MySQL/MYSQLS~1.1/ Preferred POSIX equivalent is: /cygdrive/c/PROGRA~2/MySQL/MYSQLS~1.1/ 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 ** 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:/Users/sgraves/R/R-212~1.0/etc/x64/Makeconf Preferred POSIX equivalent is: /cygdrive/c/Users/sgraves/R/R-212~1.0/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 x86_64-w64-mingw32-gcc -I"C:/Users/sgraves/R/R-212~1.0/include" -I"C:/PROGRA~2/MySQL/MYSQLS~1.1/"/include-O2 -Wall -std=gnu99 -c RS-DBI.c -o RS-DBI.o x86_64-w64-mingw32-gcc -I"C:/Users/sgraves/R/R-212~1.0/include" -I"C:/PROGRA~2/MySQL/MYSQLS~1.1/"/include-O2 -Wall -std=gnu99 -c RS-MySQL.c -o RS-MySQL.o x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o RMySQL.dll tmp.def RS-DBI.o RS-MySQL.o C:/PROGRA~2/MySQL/MYSQLS~1.1//bin/libmySQL.dll -LC:/Users/sgraves/R/R-212~1.0/bin/x64 -lR RS-MySQL.o:RS-MySQL.c:(.text+0xb0): undefined reference to `mysql_more_results' RS-MySQL.o:RS-MySQL.c:(.text+0x2c6): undefined reference to `mysql_init' RS-MySQL.o:RS-MySQL.c:(.text+0x2d9): undefined reference to `mysql_options' RS-MySQL.o:RS-MySQL.c:(.text+0x2ef): undefined reference to `mysql_options' RS-MySQL.o:RS-MySQL.c:(.text+0x305): undefined reference to `mysql_options' RS-MySQL.o:RS-MySQL.c:(.text+0x338): undefined reference to `mysql_real_connect' RS-MySQL.o:RS-MySQL.c:(.text+0x399): undefined reference to `mysql_close' RS-MySQL.o:RS-MySQL.c:(.text+0x3d1): undefined reference to `mysql_error' RS-MySQL.o:RS-MySQL.c:(.text+0x7a2): undefined reference to `mysql_close' RS-MySQL.o:RS-MySQL.c:(.text+0x80f): undefined reference to `mysql_fetch_fields' RS-MySQL.o:RS-MySQL.c:(.text+0x823): undefined reference to `mysql_field_count' RS-MySQL.o:RS-MySQL.c:(.text+0xae7): undefined reference to `mysql_next_result' RS-MySQL.o:RS-MySQL.c:(.text+0xb0b): undefined reference to `mysql_use_result' RS-MySQL.o:RS-MySQL.c:(.text+0xb16): undefined reference to `mysql_field_count' RS-MySQL.o:RS-MySQL.c:(.text+0xbff): undefined reference to `mysql_affected_rows' RS-MySQL.o:RS-MySQL.c:(.text+0xd27): undefined reference to `mysql_fetch_row' RS-MySQL.o:RS-MySQL.c:(.text+0xd3d): undefined reference to `mysql_fetch_lengths' RS-MySQL.o:RS-MySQL.c:(.text+0xf2e): undefined reference to `mysql_errno' RS-MySQL.o:RS-MySQL.c:(.text+0x1093): undefined reference to `mysql_errno' RS-MySQL.o:RS-MySQL.c:(.text+0x109e): undefined reference to `mysql_error' RS-MySQL.o:RS-MySQL.c:(.text+0x1114): undefined reference to `mysql_fetch_row' RS-MySQL.o:RS-MySQL.c:(.text+0x1121): undefined reference to `mysql_free_result' RS-MySQL.o:RS-MySQL.c:(.text+0x11f0): undefined reference to `mysql_query' RS-MySQL.o:RS-MySQL.c:(.text+0x1200): undefined reference to `mysql_use_result' RS-MySQL.o:RS-MySQL.c:(.text+0x120b): undefined reference to `mysql_field_count' RS-MySQL.o:RS-MySQL.c:(.text+0x12
Re: [Rd] R Tools & Vista_x64: Problem compiling RMySQL?
