Installation issues

Fail to start

On Ubuntu 12.04, we can use

sudo dpkg-reconfigure mysql-server-5.5

InnoDB vs MyISAM

The default is InnoDB.

Under Shell

Manual/Documentation

https://dev.mysql.com/doc/refman

MariaDB vs MySQL

Check server version

Check mySQL and MariaDB Server Version

Installation, setup root password, remove the need of 'sudo'

How to install MySQL 8 on Debian 10. It includes how to secure it and how to back up.
Installing MariaDB Database Server On Ubuntu 18.04 LTS Server
How to Install MariaDB on Ubuntu 18.04
How to Install Wallabag on Ubuntu 18.04 LTS
How to install MySQL server on Ubuntu 22.04 LTS Linux
The Perfect Server - Ubuntu 18.04 (Bionic Beaver) with Apache, PHP, MySQL, PureFTPD, BIND, Postfix, Dovecot and ISPConfig 3.1. Edit /etc/mysql/debian.cnf file and set the root password there in addition to setting the root password by mysql_secure_installation.
How to create MySQL admin user (superuser) account MySQL 8.x or MariaDB 10.4+

Debian 9 (Stretch) package now ships with the UNIX_SOCKET authentication plugin enabled and you are no longer asked to set a root password when installing the package. Even when setting a root password via the mysql_secure_installation script you are still denied. So we need to run 'update'; see the command below.

See a solution at Debian 9 “Stretch” and MySQL/MariaDB root password.

$ sudo apt-get install mysql-server

$ sudo systemctl status mariadb
$ sudo systemctl start mariadb.service
$ sudo systemctl enable mariadb.service

$ sudo mysql_secure_installation  # type the new root password for your MariaDB server and 
                                  # type 'Y' for all configurations
               Enter current password for root (enter for none):
               Set a root password? [y/n] y
               Remove anonymous users? [y/n] y
               Disallow root login remotely? [y/n] y
               Remove test database and access to it? [y/n] y
               Reload privilege tables now? [y/n] y

$ sudo mysql -u root mysql -e "update user set plugin='' where user='root'; flush privileges;"
## With the above command, I don't need 'sudo' in the next command
$ mysql -u root -p
...
Welcome to the MariaDB monitor.  Commands end with ; or \g.
Your MariaDB connection id is 12
Server version: 10.1.23-MariaDB-9+deb9u1 Raspbian 9.0
...
MariaDB [(none)]> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| mysql              |
| performance_schema |
+--------------------+
3 rows in set (0.02 sec)

MariaDB [(none)]> exit
Bye

Access denied for user 'root'@'localhost'

sudo service mysql stop
sudo mkdir -p /var/run/mysqldsudo chown mysql:mysql /var/run/mysqld
sudo /usr/sbin/mysqld --skip-grant-tables --skip-networking &
mysql -u root
mysql> FLUSH PRIVILEGES;
mysql> USE mysql;
mysql> UPDATE user SET authentication_string=PASSWORD("MyPASSWORDHERE") WHERE User='root';
mysql> UPDATE user SET plugin="mysql_native_password" WHERE User='root';
mysql> quit
sudo pkill mysqld
sudo service mysql start

MyPASSWORDHERE can be as short as 2 characters.

Reset root password

https://www.digitalocean.com/community/tutorials/how-to-reset-your-mysql-or-mariadb-root-password

Installing MariaDB Binary Tarballs

Authentication

MySQL 8.0. "Authentication plugin 'caching_sha2_password'
Fixing "Authentication plugin 'caching_sha2_password' cannot be loaded" errors - revert to the mysql_native_password mechanism.
Upgrading to MySQL 8.0 : Default Authentication Plugin Considerations
Authentication Plugin - SHA-256

Uninstall

sudo service mysql stop
sudo apt-get --purge remove "mysql*"
sudo mv /etc/mysql/ /tmp/mysql_configs/
sudo reboot

How do I turn off the mysql password validation?

Normally a password as short as 3 characters is enough for the root user.

https://stackoverflow.com/questions/36301100/how-do-i-turn-off-the-mysql-password-validation

Create a new local user account to grant access to a database

http://www.cyberciti.biz/faq/mysql-user-creation/

NOTE: please be mindful when creating a user name. There is no protection against creating an old user's name. If you accidentally create a same user name as say mediawiki DB user, then mediawiki will not be working.

$ mysql -u root -p
OR
$ mysql -u root -h myserver-sever.com -p

Create a new mysql database called demo;

mysql> CREATE DATABASE testdb;

Create a new user called user1 for database demo

mysql> GRANT ALL ON testdb.* TO user1@localhost IDENTIFIED BY 'mypassword';

If we quit mysql and log in again using the new account, the 'SHOW DATABASES' will only show databases that the new account can access

mysql> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| testdb             |
+--------------------+
2 rows in set (0.00 sec)

User user1 can connect to mysql server demo database using following command:

$ mysql -u user1 -p testdb
OR
$ mysql -u user1 -h mysql.server.com -p testdb

Create Remote MySQL user and grant remote access to databases

How to Allow MySQL remote connections in Ubuntu Server 18.04

Show all users

SELECT User, Host, Password FROM mysql.user; 

