On a VPS with Fedora 23 I recently upgraded my rstudio-server. After this I could no longer login.
After many attempts to repair it I decided to start with a fresh VPS, unfortunately, even here the same problem appears. From systemctl I get:
ERROR system error 13 (Permission denied); OCCURRED AT:
rstudio::core::Error
rstudio::core::system::launchChildProcess(std::string, std::string,
rstudio::core::system::ProcessConfig,
rstudio::core::system::ProcessConfigFilter, PidType*)
/root/rstudio/src/cpp/core/system/PosixSystem.cpp:1297;
LOGGED FROM: rstu lines 1-13/13 (END)
Also:
id -u rstudio-server
gives
993
I have also set the minimum user id to 100.
Any thoughts would be much appreciated.
Related
I have installed on Fedora 35 jfrog-artifactory-oss (v7.31.11-73111900.x86_64) and enabled it as a system service to start at boot. But whenever I boot up my OS, the server never starts properly. I will always need to kill the PID of the active running Artifactory process. If I then do sudo service artifactory restart it will bring up the server cleanly and everything is good. How can I avoid having to do this little dance? Is there something about OS boot up that is causing Artifactory to get thrown off?
I have looked at console.log when the server is not running properly after bootup, I see some logs like:
2022-01-27T08:35:38.383Z [shell] [INFO] [] [artifactoryManage.sh:69] [main] - Artifactory Tomcat already started
2022-01-27T08:35:43.084Z [jfac] [WARN] [d84d2d549b318495] [o.j.c.ExecutionUtils:165] [pool-9-thread-2] - Retry 900 Elapsed 7.56 minutes failed: Registration with router on URL http://localhost:8046 failed with error: UNAVAILABLE: io exception. Trying again
That shows that the server is not running properly, but doesn't give a clear idea of what to try next. Any suggestions?
2 things to check,
How is the artifactory.service file in the systemd directory
Whenever the OS is rebooted, what is the error seen in the logs, check all the logs.
Hint: From the warning shared, it seems that Router service is not able to start when OS is rebooted, so whenever OS is rebooted and issue comes up check the router-service.log for any errors/warnings.
brew
brew install not work. this is the log.
% brew install mariadb
==> Downloading https://homebrew.bintray.com/bottles/mariadb-10.4.13.mojave.bottle.tar.gz
Already downloaded: /Users/shingo/Library/Caches/Homebrew/downloads/d56104142081a8230646ac3f245adf2414e515cd5f2aeeb0637614e9966e882c--mariadb-10.4.13.mojave.bottle.tar.gz
==> Pouring mariadb-10.4.13.mojave.bottle.tar.gz
==> /usr/local/Cellar/mariadb/10.4.13/bin/mysql_install_db --verbose --user=shingo --basedir=/usr/local/Cellar/mariadb/10.4.13 --datadir=/usr/local/var/mysql --tmpdir=/tmp
Last 15 lines from /Users/shingo/Library/Logs/Homebrew/mariadb/post_install.01.mysql_install_db:
shell> /usr/local/Cellar/mariadb/10.4.13/bin/mysql -u root mysql
mysql> show tables;
Try 'mysqld --help' if you have problems with paths. Using
--general-log gives you a log in /usr/local/var/mysql that may be helpful.
The latest information about mysql_install_db is available at
https://mariadb.com/kb/en/installing-system-tables-mysql_install_db
You can find the latest source at https://downloads.mariadb.org and
the maria-discuss email list at https://launchpad.net/~maria-discuss
Please check all of the above before submitting a bug report
at http://mariadb.org/jira
Warning: The post-install step did not complete successfully
You can try again using `brew postinstall mariadb`
==> Caveats
A "/etc/my.cnf" from another install may interfere with a Homebrew-built
server starting up correctly.
MySQL is configured to only allow connections from localhost by default
To start mariadb:
brew services start mariadb
Or, if you don't want/need a background service you can just run:
mysql.server start
==> Summary
🍺 /usr/local/Cellar/mariadb/10.4.13: 744 files, 169.9MB
I have tried to execute mysql_install_db
I have tried to execute mysql_install_db without brew. this is the log.
The brew displays only the last 15 lines, so I can't help it.
% /usr/local/Cellar/mariadb/10.4.13/bin/mysql_install_db --verbose --user=shingo --basedir=/usr/local/Cellar/mariadb/10.4.13 --datadir=/usr/local/var/mysql --tmpdir=/tmp
chown: /usr/local/Cellar/mariadb/10.4.13/lib/plugin/auth_pam_tool_dir/auth_pam_tool: Operation not permitted
Couldn't set an owner to '/usr/local/Cellar/mariadb/10.4.13/lib/plugin/auth_pam_tool_dir/auth_pam_tool'.
It must be root, the PAM authentication plugin doesn't work otherwise..
Installing MariaDB/MySQL system tables in '/usr/local/var/mysql' ...
2020-05-29 22:13:03 0 [Note] /usr/local/Cellar/mariadb/10.4.13/bin/mysqld (mysqld 10.4.13-MariaDB) starting as process 45440 ...
2020-05-29 22:13:03 0 [ERROR] /usr/local/Cellar/mariadb/10.4.13/bin/mysqld: option '--innodb-large-prefix' requires an argument
2020-05-29 22:13:03 0 [ERROR] Parsing options for plugin 'InnoDB' failed.
