I have successfully installed Rstudio server (open source) on VM located on Ubuntu 16.04.2 LTS in the institute cluster. I can access the URL on port 8787. But when I try to sign in to Rstudio using my username and password, it processes for few seconds and then shows the following:
RStudio initialization error: unable to connect to service
I did not get any error when I ran command sudo rstudio-server verify-installation. But when I checked /var/log/syslog which shows the following:
ERROR system error 13 (Permission denied) [path=/home/biology/.rstudio, target-dir=]; OCCURRED AT: rstudio::core::Error rstudio::core::FilePath::createDirectory(const string&) const /home/ubuntu/rstudio/src/cpp/core/FilePath.cpp:826; LOGGED FROM: int main(int, char* const*) /home/ubuntu/rstudio/src/cpp/session/SessionMain.cpp:3303
PS: R version 3.3.2 (2016-10-31); rstudio-server-1.0.136-amd64.deb
Suggestions please.
Thanks!
I got the solution for this. I was already having the root access and I proceeded as follows:
1) mkdir /home/biology/.rstudio
2) mkdir /home/biology/.rstudio/graphics-r3
3) sudo chown -R biology:my_group .rstudio
and it worked :)
I had the same issue as #gbioinfo (R version 3.4.2; rstudio-server-1.1.383-amd64.deb; ubuntu 16.04) and had to run the first two commands as sudo.
This is most likely Permission for the home directory of the system user that you are trying to use to login to rstudio.
lets assume that the username is "rstudio_user". simply make sure that you have a home directory created for this user and this user has full permissions or ownership permission to access the directory.
At least for my experience, when I created the username, the username didn't have a home directory. so simply follow the below
sudo mkdir /home/rstudio_user
sudo chown -R rstudio_user rstudio_user
I have a single "partition" ZFS pool mounted to a directory inside /jails/www/usr/local/www/stuff (that is served by nginx) and from inside that jail I have chown'd that directory to a particular user. I have rsync periodically updating that directory from a remote server. Files are syncing fine, however there is a persistent error:
rsync: failed to set times on "/usr/local/www/stuff/file": Operation not permitted
What am I missing here?
Wasn't aware that chown doesn't touch symlinks themselves by default. Doing chown -hR /usr/local/www/stuff solved it.
This is the third time I'm setting up Postgres on a new machine (OS X 10.9 this time), and the third time I'm having problems with the connection.
Basically, I'm at the point where I've created a database cluster and can start postgres using:
postgres -D /usr/local/pgsql/data
But I want it to run in the background as a launch daemon, so I
sudo launchctl load -w /Library/LaunchDaemons/org.macports.postgresql91-server.plist
It seems like the daemon is launched successfully. But when I type psql I get the same old error message I've been dealing with every single time I try to set up Postgres:
psql: could not connect to server: No such file or directory. Is the server running locally and accepting connections on Unix domain socket "/tmp/.s.PGSQL.5432"?
Any ideas on what might be causing this?
The psql you're running is the old version bundled by Apple in Mac OS X and added to the default PATH. Use the one from Homebrew, by fixing your path or entering the path specifically.
Alternately, explicitly connect to the server by overriding the default socket directory:
psql -h /tmp
See also:
this superuser answer
How to modify PATH for Homebrew?
Update:
In this case it looks like the server is genuinely not starting. Check the permissions on the data directory (apparently /usr/local/pgsql/data) and check the Console.app logs for relevant messages from launchd.
Update:
You must fix the permissions so the postgres user (or postgres_, depending on how you installed) has ownership. Check the launchd config file to see what user it runs as, and sudo chown -R postgres /usr/local/pgsql/data to change ownership. Replace postgres with postgres_ if that's what your launchd config says
I am using UNIX in cygwin (in Windows 7). I have a syslog.conf file consisting of this line initially:
*.* /var/log/messages
All information is logged to this "messages" file. Now when I changed the path to a new file (logtest):
*.* /var/log/logtest
I restarted the syslog-ng daemon, but the information is still getting logged to /var/log/messages
What could be the problem?
I understand preserving the permissions for rsync.
However in my case my local computer does not have the user the files need to under for the webserver. So when I rsync I need the owner and group to be apache on the webserver, but be my username on my local computer. Any suggestions?
I wanted to clarify to explain exactly what I need done.
