Problem installing RODBC

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Problem installing RODBC

David Scott-6
I have a problem with some missing headers when trying to install RODBC
on my linux box.

 > install.packages("RODBC",
+                   lib="/usr/local/david/R")
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/RODBC_1.3-1.tar.gz'
Content type 'application/x-gzip' length 990220 bytes (967 Kb)
opened URL
==================================================
downloaded 967 Kb


  Read .Rprofile
* installing *source* package ‘RODBC’ ...
checking for gcc... gcc -m32 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -m32 -std=gnu99 accepts -g... yes
checking for gcc -m32 -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -m32 -std=gnu99 -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking sql.h usability... no
checking sql.h presence... no
checking for sql.h... no
checking sqlext.h usability... no
checking sqlext.h presence... no
checking for sqlext.h... no
configure: error: "ODBC headers sql.h and sqlext.h not found"
ERROR: configuration failed for package ‘RODBC’
* removing ‘/usr/local/david/R/RODBC’


Details of my setup are:

 > R.version
                _
platform       i386-redhat-linux-gnu
arch           i386
os             linux-gnu
system         i386, linux-gnu
status
major          2
minor          10.0
year           2009
month          10
day            26
svn rev        50208
language       R
version.string R version 2.10.0 (2009-10-26)

I have the following mysql setup

mysql> status;
--------------
mysql  Ver 14.12 Distrib 5.0.88, for redhat-linux-gnu (i386) using
readline 5.1

Connection id: 9
Current database:
Current user: root@localhost
SSL: Not in use
Current pager: stdout
Using outfile: ''
Using delimiter: ;
Server version: 5.0.88 Source distribution
Protocol version: 10
Connection: Localhost via UNIX socket
Server characterset: latin1
Db     characterset: latin1
Client characterset: latin1
Conn.  characterset: latin1
UNIX socket: /var/lib/mysql/mysql.sock
Uptime: 95 days 19 hours 18 min 27 sec


I am guessing my MySQL is getting a bit decrepit and needs updating, but
welcome any suggestions about sorting this out.


David Scott
--
_________________________________________________________________
David Scott Department of Statistics
                The University of Auckland, PB 92019
                Auckland 1142,    NEW ZEALAND
Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055
Email: [hidden email],  Fax: +64 9 373 7018

Director of Consulting, Department of Statistics

______________________________________________
[hidden email] 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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Re: Problem installing RODBC

Marc Schwartz-3
On Apr 19, 2010, at 7:02 PM, David Scott wrote:

> I have a problem with some missing headers when trying to install RODBC on my linux box.
>
> > install.packages("RODBC",
> +                   lib="/usr/local/david/R")
> trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/RODBC_1.3-1.tar.gz'
> Content type 'application/x-gzip' length 990220 bytes (967 Kb)
> opened URL
> ==================================================
> downloaded 967 Kb
>
>
> Read .Rprofile
> * installing *source* package ‘RODBC’ ...
> checking for gcc... gcc -m32 -std=gnu99
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc -m32 -std=gnu99 accepts -g... yes
> checking for gcc -m32 -std=gnu99 option to accept ANSI C... none needed
> checking how to run the C preprocessor... gcc -m32 -std=gnu99 -E
> checking for egrep... grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking sql.h usability... no
> checking sql.h presence... no
> checking for sql.h... no
> checking sqlext.h usability... no
> checking sqlext.h presence... no
> checking for sqlext.h... no
> configure: error: "ODBC headers sql.h and sqlext.h not found"
> ERROR: configuration failed for package ‘RODBC’
> * removing ‘/usr/local/david/R/RODBC’
>
>
> Details of my setup are:
>
> > R.version
>               _
> platform       i386-redhat-linux-gnu
> arch           i386
> os             linux-gnu
> system         i386, linux-gnu
> status
> major          2
> minor          10.0
> year           2009
> month          10
> day            26
> svn rev        50208
> language       R
> version.string R version 2.10.0 (2009-10-26)
>
> I have the following mysql setup
>
> mysql> status;
> --------------
> mysql  Ver 14.12 Distrib 5.0.88, for redhat-linux-gnu (i386) using readline 5.1
>
> Connection id: 9
> Current database:
> Current user: root@localhost
> SSL: Not in use
> Current pager: stdout
> Using outfile: ''
> Using delimiter: ;
> Server version: 5.0.88 Source distribution
> Protocol version: 10
> Connection: Localhost via UNIX socket
> Server characterset: latin1
> Db     characterset: latin1
> Client characterset: latin1
> Conn.  characterset: latin1
> UNIX socket: /var/lib/mysql/mysql.sock
> Uptime: 95 days 19 hours 18 min 27 sec
>
>
> I am guessing my MySQL is getting a bit decrepit and needs updating, but welcome any suggestions about sorting this out.
>
>
> David Scott


The missing header files are contained in the unixODBC-devel RPM, which you will need to install and then you should be able to install RODBC. Recent RH/Fedora installations use 'yum' for package management, so something like:

  yum install unixODBC-devel

as root, should get you what you need.

