R help - Oct 2003 - Problems Building RMySQL in Windows

On Wed, 15 Oct 2003, "H?ctor Villafuerte D." wrote:
> Hi all,
> Unfortunately I must use winXP at my job, so I'm trying install
> from source RMySQL. Here are some details about this problem:
> - R 1.7.1
> - RMySQL 0.5-2
> - mysql  4.1.0-alpha-max-nt
> I followed the instructions posted in 
> http://www.biostat.jhsph.edu/~kbroman/Rintro/Rwinpack.html
> and the following messages appeared. BTW, thanks in advance for your 
> help and comments.
It hasn't found the mysql entry points: have you built an import
library for the mysql client and is it in c:/mysql/lib/opt, for example.

Error messages very similar to these are covered 
in the README.windows file in the RMySQL package.

Please read the documentation in the RMySQL package and in the current
R for Windows relase (that web page is long out of date and I believe was 
never as accurate as the official documentation).
> 
> 
> C:\Program Files\R\rw1071\src\gnuwin32>make pkg-RMySQL
> 
> ---------- Making package RMySQL ------------
> 
>    **********************************************
>    WARNING: this package has a configure script
>          It probably needs manual configuration
>    **********************************************
> 
>   installing inst files
>   adding build stamp to DESCRIPTION
>   making DLL ...
> making RS-DBI.d from RS-DBI.c
> making RS-MySQL.d from RS-MySQL.c
> gcc  -Ic:/mysql/include  -IC:/PROGRA~1/R/rw1071/src/include -Wall -O2   
> -c RS-DBI.c -o RS-DBI.o
> gcc  -Ic:/mysql/include  -IC:/PROGRA~1/R/rw1071/src/include -Wall -O2   
> -c RS-MySQL.c -o RS-MySQL.o
> ar cr RMySQL.a *.o
> ranlib RMySQL.a
> windres --include-dir C:/PROGRA~1/R/rw1071/src/include  -i RMySQL_res.rc 
> -o RMySQL_res.o
> gcc  --shared -s  -o RMySQL.dll RMySQL.def RMySQL.a RMySQL_res.o  
> -LC:/PROGRA~1/R/rw1071/src/gnuwin32 -Lc:/mysql/lib/opt
>  -lmysql -liberty -lg2c -lR
> RMySQL.a(RS-MySQL.o)(.text+0x216):RS-MySQL.c: undefined reference to 
> `_mysql_get_client_info'
> RMySQL.a(RS-MySQL.o)(.text+0x7f9):RS-MySQL.c: undefined reference to 
> `_mysql_init'
> RMySQL.a(RS-MySQL.o)(.text+0x817):RS-MySQL.c: undefined reference to 
> `_mysql_options'
> RMySQL.a(RS-MySQL.o)(.text+0x879):RS-MySQL.c: undefined reference to 
> `_mysql_options'
> RMySQL.a(RS-MySQL.o)(.text+0x8e4):RS-MySQL.c: undefined reference to 
> `_load_defaults'
> RMySQL.a(RS-MySQL.o)(.text+0xb39):RS-MySQL.c: undefined reference to 
> `_mysql_real_connect'
> RMySQL.a(RS-MySQL.o)(.text+0xc3d):RS-MySQL.c: undefined reference to 
> `_mysql_close'
