I have a new version of R installed on an aws-machine (which always come with an old version for some reason and it's near impossible to just have yum or apt-get to work). I want rstudio to point to this new version which I've built from source without throwing the old version away. I therefore go to /etc/rstudio/rserver.conf (documentation) and change the contents to:
# Server Configuration File
rsession-which-r=/root/R-3.2.1/bin/R
I can confirm that at this location a new version of R is installed but then I get an error after rstudio-server restarts.
root#ip-172-31-40-49 rstudio]$ rstudio-server restart
initctl: Unknown instance:
What am I to do?
Below worked for me:
1) check the process that used 8787
sudo fuser 8787/tcp
2) with the -k option to kill all process.
sudo fuser -k 8787/tcp
3) Start RStudio Server
sudo rstudio-server start
The solution above is provided here by Leon Zhang.
The first thing to do is to check your configuration with:
rstudio-server verify-installation
a number of times when updating R or RStudio I have run into the same error as you have and get the following error message.
-bash-4.1$ sudo rstudio-server verify-installation
29 Sep 2015 18:24:11 [rserver] ERROR system error 98 (Address already in use); OCCURRED AT: rstudio::core::Error rstudio::core::http::initTcpIpAcceptor(rstudio::core::http::SocketAcceptorService<boost::asio::ip::tcp>&, const std::string&, const std::string&) /root/rstudio/src/cpp/core/include/core/http/TcpIpSocketUtils.hpp:103; LOGGED FROM: int main(int, char* const*) /root/rstudio/src/cpp/server/ServerMain.cpp:436
rstudio-server start/running, process 48632
Although I have never been able to figure out the cause, I can suggest the following workaround:
1. change the port /etc/rstudio/rserver.conf for example from 8787 to 8788
2. open the new ports in your firewall settings. (allow access to the new port in /etc/sysconfig/iptables)
3. update your firewall: sudo /sbin/service iptables restart
4. restart Rstudio server: sudo rstudio-server restart
This has worked for me each of the ~4-5 times this has happened. Although I am not 100% sure this can help with your use case, it may. As an alternative, if you can use containers in your AWS setup, you may be interested in a great off-the shelf docker image with the latest R/Rstudio.
It happened for me on my Cento-7.x machine while I upgraded from old RStudio server to the new version. Rebooting the machine seems to have fixed the problem.
Related
I created a Flask app that uses Beautiful Soup and Selenium to scrape and track Amazon product prices. The data was stored using CS50's version of SQLalchemy.
I then created an account to use Oracle's always free VM, with Ubuntu. I followed this excellent guide to the dot https://asdkazmi.medium.com/deploying-flask-app-with-wsgi-and-apache-server-on-ubuntu-20-04-396607e0e40f and set up Apache's conf file and the Wsgi file. I also added the network rules on Oracle's Virtual Cloud Network and to iptables, which I believe works fine.
Following this, the website still couldn't launch. Apache's error log showed a "PermissionError: [Errno 13] Permission denied: '/flask_session'". Based on this post Permission issue when writing file on webserver (flask, apache & wsgi) I changed the OS env to my env os.chdir('/home/ubuntu/flaskapp') and used chown to give rights
sudo chown -R ubuntu:www-data flaskapp
sudo chmod -R g+s flaskapp.
Now, my front page is accessible on http://129.150.38.171/ . However, upon any request to the server, Chrome displays "This page isn’t working 129.150.38.171 didn’t send any data." Apache's log shows a "segmentation fault (core dumped) python flask". Based on the sequence of my code, the error begins when I try to execute SQL, e.g. rows = usersdb.execute("SELECT * FROM users WHERE username = ?", request.form.get("username")).
I do not think that it is not my codes' error as it runs fine locally and the production server also worked when I set it up on Oracle VM using this guide https://docs.oracle.com/en-us/iaas/developer-tutorials/tutorials/flask-on-ubuntu/01oci-ubuntu-flask-summary.htm .
I've found this guide on debugging https://www.bustawin.com/debug-segmentation-faults-in-apache-from-mod_wsgi/ using gdb. But with source /etc/apache2/envvars
sudo -E gdb /usr/sbin/apache, it just tells me "No executable file specified".
Any ideas on what could be the error?
