Having lot of aliases might be confusing, such as when they are brought by zsh git plugin for instance. I wonder if it's possible to display the definition next to the alias for each one. I'm surprised I'm not able to find, so maybe I've used wrong terms when searching for it. If so, please apologize ...
Current behavior:
$ gg<Tab>
gg gga ggf ggfl ggl ggp ggpnp ggpull ggpur ggpush ggsup ggu
Desired behavior :
$ gg<Tab>
gg 'git gui citool'
gga 'git gui citool --amend'
ggpull 'git pull origin "$(git_current_branch)"'
ggpur ggu
ggpush 'git push origin "$(git_current_branch)"'
ggsup 'git branch --set-upstream-to=origin/$(git_current_branch)'
glgg 'git log --graph'
glgga 'git log --graph --decorate --all'
I've found a similar idea for displaying files list info that can be configured like this :
zstyle ':completion:*' file-list all. But I've found nothing in the doc for a similar feature related to alias expansion.
A similar problem is also solved for parameters completion :
docker -<Tab>
--config -- Location of client config files
--debug -D -- Enable debug mode
--help -h -- Print usage
--host -H -- tcp://host:port to bind/connect to
--log-level -l -- Logging level
--tls -- Use TLS
--tlsverify -- Use TLS and verify the remote
--userland-proxy -- Use userland proxy for loopback traffic
--version -v -- Print version information and quit
Thanks !
Related
I'm currently struggling with running a .sh script I'm trying to trigger from Jenkins.
Within the Jenkins "execute shell" section, I'm connecting to a remote server (The Jenkins agent does not have right OS to build what I need.), using:
cp -r . /to/shared/drive/to/have/access/on/remote
ssh -t -t username#servername << EOF
cd /to/shared/drive/to/have/access/on/remote
source build.sh dev
exit
EOF
Inside build.sh, I'm exporting R_LIBS to build a package for different R versions.
...
for path in "${!rVersionPaths[#]}"; do
export R_LIBS="${path}"
Rscript -e 'install.packages(c("someDependency", "someOtherDependency"), repos="http://cran.r-project.org");'
...
Setting R_LIBS should functions here like setting lib within install.packages(...). For some reason the R_LIBS export doesn't get picked up. Also setting other env variables like http_proxy are ignored. This causes any requests outside the network to fail.
Is there any particular way of achieving this?
Maybe pass those variables with env, like
env R_LIBS="${path}" Rscript -e 'install.packages(c("someDependency", .....
Well i'm not able to comment on the question, so posting it as answer.
I had similar problem when calling remote shell script from Jenkins, the problem was somehow bash_profile variables were not loaded when called the script from Jenkins but locally it worked. Loading the bash profile in ssh connection solved it for me.
Add source to bash_profile in build.sh
. ~/.bash_profile OR source ~/.bash_profile
Or
Reload bash_profile in ssh connection
`ssh -t -t username#servername << EOF
. ~/.bash_profile
your commands here
exit
EOF
You can set that variable in the same command line like this:
R_LIBS="${path}" Rscript -e \
'install.packages(c("someDependency", "someOtherDependency"), repos="http://cran.r-project.org");'
It's possible to append more variables in this way. Note that this will set those environment variables only for the command being called after them (and its children processes as well).
You said that "R_LIBS export doesn't get picked up". Question Is the value UNSET? Or is it set to some other value & you are trying to override it?
It is possible that SSH may be invoking "/bin/sh -c". Based on the second answer to: Why does 'cd' command not work via SSH?, you can simplify the SSH command and explicitly invoke the build.sh script in Bash:
cp -r . /to/shared/drive/to/have/access/on/remote
ssh -t -t username#servername "cd /to/shared/drive/to/have/access/on/remote && bash -f build.sh dev"
This makes the SSH invocation more similar to invoking the command within a remote interactive shell. (You can avoid sourcing scripts and exporting variables.)
You don't need to export R_LIBSor env R_LIBS when it is possible to prefix any command with local environment variable overrides (agrees with Luis' answer):
...
for path in "${!rVersionPaths[#]}"; do
R_LIBS="${path}" Rscript -e 'install.packages(c("someDependency", "someOtherDependency"), repos="http://cran.r-project.org");'
...
The Rscript may be doing a lot with env vars. You can verify that you are setting the R_LIBS env var by replacing Rscript with the env command and observe the output:
...
for path in "${!rVersionPaths[#]}"; do
R_LIBS="${path}" env
...
