Question

error when using ensembldb with a MySQL server

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Didi ▴ 10

@didi-10905

Last seen 2.2 years ago

Spain

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)

ensembldb rmysql • 1.9k views

ADD COMMENT • link updated 6.3 years ago by James W. MacDonald 65k • written 6.3 years ago by Didi ▴ 10

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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 REPLY • link 6.3 years ago Johannes Rainer ★ 2.0k

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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 REPLY • link 6.3 years ago Didi ▴ 10

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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 REPLY • link 6.3 years ago Johannes Rainer ★ 2.0k

score 0 · Answer 1 · 2017-12-28

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 13 minutes ago

United States

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.