How to select MySQL version when installing RMySQL in linux - mysql

Question

I am running an R application in a Docker container and would like to connect to a MySQL 8 database using the RMySQL library. I can connect to the database from the container using the mysql terminal command without any problems, but when I call dbConnect() in my R script I get an unknown SSL connection error (see below).
As I am using the same SSL certificates with the terminal command as well as in my R script, it must have something to do with the MySQL version used by RMySQL. I need to have MySQL 5.7 installed in the container, too, as some other R packages cannot be built otherwise. However, according to the thread below you can specify the directory of the MySQL version to be used when installing RMySQL:
adding RMySQL package to R fails (on Windows)?
So I set $MYSQL_HOME in /etc/R/Renviron.site and called install.packages('RMySQL',type='source').
Apparently you also need to copy some .lib and .dll files to make it work in Windows, but where do I find the equivalent files in Linux?
Database handler script:
#' #import DBI
#' #import RMySQL
connectToDatabase <- function(myproject.db_config) {
dbConfig <- read.properties(myproject.db_config)
print(dbConfig)
dbHandle <- dbConnect(
MySQL(),
dbname = dbConfig$databaseName,
host = dbConfig$host,
port = as.integer(dbConfig$port),
user = dbConfig$user,
password = dbConfig$password
)
return(dbHandle)
}
Config file passed to the read.properties() command:
host=domain.subdomain.de
port=3306
user=john.doe
password=mypassword
databaseName=my_db
ssl-ca=/staging/mysql-ssl/ca.pem
ssl-cert=/staging/mysql-ssl/client-cert.pem
ssl-key=/staging/mysql-ssl/client-key.pem
Error message in R:
Error in connection_create(host, username, password, dbname, as.integer(port), :
Failed to connect: SSL connection error: unknown error number

Answer 1

I found the solution by myself. The SSL certificates were not applied in the dbConnect() call. They need to be defined in a mysql.cnf file which is passed to dbConnect() in the default.file parameter:
dbHandle <- dbConnect(
MySQL(),
dbname = dbConfig$databaseName,
host = dbConfig$host,
port = as.integer(dbConfig$port),
user = dbConfig$user,
password = dbConfig$password,
default.file = dbConfig$configFile
)
Config file passed to the read.properties() command:
host=domain.subdomain.de
port=3306
user=john.doe
password=mypassword
databaseName=my_db
configFile=/staging/config/mysql.cnf
mysql.cnf:
[mysqld]
ssl-ca=/staging/mysql-ssl/ca.pem
ssl-cert=/staging/mysql-ssl/client-cert.pem
ssl-key=/staging/mysql-ssl/client-key.pem