According to this manual "Initialization at Start of an R Session", Rscript looks in several places to load "site and user files":
$R_PROFILE
$R_HOME/etc/Renviron
$R_HOME/etc/Renviron.site
$R_ENVIRON_USER
$R_PROFILE_USER
./.Rprofile
$HOME/.Rprofile
./.RData
The "Examples" section of that manual shows this:
## Not run:
## Example ~/.Renviron on Unix
R_LIBS=~/R/library
PAGER=/usr/local/bin/less
If you add the --vanilla command-line option to ignore all of these files, then you may get different results and know something in the site/init/environ files is affecting your R_LIBS! I cannot run this system myself. Hopefully we have given you some areas to investigate.
You probably don't want to source build.sh, just invoke it directly (i.e. remove the source command).
By source-ing the file your script is executed in the SSH shell (likely sh) rather than by bash, which it sounds like is what you intended.
I had been using a proxy for a long time. Now I need to remove it. I have forgotten how I have added the proxy to wget. Can someone please help me get back to the normal wget where it doesn't use any proxy. As of now, I'm using
wget <link> --proxy=none
But I'm facing a problem when I'm installing using a pre-written script. It's painstaking to search all through the scripts and change each command.
Any simpler solution will be very much appreciated.
Thanks
Check your
~/.wgetrc
/etc/wgetrc
and remove proxy settings.
Or use wget --no-proxy command line option to override them.
In case your OS is alpine/busybox then the wget might vary from the one used by #Logu.
There the correct command is
wget --proxy off http://server:port/
Running wget --help outputs:
/ # wget --help
BusyBox v1.31.1 () multi-call binary.
Usage: wget [-c|--continue] [--spider] [-q|--quiet] [-O|--output-document FILE]
[-o|--output-file FILE] [--header 'header: value'] [-Y|--proxy on/off]
[-P DIR] [-S|--server-response] [-U|--user-agent AGENT] [-T SEC] URL...
Retrieve files via HTTP or FTP
--spider Only check URL existence: $? is 0 if exists
-c Continue retrieval of aborted transfer
-q Quiet
-P DIR Save to DIR (default .)
-S Show server response
-T SEC Network read timeout is SEC seconds
-O FILE Save to FILE ('-' for stdout)
-o FILE Log messages to FILE
-U STR Use STR for User-Agent header
-Y on/off Use proxy
I have RStudio server installed on a remote aws server (ubuntu) and want to run several projects at the same time (one of which takes lots of time to finish). On Windows there is a simple GUI solution like 'Open Project in New Window'. Is there something similar for rstudio server?
Simple question, but failed to find a solution except this related question for Macs, which offers
Run multiple rstudio sessions using projects
but how?
While running batch scripts is certainly a good option, it's not the only solution. Sometimes you may still want interactive use in different sessions rather than having to do everything as batch scripts.
Nothing stops you from running multiple instances of RStudio server on your Ubuntu server on different ports. (I find this particularly easy to do by launching RStudio through docker, as outlined here. Because an instance will keep running even when you close the browser window, you can easily launch several instances and switch between them. You'll just have to login again when you switch.
Unfortunately, RStudio-server still prevents you having multiple instances open in the browser at the same time (see the help forum). This is not a big issue as you just have to log in again, but you can work around it by using different browsers.
EDIT: Multiple instances are fine, as long as they are not on the same browser, same browser-user AND on the same IP address. e.g. a session on 127.0.0.1 and another on 0.0.0.0 would be fine. More importantly, the instances keep on running even if they are not 'open', so this really isn't a problem. The only thing to note about this is you would have to log back in to access the instance.
As for projects, you'll see you can switch between projects using the 'projects' button on the top right, but while this will preserve your other sessions I do not think the it actually supports simultaneous code execution. You need multiple instances of the R environment running to actually do that.
UPDATE 2020 Okay, it's now 2020 and there's lots of ways to do this.
For running scripts or functions in a new R environment, check out:
the callr package
The RStudio jobs panel
Run new R sessions or scripts from one or more terminal sessions in the RStudio terminal panel
Log out and log in to the RStudio-server as a different user (requires multiple users to be set up in the container, obviously not a good workflow for a single user but just noting that many different users can access the same RStudio server instance no problem.
Of course, spinning up multiple docker sessions on different ports is still a good option as well. Note that many of the ways listed above still do not allow you to restart the main R session, which prevents you from reloading installed packages, switching between projects, etc, which is clearly not ideal. I think it would be fantastic if switching between projects in an RStudio (server) session would allow jobs in the previously active project to keep running in the background, but have no idea if that's in the cards for the open source version.
