I configure an Ubuntu VM in oracle VM in a windows server. I want to install shiny server in this machine so I made the following steps in the terminal:
sudo su - \ -c "R -e \"install.packages('shiny', repos='https://cran.rstudio.com/')\""
sudo apt-get install gdebi-core
wget https://download3.rstudio.org/ubuntu-12.04/x86_64/shiny-server-1.5.6.875-amd64.deb
sudo gdebi shiny-server-1.5.6.875-amd64.deb
After that what command I need to open/run the server? I tried to type in the web browser http://10.10.88:3838 but it is not working.
I tried in the terminal sudo systemctl start shiny-server but nothing happening nothing opened or in terminal
if I type sudo start shiny server I receive this error:
start: Unable to connect to Upstart: Failed to connect to socket /com/ubuntu/upstart: Connection refused
Related
I'm trying to access a SQL Server on a local intranet with R, where R is loaded in a docker file with R-base.
On my desktop, I create a ODBC driver and it recognizes my windows credentials with the following:
odbcDriverConnect('driver={SQL Server};server=<serverName>;database=<dbName>;trusted_connection=yes')
Using R-base, after a lot of trial and error I was able to get RODBC installed, but I have no idea how to connect to this server.
Warning messages:
[RODBC] ERROR: state 01000, code 0, message [unixODBC][Driver Manager]Can't open lib 'SQL Server' : file not found
The DockerFile, which was built with a lot of trial and error. I'm sure much of it is redundant. Also I exposed ports which I found doing some research but I have no idea if they are needed to be exposed.
FROM openanalytics/r-base
# system libraries of general use
RUN apt-get update && apt-get install -y \
sudo \
libcairo2-dev \
libxt-dev \
libcurl4-gnutls-dev \
libssl-dev \
libssh2-1-dev \
libssl1.0.0
# RODBC
RUN apt-get update && \
apt-get install -y --no-install-recommends \
unixodbc \
unixodbc-dev \
unixodbc \
unixodbc-dev \
r-cran-rodbc \
apt-transport-https \
libssl-dev \
libsasl2-dev \
openssl \
curl \
unixodbc \
gnupg \
libc6 libc6-dev libc6-dbg
RUN curl https://packages.microsoft.com/keys/microsoft.asc | apt-key add -
RUN curl https://packages.microsoft.com/config/ubuntu/18.04/prod.list > /etc/apt/sources.list.d/mssql-release.list
#RUN curl https://packages.microsoft.com/config/ubuntu/19.10/prod.list > /etc/apt/sources.list.d/mssql-release.list
RUN apt-get update -y
RUN ACCEPT_EULA=Y apt-get install -y msodbcsql17 unixodbc-dev mssql-tools
EXPOSE 3838
EXPOSE 8787
Once I build the file, I enter R studio and use install.packages("RODBC")
How can I connect to the SQL server from the docker file?
----------Update
after creating a docker container with Ubuntu, I found that I was not able to ping the server name. I was however, able to ping the server ip address.
I modified the search string to ping the ip address, and changed the driver, as follows:
odbcDriverConnect('driver={ODBC Driver 17 for SQL Server};server=<serverName>;database=<dbName>;trusted_connection=yes')
This still did not work.
I could not figure out how to connect to the database with the Windows credentials of the docker host inside of the docker virtual machine.
I had to make a username and password for the database and connect with that.
I think if you change your driver to FreeTDS this will work. R doesn't support Sql Server drivers unless its a pro plan.
I followed the instruction here to install mariadb on WSL after following the steps. and I run this
sudo service mysql start
I got
mysql: unrecognized service
Any idea how to solve this?
It's just a simple problem as you see but it takes me 24 hours to diagnose the problem.
Solution:
I uninstall mariadb with this command
sudo apt-get remove --auto-remove mariadb-server
and install sudo apt install mysql-server instead but it leads to a more problems
Successfully install mysql but can't start
dpkg: error processing package mysql-server (--configure):
dependency problems - leaving unconfigured
No apport report written because the error message indicates its a followup error from a previous failure.