SELECT DISTINCT User FROM mysql.user;

Show the privileges of a user

mysql> SHOW GRANTS FOR 'user1'@'localhost';
+--------------------------------------------------------------------------------------------------------------+
| Grants for user1@localhost                                                                                   |
+--------------------------------------------------------------------------------------------------------------+
| GRANT USAGE ON *.* TO 'user1'@'localhost' IDENTIFIED BY PASSWORD '*FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF' |
| GRANT ALL PRIVILEGES ON `testdb`.* TO 'user1'@'localhost'                                                    |
+--------------------------------------------------------------------------------------------------------------+
2 rows in set (0.00 sec)

Another way is through phpMyAdmin. Click on 'Databases' and in the Action column click 'Check Privileges' in the corresponding row of the desired database.

Remove an account

DROP USER 'jeffrey'@'localhost';

Remove a database

mysql> DROP DATABASE db_name;
mysql> SHOW DATABASES;

Show the current user

mysql> SELECT USER();

Show the current database

mysql> SELECT DATABASE();

Note on MariaDB it shows the current database.

MariaDB [(none)]> use mysql
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
MariaDB [mysql]>

How do you deselect MySQL database?

https://stackoverflow.com/questions/27895328/how-do-you-deselect-mysql-database. Ans: You just select another database and USE it.

Version vs Distrib number of MySQL

https://stackoverflow.com/questions/8645184/version-vs-distrib-number-of-mysql

Ver refers to the version of the mysql command line client - what you are envoking by typing 'mysql'
Distrib refers to the mysql server version your client was built with. This is not to be confused with the mysql server you are connected to, which can be obtained with SELECT VERSION();

On Ubuntu 14.04

$ mysql --version
mysql  Ver 14.14 Distrib 5.5.58, for debian-linux-gnu (x86_64) using readline 6.3

$ mysql -u root -p -e 'select version()'
Enter password: 
+-------------------------+
| version()               |
+-------------------------+
| 5.5.58-0ubuntu0.14.04.1 |
+-------------------------+

On Docker's MySQL

# mysql --version
mysql  Ver 14.14 Distrib 5.7.20, for Linux (x86_64) using  EditLine wrapper

# mysql --user=root --password=$MYSQL_ROOT_PASSWORD -e 'select version()'
mysql: [Warning] Using a password on the command line interface can be insecure.
+-----------+
| version() |
+-----------+
| 5.7.20    |
+-----------+

MYSQL commands

Find out about your MySQL version and all installed plugins:

mysql> select version();
mysql> show plugins;

Executing SQL Statements from a Text File

$ mysql db_name

$ mysql -h host -u user -p db_name # db_name is not a password !

$ mysql -h host -u user -pPASSWORD db_name # no space after "-p"

$ mysql db_name < text_file # text_file that contains the statements you wish to execute/Batch mode
$ mysql db_name < text_file > output.txt
mysql> source file_name

Note when I test it on raspbian, I get errors Access denied for user 'testuser'@'localhost' (using password: YES).

It works after I follow these 2 suggestions

https://stackoverflow.com/questions/6091427/mysql-into-outfile-access-denied-but-my-user-has-all-access-and-the-fold GRANT FILE ON *.* TO 'asdfsdf'@'localhost';
https://www.raspberrypi.org/forums/viewtopic.php?p=1326803 Creating a new directory and change directory attributes mkdir /tmp/data; chmod 777 /tmp/data

Following the exercise here,

$ mysql -u testuser -ptestpass -e \
  "Use testrdb; SELECT * FROM motortrend WHERE model = 'RX4' INTO OUTFILE '/tmp/data/rx4.csv'"
$ cat /tmp/data/rx4.csv
Mazda RX4	21	6	160	110	3.9	2.62	16.46	0	1	4	4	Mazda	RX4
newrow	21	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	RX4

Create a table

Note that a database have multiple tables.

mysql> CREATE DATABASE testdb;
mysql> USE testdb
mysql> CREATE TABLE pet (name VARCHAR(20), owner VARCHAR(20),
    -> species VARCHAR(20), sex CHAR(1), birth DATE, death DATE);

OR put it in a text file

mysql> CREATE TABLE pet
{
    name VARCHAR(20),
    owner VARCHAR(20),
    species VARCHAR(20), 
    sex CHAR(1), 
    birth DATE, 
    death DATE
}

Show all tables.

mysql> SHOW TABLES;

Verify your table

mysql> DESCRIBE pet;

Loading data into a table

https://dev.mysql.com/doc/refman/5.7/en/loading-tables.html

mysql> LOAD DATA LOCAL INFILE '/path/pet.txt' INTO TABLE pet;

OR using the mysqlimport utility from the shell

$ mysqlimport --local pet /path/pet.txt

You could add a new record using an INSERT statement like this:

mysql> INSERT INTO pet
    -> VALUES ('Puffball','Diane','hamster','f','1999-03-30',NULL);

Retrieve data

https://dev.mysql.com/doc/refman/5.7/en/retrieving-data.html General form

SELECT what_to_select
FROM which_table
WHERE conditions_to_satisfy;