Often you don't need several instances of Rstudio - in this case just save your code in .R file and launch it using ubuntu command prompt (maybe using screen)
Rscript script.R
That will launch a separate R session which will do the work without freezing your Rstudio. You can pass arguments too, for example
# script.R -
args <- commandArgs(trailingOnly = TRUE)
if (length(args) == 0) {
start = '2015-08-01'
} else {
start = args[1]
}
console -
Rscript script.R 2015-11-01
I think you need R Studio Server Pro to be able to log in with multiple users/sessions.
You can see the comparison table below for reference.
https://www.rstudio.com/products/rstudio-server-pro/
Installing another instance of rstudio server is less than ideal.
Linux server admins, fear not. You just need root access or a kind admin.
Create a group to use: groupadd Rwarrior
Create an additional user with same home directory as your primary Rstudio login:
useradd -d /home/user1 user2
Add primary and new user into Rwarrior group:
gpasswd -a user2 Rwarrior
gpasswd -a user1 Rwarrior
Take care of the permissions for your primary home directory:
cd /home
chown -R user1:Rwarrior /home/user1
chmod -R 770 /home/user1
chmod g+s /home/user1
Set password for the new user:
passwd user2
Open a new browser window in incognito/private browsing mode and login to Rstudio with the new user you created. Enjoy.
I run multiple RStudio servers by isolating them in Singularity instances. Download the Singularity image with the command singularity pull shub://nickjer/singularity-rstudio
I use two scripts:
run-rserver.sh:
Find a free port
#!/bin/env bash
set -ue
thisdir="$(dirname "${BASH_SOURCE[0]}")"
# Return 0 if the port $1 is free, else return 1
is_port_free(){
port="$1"
set +e
netstat -an |
grep --color=none "^tcp.*LISTEN\s*$" | \
awk '{gsub("^.*:","",$4);print $4}' | \
grep -q "^$port\$"
r="$?"
set -e
if [ "$r" = 0 ]; then return 1; else return 0; fi
}
# Find a free port
find_free_port(){
local lower_port="$1"
local upper_port="$2"
for ((port=lower_port; port <= upper_port; port++)); do
if is_port_free "$port"; then r=free; else r=used; fi
if [ "$r" = "used" -a "$port" = "$upper_port" ]; then
echo "Ports $lower_port to $upper_port are all in use" >&2
exit 1
fi
if [ "$r" = "free" ]; then break; fi
done
echo $port
}
port=$(find_free_port 8080 8200)
echo "Access RStudio Server on http://localhost:$port" >&2
"$thisdir/cexec" \
rserver \
--www-address 127.0.0.1 \
--www-port $port
cexec:
Create a dedicated config directory for each instance
Create a dedicated temporary directory for each instance
Use the singularity instance mechanism to avoid that forked R sessions are adopted by PID 1 and stay around after the rserver has shut down. Instead, they become children of the Singularity instance and are killed when that shuts down.
Map the current directory to the directory /data inside the container and set that as home folder (this step might not be nessecary if you don't care about reproducible paths on every machine)
#!/usr/bin/env bash
# Execute a command in the container
set -ue
if [ "${1-}" = "--help" ]; then
echo <<EOF
Usage: cexec command [args...]
Execute `command` in the container. This script starts the Singularity
container and executes the given command therein. The project root is mapped
to the folder `/data` inside the container. Moreover, a temporary directory
is provided at `/tmp` that is removed after the end of the script.
EOF
exit 0
fi
thisdir="$(dirname "${BASH_SOURCE[0]}")"
container="rserver_200403.sif"
# Create a temporary directory
tmpdir="$(mktemp -d -t cexec-XXXXXXXX)"