Errors were encountered while processing:
mysql-server-5.7
mysql-server
E: Sub-process /usr/bin/dpkg returned an error code (1)
so by removing mariadb's deb sources and purging mysql-common and then reinstalling it.
do:
sudo apt edit-sources
and look for anything containing mariadb like: deb [arch=amd64,arm64,ppc64el] http://ftp.nluug.nl/db/mariadb/repo/10.3/ubuntu bionic main
comment it out by putting a # in front of it. then run
sudo apt update
sudo apt purge mysql-common
sudo apt install mysql-common
after that you can installed mysql-server properly via sudo apt install mysql-server, then do:
sudo apt purge mysql-server mysql-server-5.7
sudo apt purge mysql-server mysql-client mysql-common mysql-server-core-5.7 mysql-client-core-5.7
sudo rm -rfv /etc/mysql /var/lib/mysql
sudo apt autoremove
sudo apt autoclean
Finally:
sudo apt update
sudo apt install mysql-server mysql-client --fix-broken --fix-missing
References:
https://askubuntu.com/questions/980314/cannot-install-mysql-server-in-ubuntu16-0-4
https://askubuntu.com/questions/763534/cannot-reinstall-mysql-server-after-its-purge
Which Linux distribution are you using on your WSL?
First, try the following:
systemctl {start|stop|restart|status} mysql
OR
service mysql {start|stop|restart|status}
to manage the MySQL service.
The reasons can be the following:
Wrong service name:
On some Linux distributions, the service is named as mysqld instead of mysql.
To check: Run chkconfig --list on your WSL and identify the correct service name.
File permission issues:
Please ensure that the files in /var/lib/mysql have 770 permissions and ownership set to mysql user.
To fix:
chmod -R 770 /var/lib/mysql
chgrp -R mysql /var/lib/mysql
In addition to that, ensure that the /etc/rc.d/init.d/mysqld script has executable permissions to modify mysqld.
To fix:
chmod 755 /etc/rc.d/init.d/mysqld
Missing/Corrupted MySQL server package:
Reinstall MySQL!
I need to create an AMI with a clean install of R and RStudio Server. I have tried this on Amazon Linux 2 AMI (HVM), Amazon Linux AMI 2018.03.0 (HVM), and Ubuntu Server 18.04 LTS (HVM) but none of them work. I do not get any errors (that I notice) in my installs but when I try to access RStudio Server via http://ec2-XX-XX-XX-XX.compute-1.amazonaws.com:8787 there's nothing to connect to. I have even tried opening all ports to all IPs to make sure it wasn't a networking issue.
My Amazon API install scripts are below
Amazon Linux AMI 2018.03.0 (HVM)
sudo yum install -y R
wget https://download2.rstudio.org/server/centos6/x86_64/rstudio-server-rhel-1.2.1335-x86_64.rpm
sudo yum install -y rstudio-server-rhel-1.2.1335-x86_64.rpm
rm rstudio-server-rhel-1.2.1335-x86_64.rpm
Amazon Linux 2 AMI
sudo amazon-linux-extras install -y R3.4
wget https://download2.rstudio.org/server/centos6/x86_64/rstudio-server-rhel-1.2.1335-x86_64.rpm
sudo yum install -y rstudio-server-rhel-1.2.1335-x86_64.rpm
rm rstudio-server-rhel-1.2.1335-x86_64.rpm
I get this as part of the result:
Running transaction
Installing : rstudio-server-1.0.153-1.x86_64 1/1
groupadd: group 'rstudio-server' already exists
rsession: no process found
rstudio-server start/running, process 4990
Verifying : rstudio-server-1.0.153-1.x86_64 1/1
Installed:
rstudio-server.x86_64 0:1.0.153-1
Complete!
I think the issue is the rsession: no process found portion but I can't figure out how to resolve it.
Would anyone know or like to share their note on installing opencpu cloud server on ubuntu 16.04?
I thought it is easy, but we saw many error here and there when following the instructions. I am new to opencpu. And, I don't have much experience on apache and nignx.