> RMySQL.a(RS-MySQL.o)(.text+0xd31):RS-MySQL.c: undefined reference to 
> `_mysql_options'
> RMySQL.a(RS-MySQL.o)(.text+0xde1):RS-MySQL.c: undefined reference to 
> `_mysql_close'
> RMySQL.a(RS-MySQL.o)(.text+0xf89):RS-MySQL.c: undefined reference to 
> `_mysql_query'
> RMySQL.a(RS-MySQL.o)(.text+0xfa4):RS-MySQL.c: undefined reference to 
> `_mysql_use_result'
> RMySQL.a(RS-MySQL.o)(.text+0xfbe):RS-MySQL.c: undefined reference to 
> `_mysql_field_count'
> RMySQL.a(RS-MySQL.o)(.text+0x106a):RS-MySQL.c: undefined reference to 
> `_mysql_affected_rows'
> RMySQL.a(RS-MySQL.o)(.text+0x10de):RS-MySQL.c: undefined reference to 
> `_mysql_error'
> RMySQL.a(RS-MySQL.o)(.text+0x116f):RS-MySQL.c: undefined reference to 
> `_mysql_fetch_fields'
> RMySQL.a(RS-MySQL.o)(.text+0x1188):RS-MySQL.c: undefined reference to 
> `_mysql_field_count'
> RMySQL.a(RS-MySQL.o)(.text+0x155c):RS-MySQL.c: undefined reference to 
> `_mysql_fetch_row'
> RMySQL.a(RS-MySQL.o)(.text+0x1576):RS-MySQL.c: undefined reference to 
> `_mysql_fetch_lengths'
> RMySQL.a(RS-MySQL.o)(.text+0x17c3):RS-MySQL.c: undefined reference to 
> `_mysql_errno'
> RMySQL.a(RS-MySQL.o)(.text+0x19e4):RS-MySQL.c: undefined reference to 
> `_mysql_errno'
> RMySQL.a(RS-MySQL.o)(.text+0x19ef):RS-MySQL.c: undefined reference to 
> `_mysql_error'
> RMySQL.a(RS-MySQL.o)(.text+0x1a64):RS-MySQL.c: undefined reference to 
> `_mysql_fetch_row'
> RMySQL.a(RS-MySQL.o)(.text+0x1a74):RS-MySQL.c: undefined reference to 
> `_mysql_free_result'
> RMySQL.a(RS-MySQL.o)(.text+0x1d1b):RS-MySQL.c: undefined reference to 
> `_mysql_get_client_info'
> RMySQL.a(RS-MySQL.o)(.text+0x1f4e):RS-MySQL.c: undefined reference to 
> `_mysql_get_host_info'
> RMySQL.a(RS-MySQL.o)(.text+0x1f78):RS-MySQL.c: undefined reference to 
> `_mysql_get_server_info'
> RMySQL.a(RS-MySQL.o)(.text+0x1fa5):RS-MySQL.c: undefined reference to 
> `_mysql_get_proto_info'
> RMySQL.a(RS-MySQL.o)(.text+0x1fb6):RS-MySQL.c: undefined reference to 
> `_mysql_thread_id'
> RMySQL.a(RS-MySQL.o)(.text+0x2c32):RS-MySQL.c: undefined reference to 
> `_mysql_fetch_lengths'
> RMySQL.a(RS-MySQL.o)(.text+0x2c59):RS-MySQL.c: undefined reference to 
> `_mysql_errno'
> RMySQL.a(RS-MySQL.o)(.text+0x2eda):RS-MySQL.c: undefined reference to 
> `_mysql_fetch_row'
> collect2: ld returned 1 exit status
> make[2]: *** [RMySQL.dll] Error 1
> make[1]: *** [src/RMySQL.dll] Error 2
> make: *** [pkg-RMySQL] Error 2
> 
> C:\Program Files\R\rw1071\src\gnuwin32>
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> 
> 
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