Some examples

mysql> SELECT * FROM pet;

mysql> UPDATE pet SET birth = '1989-08-31' WHERE name = 'Bowser';

mysql> SELECT * FROM pet WHERE name = 'Bowser';

mysql> SELECT * FROM pet WHERE birth >= '1998-1-1';

mysql> SELECT * FROM pet WHERE species = 'dog' AND sex = 'f';

mysql> SELECT * FROM pet WHERE (species = 'cat' AND sex = 'm')
    -> OR (species = 'dog' AND sex = 'f');

mysql> SELECT name, birth FROM pet;

mysql> SELECT DISTINCT owner FROM pet;

mysql> SELECT name, birth FROM pet ORDER BY birth;

mysql> SELECT name, birth FROM pet ORDER BY birth DESC;  # To sort in reverse (descending) order

mysql> SELECT name, birth FROM pet WHERE MONTH(birth) = 5;

Pattern match

mysql> SELECT * FROM pet WHERE name LIKE 'b%'; # find names beginning with b, case-insensitive

mysql> SELECT * FROM pet WHERE name LIKE '%fy'; # find names ending with fy:

mysql> SELECT * FROM pet WHERE name LIKE '%w%'; # find names containing a w:

Count rows

mysql> SELECT COUNT(*) FROM pet;

mysql> SELECT COUNT(DISTINCT owner) FROM pet;

mysql> SELECT owner, COUNT(*) FROM pet GROUP BY owner;

Retrieve information from multiple tables https://dev.mysql.com/doc/refman/5.7/en/multiple-tables.html

# suppose we have two tables event & score; each has a column called event_id
# score table has columns: name, event_id, score
# event table has columns: event_id, date, type
mysql> SELECT student_id, date, score, type 
    -> FROM event, score
    -> WHERE date = "1999-09-20"
    -> AND event.event_id = score.event_id;

Mysql list tables and sizes - order by size

https://stackoverflow.com/questions/14569940/mysql-list-tables-and-sizes-order-by-size

SELECT TABLE_NAME, table_rows, data_length, index_length, 
    round(((data_length + index_length) / 1024 / 1024),2) "Size in MB"
    FROM information_schema.TABLES WHERE table_schema = "schema_name"
    ORDER BY (data_length + index_length) DESC;

Note: replace "schema_name" with your database name.

Find first and last record from mysql table

https://stackoverflow.com/questions/2735395/how-to-find-first-and-last-record-from-mysql-table

# get the fields name
Show columns from tablename;

# To get the first record:
select col1 from tab1 order by col1 asc limit 1;   

# To get the last record:
select col1 from tab1 order by col1 desc  limit 1;

# To get the last few records
select * from tab1 order by col2 desc limit 10;

Write/save a table/query to a text file

# Method 1. mysql. Get a permission denied error 
$ mysql -u root -p
> SELECT * FROM tbl_name INTO OUTFILE '/tmp/orders.txt';

# Method 2. shell. Simple solution; does not need to change FILE privileges.
# https://stackoverflow.com/questions/9462416/shell-one-line-query
mysql -u root -pmy_password -h ip_add --port=13306 -D DATABASENAME -e "SELECT * FROM tbl_name;" > output.txt

Create a database 'demo' and a table 'employee'

http://www.thegeekstuff.com/2011/10/mysql-tutorial-basics/

mysql -u guest -p demo
show databases;
use demo;
show tables;
create table employee .............;
desc employee;
insert into employee .............;
select * from employee;

Access mysql using perl

http://www.cyberciti.biz/faq/how-to-access-mysql-database-using-perl

How to See Which MySQL Tables are Taking the Most Space

https://www.howtogeekpro.com/166/how-to-see-which-mysql-tables-are-taking-the-most-space/

Check a Value in a MySQL Database from a Linux Bash Script

Dates and times

How to Work Effectively With Dates and Times in MySQL

Administration

Default port

3306

phpMyAdmin

http://localhost/phpmyadmin with default username: root and the admin password you have chosen during the installation of phpMyAdmin.

phpMyAdmin is installed under /usr/share/phpmyadmin.

Note that index.php file does not appear in /var/www/html directory. Why? A standard Apache Alias pointing every request starting with /phpmyadmin to the phpMyAdmin installation directory. See Setting up and securing a phpMyAdmin install on Ubuntu 10.04

udooer@udoo:~$ ls -l /var/www/html
total 12
-rw-r--r-- 1 root root 11510 Dec 24 13:44 index.html
lrwxrwxrwx 1 root root    18 Dec 24 14:00 mediawiki -> /var/lib/mediawiki

