[R] Install RMySQL with R 2.4.0
Joe Byers
joe-byers at utulsa.edu
Wed Nov 8 18:37:11 CET 2006
All,
I have tried to compile the RMySQL from source as specified in the
documentation. I am receiving the following errors
******************* beginning of cygwin window ****************************
joe-byers at Byersj /cygdrive/d/Program Files/R/bin
$ Rcmd build --binary ../library/RMySQL
* checking for file '../library/RMySQL/DESCRIPTION' ... OK
* preparing '../library/RMySQL':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building binary distribution
WARNING
* some HTML links may not be found
installing R.css in c:/TEMP/Rinst346079904
Using auto-selected zip options ' RMySQL-HELP=ziponly'
/bin/sh: latex: command not found
/bin/sh: latex: command not found
/bin/sh: latex: command not found
---------- Making package RMySQL ------------
======================================================================
RMySQL configure.win:
* Using mysql libraries from d:/MySQL/lib/opt
* Using mysql dll from d:/MySQL/bin
* Copying runtime libMySQL.dll and libmysql.lib to inst/libs
* Using an existing libmysql.a in d:/MySQL/lib/opt
joe-byers at Byersj /cygdrive/d/Program Files/R/bin
$ Rcmd build --binary ../library/RMySQL
* checking for file '../library/RMySQL/DESCRIPTION' ... OK
* preparing '../library/RMySQL':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building binary distribution
WARNING
* some HTML links may not be found
installing R.css in c:/TEMP/Rinst250866757
Using auto-selected zip options ' RMySQL-HELP=ziponly'
/bin/sh: latex: command not found
/bin/sh: latex: command not found
/bin/sh: latex: command not found
---------- Making package RMySQL ------------
======================================================================
RMySQL configure.win:
* Using mysql libraries from d:/MySQL/lib/opt
* Using mysql dll from d:/MySQL/bin
* Copying runtime libMySQL.dll and libmysql.lib to inst/libs
* Using an existing libmysql.a in d:/MySQL/lib/opt
======================================================================
/bin/sh: latex: command not found
adding build stamp to DESCRIPTION
/bin/sh: latex: command not found
/bin/sh: latex: command not found
making DLL ...
/bin/sh: latex: command not found
making RS-DBI.d from RS-DBI.c
making RS-MySQL.d from RS-MySQL.c
gcc -Id:/mysql/include -Id:/PROGRA~1/R/include -Wall -O2 -std=gnu99
-c RS-DB
I.c -o RS-DBI.o
gcc -Id:/mysql/include -Id:/PROGRA~1/R/include -Wall -O2 -std=gnu99
-c RS-My
SQL.c -o RS-MySQL.o
windres --include-dir d:/PROGRA~1/R/include -i RMySQL_res.rc -o
RMySQL_res.o
gcc -shared -s -o RMySQL.dll RMySQL.def RS-DBI.o RS-MySQL.o
RMySQL_res.o -Ld:
/PROGRA~1/R/bin -Ld:/mysql/lib/opt -lmysql -liberty -lR
RS-MySQL.o:RS-MySQL.c:(.text+0xf): undefined reference to
`_mysql_get_client_inf
o'
RS-MySQL.o:RS-MySQL.c:(.text+0x26b): undefined reference to `_mysql_init'
RS-MySQL.o:RS-MySQL.c:(.text+0x288): undefined reference to `_mysql_options'
RS-MySQL.o:RS-MySQL.c:(.text+0x2fd): undefined reference to `_mysql_options'
RS-MySQL.o:RS-MySQL.c:(.text+0x33e): undefined reference to `_mysql_options'
RS-MySQL.o:RS-MySQL.c:(.text+0x593): undefined reference to
`_mysql_real_connect
'S-MySQL.o:RS-MySQL.c:(.text+0x17ab): undefined reference to
`_mysql_get_client_
RS-MySQL.o:RS-MySQL.c:(.text+0x76e): undefined reference to `_mysql_options'
RS-MySQL.o:RS-MySQL.c:(.text+0x77f): undefined reference to
`_mysql_error'ost_in
RS-MySQL.o:RS-MySQL.c:(.text+0x7dc): undefined reference to `_mysql_close'
RS-MySQL.o:RS-MySQL.c:(.text+0xa7e): undefined reference to
`_mysql_close'erver_
