I am trying to run MySQL in an R script running inside a Docker (actually Rocker) container, but am getting an error on the “install_packages(…” step. The only solution I found that was somewhat similar was specific to running RedHat Linux (I am running Mac OS X 10.15) and the solution included pointing to several directories that I do not have. Running under RStudio or from the command line, RMySQL loads without a problem.
Dockerfile:
FROM rocker/r-ver:latest
RUN mkdir /home/analysis
COPY install_packages.R /home/analysis/install_packages.R
COPY script_basic.R /home/analysis/script_basic.R
RUN Rscript /home/analysis/install_packages.R
CMD Rscript /home/analysis/script_basic.R
R files:
script_basic.R
library( RMySQL )
install_packages.R
install_packages(“RMySQL”)
Commands and responses:
$ docker build -t myapp .
…
Successfully tagged myapp:latest
$ docker run -it --rm myapp
Loading required package: DBI
Error: package or namespace load failed for ‘RMySQL’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/site-library/RMySQL/libs/RMySQL.so':
libmysqlclient.so.21: cannot open shared object file: No such file or directory
Execution halted
$
I believe that rocker/r-dev does not include the libraries you need to get this to run. Untested, but try something like this.
Dockerfile
FROM rocker/r-ver:latest
RUN mkdir /home/analysis
RUN apt-get update \
&& apt-get install -y --no-install-recommends libmariadbclient-dev
COPY install_packages.R /home/analysis/install_packages.R
COPY script_basic.R /home/analysis/script_basic.R
RUN Rscript /home/analysis/install_packages.R
CMD Rscript /home/analysis/script_basic.R
You can find the need for certain libraries on https://cran.r-project.org/web/packages/RMySQL/index.html, as
SystemRequirements: libmariadb-client-dev | libmariadb-client-lgpl-dev | libmysqlclient-dev (deb), mariadb-devel (rpm), mariadb | mysql-connector-c (brew), mysql56_dev (csw)
and a note on how to install them in RMySQL's github README.md's Installation section.
(The CRAN page references libmysqlclient-dev, but the github page suggests "the mariadb implementation is much better". I don't know the premise of the statement, just explaining why I suggested one and CRAN listed another.)
I have just installed Debian Lenny with Apache, MySQL, and PHP and I am receiving a PDOException could not find driver.
This is the specific line of code it is referring to:
$dbh = new PDO('mysql:host=' . DB_HOST . ';dbname=' . DB_NAME, DB_USER, DB_PASS)
DB_HOST, DB_NAME, DB_USER, and DB_PASS are constants that I have defined. It works fine on the production server (and on my previous Ubuntu Server setup).
Is this something to do with my PHP installation?
Searching the internet has not helped, all I get is experts-exchange and examples, but no solutions.
You need to have a module called pdo_mysql. Looking for following in phpinfo(),
pdo_mysql
PDO Driver for MySQL, client library version => 5.1.44
The dsn in your code reveals you are trying to connect with the mysql driver. Your error message indicates that this driver is unavailable.
Check that you have the mysql extension installed on your server.
In Ubuntu/Debian you check for the package with:
dpkg --get-selections | grep php | grep mysql
Install the php5-mysql package if you do not have it.
In Ubuntu/Debian you can use:
PHP5: sudo apt-get install php5-mysql
PHP7: sudo apt-get install php7.0-mysql
Lastly, to get it working, you will need to restart your web-server:
Apache: sudo /etc/init.d/apache2 restart
Nginx: sudo /etc/init.d/nginx restart
Update: newer versions should use php-sqlite3 package instead of php5-sqlite. So use this, if you are using a recent ubuntu version:
sudo apt-get install sqlite php-sqlite3
Original answer to question is here:
sudo apt-get install sqlite php5-sqlite
sudo /etc/init.d/apache2 restart
If your phpinfo() is not showing the pdo_sqlite line (in my case, on my Ubuntu Server), you just need to run the lines above and then you'll be good to go.
For newer versions of Ubuntu that have PHP 7.0 you can get the php-mysql package:
sudo apt-get install php-mysql
Then restart your server:
sudo service apache2 restart
I had the same issue. The solution depends on OS. In my case, i have debian, so to solve it:
Updated my php version from (php5 to php7)
Install php-mysql and php7.0-mysql
apt-get install php-mysql
apt-get install php7.0-mysql
I edited my php.ini locate at /etc/php/7.0/apache2/php.ini
uncomment the line : extension=php_pdo_mysql.dll
Then restart apache:
service apache2 restart
This solves my problem
On my Windows machine, I had to give the absolute path to the extension dir in my php.ini:
extension_dir = "c:\php5\ext"
Check if the module is available with php -m | grep pdo_mysql.
If not, for PHP 7.2, you can install relevant package with sudo apt install php7.2-mysql.