udooer@udoo:~$ ls -lah /etc/apache2/
total 88K
drwxr-xr-x   8 root root 4.0K Dec 24 13:44 .
drwxr-xr-x 121 root root 4.0K Dec 25 08:15 ..
-rw-r--r--   1 root root 7.0K Jan  7  2014 apache2.conf
drwxr-xr-x   2 root root 4.0K Dec 25 08:15 conf-available
drwxr-xr-x   2 root root 4.0K Dec 25 08:15 conf-enabled
-rw-r--r--   1 root root 1.8K Jan  3  2014 envvars
-rw-r--r--   1 root root  31K Jan  3  2014 magic
drwxr-xr-x   2 root root  12K Dec 24 13:45 mods-available
drwxr-xr-x   2 root root 4.0K Dec 24 13:45 mods-enabled
-rw-r--r--   1 root root  320 Jan  7  2014 ports.conf
drwxr-xr-x   2 root root 4.0K Dec 24 13:44 sites-available
drwxr-xr-x   2 root root 4.0K Dec 24 13:44 sites-enabled

udooer@udoo:~$ ls -laH /etc/apache2/sites-available/
total 20
drwxr-xr-x 2 root root 4096 Dec 24 13:44 .
drwxr-xr-x 8 root root 4096 Dec 24 13:44 ..
-rw-r--r-- 1 root root 1332 Jan  7  2014 000-default.conf
-rw-r--r-- 1 root root 6437 Jan  7  2014 default-ssl.conf

udooer@udoo:~$ ls -lah /etc/apache2/conf-enabled/
total 8.0K
drwxr-xr-x 2 root root 4.0K Dec 25 08:15 .
drwxr-xr-x 8 root root 4.0K Dec 24 13:44 ..
lrwxrwxrwx 1 root root   30 Dec 24 13:44 charset.conf -> ../conf-available/charset.conf
lrwxrwxrwx 1 root root   40 Dec 25 08:13 javascript-common.conf -> ../conf-available/javascript-common.conf
lrwxrwxrwx 1 root root   44 Dec 24 13:44 localized-error-pages.conf -> ../conf-available/localized-error-pages.conf
lrwxrwxrwx 1 root root   46 Dec 24 13:44 other-vhosts-access-log.conf -> ../conf-available/other-vhosts-access-log.conf
lrwxrwxrwx 1 root root   33 Dec 25 08:15 phpmyadmin.conf -> ../conf-available/phpmyadmin.conf
lrwxrwxrwx 1 root root   31 Dec 24 13:44 security.conf -> ../conf-available/security.conf
lrwxrwxrwx 1 root root   36 Dec 24 13:44 serve-cgi-bin.conf -> ../conf-available/serve-cgi-bin.conf

udooer@udoo:~$ cat /etc/apache2/conf-available/phpmyadmin.conf 
# phpMyAdmin default Apache configuration

Alias /phpmyadmin /usr/share/phpmyadmin

<Directory /usr/share/phpmyadmin>
	Options FollowSymLinks
	DirectoryIndex index.php

	<IfModule mod_php5.c>
		AddType application/x-httpd-php .php

		php_flag magic_quotes_gpc Off
		php_flag track_vars On
		php_flag register_globals Off
		php_admin_flag allow_url_fopen Off
		php_value include_path .
		php_admin_value upload_tmp_dir /var/lib/phpmyadmin/tmp
		php_admin_value open_basedir /usr/share/phpmyadmin/:/etc/phpmyadmin/:/var/lib/phpmyadmin/:/usr/share/php/php-gettext/:/usr/share/javascript/
	</IfModule>

</Directory>

If we want to change the URL or the port number of phpMyAdmin, follow this.

Configuration files

MySQL Docker Containers: Understanding the basics

On Ubuntu 18.04

$ sudo apt update
$ sudo apt install mariadb-server mariadb-client
$ sudo systemctl status mariadb
$ sudo mysql_secure_installation
$ mysql –u root -p
mysql  Ver 15.1 Distrib 10.1.41-MariaDB, for debian-linux-gnu (x86_64) using readline 5.2
Copyright (c) 2000, 2018, Oracle, MariaDB Corporation Ab and others.

Usage: mysql [OPTIONS] [database]

Default options are read from the following files in the given order:
/etc/my.cnf /etc/mysql/my.cnf ~/.my.cnf 
...

Ubuntu 18.04 configuration file location /etc/mysql/mariadb.conf.d/50-server.cnf

This can be found by using mysql --help or mysqld --help --verbose. On Ubuntu 16.04, it shows

$ mysql --help
...
Default options are read from the following files in the given order:
/etc/my.cnf /etc/mysql/my.cnf ~/.my.cnf
...
$ tree /etc/mysql/
/etc/mysql/
├── conf.d
│   ├── mysql.cnf
│   └── mysqldump.cnf
├── debian.cnf
├── debian-start
├── my.cnf -> /etc/alternatives/my.cnf
├── my.cnf.fallback
├── mysql.cnf
└── mysql.conf.d
    ├── mysqld.cnf
    └── mysqld_safe_syslog.cnf

2 directories, 9 files

Errors

Can't connect to local MySQL server through socket '/var/mysql/mysql.sock' (38)
Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (on Debian 10) when I run sudo mysql_secure_installation after I installed mariadb-server.

Solution: Make sure to run the following after installing mariadb-server

sudo systemctl start mariadb.service
sudo systemctl enable mariadb.service

Default database location

On Debian/Ubuntu, it is /var/lib/mysql.