RS-MySQL.o:RS-MySQL.c:(.text+0xaff): undefined reference to
`_mysql_fetch_fields
'S-MySQL.o:RS-MySQL.c:(.text+0x19ac): undefined reference to
`_mysql_get_proto_i
RS-MySQL.o:RS-MySQL.c:(.text+0xb18): undefined reference to
`_mysql_field_count'
RS-MySQL.o:RS-MySQL.c:(.text+0x19bd): undefined reference to
`_mysql_thread_id'
RS-MySQL.o:RS-MySQL.c:(.text+0xf14): undefined reference to
`_mysql_fetch_row''
RS-MySQL.o:RS-MySQL.c:(.text+0xf2e): undefined reference to
`_mysql_fetch_length
s'-MySQL.o:RS-MySQL.c:(.text+0x27cd): undefined reference to
`_mysql_fetch_lengt
RS-MySQL.o:RS-MySQL.c:(.text+0x1141): undefined reference to `_mysql_errno'
RS-MySQL.o:RS-MySQL.c:(.text+0x12d5): undefined reference to
`_mysql_errno'_id'
RS-MySQL.o:RS-MySQL.c:(.text+0x12e0): undefined reference to
`_mysql_error'to-im
RS-MySQL.o:RS-MySQL.c:(.text+0x1356): undefined reference to
`_mysql_fetch_row'
RS-MySQL.o:RS-MySQL.c:(.text+0x1362): undefined reference to
`_mysql_free_result
'nfo: resolving _R_NamesSymbol by linking to __imp__R_NamesSymbol
(auto-import)
RS-MySQL.o:RS-MySQL.c:(.text+0x143f): undefined reference to `_mysql_query'
RS-MySQL.o:RS-MySQL.c:(.text+0x145a): undefined reference to
`_mysql_use_result'
Info: resolving _R_NaInt by linking to __imp__R_NaInt (auto-import)
RS-MySQL.o:RS-MySQL.c:(.text+0x146e): undefined reference to
`_mysql_field_count
'nfo: resolving _R_DotsSymbol by linking to __imp__R_DotsSymbol
(auto-import)
RS-MySQL.o:RS-MySQL.c:(.text+0x152d): undefined reference to `_mysql_query'
RS-MySQL.o:RS-MySQL.c:(.text+0x155d): undefined reference to `_mysql_error'
RS-MySQL.o:RS-MySQL.c:(.text+0x159a): undefined reference to
`_mysql_affected_ro
ws'e[1]: *** [all] Error 2
RS-MySQL.o:RS-MySQL.c:(.text+0x17ab): undefined reference to
`_mysql_get_client_
info'nstallation of RMySQL failed ***
RS-MySQL.o:RS-MySQL.c:(.text+0x1959): undefined reference to
`_mysql_get_host_in
fo'oving 'c:/TEMP/Rinst346079904/RMySQL'
RS-MySQL.o:RS-MySQL.c:(.text+0x1981): undefined reference to
`_mysql_get_server_
info'tallation failed
RS-MySQL.o:RS-MySQL.c:(.text+0x19ac): undefined reference to
`_mysql_get_proto_i
nfo'
RS-MySQL.o:RS-MySQL.c:(.text+0x19bd): undefined reference to
`_mysql_thread_id'
RS-MySQL.o:RS-MySQL.c:(.text+0x265d): undefined reference to
`_mysql_fetch_row'
RS-MySQL.o:RS-MySQL.c:(.text+0x2687): undefined reference to `_mysql_errno'
RS-MySQL.o:RS-MySQL.c:(.text+0x27cd): undefined reference to
`_mysql_fetch_lengt
hs'
RS-MySQL.o:RS-MySQL.c:(.text+0x2b1d): undefined reference to
`_mysql_insert_id'
Info: resolving _R_RowNamesSymbol by linking to __imp__R_RowNamesSymbol
(auto-im
port)
Info: resolving _R_ClassSymbol by linking to __imp__R_ClassSymbol
(auto-import)
Info: resolving _R_NamesSymbol by linking to __imp__R_NamesSymbol
(auto-import)
Info: resolving _R_NilValue by linking to __imp__R_NilValue (auto-import)
Info: resolving _R_NaReal by linking to __imp__R_NaReal (auto-import)
Info: resolving _R_NaInt by linking to __imp__R_NaInt (auto-import)
Info: resolving _R_NaString by linking to __imp__R_NaString (auto-import)
Info: resolving _R_DotsSymbol by linking to __imp__R_DotsSymbol
(auto-import)
collect2: ld returned 1 exit status
make[3]: *** [RMySQL.dll] Error 1
make[2]: *** [srcDynlib] Error 2
make[1]: *** [all] Error 2
make: *** [pkg-RMySQL] Error 2
*** Installation of RMySQL failed ***
Removing 'c:/TEMP/Rinst250866757/RMySQL'
ERROR
* installation failed
joe-byers at Byersj /cygdrive/d/Program Files/R/bin
$
****************** end if cygwin window ***********************
Any help would be greatly appreciated.