# We delete this directory afterwards, so its important that $tmpdir
# really has the path to an empty, temporary dir, and nothing else!
# (for example empty string or home dir)
if [[ ! "$tmpdir" || ! -d "$tmpdir" ]]; then
echo "Error: Could not create temp dir $tmpdir"
exit 1
fi
# check if temp dir is empty (this might be superfluous, see
# https://codereview.stackexchange.com/questions/238439)
tmpcontent="$(ls -A "$tmpdir")"
if [ ! -z "$tmpcontent" ]; then
echo "Error: Temp dir '$tmpdir' is not empty"
exit 1
fi
# Start Singularity instance
instancename="$(basename "$tmpdir")"
# Maybe also superfluous (like above)
rundir="$(readlink -f "$thisdir/.run/$instancename")"
if [ -e "$rundir" ]; then
echo "Error: Runtime directory '$rundir' exists already!" >&2
exit 1
fi
mkdir -p "$rundir"
singularity instance start \
--contain \
-W "$tmpdir" \
-H "$thisdir:/data" \
-B "$rundir:/data/.rstudio" \
-B "$thisdir/.rstudio/monitored/user-settings:/data/.rstudio/monitored/user-settings" \
"$container" \
"$instancename"
# Delete the temporary directory after the end of the script
trap "singularity instance stop '$instancename'; rm -rf '$tmpdir'; rm -rf '$rundir'" EXIT
singularity exec \
--pwd "/data" \
"instance://$instancename" \
"$#"
I am getting below error while running gzip command over ssh
ssh 123#HPUX "gzip"
ksh: gzip: not found
whereas if i am running tar in same way it is working properly.
ssh 123#HPUX "tar"
tar: usage tar [-]{txruc}[eONvVwAfblhm{op}][0-7[lmh]] [tapefile] [blocksize] [[-C directory] file] ...
Can you please suggest why am i getting this error and how can i overcome this problem ?
When i tried following step gzip is working properly
ssh 123#HPUX
gzip
gzip: compressed data not written to a terminal. Use -f to force compression.
For help, type: gzip -h
which means that gzip is working.
Your $path may be set differently for an interactive login session, versus
executing a single command via ssh. Does it work if you specify an absolute path to gzip?
Try logging in interactively, and use the command which gzip to show where the
binary is. Perhaps it's something like /usr/local/gnu/gzip . (You might want to do
echo $path too, and make a note of it for comparison purposes.) Then try using
that path in your batch SSH command, i.e. ssh 123#HPUX "/usr/local/gnu/gzip" to see
what happens. The command ssh 123#HPUX 'echo $path' (note single quotes!) should tell you how your $path is set in that context -- if you compare that to your interactive $path, you'll probably see a difference that explains why gzip isn't found in the first version of your batch command.
Wild guess: it's ksh raising the error the first time. When you do a full ssh login, are you using ksh? Are you running any scripts that modify its path?
Is it possible to have an SSH session use all your local configuration files (.bash_profile, .vimrc, etc..) on login? That way you would have the same configuration for, say, editing files in vim in the remote session.
I just came across two alternatives to just doing a git clone of your dotfiles. I take no credit for either of these and can't say I've used either extensively so I don't know if there are pitfalls to either of these.
sshrc
sshrc is a tool (actually just a big bash function) that copies over local rc-files without permanently writing them to the remove user's $HOME - the idea being that might be a shared admin account that other people use. Appears to be customizable for different remote hosts as well.
.ssh/config and LocalCommand
This blog post suggests a way to automatically run a command when you login to a remote host. It tars and pipes a set of files to the remote, then un-tars them on the remote's $HOME:
Your local ~/.ssh/config would look like this:
Host *
PermitLocalCommand yes
LocalCommand tar c -C${HOME} .bashrc .bash_profile .exports .aliases .inputrc .vimrc .screenrc \
| ssh -o PermitLocalCommand=no %n "tar mx -C${HOME}"
You could modify the above to only run the command on certain hosts (instead of the * wildcard) or customize for different hosts as well. There might be a fair amount of duplication per host with this method - although you could package the whole tar c ... | ssh .. "tar mx .." into a script maybe.
Note the above looks like it clobbers the same files on the remote when you connect, so use with caution.
Use a dotfiles.git repo
What I do is keep all my config files in a dotfiles.git on a central server.
You can set it up so that when you ssh into a remote machine, you automatically pull the latest version of the dotfiles. I do something like this:
ssh myhost
cd ~/dotfiles
git pull --rebase
cd ~
ln -sf dotfiles/$username/linux/.* .
Note:
To put that in a shell script, you can automate the process of executing commands on a remote machine by piping to ssh.
The "$username" is there so that you can share your config files with other people you're working with.
The "ln -sf" creates symbolic links to all your dotfiles, overwriting any local ones, such that ~/.emacs is linked to the version controlled file ~/dotfiles/$username/.emacs.
The use of a "linux" subdirectory is just to allow for configuration changes across platforms. I also have a mac directory under dotfiles/$username/mac. Most of the files in the /mac directory are symlinked from the linux directory as it's very similar, but there are some exceptions.