$ mysql -uroot -p -e 'SHOW VARIABLES WHERE Variable_Name = "datadir"'

OR

mysql> select @@datadir;

Change data location

https://stackoverflow.com/questions/1795176/how-to-change-mysql-data-directory

sudo /etc/init.d/mysql stop
sudo cp -R -p /var/lib/mysql /newpath
sudo gedit /etc/mysql/my.cnf
Look for the entry for datadir, and change the path (which should be /var/lib/mysql) to the new data directory.
sudo gedit /etc/apparmor.d/usr.sbin.mysqld
Look for lines beginning with /var/lib/mysql. Change /var/lib/mysql in the lines with the new path.
sudo /etc/init.d/apparmor reload
sudo /etc/init.d/mysql restart

Full Backup and Restore with Mariabackup

The mariabackup command is a physical backup method (cf SQL command is a logical backup method)
- A physical backup involves copying the data files directly. It is faster and more efficient, but less portable. These data files are specific to the hardware, operating system, and version of MariaDB that you are using.
- A logical backup exports the data in a human-readable format such as SQL, while a physical backup copies the raw data files directly.
MariaDB Backup or here
You can restore the backup using the rsync command (as long as the MariaDB Server process is stopped on the target server, you can technically restore the backup using any file copying tool, such as cp or rysnc). sudo systemctl restart mysqld

$ mariabackup --backup \
   --target-dir=/var/mariadb/backup/ \
   --user=mariabackup --password=mypassword

$ mariabackup --prepare \
   --target-dir=/var/mariadb/backup/
$ mariabackup --copy-back \
   --target-dir=/var/mariadb/backup/

How to backup/export and load/import a single database and/or table from a MySQL database

# Export
# Method 1: directly
$ mysqldump -u USERNAME --password="PW" DB_NAME > backup.sql
# Method 2: gzip
$ mysqldump -u USERNAME --password="PW" DB_NAME | gzip --best --verbose > backup.sql.gz
# Multiple database
$ mysqldump -u USERNAME --password="PW" --all-databases > all_databases.sql

# Import 
$ mysql -u UserName -p Password -e 'Create Database DB_NAME'
# Method 1 (the database needs to be created first)
$ mysql -u UserName -p Password -h Hostname DB_NAME < backup.sql
# Method 2 (not working?)
$ mysqlimport -u UserName -p Password backup.sql
# Multiple database (no need to create an empty database)
$ mysql -u UserName -p < backup.sql

Note that

the back up file is a text file.
it seems it is common to use sql as the extension name
the user information will not be retained in the backup file.
the original database name is saved in the backup file
the database name DB_NAME in importing is required. It the database name does not to be the same as the original if only one database was dumped. However the database DB_NAME has to be created beforehand (mysql> CREATE DATABASE DB_NAME2). If the database has not existed or we omit the DB_NAME in importing, we will get an error

ERROR 1046 (3D000) at line 22: No database selected

# or
ERROR 1049 (42000): Unknown database 'testdb'

Export a CSV file

How to export a CSV file from MySQL command line

Move the MySQL data directory

SSL

How to set up MariaDB SSL and secure connections from clients

Secure Your Database

How Should You Secure Your Database?

Injection attack

SQL injection

How to Analyse MySQL Performance

How to Analyse MySQL Performance Problems

Load balance

How to Install a Load Balancing MySQL Server with ProxySQL on Debian 11

Office

LibreOffice

Introduction to Databases: LibreOffice Base Tutorial (youtube)

Use through R

Examples from r-bloggers

Installation

http://cran.r-project.org/web/packages/RMySQL/
https://db.rstudio.com/my-sql/ (more instructions)

Ubuntu/Debian

First, log in using root.

install.packages("DBI")

Go to shell and

# sudo apt-get install libdbd-mysql (this line seems not necessary)
# sudo apt-get install libmysqlclient-dev (Ubuntu 14)      
sudo apt-get install -y libmariadb-dev (Debian Stretch)
# R
# install.packages("RMySQL")

Windows

Check my note with complete screenshots at File:Install MySQL on Windows.pdf.

Open and close connection: dbConnect/dbDisconnect

con <- dbConnect(MySQL(), user="me", password="nuts2u", dbname="my_db", host="localhost")
on.exit(dbDisconnect(con))

dbListTables(con)
head(dbReadTable(con, "recentchanges"))

List tables and fields: dbListTables and dbListFields

dbListTables(mydb)
dbListFields(mydb, 'some_table')

Read and write entire tables: dbReadTable and dbWriteTable

We can create tables in the database using R dataframes.

df = dbReadTable(con, 'motortrend')
dbWriteTable(mydb, name='table_name', value=data.frame.name)

Query: dbGetQuery and dbSendQuery

You can process query results row by row, in blocks or all at once. The highly useful function dbGetQuery(con, sql) returns all query results as a data frame. With dbSendQuery, you can get all or partial results with fetch.

con <- dbConnect(MySQL(), user="network_portal", password="monkey2us", dbname=db.name, host="localhost")
rs <- dbSendQuery(con, "select name from genes limit 10;") # results in in mysql
data <- fetch(rs, n=10) # return result to R as a data frame; use n=-1 to retrieve all pending records.
huh <- dbHasCompleted(rs)
dbClearResult(rs)
dbDisconnect(con)