I installed RStudio on Linux server Ubuntu 18.04 and I couldn't access it from browser. I used
:8787 and I got the error
This site can’t be reached
ERR_CONNECTION_TIMED_OUT
I unable firewall and still the same error. when I run
$sudo rstudio-server verify-installation
I got error
11 Jul 2020 14:53:12 [rsession-rstudio-server] ERROR system error 13 (Permission denied) [path:
/home/rstudio-server/.config/rstudio/dictionaries/custom, target-dir: ]; OCCURRED AT
rstudio::core::Error rstudio::core::FilePath::createDirectory(const string&) const
src/cpp/shared_core/FilePath.cpp:634; LOGGED FROM: std::vector<std::__cx
I am new to both Linux and Rstudio. any help to figure this problem
Thank you
Which version of RStudio Server do you use ?
I had similar problem on (1.3.959) on Ubuntu 18.04. I installed the latest from https://rstudio.com/products/rstudio/download-server/debian-ubuntu/.
wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.3.1056-amd64.deb
sudo gdebi rstudio-server-1.3.1056-amd64.deb
After that I also need to restart apache2.service:
systemctl restart apache2.service
$ rstudio-server version
1.3.1056 (Water Lily) for Ubuntu Bionic
And after works fine.
Also good sources:
https://community.rstudio.com/t/rstudio-server-instal-on-ubuntu-does-not-create-home-directory-home-rstudio-server/69785
https://community.rstudio.com/t/problem-rstudio-server-installed-in-ubuntu20-04/68506
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I have a VPS hosting with a domain redirecting to it.
I have LAMP stack for my main website using WordPress CMS.
Plus I am using Odoo as my back-end with python and PostgreSQL in a sub-domain.
Everything was working fine until I installed Certbot Let’s Encrypt to obtain an SSL certificate by following these tutorials
For My Wordpress i installed this plugin:
WP Encryption – One Click single / wildcard Free SSL certificate & force HTTPS
Which got me in a loop because it forced the https i will explain it later on
So when the plugin didn't work i searched for another way for the whole VPS with these tutorials:
How To Secure Apache with Let's Encrypt on Ubuntu 16.04
How To Secure Apache with Let's Encrypt on Ubuntu 18.04
After completing the second tutorial for ubuntu 18.04 i noticed that all my domain traffic is going to https and it got stuck in a loop saying same as i said above
"ERR_TOO_MANY_REDIRECTS which means Site redirected too many times"
and couldn't access the website front-end for the wordpress in the doamin.
Then when i applied
"Step 3 — Allowing HTTPS Through the Firewall"
my internet connection got interpreted and when i got back to the ssh session i found my self locked out of the server and did not find any way to get back in.
And when i tired to use the sub-domain that has Odoo on it i have got the same error
"ERR_TOO_MANY_REDIRECTS which means Site redirected too many times"
Until here i was hopeless and did't know what to do.
I contacted my VPS server provider and told him about what exactly happened. Then some how he managed to get me into the server again with a URL to the terminal i still couldn't access the server using ssh clients like putty.. so when i entered the server after he provided me with the URL first thing noticed is that he "rebooted the VPS" will get to this in a second.
So first thing i did was removing the wordpress plugin "WP Encryption" and update the wordpress site-url in wp_options table in mysql database because the plugin changed it from http to https so i changed it back and that solved the ERR_TOO_MANY_REDIRECTS for my wordpress website.
Then the second thing i did was disabling the ufw firewall that i enabled in the tutorial in Step 3 above.
I instantly got my connection to the server back using ssh client putty but what i have noticed again is the postgres service was inactive and went down with the reboot of the VPS. i tried to start the service but it didn't a gave me this error.
Failed to start postgresql.service: Unit postgresql.service is masked.
i searched for a solution and found these commands to unmask
sudo systemctl unmask postgresql
sudo systemctl enable postgresql
sudo systemctl restart postgresql
and then the service has started and everything sames OK when i run the status command
service postgresql status
the response is
● postgresql.service - LSB: PostgreSQL RDBMS server
Loaded: loaded (/etc/init.d/postgresql; generated)
Active: active (exited) since Thu 2020-03-26 05:54:09 UTC; 2h 22min ago
Docs: man:systemd-sysv-generator(8)
Tasks: 0 (limit: 2286)
Memory: 0B
CGroup: /system.slice/postgresql.service
but when i try to connect to postgres through the default port with odoo it says:
could not connect to server: No such file or directory
Is the server running locally and accepting
connections on Unix domain socket "/var/run/postgresql/.s.PGSQL.5432"
after many searches i made i found the posgres main cluster is also inactive or down i tried to start it with this command
pg_ctlcluster 11 main start
but i get this error
Job for postgresql#11-main.service failed because the service did not take the steps required by its unit configuration. See "systemctl status postgresql#11-main.service" and "journalctl -xe" for details.
