I installed R under my home folder, and I would like to use the new R is invoked when I submit jobs to clusters. The cluster nodes all have CentOS installed.
Here is the configure I made in the .bash_profile and .bashrc:
if [ `lsb_release -i|cut -c17-20` == 'Cent' ] ; then
alias R='/home/XXX/R-3.0.2/bin/R'
alias Rscript='/home/XXX/R-3.0.2/bin/Rscript'
fi
I added following in .bash_profile:
if [ -f ~/.bashrc ]; then
source ~/.bashrc
fi
I also added this to the scripts submitted.
source $HOME/.bash_profile
I tried with qsub -I, it works perfect.
However, after I submit the job, and which R still show the original path!
How to set the environment correctly?
Aliasing doesn't affect the which command, for example:
$ which R
/usr/bin/R
$ alias R=/bin/date
$ R
Sun Jan 5 13:40:54 CET 2014 # as you see the alias works
$ which R # `which R` still returns the original path
/usr/bin/R
Instead of using aliases, I think you want to prepend /home/XXX/R-3.0.2/bin to PATH:
PATH="/home/XXX/R-3.0.2/bin:$PATH"
After this, if R and Rscript exist in /home/XXX/R-3.0.2/bin, then:
which R should return /home/XXX/R-3.0.2/bin/R
which Rscript should return /home/XXX/R-3.0.2/bin/Rscript
as they will be found in /home/XXX/R-3.0.2/bin first, before any other directory in the rest of $PATH.
Related
I'm currently struggling with running a .sh script I'm trying to trigger from Jenkins.
Within the Jenkins "execute shell" section, I'm connecting to a remote server (The Jenkins agent does not have right OS to build what I need.), using:
cp -r . /to/shared/drive/to/have/access/on/remote
ssh -t -t username#servername << EOF
cd /to/shared/drive/to/have/access/on/remote
source build.sh dev
exit
EOF
Inside build.sh, I'm exporting R_LIBS to build a package for different R versions.
...
for path in "${!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 have created below .sh file to run R code saved in separate .R file.
cat EE.sh
#!/bin/bash
VARIABLES=( 20190719 20190718 )
for i in ${VARIABLES[#]}; do
VARIABLENAME=$i
/usr/lib/R/bin/Rscript -e 'source("/home/EER.R")'
Basically what it is expected to do is, take the dates from VARIABLE and pass to the /home/EER.R file, and R will do execution based on passed date (after correct formatting)
Then I ran below code
sudo chmod a+rx EE.sh
and
sudo bash EE.sh
But I then get below error message.
sudo bash EE.sh
EE.sh: line 2: $'\r': command not found
EE.sh: line 3: $'\r': command not found
EE.sh: line 4: $'\r': command not found
Can anyone help me to resolve this issue.
I am using Ubuntu 18 with R version 3.4.4 (2018-03-15)
This problem looks to be related to carriage returns related(which come when we copy text from windows machine to unix machine), so to identify them use:
cat -v Input_file
If you see carriage returns in your file then try:
tr -d '\r' < Input_file > temp && mv temp Input_file
Once they are removed then try to run your program.
I would like to my terminal current directory follows my VIM one.
Example:
In TERMINAL:
> pwd
=> /Users/rege
> vim
Then in VIM
:cd /Users/rege/project
<Ctrl-z>(for suspend)
In terminal
> pwd
=> /Users/rege/project
I`m using MacOS, zsh, tmux.
I need this because when Im trying to use tags in VIM, tags are check in project from my terminal directory not vim one.
So I need to change terminal current directory always when I change VIM current directory.
What kind of command do you issue in your shell after you suspend Vim? Isn't Vim's :!command enough?
With set autochdir, Vim's current directory follows you as you jump from file to file. With this setting, a simple :!ctags -R . will always create a tags file in the directory of the current file.
Another useful setting is set tags=./tags,tags;$HOME which tells Vim to look for a tags file in the directory of the current file, then in the "current directory" and up and up until it reaches your ~/. You might modify the endpoint to suit your needs. This allows you to use a tags at the root of your project while editing any file belonging to the project.
So, basically, you can go a long way without leaving Vim at all.
If you really need to go back to the shell to issue your commands, :shell (or :sh) launchs a new shell with Vim's current directory. When you are done, you only have to $ exit to go back to Vim:
$ pwd
/home/romainl
$ vim
:cd Projects
:sh
$ pwd
/home/romainl/Projects
$ exit
In bash or zsh and on Unix you can do this: current working directory of the process is represented in /proc/{PID}/cwd as a symlink to a real directory. Speaking about zsh the following code will do the job:
function precmd()
{
emulate -L zsh
(( $#jobstates == 1 )) || return
local -i PID=${${${(s.:.)${(v)jobstates[1]}}[3]}%\=*}
cd $(readlink /proc/$PID/cwd)
}
. Note: with this code you won’t be able to pernamently switch directories in terminal anymore, only in vim or for duration of one command (using cd other-dir && some command).
