I have upgraded R on my Linux box from 1.5.1 to 1.6.1 using the binary
distributions for redhat 7.x.
My machine is runing:
Linux 2.4.18-3
Red Hat Linux release 7.3 (Valhalla)
After upgrading R, I executed upgrade.packages()
During the upgrading of the different packages there was an error on RMySQL.
Here is a dump of the upgrading messages:
==============================================================* Installing
*source* package 'RMySQL' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for mysql_init in -lmysqlclient... no
checking for mysql.h... no
checking for mysql_init in -lmysqlclient... no
checking for mysql_init in -lmysqlclient... yes
checking for /usr/local/include/mysql/mysql.h... no
checking for /usr/include/mysql/mysql.h... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -I/usr/lib/R/include -I/usr/include/mysql -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -fPIC -O2 -m486 -fno-strength-reduce -g -c
RS-DBI.c -o RS-DBI.o
gcc -I/usr/lib/R/include -I/usr/include/mysql -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -fPIC -O2 -m486 -fno-strength-reduce -g -c
RS-MySQL.c -o RS-MySQL.o
gcc -shared -L/usr/local/lib -o RMySQL.so RS-DBI.o RS-MySQL.o -L/usr/lib/mysql
-lmysqlclient -lz
** R
** inst
** save image
[1] TRUE
[1] "dbObjectId"
Creating a new generic function for "format" in package
RMySQL
[1] "format"
[1] "show"
Creating a new generic function for "print" in package
RMySQL
[1] "print"
Error in getProperties(ClassDef) : "slots" is not a valid slot for
this object
(or was mistakenly deleted)
Execution halted
/usr/lib/R/bin/INSTALL: line 346: 24149 Broken pipe cat
"${lib}/${pkg}/R/${pkg}"
ERROR: execution of package source for 'RMySQL' failed
====================================================
After this process if I try to use the package I get the following result:
> library(RMySQL)
Error in getProperties(ClassDef) : "slots" is not a valid slot for
this object
(or was mistakenly deleted)
Looking at the result of installed.packages() it seems that R is still using
my previous RMySQL version (0.4-6). Moreover, I cannot use it to connect to
my MySQL server anymore:
> channel<-
dbConnect(MySQL(),dbname=db,user="xxx",password="yyy")
Error in dbConnect(MySQL(), dbname = db, user = "xxx", password =
"yyy") :
couldn't find function "MySQL"
I check the mailing list for solutions but I did not find anything, although
I've noticed a similar problem report but for R1.6.0 (although there was no
answer to this other message that I could try to transpose to my problem).
Any help on solving this problem is welcome.
Thank you,
Luis Torgo
--
Luis Torgo
FEP/LIACC, University of Porto Phone : (+351) 22 607 88 30
Machine Learning Group Fax : (+351) 22 600 36 54
R. Campo Alegre, 823 email : ltorgo at liacc.up.pt
4150 PORTO - PORTUGAL WWW : http://www.liacc.up.pt/~ltorgo
