Error updating RStudio .99 - r

Running Rstudio-server and a recent version of R. With the recent upgrade possibilities of RStudio, I wanted to upgrade.
From what I've read, I should be able to do it by simply running the
sudo gdebi [package name]
However, this gives me a string of errors.
It gets down to 'Setting up studio-server (0.99.441) ...
useradd: user 'studio-server' already exists
groupadd: group 'rstudio-server' already exists
rstudio-server stop/waiting
rstudio-server start/running, process 9823
#
I have tried started or stopping the server to get it to install, performing an install without these options and can't get it to upgrade. Google and RSeek turned up nothing, so maybe there is something I'm supposed to know but don't.
Thank you.

What I did:
- extract what is in the tar or in the .deb
- rename the folder usr/lib/rstudio (just in case)
- make a new directory /rstudio
- copy all the content of the tar in the new folder
You will need sudo permissions to rename and copy.
What I use is >sudo nautilus
and as allways. Be carefull with what you change with sudo.

Related

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

How to change the post-installation script of a package and re-install it?

I am trying to install gnocchi-api, gnocchi-metricd and python-gnocchiclient with apt-get. I found that the postinst scripts in /var/lib/dpkg/info have some misconfigured ports due to which I cannot install the packages successfully. I wanted to ask if there is a way to change the post-installation scripts nad then re-install the package.
Thanks.
Ideally this kind of problems would be solved by filing a bug report (possibly with a patch) and letting the maintainer upload a fixed version that you can upgrade to.
If you need an immediate local workaround though, you could do the following:
Either apt download <package> or dpkg-repack <package> if for example this is a local package only, or the archive does not contain the version you are interested in f.ex.
dpkg-deb -R <package_version_arch>.deb bin-dir
sensible-editor bin-dir/DEBIAN/postinst
sensible-editor bin-dir/DEBIAN/control ideally to bump the version to mark this as a local modification, say by appending +local1 or similar.
dpkg-deb -b bin-dir .
dpkg -i <package_local-version_arch>.deb

RStudio Server returns "Cannot read property 'error' of null"

When I try to go into RStudio Server (1.0.44), I get the following error in the browser:
RStudio Initialization Error
(TypeError) : Cannot read property 'error' of null
This happens before logging in - it has the rotating clock thing for a minute and goes straight into that.
I have tried all sorts of remedies, including restarting the server, rebooting, uninstalling and reinstalling RStudio server, changing the port settings, deleting the .RStudio folder in my home directory, etc. I checked the system log and that didn't seem to have anything relevant. There were a few errors, of course, but nothing after I got the error.
Also, R works fine from the terminal and I have the latest version of both R and RStudio.
Anyone have any ideas?
You probably tried to restart rstudio already, but this is not enough.Follow these steps:
Do a ps -u user where user is one of the user whose session is returning the error in the browser
[root]# ps -u username
PID TTY TIME CMD
19445 ? 00:00:18 rsession
kill the rsession related to it using it's PID.
[root]# kill 19445
start rstudio using sudo rstudio-server start.
Go to the folder contained within the project you were working with last and delete the ProjectName.Rproj file.
restart rstudio using sudo rstudio-server restart
P.S:
If after second step, problem remains, you could remove the .Rproj file using command line: rm directory/of/Rproj/File/ProjectName.Rproj
rm -r .rstudio
sudo rstudio-server suspend-all
worked for me.
I first also moved .RData to a separate folder and upgraded the rstudio server. However, still the problem remained.
I went through a lot of trouble and have finally managed to get it to work again. What ultimately seems to have worked is upgrading to the newest version (1.0.136), deleting all .Rhistory and .Rproj.user files, stopping the server and deleting the .rstudio file in my user profile, and then restarting. I wish I had more info on why it stopped and what fixed it exactly, but at least it's working again. Note that when I upgraded--and before deleting the .rstudio folder (which I had already done a few times), the error message changed to:
Status code 500 returned
So that seems to be the same error--maybe this will help someone else to resolve this problem.

Permission denied to homebrew trying to acces /tmp

PROBLEM SOLVED, SEE BOTTOM OF POST FOR SOLUTION
I'm having issues with homebrew and persmissions. Some brew commands try accessing /tmp, which it doesn't have permissions for. For example, I try running brew doctor:
$ brew doctor
Error: Permission denied - /tmp/doctor20150702-2168-1se1w8u
I have a suspicion that the problem was introduced when I installed brew-rmtree, but I am not sure. A similar thing happens when I try to install rmtree:
$ brew install brew-rmtree
==> Installing brew-rmtree from beeftornado/homebrew-rmtree
Error: Permission denied - /tmp/homebrew20150702-516-1b1s5b3
This is the only package installation that causes this problem.
I don't have the slightest idea why brew tries to access /tmp, since brew is supposed to write only to usr/local. My /tmp folder is of course owned by root:
$ ls / | grep /tmp
lrwxr-xr-x# 1 root wheel 11B Apr 12 00:57 tmp# -> private/tmp
Running brew doctor is my go to solution, but now that fails as well, and I am dumbfounded. Does anyone know how to fix this?
EDIT: SOLUTION
It turns out that the issue with homebrew was merely a symptom, not the problem itself. /tmp is a symlink, tmp# -> private/tmp, and something was up with my permissions at /private/tmp (still don't know what, never figured it out).
So I ran disk permission reparation by opening Disk Utility, selecting my drive partition and running Repair Disk Permission. One of the first paths that it reported having repaired was /private/tmp, and after that it has worked fine.
This wasn't exactly a homebrew problem, then.

Completely remove openstack from system after installation from devstack script

I am installing OpenStack on my local machine via this link. But I am having trouble in completely removing installed components from my local machine. I ran following command:-
$ sudo ./unstack.sh
tgtadm: can't send the request to the tgt daemon, Transport endpoint is not connected
tgtd seems to be in a bad state, restarting...
stop: Unknown instance:
tgt start/running, process 14629
tgt stop/waiting
Volume group "stack-volumes" not found
Skipping volume group stack-volumes
And file are still present in /opt/stack and /usr/local/bin/. But manually removing these file will not be a good option.
The unstack.sh script only stops the services without removing them.
Devstack's folder contains a clean.sh script that removes openstack and dependencies so you can run something like this:
cd path/to/devstack
# There's no need to call unstack.sh explicitly
# clean.sh invokes that script itself.
./clean.sh
Follow the following 3 steps:
./clean.sh
rm -rf /opt/stack
rm -rf /usr/local/bin (careful, this will remove everything installed to your local bin folder, which might include previously installed applications).
For more info of all the impacted files and directories this link.
unstack doesn't clean out /opt/stack. or purge all dependency packages. or clean all eggs out of python.
I recommend running devstack in a VM. It's easy enough to simply remove the VM and rebuild from scratch.
Example shell script for creating a devstack VM for kvm:
#!/bin/sh
/usr/bin/vmbuilder kvm ubuntu -v --suite=oneiric --libvirt=qemu:///system --flavour=server --arch=amd64 --cpus=2 --mem=4096 --swapsize=2048 --rootsize=30480 --ip=192.168.122.236 --hostname=devstack --user=stack --name=stack --pass=stack --addpkg=git --addpkg=screen --addpkg=vim --addpkg=strace --addpkg=lsof --addpkg=nmap --addpkg=subversion --addpkg=acpid --addpkg=tcpdump --addpkg=python-pip --addpkg=wget --addpkg=htop --mirror=http://us.archive.ubuntu.com/ubuntu --components='main,universe' --addpkg=openssh-server --dns=8.8.8.8 --dest=/virts/devstack

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