Also, there is the R package RMySQL which provides an alternative interface to MySQL, if you should wish to investigate that approach.

Finally, there is the R-SIG-DB list which provides a focused audience for R and DB related matters:

  https://stat.ethz.ch/mailman/listinfo/r-sig-db

HTH,

Marc Schwartz

______________________________________________
[hidden email] 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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Re: Problem installing RODBC

David Scott-6
Marc Schwartz wrote:

> On Apr 19, 2010, at 7:02 PM, David Scott wrote:
>
>> I have a problem with some missing headers when trying to install RODBC on my linux box.
>>
>>> install.packages("RODBC",
>> +                   lib="/usr/local/david/R")
>> trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/RODBC_1.3-1.tar.gz'
>> Content type 'application/x-gzip' length 990220 bytes (967 Kb)
>> opened URL
>> ==================================================
>> downloaded 967 Kb
>>
>>
>> Read .Rprofile
>> * installing *source* package ‘RODBC’ ...
>> checking for gcc... gcc -m32 -std=gnu99
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc -m32 -std=gnu99 accepts -g... yes
>> checking for gcc -m32 -std=gnu99 option to accept ANSI C... none needed
>> checking how to run the C preprocessor... gcc -m32 -std=gnu99 -E
>> checking for egrep... grep -E
>> checking for ANSI C header files... yes
>> checking for sys/types.h... yes
>> checking for sys/stat.h... yes
>> checking for stdlib.h... yes
>> checking for string.h... yes
>> checking for memory.h... yes
>> checking for strings.h... yes
>> checking for inttypes.h... yes
>> checking for stdint.h... yes
>> checking for unistd.h... yes
>> checking sql.h usability... no
>> checking sql.h presence... no
>> checking for sql.h... no
>> checking sqlext.h usability... no
>> checking sqlext.h presence... no
>> checking for sqlext.h... no
>> configure: error: "ODBC headers sql.h and sqlext.h not found"
>> ERROR: configuration failed for package ‘RODBC’
>> * removing ‘/usr/local/david/R/RODBC’
>>
>>
>> Details of my setup are:
>>
>>> R.version
>>               _
>> platform       i386-redhat-linux-gnu
>> arch           i386
>> os             linux-gnu
>> system         i386, linux-gnu
>> status
>> major          2
>> minor          10.0
>> year           2009
>> month          10
>> day            26
>> svn rev        50208
>> language       R
>> version.string R version 2.10.0 (2009-10-26)
>>
>> I have the following mysql setup
>>
>> mysql> status;
>> --------------
>> mysql  Ver 14.12 Distrib 5.0.88, for redhat-linux-gnu (i386) using readline 5.1
>>
>> Connection id: 9
>> Current database:
>> Current user: root@localhost
>> SSL: Not in use
>> Current pager: stdout
>> Using outfile: ''
>> Using delimiter: ;
>> Server version: 5.0.88 Source distribution
>> Protocol version: 10
>> Connection: Localhost via UNIX socket
>> Server characterset: latin1
>> Db     characterset: latin1
>> Client characterset: latin1
>> Conn.  characterset: latin1
>> UNIX socket: /var/lib/mysql/mysql.sock
>> Uptime: 95 days 19 hours 18 min 27 sec
>>
>>
>> I am guessing my MySQL is getting a bit decrepit and needs updating, but welcome any suggestions about sorting this out.
>>
>>
>> David Scott
>
>
> The missing header files are contained in the unixODBC-devel RPM, which you will need to install and then you should be able to install RODBC. Recent RH/Fedora installations use 'yum' for package management, so something like:
>
>   yum install unixODBC-devel
>
> as root, should get you what you need.
>
> Also, there is the R package RMySQL which provides an alternative interface to MySQL, if you should wish to investigate that approach.
>
> Finally, there is the R-SIG-DB list which provides a focused audience for R and DB related matters:
>
>   https://stat.ethz.ch/mailman/listinfo/r-sig-db
>
> HTH,
>
> Marc Schwartz
>

Thanks Marc, super helpful and quick as well. Worked a treat.

David

--
_________________________________________________________________
David Scott Department of Statistics
                The University of Auckland, PB 92019
                Auckland 1142,    NEW ZEALAND
Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055
Email: [hidden email],  Fax: +64 9 373 7018

Director of Consulting, Department of Statistics

______________________________________________
[hidden email] 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.