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.
Related
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.
I installed Julia but cannot run a notebook in Jupyter (XUbuntu 14.04). As soon as I start a new notebook, it connects with the kernel and then crashes:
There's 2 possible things that I can think of.
First, I installed Julia like this:
$ sudo apt-add-repository ppa:staticfloat/julianightlies
$ sudo apt-add-repository ppa:staticfloat/julia-deps
$ sudo apt-get update
$ sudo apt-get install julia
and then:
julia> Pkg.add("IJulia")
julia> Pkg.build("IJulia")
when running $ jupyter notebook, it showed the messages above. I removed Julia and now I have version 0.4.6, which I can run perfectly from bash. It still crashes in Jupyter, though. And it still shows two versions of Julia:
(Python and R work just nice)
The second idea is, maybe it has something to do with being root? If I run
$ Julia
julia> using IJulia
ERROR: SystemError: opening file /home/luis/.julia/lib/v0.4/IJulia.ji: Permission denied
in open at ./iostream.jl:90
in open at iostream.jl:102
in stale_cachefile at loading.jl:439
in recompile_stale at loading.jl:474
in _require_from_serialized at loading.jl:83
in _require_from_serialized at ./loading.jl:109
in require at ./loading.jl:235
If I run:
$ sudo Julia
julia> using IJulia
it throws no errors at all.
Any ideas what could be happening?
Note: I am aware of similar questions here, but they havn't worked for me...
This can happen when files in your home directory were created by root and thus do not belong to your user. Rule of thumb is here: everything in your home directory should to belong to your user account.
You can use chown to change ownership:
sudo chown -R luis /home/luis/.julia will recursively change the owner of all files in /home/luis/.julia to the user account luis.
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.
I'm fairly new to the PCL and linux in general. I'm having trouble following the examples in documentation. None of the examples execute.The code compiles fine and a executable is generated. But I keep getting a permission denied error. The usual chmod and chown dont work. I've tried reinstalling PCL. What am I missing here ?
Here is the output from terminal https://www.dropbox.com/s/pjv8utctnokpihd/error.txt
From the dump you provide it looks like you are working in a mounted disk (/media/chaitanya/); possibly it was mounted with noexec or something. Try running mount to see.
Alternatively try working in your home directory:
cd ~
cp -r /media/chaitanya/work/learn-pcl/ ./
etc.
I wanted to install Meteor via
curl https://install.meteor.com | /bin/sh
like it's said in the documentation.
Every time I try this (also as sudo), I get this error:
**rmdir: /Users/christophz/.meteor-install-tmp: Directory not empty
Installation failed.**
The directory, of course, is empty before installation. After aborting the installation in my home folder there IS .meteor and still .meteor-install-tmp. But trying to create a new meteor app fails. My command line says it doesn't know this command.
I didn't find anything via Google. Can u help me and give me some hint?
Did you try rm -rf? With or without sudo:
rm -rf ~/.meteor-install-tmp
rm -rf ~/.meteor
Try deleting the directory. I think this happened to me once.