Hi I'm new in infrastructure and still learning. I would like to ask a question:
If there are 2 servers (both using Red Hat), 1 for RStudio and 1 for MiniCran. MiniCran server has full access to internet, but not for RStudio. RStudio Server can ping to MiniCran Server. But, when I tried to install packages in RStudio Server from MiniCran Server (All packages are already in MiniCran Server.). The error is Unable to to access index repository http://xxx.xx.xx/minicran/src/contrib.
But if I tried to install in MiniCran server using local file, it can be installed.
Is that related firewall or anything else?
Thanks so much in advance for anyone who wants to help give a suggest or answer.
Related
I am using R again after some time and need to install various packages (e.g. lumi, GENAVi, ideal, limma) and for some the installation works for some not. I receive failure notifications indicating that I the library paths are not writable or that access is denied.
installation of lumi with bioconductor fails
thus, lumi appears to be not existing
My PC uses windows 10, recently updated, and R 4.1.1
I tried the following steps (based on older forum entries):
I ran R Studio with administrator permissions
I gave R full permission through the firewall of my antivirus program
I gave R permission through the windows security settings
I reinstalled R on another harddrive (E:/) where it should have full permission for all paths.
I added a path in the xxx
I ran R inside a new environment in the “Conda” software, but the permission problems persisted.
(Outside of Conda) I installed the lumi package out of a zip file (instead of a Bioconductor download). Still didnt work...
So I now don’t know what to do anymore and barely find new ideas for solving the problem.
I appreciate your help
I'm an undergraduate research assistant working on a Linux server without root privilege. I'm trying to install the Rstudio server but the Rstudio website only provides the installation method for sudoers. Is it possible to install it without root access? I'm asking because I'm really not sure if I could get access from the manager. Any help will be appreciated!
No, you can't install it without root access. But there are a couple of things you could do to piece together a solution. Here are two options:
Extract the server and run it directly
You have to be root to install packages, so you can't install the .deb/.rpm file yourself. However, you could extract the contents of the file to a directory inside your home directory and run RStudio Server from there, by executing the rserver program in a regular shell.
Note that this will probably require an afternoon of editing the rserver.conf file to tell it where to find the rest of the files in the installation (since it presumes they are installed in /usr/lib by default). You can get some inspiration for how to do this here: https://github.com/rstudio/rstudio/blob/master/src/cpp/conf/rserver-dev.conf
Run the desktop version and forward the graphics
The other route is to run RStudio Desktop on the server; we make several builds of RStudio Desktop that are installer-less and can just be unpacked into your home directory. Then run an X11 server on your own computer and an X11 client on the RStudio server, so that the RStudio Desktop instance appears on your computer instead of the server.
Yes, you can run rserver without root priveliges.
For RStudio 1.4 I patched the following line into src/cpp/core/LogOptions.cpp
const FilePath kDefaultLogPath = core::system::xdg::userDataDir().completePath("log");
Then you need to set the system environment variables to some location read-writeable for the user, like
RSTUDIO_CONFIG_DIR=$HOME/.config/rstudio
RSTUDIO_CONFIG_HOME=$HOME/.config/rstudio
RSTUDIO_DATA_HOME=$HOME/.local/share/rstudio
And start rserver with the option
--server-data-dir={directory writeable for user}
--server-pid-file={file-path creatable for user}
--database-config-file={config-file}
With these adjustments it runs for me when I start it as a simple user (no root privileges) with
rserver --auth-none=1 --www-frame-origin=same --www-port={port} --www-verify-user-agent=0 --server-data-dir={my-tmp-path} --server-pid-file={my-tmp-path}/rstudio.pid --database-config-file={my-tmp-path}/db.conf}
ATTENTION:
But be aware, that anyone who can reach your system and the specified port from the network has access to the running RStudio in his browser and therefore can run any command in the name of the user on your system now.
I am working with Unix and from now on I need to use the University server to run some packages in R.
1.I assessed the server by ssh
2.I downloaded miniconda
3.source ~/.bashrc
4.Downloaded Rstudio
5. conda install -c r rstudio
And when I am trying to open Rstudio I am receiving the following error
'QXcbConnection: Could not connect to display'
Any help will be super useful.
Depending you your platform and your university's security policy this may or may not work
https://unix.stackexchange.com/questions/12755/how-to-forward-x-over-ssh-to-run-graphics-applications-remotely
In short you need to explicitly enable X11 forwarding (though I was under the impression that it is on by default). Also you need to run an X11 server, there are a few on windows and MacOS. If the above does not help, it is most likely due to a security policy and you may want to speak to your university's SysAdmin
How to install a particular R package on SQL Server 2016.Package like 'ggplot2'.There is the command in R is 'Install.Packages("ggplot2")'.But how we can install this package on SQL Server 2016.
Have a look at the MSDN documentation.
You can also look at a blog post I wrote about how to install Facebook Prophet on SQL Server R Services.
Hope this helps!
Niels
I kept getting errors regarding package management for SQL Server 2017 "Error: The package management feature is not enabled for the current user or not supported on SQL Server version 14".
What finally worked for me was to go to the R version installed with SQL, then install the R packages as I normally would through R, but for the System Library instead of the User Library:
install.packages("tidyverse", lib="C:\\Program Files\\Microsoft SQL Server\\MSSQL14.MSSQLSERVER\\R_SERVICES\\library")
You need to run R as admin to execute the code above, otherwise you will get an error that the folder is not writeable.
If you run in R the command:
.libPaths()
it will show you the user path and the system path. The packages you install normally forces them to go to the user path. I suspect SQL Server can't find it if it's in the user path.
I have created a custom package and would like to deploy it to a remote machine. Here is my current long workflow:
Create custom package 'my_package_0.1.0.tar.gz'
scp package to remote machine
create Remote session
install.packages("/path/to/my_package0.1.0.tar.gz")
library('my_package')
When others connect to the machine, they have to run install and library:
install.packages("/path/to/my_package0.1.0.tar.gz")
library('my_package')
Is there a way I can share a custom package and have the workflow be:
Create remote session
Load package with library('my_package')
Feedback in comments says the best practice is to install the package in a shared location.
Here is how you can find a good place to install the packages.
Running the following shows where libraries are loaded from
.libPaths()
# rserve2 rserve2 /opt/deployr/9.0.1/rserve/R
#root root /usr/lib64/microsoft-r/3.3/lib64/R/library
There are two locations the R server is looking for libraries. One is owned by root so we shouldn't deploy here. The other location rserve2 has owndership and looks promising. We should create a library subfolder to store the shared packages.
Based on this information, the work flow should be:
Create custom package 'my_package_0.1.0.tar.gz'
scp package to remote machine
create Remote session
install.packages("/path/to/my_package0.1.0.tar.gz", lib='/opt/deployr/9.0.1/rserve/R/library/')
library('my_package')
When others connect to the machine, they can load the shared library:
library('my_package')