[R] RMySQL load error
Dick Beyer
dbeyer at u.washington.edu
Tue Mar 20 22:51:24 CET 2007
I'm having trouble getting RMySQL to load. I was able to build it and install
it (RMySQL_0.5-11.tar.gz). I was also able to build and install mysql-5.0.37.
I've read many postings about this but have not found a mention of my
particular problem (some closely related). I get the "unable to load shared
library, no such file" error, but all the files do exist, RMySQL.so and
libmysqlclient.so.15.
I set these environment variables:
PKG_LIBS=-L/usr/local/lib/mysql -lmysqlclient
PKG_CPPFLAGS=-I/usr/local/include/mysql
If anyone had any suggestions, ideas, or pointers, I would be eternally
grateful for the help. Here is the relevant output from my R session and from
building the RMySQL package (I am using gcc version 3.4.6 and RedHat AS4
2.6.9-42.0.10.ELsmp):
> library(RMySQL)
Loading required package: DBI
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
'/usr/lib64/R/library/RMySQL/libs/RMySQL.so':
libmysqlclient.so.15: cannot open shared object file: No such file or
directory
Error in library(RMySQL) : .First.lib failed for 'RMySQL'
> sessionInfo()
R version 2.4.1 (2006-12-18)
x86_64-redhat-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] "stats" "graphics" "grDevices" "utils" "datasets" "methods"
[7] "base"
other attached packages:
DBI
"0.1-12"
[root at ws-bioinf-01 MySQL]# ls -l /usr/lib64/R/library/RMySQL/libs/
total 124
-rwxr-xr-x 1 root root 122497 Mar 20 11:49 RMySQL.so
[root at ws-bioinf-01 MySQL]# ll /usr/local/lib/mysql/
total 2632
-rw-r--r-- 1 root root 27208 Mar 20 11:47 libdbug.a
-rw-r--r-- 1 root root 71144 Mar 20 11:47 libheap.a
-rw-r--r-- 1 root root 465944 Mar 20 11:47 libmyisam.a
-rw-r--r-- 1 root root 41842 Mar 20 11:47 libmyisammrg.a
-rw-r--r-- 1 root root 734880 Mar 20 11:47 libmysqlclient.a
-rwxr-xr-x 1 root root 873 Mar 20 11:47 libmysqlclient.la
lrwxrwxrwx 1 root root 24 Mar 20 11:47 libmysqlclient.so ->
libmysqlclient.so.15.0.0
lrwxrwxrwx 1 root root 24 Mar 20 11:47 libmysqlclient.so.15 ->
libmysqlclient.so.15.0.0
-rwxr-xr-x 1 root root 495952 Mar 20 11:47 libmysqlclient.so.15.0.0
-rw-r--r-- 1 root root 349328 Mar 20 11:47 libmystrings.a
-rw-r--r-- 1 root root 450234 Mar 20 11:47 libmysys.a
-rw-r--r-- 1 root root 11962 Mar 20 11:47 libvio.a
[root at ws-bioinf-01 MySQL]# R CMD build RMySQL
* checking for file 'RMySQL/DESCRIPTION' ... OK
* preparing '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 'RMySQL_0.5-11.tar.gz'
[root at ws-bioinf-01 MySQL]# R CMD INSTALL RMySQL_0.5-11.tar.gz
* Installing *source* package 'RMySQL' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for compress in -lz... yes
checking for getopt_long in -lc... yes
checking for mysql_init in -lmysqlclient... no
checking for mysql.h... no
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -I/usr/lib64/R/include -I/usr/lib64/R/include -I/usr/local/include/mysql
-I/usr/local/include -fpic -O2 -g -std=gnu99 -c RS-DBI.c -o RS-DBI.o
gcc -I/usr/lib64/R/include -I/usr/lib64/R/include -I/usr/local/include/mysql
-I/usr/local/include -fpic -O2 -g -std=gnu99 -c RS-MySQL.c -o RS-MySQL.o
gcc -shared -Wl,-O1 -o RMySQL.so RS-DBI.o RS-MySQL.o -L/usr/local/lib/mysql
-lmysqlclient -lz -L/usr/lib64/R/lib -lR
** R
** inst
** save image
Loading required package: DBI
[1] "dbObjectId"
[1] "format"
[1] "show"
[1] "print"
[1] "MySQLObject"
[1] "MySQLDriver"
[1] "dbUnloadDriver"
[1] "dbGetInfo"
[1] "dbListConnections"
[1] "summary"
[1] "MySQLConnection"
[1] "dbConnect"
[1] "dbConnect"
[1] "dbConnect"
[1] "dbDisconnect"
[1] "dbSendQuery"
[1] "dbGetQuery"
[1] "dbGetException"
[1] "dbGetInfo"
[1] "dbListResults"
[1] "summary"
[1] "dbListTables"
[1] "dbReadTable"
[1] "dbWriteTable"
[1] "dbWriteTable"
[1] "dbExistsTable"
[1] "dbRemoveTable"
[1] "dbListFields"
[1] "dbCommit"
[1] "dbRollback"
[1] "dbCallProc"
[1] "MySQLResult"
[1] "dbClearResult"
[1] "fetch"
[1] "fetch"
[1] "dbGetInfo"
[1] "dbGetStatement"
[1] "dbListFields"
[1] "dbColumnInfo"
[1] "dbGetRowsAffected"
[1] "dbGetRowCount"
[1] "dbHasCompleted"
[1] "dbGetException"
[1] "summary"
[1] "dbDataType"
[1] "make.db.names"
[1] "SQLKeywords"
[1] "isSQLKeyword"
[1] "dbApply"
[1] "dbApply"
** help
>>> Building/Updating help pages for package 'RMySQL'
Formats: text html latex example
MySQL text html latex example
MySQLConnection-class text html latex example
MySQLDriver-class text html latex example
MySQLObject-class text html latex example
MySQLResult-class text html latex example
RMySQL-package text html latex example
S4R text html latex example
dbApply-methods text html latex example
dbApply text html latex example
dbBuildTableDefinition text html latex
dbCallProc-methods text html latex
dbCommit-methods text html latex example
dbConnect-methods text html latex example
dbDataType-methods text html latex example
dbDriver-methods text html latex example
dbGetInfo-methods text html latex example
dbListTables-methods text html latex example
dbObjectId-class text html latex example
dbReadTable-methods text html latex example
dbSendQuery-methods text html latex example
dbSetDataMappings-methods text html latex example
fetch-methods text html latex example
isIdCurrent text html latex example
make.db.names-methods text html latex example
mysqlDBApply text html latex example
mysqlSupport text html latex
safe.write text html latex example
summary-methods text html latex
** building package indices ...
* DONE (RMySQL)
Thanks very much,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D. University of Washington
Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100
Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer
More information about the R-help
mailing list