Aggregate and Sort

df = dbGetQuery(con, "SELECT mfg, avg(hp) AS meanHP FROM motortrend GROUP BY mfg ORDER BY meanHP DESC")
df = dbGetQuery(con, "SELECT cyl as cylinders, avg(hp) as meanHP FROM motortrend GROUP by cyl ORDER BY cyl")

dbApply()

sql = "SELECT cyl, hp FROM motortrend ORDER BY cyl"
rs = dbSendQuery(con, sql)
dbApply(rs, INDEX='cyl', FUN=function(x, grp) quantile(x$hp))

Retrieving AUTO_INCREMENT IDs

http://www.w3schools.com/sql/sql_autoincrement.asp

create.network <- function(species.id, network.name, data.source, description) {
  
  con <- dbConnect(MySQL(),
           user="super_schmuck", password="nuts2u",
           dbname="my_db", host="localhost")
  on.exit(dbDisconnect(con))

  sql <- sprintf("insert into networks
                  (species_id, name, data_source, description, created_at)
                  values (%d, '%s', '%s', '%s', NOW());",
                 species.id, network.name, data.source, description)
  rs <- dbSendQuery(con, sql)
  dbClearResult(rs)

  id <- dbGetQuery(con, "select last_insert_id();")[1,1]

  return(id)
}

Full example from Jeffrey Breen

http://www.r-bloggers.com/slides-%E2%80%9Caccessing-databases-from-r%E2%80%9D-rstats/

First, create new database & user in MySQL:

mysql> create database testrdb;
mysql> grant all privileges on testrdb.* to 'testuser'@'localhost' identified by 'testpass';
mysql> flush privileges;

In R, load the “mtcars” data.frame, clean it up, and write it to a new “motortrend” table:

library(stringr)
library(RMySQL)
 
data(mtcars)
 
# car name is data.frame's rownames. Let's split into manufacturer and model columns:
mtcars$mfg = str_split_fixed(rownames(mtcars), ' ', 2)[,1]
mtcars$mfg[mtcars$mfg=='Merc'] = 'Mercedes'
mtcars$model = str_split_fixed(rownames(mtcars), ' ', 2)[,2]

> dim(mtcars)
[1] 32 13
> mtcars[1:3,]
               mpg cyl disp  hp drat    wt  qsec vs am gear carb    mfg   model
Mazda RX4     21.0   6  160 110 3.90 2.620 16.46  0  1    4    4  Mazda     RX4
Mazda RX4 Wag 21.0   6  160 110 3.90 2.875 17.02  0  1    4    4  Mazda RX4 Wag
Datsun 710    22.8   4  108  93 3.85 2.320 18.61  1  1    4    1 Datsun     710
 
# connect to local MySQL database (host='localhost' by default)
con = dbConnect(MySQL(), "testrdb", username="testuser", password="testpass")
 
dbWriteTable(con, 'motortrend', mtcars)
 
dbDisconnect(con)

And check the database from mysql

mli@PhenomIIx6:~$ mysql -u testuser -p
Enter password:
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 153
Server version: 5.1.63-0ubuntu0.11.10.1 (Ubuntu)

Copyright (c) 2000, 2011, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| testrdb            |
+--------------------+
2 rows in set (0.00 sec)

mysql> use testrdb;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> show tables;
+-------------------+
| Tables_in_testrdb |
+-------------------+
| motortrend        |
+-------------------+
1 row in set (0.00 sec)

mysql> describe motortrend;
+-----------+--------+------+-----+---------+-------+
| Field     | Type   | Null | Key | Default | Extra |
+-----------+--------+------+-----+---------+-------+
| row_names | text   | YES  |     | NULL    |       |
| mpg       | double | YES  |     | NULL    |       |
| cyl       | double | YES  |     | NULL    |       |
| disp      | double | YES  |     | NULL    |       |
| hp        | double | YES  |     | NULL    |       |
| drat      | double | YES  |     | NULL    |       |
| wt        | double | YES  |     | NULL    |       |
| qsec      | double | YES  |     | NULL    |       |
| vs        | double | YES  |     | NULL    |       |
| am        | double | YES  |     | NULL    |       |
| gear      | double | YES  |     | NULL    |       |
| carb      | double | YES  |     | NULL    |       |
| mfg       | text   | YES  |     | NULL    |       |
| model     | text   | YES  |     | NULL    |       |
+-----------+--------+------+-----+---------+-------+
14 rows in set (0.01 sec)