Hi all,
Unfortunately I must use winXP at my job, so I'm trying install
from source RMySQL. Here are some details about this problem:
- R 1.7.1
- RMySQL 0.5-2
- mysql  4.1.0-alpha-max-nt
I followed the instructions posted in 
http://www.biostat.jhsph.edu/~kbroman/Rintro/Rwinpack.html
and the following messages appeared. BTW, thanks in advance for your 
help and comments.


C:\Program Files\R\rw1071\src\gnuwin32>make pkg-RMySQL

---------- Making package RMySQL ------------

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************

  installing inst files
  adding build stamp to DESCRIPTION
  making DLL ...
making RS-DBI.d from RS-DBI.c
making RS-MySQL.d from RS-MySQL.c
gcc  -Ic:/mysql/include  -IC:/PROGRA~1/R/rw1071/src/include -Wall -O2   
-c RS-DBI.c -o RS-DBI.o
gcc  -Ic:/mysql/include  -IC:/PROGRA~1/R/rw1071/src/include -Wall -O2   
-c RS-MySQL.c -o RS-MySQL.o
ar cr RMySQL.a *.o
ranlib RMySQL.a
windres --include-dir C:/PROGRA~1/R/rw1071/src/include  -i RMySQL_res.rc 
-o RMySQL_res.o
gcc  --shared -s  -o RMySQL.dll RMySQL.def RMySQL.a RMySQL_res.o  
-LC:/PROGRA~1/R/rw1071/src/gnuwin32 -Lc:/mysql/lib/opt
 -lmysql -liberty -lg2c -lR
RMySQL.a(RS-MySQL.o)(.text+0x216):RS-MySQL.c: undefined reference to 
`_mysql_get_client_info'
RMySQL.a(RS-MySQL.o)(.text+0x7f9):RS-MySQL.c: undefined reference to 
`_mysql_init'
RMySQL.a(RS-MySQL.o)(.text+0x817):RS-MySQL.c: undefined reference to 
`_mysql_options'
RMySQL.a(RS-MySQL.o)(.text+0x879):RS-MySQL.c: undefined reference to 
`_mysql_options'
RMySQL.a(RS-MySQL.o)(.text+0x8e4):RS-MySQL.c: undefined reference to 
`_load_defaults'
RMySQL.a(RS-MySQL.o)(.text+0xb39):RS-MySQL.c: undefined reference to 
`_mysql_real_connect'
RMySQL.a(RS-MySQL.o)(.text+0xc3d):RS-MySQL.c: undefined reference to 
`_mysql_close'
RMySQL.a(RS-MySQL.o)(.text+0xd31):RS-MySQL.c: undefined reference to 
`_mysql_options'
RMySQL.a(RS-MySQL.o)(.text+0xde1):RS-MySQL.c: undefined reference to 
`_mysql_close'
RMySQL.a(RS-MySQL.o)(.text+0xf89):RS-MySQL.c: undefined reference to 
`_mysql_query'
RMySQL.a(RS-MySQL.o)(.text+0xfa4):RS-MySQL.c: undefined reference to 
`_mysql_use_result'
RMySQL.a(RS-MySQL.o)(.text+0xfbe):RS-MySQL.c: undefined reference to 
`_mysql_field_count'
RMySQL.a(RS-MySQL.o)(.text+0x106a):RS-MySQL.c: undefined reference to 
`_mysql_affected_rows'
RMySQL.a(RS-MySQL.o)(.text+0x10de):RS-MySQL.c: undefined reference to 
`_mysql_error'
RMySQL.a(RS-MySQL.o)(.text+0x116f):RS-MySQL.c: undefined reference to 
`_mysql_fetch_fields'
RMySQL.a(RS-MySQL.o)(.text+0x1188):RS-MySQL.c: undefined reference to 
`_mysql_field_count'
RMySQL.a(RS-MySQL.o)(.text+0x155c):RS-MySQL.c: undefined reference to 
`_mysql_fetch_row'
RMySQL.a(RS-MySQL.o)(.text+0x1576):RS-MySQL.c: undefined reference to 
`_mysql_fetch_lengths'
RMySQL.a(RS-MySQL.o)(.text+0x17c3):RS-MySQL.c: undefined reference to 
`_mysql_errno'
RMySQL.a(RS-MySQL.o)(.text+0x19e4):RS-MySQL.c: undefined reference to 
`_mysql_errno'
RMySQL.a(RS-MySQL.o)(.text+0x19ef):RS-MySQL.c: undefined reference to 
`_mysql_error'
RMySQL.a(RS-MySQL.o)(.text+0x1a64):RS-MySQL.c: undefined reference to 
`_mysql_fetch_row'
RMySQL.a(RS-MySQL.o)(.text+0x1a74):RS-MySQL.c: undefined reference to 
`_mysql_free_result'
RMySQL.a(RS-MySQL.o)(.text+0x1d1b):RS-MySQL.c: undefined reference to 
`_mysql_get_client_info'
RMySQL.a(RS-MySQL.o)(.text+0x1f4e):RS-MySQL.c: undefined reference to 
`_mysql_get_host_info'
RMySQL.a(RS-MySQL.o)(.text+0x1f78):RS-MySQL.c: undefined reference to 
`_mysql_get_server_info'
RMySQL.a(RS-MySQL.o)(.text+0x1fa5):RS-MySQL.c: undefined reference to 
`_mysql_get_proto_info'
RMySQL.a(RS-MySQL.o)(.text+0x1fb6):RS-MySQL.c: undefined reference to 
`_mysql_thread_id'
RMySQL.a(RS-MySQL.o)(.text+0x2c32):RS-MySQL.c: undefined reference to 
`_mysql_fetch_lengths'
RMySQL.a(RS-MySQL.o)(.text+0x2c59):RS-MySQL.c: undefined reference to 
`_mysql_errno'
RMySQL.a(RS-MySQL.o)(.text+0x2eda):RS-MySQL.c: undefined reference to 
`_mysql_fetch_row'
collect2: ld returned 1 exit status
make[2]: *** [RMySQL.dll] Error 1
make[1]: *** [src/RMySQL.dll] Error 2
make: *** [pkg-RMySQL] Error 2