and when i run the command as requested
systemctl status postgresql#11-main.service
i get this error
● postgresql#11-main.service - PostgreSQL Cluster 11-main Loaded: loaded (/lib/systemd/system/postgresql#.service; disabled; vendor preset: enabled) Active: failed (Result: protocol) since Thu 2020-03-26 15:22:15 UTC; 14s ago Process: 18930 ExecStart=/usr/bin/pg_ctlcluster --skip-systemctl-redirect 11-main start (code=exited, status=1/FAILURE)
alone with
systemd[1]: Starting PostgreSQL Cluster 11-main...
postgresql#11-main[18930]: Error: Could not find pg_ctl executable for version 11
systemd[1]: postgresql#11-main.service: Can't open PID file /run/postgresql/11-main.pid (yet?) after start: No such file or
systemd[1]: postgresql#11-main.service: Failed with result 'protocol'.
systemd[1]: Failed to start PostgreSQL Cluster 11-main.
I guessed Let's Encrypt added an ssl configuration to the pg_hba.conf and postgres.conf like id did with apache so i searched for them and commented the "ssl on" lines and restarted postgres service along with the main cluster but nothing happened still the the same error which is
Error: Could not find pg_ctl executable for version 11
I know i shouldn't run pg_ctl directly under Ubuntu/Debian. I must use pg_ctlcluster instead, which is installed by postgresql-common. I saw the main page documentation. But when i run "sudo pg_ctlcluster 11 main reload" command i always get the above Error telling me that he could not find pg_ctl executable
I have searched a lot for this problem but nothing worked how can i solve the pg_ctl executable in version 11 ??
Ps:
I am using Ubuntu 19.10 (GNU/Linux 5.3.0-24-generic x86_64)
Odoo 11 with postgres 11 as the database odoo can't connect to postgres as i mentioned before
edit:
Unfortunately i can't do a restore or recover the server to fix postgres package because my last backup of the server was on 19/3 and today is 26/3 i have an important data between this period
Update 27/3/2020 4:06 AM
I compared my last server backup with the production server and found a lot of postgres files missing!! like int this path /usr/lib/postgres/11/ and /etc/postgres/11/ i think postgres some how got damaged and lost some files in the reboot of the server >>> but found the data files of the database located in /var/lib/postgres/11/ <<< Can i read them in my backup server ? i will try and let you know
So finally after a hours of digging
All PostgreSQL files where damaged and missing and i lost hope of repairing them i don't know what caused that but it has a relation with the accidental reboot of the server.
So i managed to find the main cluster data file for my important database information for the production server in this path
/var/lib/postgres/11/
and i took a backup from it by zipping the whole folder using this command
zip -r main.zip main/
then i did a full purge and reinstall for postgres usuing these commands from here
apt-get --purge remove postgresql\*
to remove everything PostgreSQL from your system. Just purging the postgres package isn't enough since it's just an empty meta-package.
Once all PostgreSQL packages have been removed, run:
rm -r /etc/postgresql/
rm -r /etc/postgresql-common/
rm -r /var/lib/postgresql/
userdel -r postgres
groupdel postgres
Then i installed postgres with this command to match odoo11
sudo apt-get install postgresql libpq-dev -y
then creating the ODOO PostgreSQL User
sudo su - postgres -c "createuser -s odoo" 2> /dev/null || true
Now everything is okay odoo should work fine but you still don't have any database
So to bring back the backup from the cluster folder we took earlier we need to move the zip file to the same directory we took it from which is
/var/lib/postgres/11/
but before that you should stop postgres service
sudo systemctl stop postgresql
and make sure it has stopped
sudo systemctl status postgresql
after that rename the main cluster that postgres uses right now because its empty and we don't need it because we are replacing it with our backed up cluster
mv /var/lib/postgres/11/main /var/lib/postgres/11/main_old
then move the zip file from where you backed it up to the postgres cluster folder with this command
mv /backups/main.zip /var/lib/postgres/11/
unzip the folder in the same path by using this command
unzip -a /var/lib/postgres/11/main.zip
after unzipping the folder give the ownership to your postgres user and group
chown -R postgres:postgres main
Then you are good to go. Start Postgres service
sudo systemctl start postgresql
sudo systemctl status postgresql
and make sure you also start the main cluster service
pg_ctlcluster 11 main start
if you stopped odoo make sure to start it also
service odoo-server start
Ps: I solved ERR_TOO_MANY_REDIRECTS for the odoo sub-domain by commenting ssl configurations in my odoo.config Apache2 virtual host that lets encrypt updated before and everything got back to where left it before installing lets encrypt.