Finally, note that you can make this even more sophisticated with hostnames and the like rather than just a generic 'linux'. With a dotfiles.git, you can also raid dotfiles from your friends, which is awesome -- everyone has their own set of little tricks and hacks.
No, because it's not SSH using your config files, but the remote shell.
I suggest keeping your config files in Subversion or some other VCS. Here's how I do it.
Well, no, because as Andy Lester says, the remote machine is the one doing the work, and it has no access back to your local machine to get .vimrc ...
On the other hand, you could use sshfs to mount the remote file system locally and edit the files locally. This doesn't require you to install anything on the remote machine. Not sure how efficient it is, maybe not great for editing big files over slow links.
Or Komodo IDE has a neat "Open >> Remote File" option which lets you edit files on remote
machines by scping them back and forth automatically.
I do this kind of things every day. I have about 15 bash rc files and .vimrc, a few vim plugin scripts, .screenrc and some other rc files. I have a sync script (written in bash) which uses the cool rsync command to sync all these files to remote servers. Every time I update some files on my main server, I would call the script to sync them to remote servers.
Setting up a svn/git/hg repository on the main server also works for me but my remote servers need to be repeatedly reinstalled for testing. So I find it's more convenient to use rsync.
A few years ago I also used the rdist tool which can also meet the requirement for most of the time. But now I prefer rsync as it supports incremental sync which is very efficient.
ssh can be configured to pass certain environment variables through to the other (remote side). And since most shells will check some environment variables for additional settings to apply, you can hack that into applying some local settings remotely. But its a bit complicated and most administrators turn off the ssh environment variable pass-through in the sshd config anyways.
You could always just copy the files to the machine before connecting with ssh:
#!/bin/bash
scp ~/.bash_profile ~/.vimrc user#host:
ssh user#host
This works best if you are using keys to login and no one else logs in as that user.
Here's a simple bash script I've used for this purpose. It syncs over some folders I like to have copied over using rsync and then adds the ~/bin folder to the remote machines .bashrc if it's not there already. It works best if you have have copied your ssh keys to each server. I use this approach instead of a "dotfiles repo" as lots of the servers I connect to don't have git on them.
So to use it, you'd do something like this:
./bin_sync_to_machine.sh server1
bin_sync_to_machine.sh
function show_help()
{
echo ""
echo "usage: SERVER {SERVER2 SERVER3 etc...}"
echo ""
exit
}
if [ "$1" == "help" ]
then
show_help
fi
if [ -z "$1" ]
then
show_help
fi
# Sync ~/bin and some dot files to remote server using rsync
for SERVER in $*; do
rsync -avrz --progress ~/bin/ -e ssh $SERVER:~/bin
rsync -avrz --progress ~/.vim/ -e ssh $SERVER:~/.vim
rsync -avrz --progress ~/.vimrc -e ssh $SERVER:~/.vimrc
rsync -avrz --progress ~/.aliases $SERVER:~/.aliases
rsync -avrz --progress ~/.aliases $SERVER:~/.bash_aliases
# Ensure remote server has ~/bin in the path
ssh $SERVER '~/bin/path_add_to_path.sh'
done
path_add_to_path.sh
pathadd() {
if [ -d "$1" ] && [[ ":$PATH:" != *":$1:"* ]]; then
PATH="${PATH:+"$PATH:"}$1"
fi
}
# Add to current path if running in a shell
pathadd ~/bin
# Add to ~/.bashrc
if ! grep -q PATH:~/bin ~/.bashrc; then
echo "PATH=\$PATH:~/bin" >> ~/.bashrc
fi
if ! grep -q source ~/.aliases ~/.bashrc; then
echo "source ~/.aliases" >> ~/.bashrc
fi
I wrote an extremely simple tool for this that will allow you to natively transport your .vimrc file whenever you ssh, by using SSHd built-in config options in a non-standard way.
No additional svn,scp,copy/paste, etc required.
It is simple, lightweight, and works by default on all server configurations I have tested so far.
https://github.com/gWOLF3/viSSHous
I think that https://github.com/fsquillace/kyrat does what you need.
I wrote it long time ago before sshrc was born and it has more benefits compared to sshrc:
It does not require dependencies on xxd for both hosts (which can be unavailable on remote host)
Kyrat uses a more efficient encoding algorithm
It is just ~20 lines of code (really easy to understand!)
No need of root access or any installations to the remote host
For instance:
$> echo "alias q=exit" > ~/.config/kyrat/bashrc
$> kyrat myuser#myserver.com
myserver.com $> q
exit