Here is the long story:
I created a new and clean ubuntu 16.04 server from microsoft azure vm, and installed opencpu cloud server following:
# Requires Ubuntu 14.04 (Trusty) or 16.04 (Xenial)
sudo add-apt-repository -y ppa:opencpu/opencpu-1.6
sudo apt-get update
sudo apt-get upgrade
# Installs OpenCPU server
sudo apt-get install -y opencpu
The server reported insserv error when running opencpu init script
update-rc.d: error: insserv rejected the script header dpkg
We then did some goolge and fix around, we got apache2 running, but when called:
curl http://localhost/ocpu/info
received 404 error.
FYI, the single user server runs fine.
The solution we found is that opencpu need mod_R to be turned on from apache2:
sudo a2enmod R
You need first to change to dir:
/etc/apache2/mods-available
And, make sure R.load file exists.
After running a2enmod command, should see a link to R.load (R module) in
/etc/apache2/mods-enable
Thank you y g for your question and response .. I had the same problem i try what you have mentioned in your comment but
curl http://localhost/cpu/info
takes along time without no response.
Thank you.
I used opencpu 1.5 works without bugs on ubuntu 16.04
sudo add-apt-repository -y ppa:opencpu/opencpu-1.5
sudo apt-get update
sudo apt-get upgrade
Install R and then install opencpu
sudo apt-get install r-base r-base-dev
sudo apt-get install -y opencpu
Also you should probably install Rstudio for IDE access
sudo apt-get install rstudio-server
To login to R you'll need to make a new user - follow the prompts
sudo adduser myname
Now just to make sure its all working
sudo service opencpu restart
sudo service rstudio-server restart
And try something like to check if its working
curl -L -v localhost/ocpu/library/
which should return a list of packages now installed on Ubuntu like this
Final Screenshot
Set up using AWS instance running centOS 6.4 with R and shiny server using my Macbook and trying to figure out what is wrong with it as there are issues with this process
# set up AWS Redhat 6.4 instance (dont forget to download .pem)
# set the .pem file into your ~/.ssh/ folder and make sure you chmod the file
chmod 400 ~/.ssh/myshinypemexample.pem
ssh into machine
ssh -i ~/.ssh/myshinypemexample.pem root#yourPublicDNS
# the first time you run this, just press yes, don't be scared :)
# use ec2-user and log into machine
ssh -i ~/.ssh/myshinypemexample.pem ec2-user#yourPublicDNS
Get the EPEL rpm
wget http://mirror.us.leaseweb.net/epel/6/i386/epel-release-6-8.noarch.rpm
rpm -ivh epel-release-6-8.noarch.rpm --test
Import the EPEL GPG key
wget https://www.fedoraproject.org/static/0608B895.txt
sudo mv 0608B895.txt /etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL-6
sudo rpm --import /etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL-6
Verify that the key has been imported.
rpm -qa gpg*
## You should see a line like this: gpg-pubkey-0608b895-4bd22942
Install the rpm
sudo rpm -ivh epel-release-6-8.noarch.rpm
Install shiny server
sudo su - -c "R -e \"install.packages('shiny', repos='http://cran.rstudio.com/')\""
# this gives error and have to install Rcpp and httr manually
wget http://cran.r-project.org/src/contrib/Rcpp_0.11.1.tar.gz
sudo R CMD INSTALL --build Rcpp_0.11.1.tar.gz
wget http://cran.r-project.org/src/contrib/httpuv_1.2.3.tar.gz
sudo R CMD INSTALL --build httpuv_1.2.3.tar.gz
run shiny server again
sudo su - -c "R -e \"install.packages('shiny', repos='http://cran.rstudio.com/')\""
Install Shiny Server
wget http://download3.rstudio.org/centos-5.9/x86_64/shiny-server-1.0.0.42-x86_64.rpm
sudo yum install --nogpgcheck shiny-server-1.0.0.42-x86_64.rpm
# test server
sudo status shiny-server
check location of example shiny app
sudo R -e "system.file('examples/01_hello', package='shiny')"
[1] "/usr/lib64/R/library/shiny/examples/01_hello"
#copy example file from R to /srv as Shiny looks for this location to work
sudo cp -R /usr/lib64/R/library/shiny/examples/01_hello /srv/shiny-server/
MYIP:3838 does not resolve. Why?