I've removed R-sig-db. PLEASE don't cross-post, not least because the R-sig-db moderator (me) ends up having to approve all the non-subscribed replies such as Duncan's. On Fri, 26 Nov 2010, Duncan Murdoch wrote: On 26/11/2010 1:06 PM, Spencer Graves wrote: Hello: What do I need to do to compile R packages (especially RMySQL) for the 64-bit version of R 2.12.0 under Vista_x64? The symptoms you're seeing are because the linker can't functions in libmySQL.dll which it is looking for in the somewhat strange path C:/PROGRA~2/MySQL/MYSQLS~1.1//bin/libmySQL.dll Does that file exist? Is it a 64 bit dll, compatible with MinGW? Is it compiled under the same convention as R, where no underscores are used in external names? (The latter two questions can probably be answered by looking at "objdump -x libmySQL.dll". objdump.exe is distributed as part of the MinGW distribution in Rtools.) For x64, you need (or at least, it is more correct to use) x86_64-w64-mingw32-objdump. But I think he has pretty much told us that it is a 32-bit DLL. To install RMySQL on x64 Windows you need the 64-bit client DLLs. The standard MySQL installers do not allow you to install 32-bit and 64-bit MySQL on the same machine, but once you manage that, 32bit RMySQL can talk to a 64-bit MySQL server, and v.v. BTW, the underscore convention does not matter for DLLs, only object files (.o, .a). This does all work (I passed patches back to the maintainer so that it does). I do have a bi-arch Windows install of RMySQL on my machine talking to a 64-bit MySQL server. But we've had far too much frustration with (even very minor) MySQL version mismatches to even think about distributing such a build. Duncan Murdoch I upgraded to "Rtools212.exe" yesterday but immediately got errors from "R CMD check RMySQL_0.7-5.tar.gz". After the first error, I installed it a second time, then got "undefined reference to" roughly 50 different names beginning "mysql_"; copied below. I see two possible sources for this problem: (1) RTools212 may not be installed properly. (2) RMySQL may be incompatible with R x64 2.12.0, especially with a 32-bit version of MySQL. NOTE: RMySQL worked with R2.11.1 (and MySQL 5.1.50-community server) But you failed to tell us the 'at a minimum' information we asked for about either version of R. If that was i386 R, then yes, your MySQL is 32-bit. before I installed R2.12.0. I'm reasonably sure that my local installation of MySQL is only 32-bit. What do you suggest? I use the 32-bit version of R2.12.0? Thanks, Spencer # * installing *source* package 'RMySQL' ... checking for $MYSQL_HOME... C:/PROGRA~2/MySQL/MYSQLS~1.1/ cygwin warning: MS-DOS style path detected: C:/PROGRA~2/MySQL/MYSQLS~1.1/ Preferred POSIX equivalent is: /cygdrive/c/PROGRA~2/MySQL/MYSQLS~1.1/ 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 ** 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:/Users/sgraves/R/R-212~1.0/etc/x64/Makeconf Preferred POSIX equivalent is: /cygdrive/c/Users/sgraves/R/R-212~1.0/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 x86_64-w64-mingw32-gcc -I"C:/Users/sgraves/R/R-212~1.0/include" -I"C:/PROGRA~2/MySQL/MYSQLS~1.1/"/include-O2 -Wall -std=gnu99 -c RS-DBI.c -o RS-DBI.o x86_64-w64-mingw32-gcc -I"C:/Users/sgraves/R/R-212~1.0/include" -I"C:/PROGRA~2/MySQL/MYSQLS~1.1/"/include-O2 -Wall -std=gnu99 -c RS-MySQL.c -o RS-MySQL.o x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o RMySQL.dll tmp.def RS-DBI.o RS-MySQL.o C:/PROGRA~2/MySQL/MYSQLS~1.1//bin/libmySQL.dll -LC:/Users/sgraves/R/R-212~1.0/bin/x64 -lR RS-MySQL.o:RS-MySQL.c:(.text+0xb0): undefined reference to `mysql_more_results' RS-MySQL.o:RS-MySQL.c:(.text+0x2c6): undefined reference to `mysql_init' RS-MySQL.o:RS-MySQL.c:(.text+0x2d9): undefined reference to `mysql_options' RS-MySQL.o:RS-MySQL.c:(.text+0x2ef): undefined reference to `mysql_options' RS-MySQL.o:RS-MySQL.c:(.text+0x305): undefined reference to `mysql_options' RS-MySQL.o:RS-MySQL.c:(.text+0x338): undefined reference to `mysql_real_connect' RS-MySQL.o:RS-MySQL.c:(.text+0x399): undefined reference to `mysql_close' RS-MySQL.o:RS-MySQL.c:(.text+0x3d1): undefined reference to `mysql_error' RS-MySQL.o:RS-MySQL.c:(.text+0x7a2): undefined reference to `mysql_close' RS-MySQL.o:RS-MySQL.c:(.text+0x80f): undefined reference to `mysql_fetch_fields' RS-MySQL.o:RS-MySQL.c:(.text+0x823): un
Re: [Rd] R Tools & Vista_x64: Problem compiling RMySQL?