2020-05-29 22:13:03 0 [ERROR] /usr/local/Cellar/mariadb/10.4.13/bin/mysqld: unknown variable 'mysqlx-bind-address=127.0.0.1'
2020-05-29 22:13:03 0 [ERROR] Aborting
Installation of system tables failed! Examine the logs in
/usr/local/var/mysql for more information.
The problem could be conflicting information in an external
my.cnf files. You can ignore these by doing:
shell> /usr/local/Cellar/mariadb/10.4.13/bin/mysql_install_db --defaults-file=~/.my.cnf
You can also try to start the mysqld daemon with:
shell> /usr/local/Cellar/mariadb/10.4.13/bin/mysqld --skip-grant-tables --general-log &
and use the command line tool /usr/local/Cellar/mariadb/10.4.13/bin/mysql
to connect to the mysql database and look at the grant tables:
shell> /usr/local/Cellar/mariadb/10.4.13/bin/mysql -u root mysql
mysql> show tables;
Try 'mysqld --help' if you have problems with paths. Using
--general-log gives you a log in /usr/local/var/mysql that may be helpful.
The latest information about mysql_install_db is available at
https://mariadb.com/kb/en/installing-system-tables-mysql_install_db
You can find the latest source at https://downloads.mariadb.org and
the maria-discuss email list at https://launchpad.net/~maria-discuss
Please check all of the above before submitting a bug report
at http://mariadb.org/jira
I noticed that the system can not chown for auth_pam_tool because Operation not permitted.
auth_pam_tool permission
this is my permission the directory.
% ls -l /usr/local/Cellar/mariadb/10.4.13/lib/plugin/auth_pam_tool_dir/auth_pam_tool
-r-xr-xr-x 1 shingo staff 13608 5 10 04:28 /usr/local/Cellar/mariadb/10.4.13/lib/plugin/auth_pam_tool_dir/auth_pam_tool
How to fix Operation not permitted?
Or is there any other reason why it cannot be installed?
Self resolved.
Anyway I gave it try start
Even though the installation was not successful, anyway I gave it try % mysql.server start.
A error log file was created.
A error log file was created by starting mysql server.
the error log shows:
2020-05-30 8:47:10 0 [Warning] InnoDB: innodb_open_files 300 should not be greater than the open_files_limit 256
2020-05-30 8:47:10 0 [ERROR] /usr/local/Cellar/mariadb/10.4.13/bin/mysqld: unknown variable 'mysqlx-bind-address=127.0.0.1'
2020-05-30 8:47:10 0 [ERROR] Aborting
An unknown value in the mysqlx-bind-address seems to be causing the error.
How to fix unknown variable
I found
the same error question. This question discussed a my.conf file.
~/.my.conf did not exist on my mac
/etc/my.conf did not exist on my mac
this question teach me the my.conf location.
Finally I found my.conf in /usr/local/etc/my.cnf.Certainly the settings for mysqlx-bind-address were written in my.conf.
So rm /usr/local/etc/my.cnf, then brew reinstall SUCCESS!.
The permission was irrelevant at all.
this work for me:
rm /opt/homebrew/etc/my.cnf
I have an error, where I cant find anything related to it on the www:
The error pops up everythime I start/login into Rstudio-Server(installed on an Linux-Server). It worked for month.
05 Jan 2016 07:13:38 [rsession-me] ERROR system error 24 (Too many open files); OCCURRED AT: core::system::file_monitor::Handle core::system::file_monitor::detail::registerMonitor(const core::FilePath&, bool, const boost::function<bool(const core::FileInfo&)>&, const core::system::file_monitor::Callbacks&) /home/ubuntu/rstudio/src/cpp/core/system /file_monitor/LinuxFileMonitor.cpp:455; LOGGED FROM: void session::module_context::<unnamed>::onMonitoringError(const core::Error&) /home/ubuntu/rstudio/src/cpp/session/SessionModuleContext.cpp:360
I tried:
sudo rstudio-server suspend-all
sudo rstudio-server stop
sudo rstudio-server restart
But the error still pops up.
I am having issues connecting to a rstudio server I just installed. Can you please let me know if you know how to solve this? Thanks!
I just installed Rstudio server 0.99.485 64-bit on Ubuntu 13.10 (saucy) and am getting this error below:
The error in /var/log/syslog says:
ERROR Unexpected exception: locale::facet::Screateclocale name not valid;
LOGGED FROM: int main(int, char* const*) /home/ubuntu/rstudio/src/cpp/session/SessionMain.cpp:3166
The symptom is that the web UI says it's "unable to connect to service"
I have followed everything mentioned on this post, but it doesn't seem to work.
When I trace the rstudio-server process using sudo strace -f -e 'trace=!clockgettime,gettimeofday,futex,timerfdsettime,epollwait,epollctl' -p 10208 -o trace.txt, I am seeing this in the trace.txt ( below is what I used to log in:
10226 connect(10, {safamily=AFLOCAL, sunpath="/tmp/rstudio-rsession/"}, 28) = -1 ECONNREFUSED (Connection refused)
I've tried logged in using an invalid id to confirm that pam authentication is working fine
Also looked at this question and made sure there exists /home/<USERID> but still the problem is there.
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.