I guess i will leave it here and won't use ssl in production again till i figure out how to use it in a test server .. thanks for your time i hope my question and answer helps someone in the future
Try adding 'pg_path' in your odoo configuration file.
Like: pg_path = /path/to/postgresql/binaries
Generally '/usr/lib/posrgresql/11/bin' is the binary directory.
I am trying to connect R from a browser using opencpu js. I cannot have opencpu in local mode and I need it to run in remote host so that my javascript based app server can be access by multiple users from where bunch of input data needs to be sent to openCPU server and R modules should work independently for each user.
I have a centOS6 instance where I have R installed properly.
I have managed to install openCPU as well using the rpm binary https://archive.opencpu.org/centos-6/.
The installation was successful but ended with:
sudo rpm -ivh opencpu-server-2.1.0-rpm0.x86_64.rpm
Preparing... ########################################### [100%]
1:opencpu-server ########################################### [100%]
/var/tmp/rpm-tmp.T2qZY9: line 13: systemctl: command not found
/var/tmp/rpm-tmp.T2qZY9: line 14: systemctl: command not found
/var/tmp/rpm-tmp.T2qZY9: line 13: systemctl: command not found
/var/tmp/rpm-tmp.T2qZY9: line 14: systemctl: command not found
,which means the stage where after successful installation the server gets started, has failed as systemctl is not present in centOS.
So my questions are:
- what is the best way to start the openCPU server ?
- how can i change the port as i don't have all ports open ?
- Is this approach of connecting remote openCPU server instance from browser feasible or am I in a wrong direction?
Any pointers would be very helpful.
Thanks in advance.
You can probably ignore this error. Does this work on your server?
curl http://localhost/opcu/info
What do you see if you run sudo apachectl restart?
I have OSX El Capitan. I installed Nginx-Full via homebrew. I am supposed to be able to start and stop services with
brew services Nginx-Full Start
I run that command and it seems to start no problem. I check the running services with
brew services list
That indicates that the Nginx-Full services is running. When i run
htop
to look at everything that is running Nginx does not show up and the server is not handling requests.
nginx is failing to launch because of an error, but brew-services is not communicating that to you.
Running it with sudo, as other users have suggested, is just masking the problem. If you just run nginx directly, you may see that there is actually a configuration or permissions issue that is causing nginx to abort. In my case, it was because it couldn't write to the error log:
nginx: [alert] could not open error log file: open() "/usr/local/var/log/nginx/error.log" failed (13: Permission denied)
2020/04/02 13:11:53 [warn] 19989#0: the "user" directive makes sense only if the master process runs with super-user privileges, ignored in /usr/local/etc/nginx/nginx.conf:2
2020/04/02 13:11:53 [emerg] 19989#0: open() "/usr/local/var/log/nginx/error.log" failed (13: Permission denied)
The last error is causing nginx to fail to launch. You can make yourself the owner of the logs with:
sudo chown -R $(whoami) /usr/local/var/log/nginx/
This should cause subsequent config errors to be written to the error log, even if homebrew services is not reporting them in stderr/stdout for now.
I've opened an issue about this: https://github.com/Homebrew/homebrew-services/issues/215
The log path may not the same for everyone. You can check the path to log file by checking the config file /usr/local/etc/nginx/nginx.conf. You can find a line like:
error_log /Users/myusername/somepath/nginx.log;. Change the chown command above accordingly. If even this didn't solve the problem, you may have to do the same for any other log files specified in the server blocks in your nginx configuration
Try launching it with "sudo", even if the formula say
The default port has been set in /usr/local/etc/nginx/nginx.conf to 8080 so that
nginx can run without sudo.
sudo brew services Nginx-Full start
this worked for me:
sudo brew services start nginx
Running sudo nginx worked for me, it initially gave some error stating certain file in certain directory is missing, creating that file, and then another file is asked for to be created and then it runs properly.
I had similar problem, running it brew services start nginx used to show nginx running.
but brew services list used to show error.
running with sudo nginx solved my issue