Thanks for the reminder not to cross post; by now, I should know better. Thanks to Duncan for his reply, which helped convince me that I should compile for i386 only. The problem seemed to disappear after I modified the path. Spencer On 11/26/2010 12:44 PM, Prof Brian Ripley wrote: I've removed R-sig-db. PLEASE don't cross-post, not least because the R-sig-db moderator (me) ends up having to approve all the non-subscribed replies such as Duncan's. On Fri, 26 Nov 2010, Duncan Murdoch wrote: On 26/11/2010 1:06 PM, Spencer Graves wrote: Hello: What do I need to do to compile R packages (especially RMySQL) for the 64-bit version of R 2.12.0 under Vista_x64? The symptoms you're seeing are because the linker can't functions in libmySQL.dll which it is looking for in the somewhat strange path C:/PROGRA~2/MySQL/MYSQLS~1.1//bin/libmySQL.dll Does that file exist? Is it a 64 bit dll, compatible with MinGW? Is it compiled under the same convention as R, where no underscores are used in external names? (The latter two questions can probably be answered by looking at "objdump -x libmySQL.dll". objdump.exe is distributed as part of the MinGW distribution in Rtools.) For x64, you need (or at least, it is more correct to use) x86_64-w64-mingw32-objdump. But I think he has pretty much told us that it is a 32-bit DLL. To install RMySQL on x64 Windows you need the 64-bit client DLLs. The standard MySQL installers do not allow you to install 32-bit and 64-bit MySQL on the same machine, but once you manage that, 32bit RMySQL can talk to a 64-bit MySQL server, and v.v. BTW, the underscore convention does not matter for DLLs, only object files (.o, .a). This does all work (I passed patches back to the maintainer so that it does). I do have a bi-arch Windows install of RMySQL on my machine talking to a 64-bit MySQL server. But we've had far too much frustration with (even very minor) MySQL version mismatches to even think about distributing such a build. Duncan Murdoch I upgraded to "Rtools212.exe" yesterday but immediately got errors from "R CMD check RMySQL_0.7-5.tar.gz". After the first error, I installed it a second time, then got "undefined reference to" roughly 50 different names beginning "mysql_"; copied below. I see two possible sources for this problem: (1) RTools212 may not be installed properly. (2) RMySQL may be incompatible with R x64 2.12.0, especially with a 32-bit version of MySQL. NOTE: RMySQL worked with R2.11.1 (and MySQL 5.1.50-community server) But you failed to tell us the 'at a minimum' information we asked for about either version of R. If that was i386 R, then yes, your MySQL is 32-bit. before I installed R2.12.0. I'm reasonably sure that my local installation of MySQL is only 32-bit. What do you suggest? I use the 32-bit version of R2.12.0? Thanks, Spencer # * installing *source* package 'RMySQL' ... checking for $MYSQL_HOME... C:/PROGRA~2/MySQL/MYSQLS~1.1/ cygwin warning: MS-DOS style path detected: C:/PROGRA~2/MySQL/MYSQLS~1.1/ Preferred POSIX equivalent is: /cygdrive/c/PROGRA~2/MySQL/MYSQLS~1.1/ 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 ** 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:/Users/sgraves/R/R-212~1.0/etc/x64/Makeconf Preferred POSIX equivalent is: /cygdrive/c/Users/sgraves/R/R-212~1.0/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 x86_64-w64-mingw32-gcc -I"C:/Users/sgraves/R/R-212~1.0/include" -I"C:/PROGRA~2/MySQL/MYSQLS~1.1/"/include-O2 -Wall -std=gnu99 -c RS-DBI.c -o RS-DBI.o x86_64-w64-mingw32-gcc -I"C:/Users/sgraves/R/R-212~1.0/include" -I"C:/PROGRA~2/MySQL/MYSQLS~1.1/"/include-O2 -Wall -std=gnu99 -c RS-MySQL.c -o RS-MySQL.o x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o RMySQL.dll tmp.def RS-DBI.o RS-MySQL.o C:/PROGRA~2/MySQL/MYSQLS~1.1//bin/libmySQL.dll -LC:/Users/sgraves/R/R-212~1.0/bin/x64 -lR RS-MySQL.o:RS-MySQL.c:(.text+0xb0): undefined reference to `mysql_more_results' RS-MySQL.o:RS-MySQL.c:(.text+0x2c6): undefined reference to `mysql_init' RS-MySQL.o:RS-MySQL.c:(.text+0x2d9): undefined reference to `mysql_options' RS-MySQL.o:RS-MySQL.c:(.text+0x2ef): undefined reference to `mysql_options' RS-MySQL.o:RS-MySQL.c:(.text+0x305): undefined reference to `mysql_options' RS-MySQL.o:RS-MySQL.c:(.text+0x338): undefined reference to `mysql_real_connect' RS-MySQL.o:RS-MySQL.c:(.text+0x399): undefined refer