Note 2: I have no idea how to express this in bash. The straightforward way is to get PIDs of all children of the shell (using ps --ppid $$ -o CMD), filter out the ps process (it will be shown as a child as well), check that there is only one other child and use its PID like in the last line above. But I am pretty sure there is a better way using some shell builtins like I did with zsh’s $jobstates associative array. I also don’t remember what is the analogue of precmd in bash.
Another idea would be making vim save its current directory into some file when you do <C-z> and make shell read this in precmd:
" In .vimrc:
function s:CtrlZ()
call writefile([fnamemodify('.', ':p')], $CWDFILE, 'b')
return "\<C-z>"
endfunction
nnoremap <expr> <C-z> <SID>CtrlZ()
# In .zshrc
function vim()
{
local -x CWDFILE=~/.workdirs/$$
test -d $CWDFILE:h || mkdir $CWDFILE:h
vim $#
}
function precmd()
{
local CWDFILE=~/.workdirs/$$
test -e $CWDFILE && cd "$(cat $CWDFILE)"
}
. It should be easier to port above code to bash.
you can open a new terminal like this
:!xterm -e bash -c "cd %:p:h;bash" &
actually I write this in my .vimrc
nmap <F3> :!xterm -e bash -c "cd %:p:h;bash" &<CR> | :redraw!
For bash users coming by:
Vim: Save pwd at <c-z> (with map and getpwd()).
Bash: Before prompt command, goto directory indicated by vim with PROMPT_COMMAND.
.bashrc
PROMPT_COMMAND='read -r line 2>/dev/null </tmp/cd_vim'\
'&& > /tmp/cd_vim && cd ${line##\r};'$PROMPT_COMMAND
vimrc
function! s:CtrlZ() call writefile([getcwd(),''], '/tmp/cd_vim', 'b')
return "\<C-z>"
endfunction
nnoremap <expr> <C-z> <SID>CtrlZ()
This is ZyX answer edited for bash https://stackoverflow.com/a/12241861/2544873
Tried using the answer found here:
How to run 'cd' in shell script and stay there after script finishes?
When I add the 'source' command, the directory is still unchanged after script runs, regardless of whether I execute 'source ' or call the script using an alias coded in cshrc.
Any help is much appreciated!
As you can see below, make sure your call to cd is not executing within a subshell. If it is, this won't work, source or not.
Script with cd in subshell
#!/bin/bash
( cd /etc ) # thie exec's in a subshell
Output
$ pwd
/home/siegex
$ source ./cdafterend.sh && pwd
/home/siegex
Script with cd not in subshell
#!/bin/bash
cd /etc # no subshell here
Output
$ pwd
/home/siegex
$ source ./cdafterend.sh && pwd
/etc
It was necessary to remove "/bin/" from the cd command within this script, in order for the command to work as intended. Removing this removes the subshell issue for this script. Also, coding "$1" in the ls command was invalid in this context.
I got this far:
:~ curl -u username:password -d status="new_status" http://twitter.com/statuses/update.xml
Now, how can I alias this with variables so I can easily twit from Terminal? How can I make the alias working through different sessions (when I close Terminal aliases reset).
Thanks!
Basic Authentication is no longer supported by twitter. Please use OAuth.
You clearly have the alias command: stick it in your ~/.bashrc and it will be set up when your bash shell starts. (.shrc should also work for sh-like shells.)
If you stick it in a script file as the previous answer suggests:
(a) add the line
#!/bin/sh
at the top;
(b) make sure it's on your path or you'll have to type the whole path to the script when you want to run it.
(c) to make it executable,
chmod +x tweet.sh
what about putting it a file and using argument 1 as $1:
# tweet.sh "post my status, moron!":
curl -u username:password -d status="$1" http://twitter.com/statuses/update.xml
will that work?
You need to create a file in your home directory that will get referenced each time a new terminal opens.
Do a bit of research as to what to name the file, according to what type of shell you are using (tcsh looks for a file called .tcshrc while bash looks for .bashrc).
Once you have that file, make it executable by running:
chmod +x name_of_file
Then, in that file, create your alias (again, you'll need to research how to do this depending on what type of shell you are using). For tcsh, my alias looks like this:
alias tw 'curl -u username:password -d status=\!^ http://twitter.com/statuses/update.xml'
Bash aliases use an equals sign. A bash alias would look something more like this:
alias tw='curl -u username:password -d status=\!^ http://twitter.com/statuses/update.xml'
Note the change in the command after "status=". The \!^ tells the line of code to insert the first argument passed after the alias itself.
Save your file.
You could then run an update to twitter by typing the following in a new terminal:
tw 'my first post to twitter via the terminal, using aliases'
Don't forget to escape 'special' characters (like exclamations) with the escape character, \ (i.e. \!)
Since Basic Authentication is no longer supported by twitter, you have to use OAuth to achieve your goal.
But if you just want to post to Twitter using terminal, there are many application can do it.
Take a look at Rainbowstream or t
With rainbowstream, the following lines will let you tweet from console:
$ sudo pip install rainbowstream
$ rainbowstream
[#yourscreenname]t whatever you want