[R] Compiling RMySQL on Win7 64bits RS-DBI.c:1:0: sorry, unimplemented: 64-bit mode not compiled in

[Uwe Ligges]

On 24.04.2012 20:13, Ben Rhelp wrote:
> Hi Uwe,
>
> I tried removing D:\BenSave\Rtools\MinGW64\bin (and replacing it with D:\BenSave\Rtools\MinGW\bin) but the result is the same.
>
> If I try to run "install.packages('RMySQL', type = 'source')" on my R 32bits instance I get the following which seems to be due to having a MySQL server 64bits as expected.
 >
> any other suggestions?

Yes, do not replace but delete that part, you have gcc-4.6.3 in your 
path which should be sufficient.
I do not know if it is possible to compile RMySQL afterwards (untested, 
and it depends on the MySQL you are linking against.

best,
Uwe Ligges



> thanks in advance,
>
> Ben
>
>
> install.packages('RMySQL', type = 'source')
> --- Please select a CRAN mirror for use in this session ---
> trying URL 'http://cran.ma.imperial.ac.uk/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... D:/MySQL/forR55
> ** libs
> Warning: this package has a non-empty 'configure.win' file,
> so building only the main architecture
>
> gcc  -I"D:/BenSave/R/R-215~1.0/include" -DNDEBUG -I"D:/MySQL/forR55"/include         -O3 -Wall  -std=gnu99 -mtune=core2 -c RS-DBI.c -o RS-DBI.o
> gcc  -I"D:/BenSave/R/R-215~1.0/include" -DNDEBUG -I"D:/MySQL/forR55"/include         -O3 -Wall  -std=gnu99 -mtune=core2 -c RS-MySQL.c -o RS-MySQL.o
> gcc -shared -s -static-libgcc -o RMySQL.dll tmp.def RS-DBI.o RS-MySQL.o D:/MySQL/forR55/lib/opt/libmysql.lib -LD:/BenSave/R/R-215~1.0/bin/i386 -lR
> RS-MySQL.o:RS-MySQL.c:(.text+0xba): undefined reference to `mysql_more_results at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x352): undefined reference to `mysql_init at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x36f): undefined reference to `mysql_options at 12'
> RS-MySQL.o:RS-MySQL.c:(.text+0x38d): undefined reference to `mysql_options at 12'
> RS-MySQL.o:RS-MySQL.c:(.text+0x3ab): undefined reference to `mysql_options at 12'
> RS-MySQL.o:RS-MySQL.c:(.text+0x3e6): undefined reference to `mysql_real_connect at 32'
> RS-MySQL.o:RS-MySQL.c:(.text+0x44a): undefined reference to `mysql_close at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x5b8): undefined reference to `mysql_error at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x9c4): undefined reference to `mysql_close at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0xa3d): undefined reference to `mysql_fetch_fields at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0xa55): undefined reference to `mysql_field_count at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0xd5b): undefined reference to `mysql_next_result at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0xd85): undefined reference to `mysql_use_result at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0xd93): undefined reference to `mysql_field_count at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0xe7b): undefined reference to `mysql_affected_rows at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0xf56): undefined reference to `mysql_fetch_row at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0xf73): undefined reference to `mysql_free_result at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0xfd7): undefined reference to `mysql_query at 8'
> RS-MySQL.o:RS-MySQL.c:(.text+0xfea): undefined reference to `mysql_use_result at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0xffb): undefined reference to `mysql_field_count at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x109d): undefined reference to `mysql_error at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x1146): undefined reference to `mysql_affected_rows at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x12bd): undefined reference to `mysql_fetch_row at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x12d8): undefined reference to `mysql_fetch_lengths at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x154f): undefined reference to `mysql_errno at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x16e4): undefined reference to `mysql_errno at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x16f2): undefined reference to `mysql_error at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x1766): undefined reference to `mysql_fetch_row at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x1775): undefined reference to `mysql_free_result at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x1990): undefined reference to `mysql_get_client_info at 0'