Thank you
Joe
Dan Rie wrote:
> I have not replied to the list with this response, because, it's kind
of vacuous. But here are my thoughts:
>
> When I was working on getting RMySQL installed, I decided to do the
install on a machine on my LAN that did not have MySQL installed. I
retrieved all the tools to do R builds with Windows (the biggest hurdle
I faced in the whole process of trying to install RMySQL was getting
prepared to build R packages under Windows). So far I have not
succeeded on that machine. However, I did succeed on another machine
that had MySQL installed.
>
> So, I suggest that there are two possible approaches: Copy the MySQL
files that you will need onto the machine that does not have MySQL
installed. That may sound weird, but it is actually not all that
demanding. On Windows, these are the folders like "C:\Program
Files\MySQL\MYSQLS~1.0\lib", "C:\Program
Files\MySQL\MYSQLS~1.0\include", and "C:\Program
Files\MySQL\MYSQLS~1.0\bin" (there may be a few others as well). You
will need to have the various header files (for C) and the library files
and definitions. I was working with Windows and I think that you are
working with Linux, but the principle is the same - you need to have the
MySQL resource files available in order to build the RMySQL package.
There are lots of clues in the RMySQL readme and help files.
>
> It's probably easier to just install MySQL on your machine and then
you will have the files appropriate to building RMySQL available. I
don't think that you actually need to have the same version of MySQL
installed as you may be accessing on a server. However, you do have to
have some version of the libmysql library to link with the RMySQL
package in order to generate the appropriate messages to send to the server.
>
> It's not really very hard to install MySQL on your machine, even if
you don't plan to use it. I believe that when you install it it will
default to running the MySQL server on boot, but you can fix that easily
if you don't want it running (a possible security and configuration issue).
>
> If you don't have MySQL installed on your machine at all, then you
have fewer issues of incompatibility to worry about than I did. Perhaps
a fresh update of the RMySQL package will deliver a working install. I
know that the package was recently rebuilt for distribution, and the
latest version may resolve the problem if it is different from the one
that you are using.
>
> If you are still having a problem, send more specific info, and I'll
try to comment, but I am certainly no expert in R package installation
(although I do have this one success to my credit).
>
> Dan Rie
> Scituate, MA
>
>
> ----- Original Message ----- From: "Joe Byers" <joe-byers at utulsa.edu>
> To: "Dan Rie" <drie at portfoliointelligence.com>
> Cc: <r-help at stat.math.ethz.ch>
> Sent: Monday, November 06, 2006 6:25 PM
> Subject: Re: [R] Install RMySQL with R 2.4.0
>
>
>>
>> Dan Rie wrote:
>>> I had a very similar problem installing RMySQL with R 2.4.0 on
Windows XP.
>>> I beleive that the cause may have been that the RMySQL build used a
slightly older version of the MySQL compiled library functions than was
installed on my machine (I updated both MySQL, DBI, and RMySQL to latest
versions prior to attempting the install). Since RMySQL links to the
compiled MySQL library, slight differences could affect the linked
references. I do not know that this is the source of the problem, but
it was one obvious point of fraility.
>>>
>>> The solution, suggested by Prof. Brian Ripley on the r-sig-db list,
was to rebuild the RMySQL library from source prior to doing the
install. After completing the recompilation of the RMySQL package, the
install worked as it should. I believe that the binaries for RMySQL may
have been updated since I had those problems, so you might also want to
make sure that you have the latest version of all the packages.
>>>
>> What do you do if you are accessing the Mysql server remotely from
the machine that R is install upon. No MYsql libraries or other files
are stored on either of my computers.