C:\Program Files\R\rw1071\src\gnuwin32>

David James wrote:
>Hi,
>
>I'm attaching a Windows binary version of RMySQL.  It was compiled
>against MySQL 2.23.56 (recall that you must also install the DBI
>package). Let me know if it works.
>
>Hope this helps,
>
>--
>David
>
Thanks David,
I tried the binaries you sent me. Here's the warning it gave me:

    > library(RMySQL)
    Warning message:
    DLL attempted to change FPU control word from 8001f to 9001f

Then I tried to do this:

    > con <- dbConnect(dbDriver("MySQL"), dbname =
"test")

but it crashed R.
I got back to the sources then (but now using RCMD.EXE)... but again
it seems I'm missing something important:

    C:\Program Files\R\rw1071\bin>rcmd INSTALL ..\src\library\RMySQL

    make: *** No rule to make target `Files/R/rw1071/src/library'.  Stop.
    *** Installation of RMySQL failed ***

    C:\Program Files\R\rw1071\bin>

Thank you so much for your help.

David James wrote:
>"H?ctor Villafuerte D." wrote:
>  
>
>>Thanks David,
>>I tried the binaries you sent me. Here's the warning it gave me:
>>
>>    > library(RMySQL)
>>    Warning message:
>>    DLL attempted to change FPU control word from 8001f to 9001f
>>    
>>
>
>I have seen this, but it has not caused any problem to me, so my
>reaction is that it may be ok to ignore.
>
>  
>
>>Then I tried to do this:
>>
>>    > con <- dbConnect(dbDriver("MySQL"), dbname =
"test")
>>
>>but it crashed R.
>>    
>>
>
>I've seen this too.  Typically it is a *.dll conflict between the
>version of the MySQL library included and used for compiling RMySQL
>(MySQL 3.23.56) and the runtime MySQL library you use (say, 4.0.x).
>If this is the problem, you can easily fix it by making sure your
>PATH variable picks the *.dll used in the RMySQL package first
>(ahead of the 4.0.x *.dll).
>
>Hope this helps,
>
>--
>David
>  
>
Here is a  copy of my PATH environment variable:
C:\Perl\bin\;%SystemRoot%\system32;%SystemRoot%;%SystemRoot%\System32\Wbem;
"C:\Program Files\NMapWin\bin";c:\cygwin\bin;C:\Python23;
"C:\Program Files\R\rw1071\library\RMySQL\libs";C:\mysql\bin

And yes... running dbConnect still crashes R...
Thanks again for your help.

David Whiting wrote:
>Can you use RODBC instead?  I use it all the time and find it works
>very well.  I installed it some time ago and have forgotten the exact
>details but I remember that it was easy to do following the
>instructions.  I also can't remember why I choose RODBC instead of
>RMySQL and whether there are advantages of RMySQL over RODBC.
>  
>
Ok, I think I'll try RODBC. For what I have read of ODBC's I pressume 
RODBC will be
easier to use, but slower (since it is a higher layer of abstraction... 
or something like that).
I'll let you know if I succeed (to be honest, I'll let you know if I 
fail too!)
Thanks,
Hector

David Whiting wrote:
>Can you use RODBC instead?  I use it all the time and find it works
>very well.  I installed it some time ago and have forgotten the exact
>details but I remember that it was easy to do following the
>instructions.  I also can't remember why I choose RODBC instead of
>RMySQL and whether there are advantages of RMySQL over RODBC.
>  
>
Great! Using RODBC is really easy!
Would someone please comment on the pros and cons of RODBC compared with 
RMySQL?
Thanks in advance.
Hector