Use similar command on other PHP versions and package managers.
On Ubuntu just execute
sudo apt-get install php5-mysql
sudo apt-get install php-mysql
worked well on ubuntu and php 7
When adding these into your php.ini ensure the php_pdo.dll reference is first before the db drivers dlls otherwise this will also cause this error message too. Add them like this:
[PHP_PDO]
extension=php_pdo.dll
[PHP_PDO_MYSQL]
extension=php_pdo_mysql.dll
for Windows 8.1/10 in :\\php.ini file you should uncomment line "extension=pdo_mysql"
Did you check your php.ini (check for the correct location with phpinfo()) if MySQL and the driver is installed correctly?
For PHP 5.5 on CentOS I fixed this by installing the php55-mysqlnd package.
sudo yum -y install php55w-mysqlnd # For Webtatic
sudo yum -y install php55u-mysqlnd # For Remi
For help installing, write a comment as it depends on the way PHP is installed on your system. Available repo's are webtatic and remi.
Check if extension_dir in php configuration file set correctly. Try to comment/uncomment some extensions and see if it's reflected on phpinfo().
If it doesn't then either php config file cannot be loaded (wrong location) extension_dir is commented or set to the wrong location.
In my case my DSN string was incorrect, specifically it did not contain mysql://. I would have expected a different error message, perhaps something like 'DSN string does not specify driver/protocol.'
Adding mysql:// to the beginning of the DSN string resolved the issue.
I had the same problem during running tests with separate php.ini. I had to add these lines to my own php.ini file:
[PHP]
extension = mysqlnd.so
extension = pdo.so
extension = pdo_mysql.so
Notice: Exactly in this order
I spent the last day trying to figure out why I was getting the following error. I am running Ubuntu 14.04.
The Problem:
I noticed that my PHP-CLI version was running php7.0 but php_info() (the web version) was displaying php 5.5.9. Even though php_info() said pdo was enabled, using the command line (CLI) wasn't recognizing the pdo_mysql command. It turns out that mysql was enabled for my old version but not the CLI version. All I did was install mysql for php7.0 and it was able to work.
This is what worked:
To check the version:
php -v
To install mysql for php7.0
sudo apt-get install php7.0-mysql
1) make sure your CLI version is the same as your web version
2) If they are different, make sure your CLI version has the mysql plug-in since it doesn't come with it as a default.
Incorrect installation of PHP was being called
I was experiencing the same problem. And I hope this would help someone who is having a similar issue as me.
Scenario
OS = Windows 10
Platform = XAMPP
PHP Version = 7 (Multiple Version seem to have been installed in the PC)
I created phpinfo.php file in the public folder and run the phpinfo() to look for the location of my php.ini file.
PHP.ini Location = c:\xampp\php\php.ini
Problem
Calling c:\xampp\htdocs> php -v returned PHP 7.2.3 but phpinfo.php showed PHP 7.2.2.
Solution
Instead of calling
php artisan migrate:install
which gave me this error, I used
c:\xampp\php\php artisan migrate:install
and it worked.
The problem is a missing php to mysql library. In CentOs i fixed it by running
# yum install php-mysql and then restarting apache with # /bin/systemctl restart httpd.service Note that the naming is slightly different from debian/ubuntu based distros, php->php5 and httpd->apache2.
I extremely recommend mysqllnd instead of mysql because of you would have a lot of problems like number converting and bit type evaluates problem with mysql extension.
on ubuntu install mysqllnd with following command:
sudo apt-get install php5-mysqlnd
In my case, I was using PDO with php-cli, and it worked fine.
Only when I tried to connect from apache, I got the "missing driver" issue, which I didn't quite understand.
A simple apt-get install php-mysql solved it. (Ubuntu 16.04 / PHP7. credits go to the selected answer & Ivan's comment)
Hope it can help.
PHP Fatal error: Uncaught PDOException: could not find driver
I struggled and struggled with "apt install php-mysql php7toInfinity and don't forget sqlite-what-ever's" and just could not get rid of this error message until I went back to basics and reset the file-permissions on the web-site in question.
These 3 commands reset file and folder permissions on the web-site and got it to work again.
cd /var/www/web-site-name.com/web/
# find (sub) directories and change permissions
find . -type d -exec chmod 755 {} \;
# find files and change permissions
find . -type f -exec chmod 664 '{}' \;
I Fixed this issue on my Debian 6.
Normally I just had installed php5-common package. After installation, you have to restart your web server (apache or nginx depending on which one you installed).
