I am using MySQL and R, with the package RMySQL... (naturally)
After a computer update, and when loading RMySQL, I started getting this warning message:
RMySQL was compiled with MySQL 5.5.40 but loading MySQL 5.6.24 instead!
This may cause problems with your database connections.
Please install MySQL 5.5.40.
I would rather not have to downgrade MySQL, and was wondering if I should just compile RMySQL in order to use the newer version. Still, I couldn't find how to do it, and therefore look for a more direct answer.
Best regards,
Related
Perhaps it's a silly question, but at least for me is not that obvious. Perhaps for the naming.
I'm trying to figure out what is the correct package I'm need to use to connect my R code to a MySQL database.
I've read in the RMySQL package that:
NOTE: this package is being phased out in favor of the new RMariaDB package.
So in other words, from now on do I need to use RMariaDB package even if I'm connecting to MySQL or MySQL support is going to be dropped at some point since the databases are diverging a little bit on each version.
I specially ask in the context of MySQL 8.
Thanks!
Yes, you should use RMariaDB instead of RMySQL.
Both RMariaDB and RMySQL are using the same database driver, the MariaDB Connector/C client library for client/server communication:
MariaDB Connector/C supports all MySQL and MariaDB specific authentication methods, so connecting to a MySQL 8.0 database server shouldn't be a problem.
Beside the X-Protocol, which isn't used in R, MariaDB Connector/C also supports all MySQL specific api features.
RMariaDB supports text and binary protocol for client/server communication. Differences between MySQL and MariaDB binary protocol are handled in MariaDB Connector/C, text protocol is still the same.
RMariaDB will be a replacement for RMySQL, so in near future you will not get bug or security fixes for RMySQL anymore.
I'm installing Jira locally with the latest version (7.13 x64 version).
When doing the custom install and trying to switch to using MySQL as the database,
I get the error:
You have specified a database that is not empty, please specify an empty database.
The database is brand new, I literally just created it and if I query it I can see it has no tables created.
I created the database (and several others) using either the standard CREATE DATABASE ... or be specifying UTF-8 as well, which is how the Atlassisn docs suggest it is done.
But, no matter what I do, the same error keeps appearing. Topics on the Atlassian site mentioning this error haven't been any help and all seem to do with version conflicts which aren't relevant here.
I have installed the Java/MySQL connector version 8.0.13. Is it something to do with that?
Thanks in advance.
It was the JDBC connector that was the problem. I downloaded and installed the latest (version 8.0.13) but it was causing the error.
Installing version 5.1.47 works just fine, even though it isn't recommended for use with MySQL 5.6, which I'm using.
But, using that connector, I have a database installed and Jira is functioning as it should.
I know is so late for answer but say answer to other searcher this question
I found this error in the logs which lead me to https://jira.atlassian.com/browse/JRASERVER-67274
Loading class com.mysql.jdbc.Driver'. This is deprecated. The new driver class is com.mysql.cj.jdbc.Driver'. The driver is automatically registered via the SPI and manual loading of the driver class is generally unnecessary.
The long and short of it is you need an older mysql-connector-java-5.1.x.jar driver instead of the latest mysql-connector-java-8.0.x.jar that the documentation would lead you to install.
Reverting my driver to mysql-connector-java-5.1.49.jar fixed the issue for me.
Basically I want to know where I can find a distribution of XAMPP that uses good ol' MySQL instead of MariaDB. I have a Drupal site that runs fine on MySQL 5.5.16, but when I run it on MySQL 10.1.0-MariaDB (which was what the newer XAMPP I downloaded came with), I can't clear the caches without it corrupting the database. I know MariaDB is supposedly the same as MySQL, but this error is happening with one and not the other, and nothing else is different. Where can I get that distribution?
I am presuming you are using Windows.
According to WikiPedia, MySQL 5.5.16 came installed with XAMPP 1.7.7 and the last version of XAMPP to come with MySQL (5.6.26) was XAMPP 5.6.12. (Source)
You can find all the older versions of XAMPP on Sourceforge.
I just did a clean install of CentOS Linux. The first thing I did after installing CentOS was to download MySQL and try to install the -server rpm file. But the installation fails with a lot of messages stating conflicts with MariaDB packages which seem to be redundant to those in MySQL. I want to use MySQL as my database.
Are there any reasons why I should not just delete mariadb, so that the conflicts can be resolved? If mariadb performs some important functions in CentOS, I do not want to end up having my system crash.
You could use MariaDB as mysql version 5.5 for it is just another MYSQL branch...
In Centos 7, it is a alternative project of oracle mysql. It contains all mysql functions and optimize structures, data processing, Algorithm etc..
you could even login the server with a "mysql" command.
you don't need to pay attentions on the name, it is no problem to your former mysql projects.
ps:
I don't think that a linux system will have a "clean", "pure" os environment. Linux is a free and open source system which means you could install and remove every thing with no problem.
To have MySQL database functionality you can install either the MySQL packages or the MariaDB packages. MariaDB is a fork originating from the same MySQL code base. For compatibility see https://mariadb.com/kb/en/mariadb/mariadb-vs-mysql-compatibility/
Yes, you can remove MariaDB packages and replace them by MySQL packages.
I'm trying to install RMySQL on Windows 7 (64 bit), following the instructions at http://biostat.mc.vanderbilt.edu/wiki/Main/RMySQL. I'm using R 2.15.1, RTools 2.15, and a full installation of the latest MySQL 5.5.28 and Connector C 6.0.2, and have done the extra step of copying lib and dll files. When I run install.packages('RMySQL',type='source'), it builds but with the warning:
RMySQL was compiled with MySQL 5.5.28 but loading MySQL 6.0.0 instead!
This may cause problems with your database connections.
Please install MySQL 5.5.28.
If you have already done so, you may need to set your environment
variable MYSQL_HOME to the proper install directory.
This confuses me, as I believe I'm using a consistent and up-to-date installation of MySQL, based on the MySQL Installer (which I have also re-run to check for updates). My MYSQL_HOME variable is set to "C:/PROGRA~1/MySQL/MYSQLS~1.5/" and so also looks correct.
I'm not sure where the 6.0.0 version number in the warning is coming from. Based on searches, this appears to be an old 32-bit version of MySQL.
Is anyone able to help?
RMySQL seems to be compiled not with the latest version of MySQL that you are using. As the error message says: Install a MySQL version that is compatible with RMySQL.