[R] RMySQL 0.6-1 Package Install Fails in R 2.5.1 (pclinuxos)

From: Matt Cook <mcook_at_cymat.com>
Date: Wed, 19 Nov 2008 08:25:57 -0500

I am having difficulties installing the RMySQL package (0.6-1) on a clean install of pclinuxos with R version 2.5.1. My version of the OS came with R-base already installed along the RKWard GUI front end.I have attempted to install the package through RKWard however I have had some problems.

I have searched google and various forums extensively but I have not found anyone with the exact same problem as myself. I am a relative novice with both Linux and R, so I am at a loss with where I should begin troubleshooting. I am fairly certain that I have installed all the required devel libraries for both R and MySQL. The package install seems to pass all the checks save for the /usr/local/include/mysql/mysql.h check. I have looked and this location does not exist. However the following check does find MySQL.h in another locale (/usr/include/mysql/mysql.h).

The package attempted install log and some relevant code are attached below. Anyhelp or suggestions provided will be greatly appreciated.

I should also mention that other packages install with no difficulties, including RMySQL's dependency, DBI.

The following is the transcript of my attempted RMySQL install:


RS-DBI.c -o RS-DBI.o
In file included from RS-DBI.c:22:
RS-DBI.h:263: error: expected ) before c RS-DBI.h:263: error: expected expression before ) token make: *** [RS-DBI.o] Error 1
chmod: cannot access `/usr/local/lib/R/library/RMySQL/libs/*': No such file or directory
ERROR: compilation failed for package 'RMySQL' ** Removing '/usr/local/lib/R/library/RMySQL'

*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_* I am very confused by the last portion of the install attempt where it seems to have problems with the RS-DBI header & C files. I will include the suspect code lines that that are identified:

RS-DBI.c line 22 --> #include "RS-DBI.h"

/* We now define a generic data type name-Id mapping struct
* and initialize the RS_dataTypeTable[]. Each driver could

struct data_types {
char *typeName;
Sint typeId;

/* return the primitive type name for a primitive type id */ char *RS_DBI_getTypeName(Sint typeCode, const struct data_types table[]); /* same, but callable from S/R and vectorized */

s_object *RS_DBI_SclassNames(s_object *types); s_object *RS_DBI_createNamedList(char

**names, Stype *types, Sint *lengths, Sint n); s_object *RS_DBI_copyFields(RS_DBI_fields *flds); void RS_na_set(void *ptr, Stype type);
int RS_is_na(void *ptr, Stype type);
extern const struct data_types RS_dataTypeTable[];

int isalpha(int c); <-------------------------------------LINE 263

#ifdef __cplusplus


Matt Cook
Junior Engineer

Cymat Technologies Ltd.
6320-2 Danville Road
Mississauga, Ontario, Canada, L5T 2L7
P: (905) 696-9900 x2425 / F: (905) 696-9300

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Received on Wed 19 Nov 2008 - 13:30:04 GMT

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