My personal computer: named 'home' with the user account 'michael'
My web server: named 'server' with the user account 'remote' and user account 'apache'
Current situation: My website is on 'home' with the owner 'michael' and on 'server' with the owner 'apache'. 'home' needs to be using the user 'michael' and 'server' needs to be using the user 'apache'
Task: rsync my website on 'home' to 'server' but have all the files owner by 'apache' and the group 'apache'
Problem: rsync will preseve the permissions, owner, and group; however, I need all the files to be owner by apache. I know the not preserving the owner will put the owner of the user on 'server' but since that user is 'remote' then it uses that instead of 'apache'. I can not rsync with the user 'apache' (which would be nice), but a security risk I'm not willing to open up.
My only idea on how to solve: after each rsync manually chown -R and chgrp -R, but it's a huge system and this takes a long time, especially since this is going to production.
Does anyone know how to do this?
Current command I use to rsync:
rsync --progress -rltpDzC --force --delete -e "ssh -p22" ./ remote#server.com:/website
If you have access to rsync v.3.1.0 or later, use the --chown option:
rsync -og --chown=apache:apache [src] [dst]
More info in an answer from a similar question here: ServerFault: Rsync command issues, owner and group permissions doesn´t change
There are hacks you could put together on the receiving machine to get the ownership right -- run 'chmod -R apache /website' out of cron would be an effective but pretty kludgey option -- but instead, I'd recommend securely allowing rsync-over-ssh-as-apache.
You'd create a dedicated ssh keypair for this:
ssh-keygen -f ~/.ssh/apache-rsync
and then take ~/.ssh/apache-rsync.pub over to the webserver, where you'd put it into ~apache/.ssh/authorized_keys and carefully specify the allowed command, something like so, all on one line:
command="rsync --server -vlogDtprCz --delete . /website",from="IP.ADDR.OF.SENDER",no-port-forwarding,no-X11-forwarding,no-pty ssh-rsa AAABKEYPUBTEXTsVX9NjIK59wJ+fjDgTQtGwhATsfidQbO6u77dbAjTUmWCZjKAQ/fEFWZGSlqcO2yXXXXXXXXXXVd9DSS1tjE6vAQaRdnMXBggtn4M9rnePD2qlR5QOAUUwhyFPhm6U4VFhRoa3wLvoqCVtCV0cuirB6I45On96OPijOwvAuz3KIE3+W9offomzHsljUMXXXXXXXXXXMoYLywMG/GPrZ8supIDYk57waTQWymUyRohoQqFGMzuDNbq+U0JSRlvLFoVUZ5Piz+gKJwwiFwwAW2iNag/c4Mrb/BVDQAyEQ== comment#email.address
and then your rsync command on your "home" machine would be something like
rsync -av --delete -e 'ssh -i ~/.ssh/apache-rsync apache#server' ./ /website
There are other ways to skin this cat, but this is the clearest and involves the fewest workarounds, to my mind. It prevents getting a shell as apache, which is the biggest security concern, natch. If you're really deadset against allowing ssh as apache, there are other ways ... but this is how I've done it.
References here: http://ramblings.narrabilis.com/using-rsync-with-ssh, http://www.sakana.fr/blog/2008/05/07/securing-automated-rsync-over-ssh/
Last version (at least 3.1.1) of rsync allows you to specify the "remote ownership":
--usermap=tom:www-data
Changes tom ownership to www-data (aka PHP/Nginx). If you are using Mac as the client, use brew to upgrade to the last version. And on your server, download archives sources, then "make" it!
The solution using rsync --chown USER:GROUP [src] [dst] only works if the remote user has write access to the the destination directory which in most cases is not the case.
Here's another solution:
Overview
(srcmachine) (rsync) (destmachine)
srcuser -- SSH --> destuser
|
| sudo su jenkins
|
v
jenkins
Let's say that you want to rsync:
From:
Machine: srcmachine
User: srcuser
Directory: /var/lib/jenkins
To:
Machine: destmachine
User: destuser to establish the SSH connection.
Directory: /tmp
Final files owner: jenkins.
Solution
rsync --rsync-path 'sudo -u jenkins rsync' -avP --delete /var/lib/jenkins destuser#destmachine:/tmp
Read more here:
https://unix.stackexchange.com/a/546296/116861
rsync version 3.1.2
I mostly use windows in local, so this is the command line i use to sync files with the server (debian) :
user#user-PC /cygdrive/c/wamp64/www/projects
$ rsync -rptgoDvhnP --chown=www-data:www-data --exclude=.env --exclude=vendor --exclude=node_modules --exclude=.git --exclude=tests --exclude=.phpintel --exclude=storage ./website/ username#hostname:/var/www/html/website
-n : perform a trial run with no changes made, to really execute the command remove the -n option