mysql> SELECT * FROM motortrend WHERE row_names like "Mazda%" order by mpg;
+---------------+------+------+------+------+------+-------+-------+------+------+------+------+-------+---------+
| row_names     | mpg  | cyl  | disp | hp   | drat | wt    | qsec  | vs   | am   | gear | carb | mfg   | model   |
+---------------+------+------+------+------+------+-------+-------+------+------+------+------+-------+---------+
| Mazda RX4     |   21 |    6 |  160 |  110 |  3.9 |  2.62 | 16.46 |    0 |    1 |    4 |    4 | Mazda | RX4     |
| Mazda RX4 Wag |   21 |    6 |  160 |  110 |  3.9 | 2.875 | 17.02 |    0 |    1 |    4 |    4 | Mazda | RX4 Wag |
+---------------+------+------+------+------+------+-------+-------+------+------+------+------+-------+---------+
2 rows in set (0.00 sec)
mysql> SELECT row_names, wt, model  FROM motortrend WHERE row_names like "Mazda%" order by wt;
+---------------+-------+---------+
| row_names     | wt    | model   |
+---------------+-------+---------+
| Mazda RX4     |  2.62 | RX4     |
| Mazda RX4 Wag | 2.875 | RX4 Wag |
+---------------+-------+---------+
2 rows in set (0.00 sec)

mysql>

Setting Up Raspberry Pi Temperature/Humidity Sensors for Data Analysis in R

How does importing a database affect the current database?

Continue from the database (testrdb) from the previous section.

$ mysql -u testuser -ptestpass -e "use testrdb; select count(*) from motortrend"
+----------+
| count(*) |
+----------+
|       32 |
+----------+

$ mysql -u testuser -ptestpass -e "use testrdb; select * FROM motortrend WHERE model = 'RX4'"
+-----------+------+------+------+------+------+------+-------+------+------+------+------+-------+-------+
| row_names | mpg  | cyl  | disp | hp   | drat | wt   | qsec  | vs   | am   | gear | carb | mfg   | model |
+-----------+------+------+------+------+------+------+-------+------+------+------+------+-------+-------+
| Mazda RX4 |   21 |    6 |  160 |  110 |  3.9 | 2.62 | 16.46 |    0 |    1 |    4 |    4 | Mazda | RX4   |
+-----------+------+------+------+------+------+------+-------+------+------+------+------+-------+-------+

# Modify a record
$ mysql -u testuser -ptestpass -e "use testrdb; update motortrend SET mpg=22 WHERE model = 'RX4'"
$ mysql -u testuser -ptestpass -e "use testrdb; update motortrend SET mfg='toyota' WHERE model = 'RX4'"

# Remove a record. Use 'Limit' if necessary
# https://stackoverflow.com/questions/18378190/how-to-delete-a-certain-row-from-mysql-table-with-same-column-values
$ mysql -u testuser -ptestpass -e "use testrdb; DELETE FROM motortrend WHERE model = 'Corona'";

# Insert a record
$ mysql -u testuser -ptestpass -e \
 "use testrdb; INSERT INTO motortrend VALUES ('newrow',21, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 'RX4')";
$ mysql -u testuser -ptestpass -e "use testrdb; select * FROM motortrend WHERE model = 'RX4'"
+-----------+------+------+------+------+------+------+-------+------+------+------+------+--------+-------+
| row_names | mpg  | cyl  | disp | hp   | drat | wt   | qsec  | vs   | am   | gear | carb | mfg    | model |
+-----------+------+------+------+------+------+------+-------+------+------+------+------+--------+-------+
| Mazda RX4 |   22 |    6 |  160 |  110 |  3.9 | 2.62 | 16.46 |    0 |    1 |    4 |    4 | toyota | RX4   |
| newrow    |   21 | NULL | NULL | NULL | NULL | NULL |  NULL | NULL | NULL | NULL | NULL | NULL   | RX4   |
+-----------+------+------+------+------+------+------+-------+------+------+------+------+--------+-------+

# Import.
$ mysql -u testuser -ptestpass testrdb < testrdb.sql
$ mysql -u testuser -ptestpass -e "use testrdb; select * FROM motortrend WHERE model = 'RX4'"
+-----------+------+------+------+------+------+------+-------+------+------+------+------+-------+-------+
| row_names | mpg  | cyl  | disp | hp   | drat | wt   | qsec  | vs   | am   | gear | carb | mfg   | model |
+-----------+------+------+------+------+------+------+-------+------+------+------+------+-------+-------+
| Mazda RX4 |   21 |    6 |  160 |  110 |  3.9 | 2.62 | 16.46 |    0 |    1 |    4 |    4 | Mazda | RX4   |
+-----------+------+------+------+------+------+------+-------+------+------+------+------+-------+-------+
$ mysql -u testuser -ptestpass -e "use testrdb; select count(*) from motortrend"
+----------+
| count(*) |
+----------+
|       32 |
+----------+

dbplyr

Generating SQL with {dbplyr} and sqlfluff

RODBC

SQLite

How and When to Use Sqlite
RSQLite package
readwritesqlite: Enhanced Reading and Writing for 'SQLite' Databases
pi-hole is using SQLite3
How to Install SQLite and SQLite Browser on Ubuntu 20.04
What Is SQLite and Why Is It So Popular?

How to Use DB Browser for SQLite

How to Use DB Browser for SQLite on Linux

PostgreSQL

pgcli

Pgcli: a command line interface for Postgres with auto-completion and syntax highlighting.

