rsession: no process found - R Studio - r

I am installing R Studio on AWS ec2 instance running Ubuntu. While installation I get an error "rsession: no process found".
After installation I opened "server_ip:8787" in browser, R Studio asked me for login credentials. I am unable to login as it always shows "RStudio initialization error : Unable to connect to server".
In terminal when I enter sudo rstudio-server verify-installation nothing happens.
sudo rstudio-server restart gives rsession: no process found.
I also tried sudo ufw allow 8787 but no success.

you've probably already fix your issue, but have you actually installed R BEFORE RStudio?

I had the same problem (using Hetzner server) and sudo ufw allow 8787 did the trick for me. Thanks!

Related

What is LD_LIBRARY_PATH for R in a conda envrionment?

I have an a GCP virtual machine running RStudio Server. It has a public IP and I was accessing it at #.#.#.#:8787. During an ubuntu (22.04) update the server stopped working via the public IP. sudo rstudio-server verify installation showed that libR.so could not be found. However, if I ssh tunnel to the vm I can access RSS at localhost:8787.
According to the folks at RStudio, the problem may have to do with setting the LD_LIBRARY_PATH for R in the /etc/rstudio/rserver.conf file. However, I can't seem to figure out what that should be set to.
I tried /home/balter/conda/lib/R/lib, but that did not fix the problem.
There is more detail in the issue I filed.
My question here is what to try instead of rsession-ld-library-path=/home/balter/conda/lib/R/lib in the /etc/rstudio/rserver.conf file?

How do I fix the CondaHTTPError [duplicate]

