Question: error when using ensembldb with a MySQL server
0
gravatar for Didi
16 months ago by
Didi10
Didi10 wrote:

Hi, 

When trying to run this script through R, I've got the error highlighted in yellow. Any idea how to solve this issue?

Thanks a lot.

Cheers,

Didi

> library(ensembldb)
> library(RMySQL)
> dbcon <- dbConnect(MySQL(), host = "localhost", user = "readonly",
+                                  pass = "readonly")
Error in .local(drv, ...) : 
  Failed to connect to database: Error: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
rmysql ensembldb • 462 views
ADD COMMENTlink modified 16 months ago by James W. MacDonald49k • written 16 months ago by Didi10

This sounds like there is a problem connecting to MySQL which is independent of R. Is the MySQL server running? Can you connect using mysql -h localhost -u readonly -p ? or if you use 127.0.0.1 instead of localhost?
 

ADD REPLYlink modified 16 months ago • written 16 months ago by Johannes Rainer1.4k

Thanks a lot. When using  mysql -h localhost -u readonly -p I'm getting this error:
ERROR 1045 (28000): Access denied for user 'readonly'@'localhost' (using password: YES)

 

ADD REPLYlink written 16 months ago by Didi10

You need to create a user. Please refer to the mysql documentation for that - you'll find a lot information on the internet how to create a new user in mysql.

ADD REPLYlink written 16 months ago by Johannes Rainer1.4k
Answer: error when using ensembldb with a MySQL server
0
gravatar for James W. MacDonald
16 months ago by
United States
James W. MacDonald49k wrote:

RMySQL is a CRAN package, not Bioconductor. So you should ask your question on either r-help (r-help@r-project.org) or stackoverflow.com.

ADD COMMENTlink written 16 months ago by James W. MacDonald49k

Thanks a lot.

ADD REPLYlink written 16 months ago by Didi10
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