>>
>> Thank you
>>
>>>
>>> Date: Sat, 04 Nov 2006 23:53:11 -0600
>>> From: "Joe W. Byers" <Joe-Byers at utulsa.edu>
>>> Subject: Re: [R] Install RMySQL with R 2.4.0
>>> To: r-help at stat.math.ethz.ch
>>> Message-ID: <eiju5b$ruk$1 at sea.gmane.org>
>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>
>>> Seth Falcon wrote:
>>>> "Joe W. Byers" <Joe-Byers at utulsa.edu> writes:
>>>>
>>>>> I am having trouble as well with the new version of R 2.4. I
downloaded
>>>>> the gz file from the cran website, followed the instructions in the
>>>>> README.win file and installed RMySQL. I have mysql installed under
>>>>> c:\mysql not the program files directory which is the only
difference.
>>>>>
>>>>> I get the following error when I attempt to connect to the MySQL Db
>>>>> > ## open a connection to a MySQL database
>>>>> > con <- dbConnect(dbDriver("MySQL"),host='localhost',
>>>>> + username='XXXX',dbname = 'StorageSims');
>>>>> Error in function (classes, fdef, mtable) :
>>>>> unable to find an inherited method for function "dbConnect",
>>>>> for signature "MySQLDriver"
>>>>> >
>>>>>
>>>>> Any help will be appreciated. I would like to note that there are no
>>>>> problems with RMySQL on my linux system, only on XP's.
>>>>
>>>> Just to make sure:
>>>>
>>>> Before trying the code you posted, you did library("RMySQL"), right?
>>> YES
>>>>
>>>> Also, what versions of DBI and RMySQL are you using?
>>> RMySQL from
http://cran.r-project.org/src/contrib/Descriptions/RMySQL.html
>>> DBI Version 0.1-10 according to the NEWS file in ../R/library
>>>>
>>>> ______________________________________________
>>>> R-help at stat.math.ethz.ch 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.
>>>>
>>>
>>>
>>>
>>
>>
>>
>
>
Dan Rie wrote:
> I had a very similar problem installing RMySQL with R 2.4.0 on Windows XP.
> I beleive that the cause may have been that the RMySQL build used a slightly
> older version of the MySQL compiled library functions than was installed on
> my machine (I updated both MySQL, DBI, and RMySQL to latest versions prior
> to attempting the install). Since RMySQL links to the compiled MySQL
> library, slight differences could affect the linked references. I do not
> know that this is the source of the problem, but it was one obvious point of
> fraility.
>
> The solution, suggested by Prof. Brian Ripley on the r-sig-db list, was to
> rebuild the RMySQL library from source prior to doing the install. After
> completing the recompilation of the RMySQL package, the install worked as it
> should. I believe that the binaries for RMySQL may have been updated since
> I had those problems, so you might also want to make sure that you have the
> latest version of all the packages.
>
>
> Date: Sat, 04 Nov 2006 23:53:11 -0600
> From: "Joe W. Byers" <Joe-Byers at utulsa.edu>
> Subject: Re: [R] Install RMySQL with R 2.4.0
> To: r-help at stat.math.ethz.ch
> Message-ID: <eiju5b$ruk$1 at sea.gmane.org>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Seth Falcon wrote:
>> "Joe W. Byers" <Joe-Byers at utulsa.edu> writes:
>>
>>> I am having trouble as well with the new version of R 2.4. I downloaded
>>> the gz file from the cran website, followed the instructions in the
>>> README.win file and installed RMySQL. I have mysql installed under
>>> c:\mysql not the program files directory which is the only difference.
>>>
>>> I get the following error when I attempt to connect to the MySQL Db
>>> > ## open a connection to a MySQL database
>>> > con <- dbConnect(dbDriver("MySQL"),host='localhost',
>>> + username='XXXX',dbname = 'StorageSims');
>>> Error in function (classes, fdef, mtable) :
>>> unable to find an inherited method for function "dbConnect",
>>> for signature "MySQLDriver"
>>> >
>>>
>>> Any help will be appreciated. I would like to note that there are no
>>> problems with RMySQL on my linux system, only on XP's.
>> Just to make sure:
>>
>> Before trying the code you posted, you did library("RMySQL"), right?
> YES
>> Also, what versions of DBI and RMySQL are you using?
> RMySQL from http://cran.r-project.org/src/contrib/Descriptions/RMySQL.html
> DBI Version 0.1-10 according to the NEWS file in ../R/library
>> ______________________________________________
>> R-help at stat.math.ethz.ch 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.
>>
>
> ______________________________________________
> R-help at stat.math.ethz.ch 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.
>
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