I'd like to install the pymongo library but I'm getting the following error:
(C:\Users\xxxxxxx\AppData\Local\Continuum\anaconda3) C:\Users\xxxxxxx>
conda install -c anaconda pymongo
Fetching package metadata ...
CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/a
naconda/win-64/repodata.json>
Elapsed: -
An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
ConnectTimeout(MaxRetryError("HTTPSConnectionPool(host='conda.anaconda.org', por
t=443): Max retries exceeded with url: /anaconda/win-64/repodata.json (Caused by
ConnectTimeoutError(<urllib3.connection.VerifiedHTTPSConnection object at 0x000
00000054D6128>, 'Connection to conda.anaconda.org timed out. (connect timeout=9.
15)'))",),)
Steps taken to resolve:
1. Update C:\Users\\xxxxxxx\.condarc file with the following:
channels:
- defaults
ssl_verify: false
proxy_servers:
http: http://sproxy.fg.xxx.com:1000
https: https://sproxy.fg.xxx.com:1000
2. (C:\Users\xxxxxxx\AppData\Local\Continuum\anaconda3) C:\Users\xxxxxxx>
conda config --set ssl_verify False
Additional Info:
(C:\Users\xxxxxxx\AppData\Local\Continuum\anaconda3) C:\Users\xxxxxxx>
conda info
Current conda install:
platform : win-64
conda version : 4.3.27
conda is private : False
conda-env version : 4.3.27
conda-build version : 3.0.22
python version : 3.6.2.final.0
requests version : 2.18.4
config file : C:\Users\xxxxxxx\.condarc
netrc file : None
offline mode : False
user-agent : conda/4.3.27 requests/2.18.4 CPython/3.6.2 Windows/7 W
indows/6.1.7601
administrator : False
A number of posts online simply reinstalled Anaconda, any other options apart from a fresh install?
This works a charm:-
Just copy these:-
libcrypto-1_1-x64.dll
libssl-1_1-x64.dll
from D:\Anaconda3\Library\bin to D:\Anaconda3\DLLs.
Execute the following command in the cmd prompt/terminal:
conda config --set ssl_verify no
I try to create a virtual env with python 2.7 with anaconda, the base env is python 3.7. I encounter the exactly same problem. It turns out that there isn't such problem with other virtual envs with python 3.7 or 3.6.
This post works perfectly to solve my problem on win7 with anaconda prompt.
It basically says you need to add the following directories into your user environment path in windows (go to Start and type in: View Advanced System Settings, then select Environmental Variables: then select Path and click Edit: finally you can click New and add a path):
C:\your_directory_to_anaconda3\Anaconda3\Scripts
C:\your_directory_to_anaconda3\Anaconda3\
C:\your_directory_to_anaconda3\Anaconda3\Library\bin -- This is the directory for openssl
If you added conda to your PATH variables, remove it and use the "Anaconda Prompt". This solved the problem for me.
See: https://github.com/conda/conda/issues/8046#issuecomment-450582208
I faced this issue when I tried to create environment. I solved it by first activating conda base environment by using:
conda activate base
then I created the environment
conda create -n myenv python=3.7
Check the proxy URL
Verify .condarc file
For me, the problem was with the indentation in the .condarc file.
proxy_servers:
http: http://testproxy:8080
https: https://testproxy:8080
My authenticated proxy server is configured with a domain whitelist for massive and repeated downloads so root or local sudoer doesn't need to be authenticated.
Adding conda.anaconda.org is not enough as this repo redirect its traffic to amazonaws.com.
In my case, adding ".amazonaws.com" to the whitelist solved the issue.
The issue was resolved by adding a username and password to file C:\Users\xxxxx.condarc
channels:
- defaults
ssl_verify: false
proxy_servers:
http: http://xxxxx:password#sproxy.fg.abc.com:yyyy
https: https://xxxxx:password#sproxy.fg.abc.com:yyyy
I had the same problem on Windows 10-64 bit and intuitively installed the 64-bit version of miniconda. However, it results in exactly the same error above. Installing 32 bit conda installer has resolved the issue
Before installing some package (pydicom) the installation run just fine. After
it I tried to install matplotlib, but I got the same error as yours.
I tried conda config --set ssl_verify no but it didn't solve the problem so I set it again to true.
Fortunately, I had a virtual environment where I installed my packages. I closed all Anaconda prompts and tried in a new test environment. Magically, the install worked. I came back to my original virtual env and run the install again, and it worked!.
It might be that I just had to wait for some time before I could use conda install again.
One other thing I could do is remove the package that caused the problem, but I didn't have the chance to try it. If it has anything to do with some virtual environments not being affected, then one possible way to guard against this is to clone the environment before installing any new package.
Edit: I tried the same solution but It did not work. But instead of showing the error immediately, it asks me whether I want to proceed. I deactivated the env, and re-opened anaconda prompt, then did the same steps as above and worked again.
I also had the Same Issue, I resolved by installing 32 bit Anaconda Installer.
Which resolved the CondaHTTPError: HTTP 000 CONNECTION, on Windows 64 bit.
I faced this issues after "conda clean -a" on win-64.
Activating and deactivating existing conda env resolved the issue.
You might need to upgrade your openssl installation
You can download it here (Try the latest version):
https://slproweb.com/products/Win32OpenSSL.html
Source:
https://github.com/ContinuumIO/anaconda-issues/issues/6424#issuecomment-464660808
My issue was simply not running the conda init command prior to attempting to create an environment.