> RS-MySQL.o:RS-MySQL.c:(.text+0x1b84): undefined reference to `mysql_get_host_info at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x1bae): undefined reference to `mysql_get_server_info at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x1bde): undefined reference to `mysql_get_proto_info at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x1bf5): undefined reference to `mysql_thread_id at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x294a): undefined reference to `mysql_fetch_row at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x2977): undefined reference to `mysql_errno at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x2aca): undefined reference to `mysql_fetch_lengths at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x315c): undefined reference to `mysql_insert_id at 4'
> RS-MySQL.o:RS-MySQL.c:(.text+0x324d): undefined reference to `mysql_real_escape_string at 16'
> RS-MySQL.o:RS-MySQL.c:(.text+0x3317): undefined reference to `mysql_get_client_info at 0'
> RS-MySQL.o:RS-MySQL.c:(.text+0x335d): undefined reference to `mysql_get_client_version at 0'
> RS-MySQL.o:RS-MySQL.c:(.text+0x33ae): undefined reference to `mysql_server_init at 12'
> RS-MySQL.o:RS-MySQL.c:(.text+0x33b6): undefined reference to `mysql_get_client_version at 0'
> RS-MySQL.o:RS-MySQL.c:(.text+0x33d7): undefined reference to `mysql_get_client_info at 0'
> RS-MySQL.o:RS-MySQL.c:(.text+0x3408): undefined reference to `mysql_server_end at 0'
> collect2: ld returned 1 exit status
> ERROR: compilation failed for package 'RMySQL'
> * removing 'D:/BenSave/R/R-2.15.0/library/RMySQL'
>
> The downloaded source packages are in
>          ‘C:\Users\BenSave\TempFolder\RtmpS8df20\downloaded_packages’
> Warning messages:
> 1: running command 'D:/BenSave/R/R-2.15.0/bin/i386/R CMD INSTALL -l "D:/BenSave/R/R-2.15.0/library"   C:\Users\BenSave\TempFolder\RtmpS8df20/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
>
>
>
>
>
>> ________________________________
>> From: Uwe Ligges<ligges at statistik.tu-dortmund.de>
>> To: Ben Rhelp<benrhelp at yahoo.co.uk>
>> Cc: "r-help at r-project.org"<r-help at r-project.org>
>> Sent: Tuesday, 24 April 2012, 18:22
>> Subject: Re: [R] Compiling RMySQL on Win7 64bits RS-DBI.c:1:0: sorry, unimplemented: 64-bit mode not compiled in
>>
>>
>>
>> On 24.04.2012 16:40, Ben Rhelp wrote:
>>> Hi,
>>>
>>> On a Win7 64 bit, I have installed:
>>> *R-15.0 and I am running it in 64bits
>>> *Rtools215.exe*MySQL 5.5.23 64bits
>>>
>>> My PATH start with D:\BenSave\Rtools\bin;D:\BenSave\Rtools\MinGW64\bin;D:\BenSave\R\R-2.15.0\bin;D:\BenSave\Rtools\MinGW\bin;D:\BenSave\Rtools\gcc-4.6.3\bin;
>>
>>
>> What is D:\BenSave\Rtools\MinGW64\bin? Probably it needs to go out of
>> the way.
>>
>> Uwe Ligges
>>
>>>
>>> Note that I place MinGW64\bin has I want the package in 64 bits, so just in case it helps...
>>>
>>>
>>> To install RMySQL 64 bits, I then followed the steps described in http://stackoverflow.com/questions/4785933/adding-rmysql-package-to-r-fails, namely:
>>>
>>>      1. Install latest RTools from http://cran.r-project.org/bin/windows/Rtools/
>>>      2. install MySQL or header and library files of mysql
>>>      3. create or edit file C:\Program Files\R\R-2.15\etc\Renviron.site and add line like MYSQL_HOME=C:/mysql (path to your mysql files)
>>>      4. copy libmysql.lib from mysql/lib to mysql/lib/opt to meet dependencies.
>>>      5. copy libmysql.dll to C:\Program Files\R\R-2.15\bin directory.
>>>      6. run install.packages('RMySQL',type='source') and wait while compilation will end.
>>>
>>>> install.packages('RMySQL', type = 'source')
>>> --- Please select a CRAN mirror for use in this session ---
>>> trying URL 'http://cran.ma.imperial.ac.uk/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... D:/MySQL/forR55
>>> ** libs
>>> Warning: this package has a non-empty 'configure.win' file,
>>> so building only the main architecture
>>>
>>> gcc -m64 -I"D:/BenSave/R/R-215~1.0/include" -DNDEBUG -I"D:/MySQL/forR55"/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:1:0: sorry, unimplemented: 64-bit mode not compiled in
>>> make: *** [RS-DBI.o] Error 1
>>> ERROR: compilation failed for package 'RMySQL'
>>> * removing 'D:/BenSave/R/R-2.15.0/library/RMySQL'
>>>
>>> The downloaded source packages are in
>>>         ‘C:\Users\Bvinsonneau\TempFolder\RtmpwPJoVe\downloaded_packages’
>>> Warning messages:
>>> 1: running command 'D:/BenSave/R/R-2.15.0/bin/x64/R CMD INSTALL -l "D:/BenSave/R/R-2.15.0/library"Â Â  C:\Users\BenSave\TempFolder\RtmpwPJoVe/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
>>>>
>>>
>>>
>>>
>>> I seems to have the same error than the reporter on
>>>
>>> http://r.789695.n4.nabble.com/Installing-RMySQL-64-bit-Windows-7-td4466352.html
>>> and Prof Brian Ripley suggests that the reporter should re-read the the instructions in 'R Installation and
>>> Administration'. I did so but no luck. I am not sure what I am missing.Â
>>>
>>> Does anyone have a suggestion?
>>>
>>> Regards,
>>>
>>> Ben
>>>      [[alternative HTML version deleted]]
>>>
>>>
>>>
>>>
>>> ______________________________________________
>>> 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.
>>
>>
>>