Then I just do an lsof on the apache process id (lsof -p process_id) as followed :
sudo lsof -p 1399 #replace 1399 by your apache process id
apache2 1399 root mem REG 254,2 80352 227236 /usr/lib/php5/20090626/xmlrpc.so
apache2 1399 root mem REG 254,2 166496 227235 /usr/lib/php5/20090626/suhosin.so
apache2 1399 root mem REG 254,2 31120 227233 /usr/lib/php5/20090626/pdo_mysql.so
apache2 1399 root mem REG 254,2 100776 227216 /usr/lib/php5/20090626/pdo.so
apache2 1399 root mem REG 254,2 135864 227232 /usr/lib/php5/20090626/mysqli.so
As you can see above, the modules are installed on a file path not known or guided by common library path: /usr/lib/php5/20090626/. For your installation, it may be different, but only the path of pdo_mysql.so, pdo.so, mysqli.so. So, this is why Drupal or any other php engine couldn't find the library and shows that error: PDOException: could not find driver
I just don't know why it is installed on such a weird path, for me it's just a bug in the library package installation script in debian 6.
I solved the issue by creating a symbolic for all the files under /usr/lib/php5/20090626/ to
/usr/lib/php5/ with this command :
ln -s /usr/lib/php5/20090626/* /usr/lib/php5/
$DB_TYPE = 'mysql'; //Type of database<br>
$DB_HOST = 'localhost'; //Host name<br>
$DB_USER = 'root'; //Host Username<br>
$DB_PASS = ''; //Host Password<br>
$DB_NAME = 'database_name'; //Database name<br><br>
$dbh = new PDO("$DB_TYPE:host=$DB_HOST; dbname=$DB_NAME;", $DB_USER, $DB_PASS); // PDO Connection
This worked for me.
I faced the same issue after I removed the php5 package (that includes all the drivers as well) in order to install php7 package. I actually installed php7 package without a mysql module.
I managed to solve it by typing in the terminal:
1) $ apt-cache search php7
which lists all the modules, looking through the modules I found,
php7.0-mysql - MySQL module for PHP
2) $ sudo apt-get install php7.0-mysql
That's it. It worked for me in my linux system.
(use the appropriate php version, yours could be php5)
Just one other thing to confirm as some people are copy/pasting example code from the Internet to get started. Make sure you have MySQL entered here:
... $dbh = new PDO ("mysql: ...
In some examples this shows
$dbh = new PDO ("dblib ...
For those using Symfony2/3 and wondering why you're getting this error. If you're using "mapping_types", you might encounter this error. The reason is that "mapping_types" is placed at the wrong level. For instance :
doctrine:
dbal:
mapping_types:
set: string
This "mapping_types" must be placed at this level :
doctrine:
dbal:
#To counter the error caused by 'mapping_types'
connections:
default:
server_version: %database_server_version%
mapping_types:
set: string
I hope this helps
I found the solution here : https://github.com/doctrine/DoctrineBundle/issues/327
Everywhere I go I read that the path of extension_dir should be changed from ext to an absolute path. It worked for me. However, when trying to build a server of my colleague's PC, I had to let the value to ext instead of putting an absolute path.
If you did put an absolute path and it does the extension is still not found, considerer trying both with the absolute path and ext.
Check correct path in extension_dir in you phpinfo().
Had the same issue, because I forgot to go into my virtual machine. If I go to my local directory like this:
cd /www/homestead/my_project
php artisan migrate
that error will appear. But it works on my virtual machine
cd ~/homestead
vagrant ssh
cd /www/homestead/my_project
php artisan migrate
I'd like to install the following UDF's from sam J levy's site
I have run through the windows (32 bit) installation with wamp for my testing server with no problem. Now I have my proper server running centOs 6.4. I have copied the .so files to
usr/lib64/mysql/plugin/damlev.so
I then try to run one of the sql statements to create the function
CREATE FUNCTION damlev RETURNS INTEGER SONAME 'damlev.so';
And get the following error
1126 - Can't open shared library 'damlev.so' (errno: 22 /usr/lib64/mysql/plugin/damlev.so: wrong ELF class: ELFCLASS32)
What Am I doing wrong. Is it because the server is 64bit?
Edit Bounty Started:
If more details about the server are required I can gladly supply them. I need this function installed.
It seems that you're trying to use the damlev.so library included in the damlev.zip file of the Levi's site, but that library is for an Ubuntu 32-bit system, therefore it cannot work on your Centos 64-bit system, so you'll have to compile from sources.
As a prerequisite, you must install the g++ compiler and the mysql development libraries:
yum install gcc-c++ mysql-devel
Also, if you don't have wget and unzip, install them with the following command:
yum install wget unzip
Then download the source code and unzip it somewhere:
cd tmp
mkdir damlev
cd damlev
wget http://samjlevy.com/wp-content/uploads/2011/03/damlev.zip
unzip damlev.zip
cd src
Finally compile, install the plugin and restart the mysql server:
g++ -fPIC -I /usr/include/mysql/ -o damlev.so -shared damlev.cpp
cp damlev.so /usr/lib64/mysql/plugin/
service mysql restart
Please note that all the above command must be run as "root".