Came across the CondaHTTP Connection error after installing Anaconda environment on a new Windows 10 computer. I tried virtually all the recommendations above unsuccessfully! Looking up the Anaconda archives ( https://repo.continuum.io/archive/ ), I downloaded the immediate previous release .... and on installation and rebooting my PC, all is now wellscreenshot of release
In short - installing Microsoft Visual C++ Redistributable for Visual Studio solved my problem.
In more detail: upon trying a suggested solution of installing a new version of OpenSSL, the installation process told me I was missing a dependency - the Visual Studio Redistributable package. The installer led me to a direct download page of the 2017 version. I can't find that page now, but the official release of 2019 can be found here, and should work as well (found under Other Tools and Frameworks).
Uninstalling and reinstalling anaconda for all users (instead, of current user only, requires admin privileges) and activating the option to add Anaconda to PATH during the installation process, fixed the issues for me.
Thank you everyone for your responses. In my case, I found out that my Kaspersky Internet Security was blocking it the whole time. The moment I quit the application all applications were downloaded. Please check your firewall settings before trying all the above options.
I tried all of these solutions and none worked for me. After running the command
conda config --remove-key channels
in the Anaconda Prompt, everything started working for me on my next attempt.
Adding that I had the same problem on ubuntu on WSL. None of the solutions worked for me, until I realized I was working on WSL version 1 (I thought I'd already upgraded). Upgrading from WSL 1 to WSL 2 solved the problem for me.
Running following these two commands worked for me.
conda config --remove-key proxy_servers
conda clean --source-cache
I'd tried all of the advice on this and many other webpages.
In the end I broadcast a "help me Obiwan Kenobi, you're my only hope message" to a large group of people at work and one of them who used python all the time was able to help me
The trick was to set several windows environmental variables
CURL_CA_BUNDLE
REQUESTS_CA_BUNDLE
SSL_CERT_FILE
To my company's root certificate (a .cer or .crt) which I had downloaded to a spot on my disk
You may also need to add (in my case)
C:\Users\kdalbey\Anaconda3\Scripts
(or your particular \Anaconda3\Scripts) to your path.
And then I set proxies just for good measure
note I previously copied libcrypto-1_1-x64.dll, libcrypto-1_1-x64.pdb, libssl-1_1-x64.dll, libssl-1_1-x64.pdb from anaconda3\Library\bin to anaconda3\DLLs so that could be part of the secret sauce
and it didn't work until I killed and restarted anaconda-navigator
Two steps to deal with this error.
The Anaconda prompt configures the path, to include all the necessary executable files (for instance Library\bin - On Windows, launch it with admin permission). So that you need to use it to execute conda :
Update conda with conda update conda
Exit my proxy software which solved the issue.
I would like summarize some of the proposed answers in this post and propose my experience on that. As it can be understood from the error explanation, the error is related to the connection and I strongly believe that no need to uninstall and reinstall anything if the real cause of the problem be known. My problem gone away after the system powered off and powered on again one day later. So, some possible causes and their solutions (these solutions could be tested in order based on the written bulleted order) could be as follows:
Crash in anaconda prompt:
Probable solutions:
Deactivating and activating the environment, without removing all packages or …, or
Closing/reopening the prompt (Michael Heidelberg) or
Using cmd.exe instead, perhaps
Non-responsiveness of the anaconda site:
Massive site traffics related probable issues, that could be the reason of non-responsiveness or to temporary block some IPs
Probable solutions:
Retying as recommended in the error: HTTP errors are often intermittent, and a simple retry will get you on your way. It solves my problem sometimes. or
Activate or deactivate VPNs or Proxies (like use in .condarc; see: Github sroder, Nandhan Thiravia, Vinod Sangale, Peter Lucas, Sunding Wei).
Try after a while if you have time
System firewall block the site:
That might be happened by activating and deactivating of VPNs, repeatedly or by some other works
Probable solutions:
Finding the issue in system firewall and allowing the connection in the firewall settings (ScienceJedi, Github)
Reboot, perhaps
If the aforementioned ways didn't solve the problem, testing the related answers in the following order:
Add ...\Anaconda3\Scripts, ...\Anaconda3\, and ...\Anaconda3\Library\bin to the path (talentcat, skerjj, Victor Ochieng, jankap), perhaps need a reboot after (lightarrow)
Copying libcrypto-1_1-x64.dll and libssl-1_1-x64.dll from D:\Anaconda3\Library\bin into D:\Anaconda3\DLLs (Swapnil)
I think it could be used in the first step because It is unlikely to be cause of any other problem. The reason I didn't mention this at the beginning is that the developers could placed these files in that directory during installation, too, in default, but they didn't; perhaps it had some reasons (Github).
Note: these files are for Python >3, and I didn't find them for Python 2. Perhaps they have another names.
It must be said that my problem didn't solve by this solution.
Keep your SSL stack up-to-date (kamal dua, Anaconda troubleshooting, update openssl, Abdulrahman Bres, Update to openssl 1.1.1)
I didn't recommend it at first because Its not a good idea to unset ssl verification unless you know what you are doing (Pratyush comment) and somewhere I read that it couldn't return to True again.
It must be said that my problem didn't solve by this solution, too.
conda config --set ssl_verify false
conda update openssl ca-certificates certifi