Docker server + R client

clientsdb - A docker image with clients comments, github, docker

This requires

Installation of some library: "sudo apt install libpq-dev" (PostgreSQL library in Ubuntu)
R's packages "DBI" and "RPostgres"

CouchDB

How to Install Apache CouchDB on Ubuntu 18.04 LTS

InFluxDB

MongoDB

SQL vs. NoSQL: What's the Best Database for Your Next Project?. NoSQL's schemaless structure allows you to insert additional arbitrary data into documents.
How to Install MongoDB on Ubuntu
{hexmake} is one of the 5 Grand Prizes of the 2020 Shiny Contest
How To Backup and Migrate a MongoDB Database
Learning MongoDB from Lynda.com
mongolite: Fast and Simple 'MongoDB' Client for R
mongo Docker Official Images

DuckDB

Joining the flock from R: working with data on MotherDuck

Redis

Find database online

Install Apache HBase

Follow the Quick Start to downloaded hbase tar ball. Suppose we save the tar ball under ~/Downloads folder and extract it in the same directory. We shall edit conf/hbase-site.xml file according to their instruction. The following is my case.

$ tar xzvf hbase-0.98.3-hadoop2-bin.tar.gz 
$ cd hbase-0.98.3-hadoop2/
$ cat conf/hbase-site.xml 
<?xml version="1.0"?>
<?xml-stylesheet type="text/xsl" href="configuration.xsl"?>
<configuration>
  <property>
    <name>hbase.rootdir</name>
    <value>file:///home/brb/Downloads/hbase-0.98.3-hadoop2/hbase</value>
  </property>
  <property>
    <name>hbase.zookeeper.property.dataDir</name>
    <value>/home/brb/Downloads/hbase-0.98.3-hadoop2/zookeeper</value>
  </property>
</configuration>

Before we follow the getting started guide to launch HBase, we shall make sure JAVA_HOME environment variable is created.

$ ls /usr/lib/java
$ export JAVA_HOME=/usr/lib/jvm/java-6-openjdk-amd64

Note that the last line may be replaced by

export JAVA_HOME=$(readlink -f /usr/bin/javac | sed "s:bin/javac::")

Then we can launch HBase,

$ ./bin/start-hbase.sh 

starting master, logging to /home/brb/Downloads/hbase-0.98.3-hadoop2/bin/../logs/hbase-brb-master-brb-P45T-A.out
brb@brb-P45T-A:~/Downloads/hbase-0.98.3-hadoop2$ ./bin/hbase shell
2014-07-06 09:51:34,621 INFO  [main] Configuration.deprecation: hadoop.native.lib is deprecated. Instead, use io.native.lib.available
HBase Shell; enter 'help<RETURN>' for list of supported commands.
Type "exit<RETURN>" to leave the HBase Shell
Version 0.98.3-hadoop2, rd5e65a9144e315bb0a964e7730871af32f5018d5, Sat May 31 19:56:09 PDT 2014

hbase(main):001:0> create 'test', 'cf'
2014-07-06 09:51:49,510 WARN  [main] util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
0 row(s) in 2.0770 seconds

=> Hbase::Table - test
hbase(main):002:0> list 'test'
TABLE                                                                           
test                                                                            
1 row(s) in 0.0530 seconds

=> ["test"]
hbase(main):003:0> exit

brb@brb-P45T-A:~/Downloads/hbase-0.98.3-hadoop2$ ./bin/hbase 

shell2014-07-06 09:53:37,480 INFO  [main] Configuration.deprecation: hadoop.native.lib is deprecated. Instead, use io.native.lib.available
HBase Shell; enter 'help<RETURN>' for list of supported commands.
Type "exit<RETURN>" to leave the HBase Shell
Version 0.98.3-hadoop2, rd5e65a9144e315bb0a964e7730871af32f5018d5, Sat May 31 19:56:09 PDT 2014

hbase(main):001:0> list 'test'
TABLE                                                                           
2014-07-06 09:53:44,373 WARN  [main] util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
test                                                                            
1 row(s) in 1.4800 seconds

=> ["test"]
hbase(main):002:0> put 'test', 'row1', 'cf:a', 'value1'
0 row(s) in 0.4460 seconds

hbase(main):003:0> put 'test', 'row2', 'cf:b', 'value2'
0 row(s) in 0.0140 seconds

hbase(main):004:0> put 'test', 'row3', 'cf:c', 'value3'
0 row(s) in 0.0050 seconds

hbase(main):005:0> scan 'test'
ROW                   COLUMN+CELL                                               
 row1                 column=cf:a, timestamp=1404654837532, value=value1        
 row2                 column=cf:b, timestamp=1404654856976, value=value2        
 row3                 column=cf:c, timestamp=1404654866298, value=value3        
3 row(s) in 0.0560 seconds

hbase(main):006:0> get 'test', 'row1'
COLUMN                CELL                                                      
 cf:a                 timestamp=1404654837532, value=value1                     
1 row(s) in 0.0280 seconds

hbase(main):007:0> disable 'test'
0 row(s) in 1.6050 seconds

hbase(main):008:0> drop 'test'
0 row(s) in 0.2290 seconds

hbase(main):009:0> exit
brb@brb-P45T-A:~/Downloads/hbase-0.98.3-hadoop2$