Virtuoso installation stuck on "VAD Sticker vad_dav.xml creation" on 2nd attempt

I've been attempting to install virtuoso-opensource as per the README here: https://github.com/openlink/virtuoso-opensource
The first time I ran make, it breezed passed "VAD Sticker vad_dav.xml creation" to "Starting Virtuoso Server" and then complained netstat: command not found.
I installed netstat via sudo apt-get install net-tools, ran make again and now it's always stuck on "VAD Sticker vad_dav.xml creation" even after starting from scratch after deleting the repo folder and re-cloning it again. make install gets stuck at the same point.
Does anyone have any ideas as to how to get past this?
I'm running Ubuntu Server 20.04.1 LTS on an AWS EC2 instance.
I'll note the requirement for netstat to build VADs.
By far the most common cause of hang at that stage is a stagnant virtuoso pid lurking.
pkill virtuoso and run make again.
HTH

Getting auth sign message when connecting cloud server using opencpu

I am trying to expose a sample r model as API so I created R package. In my local machine , I am able to get the output using the command :
curl http://local host/5656/ocpu/library/mypackage/R/tv/json -F "input=#test.csv"
But when I am trying the same in my AWS linux cloud server on CentOS , I am not getting the output. I tried the command :
curl 13.228.109.233:8787/p/5656/ocpu/library/mypackage/R/tv/json -F "input=#test.csv"
and I get the output as
http://13.228.109.233:8787/auth-sign-in?appUr‌​i=%2Fp%2F5656%2Focpu‌​%2Flibrary%2Fmypacka‌​ge%2FR%2Ftv%2Fjson .
The R package is loaded into the my R studio server and I am trying to access it using putty. I installed the open cpu using the command :
yum install opencpu-server
It looks like it is asking for some authentication but I am not able to get what it means. Am I missing something here?
Thanks
If one visits the URL with a browser, one sees the RStudio-Server login screen. And indeed, you are connecting to port 8787, which is the default port for Rstudio Server. Try URLs below http://13.228.109.233/ocpu/ instead.
As Ralf suggests, that was the error , I was giving the wrong URL . Also, whenever we install opencpu in CentOS , just doing a 'yum install opencpu-server' might not be sufficient. We need to execute the entire built script: https://github.com/opencpu/opencpu-server/blob/master/rpm/buildscript.sh
Without executing the build script , I was not able to connect to opencpu server.
Just in case someone gets the same issue.

RStudio Server Initialization Error: Status code 500 returned

When I login to RStudio server installed as an Amazon Machine Image, I, I see the message "RStudio Server Initialization Error" and "Status code 500 returned," as in the screenshot. When I click OK, nothing changes.
What does this mean and how can I fix this?
Refer the following link. It will guide you about the complete installation of R-Studio Server along with required dependencies.
Automated Installation of R-Studio Using Shell Script
It would be useful if you could state which version of RStudio Server you are using. Neverthless, you can try the following:
Install the most recent version using: wget http://download2.rstudio.org/rstudio-server-0.98.1103-amd64.deb. If you want 32-bit version wget http://download2.rstudio.org/rstudio-server-0.98.1103-i386.deb.
Delete the startup files (.Rprofile, .Renviron, and .RData) from your initial working directory, which should be user's home.
Check if you can run R from command line and if your are getting any error messages - fix that first

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