I often happen to run a command like source mydirectory, where mydirectory is a ...directory, and not a shell script file (I guess I'm not that good at predicting autocompletion :p)
What puzzles me is that zsh does not complain, and returns 0 as status code; although that does not seem a normal call to source AFAIK.
# in zsh shell
# create an empty dir
$ mkdir /tmp/mydir
# "source" it
$ source /tmp/mydir && echo "success"
# output: 'success'
Meanwhile, bash will complain when asked to "source"
# in bash
$ source /tmp/mydir/ && echo "success"
# output: 'bash: source: /tmp/mydir/: is a directory'
Does someone know why this is a valid call in ZSH?
References I looked in
SO itself
the documentation of ZSH builtin commands https://zsh.sourceforge.io/Doc/Release/Shell-Builtin-Commands.html
multiple tutorials about source
... to no avail
Related
I have a '.js' script that I usually activate from the terminal using the command node script.js. As this is part of a process where I first do some data analysis in R, I want to avoid the manual step of opening the terminal and typing the command by simply having R do it for me. My goal would be something like this:
...R analysis
write.csv(df, "data.csv")
system('node script.js')
However, when I use that specific code, I get the error:
sh: 1: node: not found
Warning message:
In system("node script.js") : error in running command
Of course, the same command runs without problem if I type it directly on the terminal.
About my Software
I am using:
Linux computer with the PopOS!
RStudio 2021.09.1+372 "Ghost Orchid"
R version 4.0.4.
The error message node: not found indicates that it couldn't find the program node. It's likely in PATH in your terminal's shell, but not in system()'s shell (sh).
In your terminal, locate node by executing which node. This will show the full path to the executable. Use that full path in system() instead.
Alternatively, run echo $PATH in your terminal, and run system('echo $PATH') or Sys.getenv('PATH') in R. Add any missing directories to R's path with Sys.setenv(PATH = <your new path string>)
Note that system2() is recommended over system() nowadays - but for reasons unimportant for your case. See ?system and ?system2 for a comparison.
Examples
Terminal
$ which node
/usr/bin/node
R
system('/usr/bin/node script.js')
# alternatively:
system2('/usr/bin/node', c('script.js'))
or adapt your PATH permanently:
Terminal
% echo $PATH
/usr/local/bin:/home/caspar/programs:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
R
> Sys.getenv('PATH')
[1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/RStudio.app/Contents/MacOS/postback"
> Sys.setenv(PATH = "/home/caspar/programs:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/RStudio.app/Contents/MacOS/postback")
When I open terminal, I receive this message:
Last login: Fri Jan 17 11:02:25 on ttys000
(eval):1: parse error near `)'
(eval):1: parse error near `)'
It prints twice, but I only have four ")" in my .zshrc file, and none of them seem to be causing any issues. I've looked around the web for solutions, but I haven't found many that seem to address this problem.
My .zshrc file looks like this:
# If you come from bash you might have to change your $PATH.
# export PATH=$HOME/bin:/usr/local/bin:$PATH
# Path to your oh-my-zsh installation.
export ZSH=$HOME/.oh-my-zsh
(Some code removed for brevity...)
# Which plugins would you like to load?
source $ZSH/oh-my-zsh.sh
# My personal Add-ons:
# open VSCode via "code"
function code {
if [[ $# = 0 ]]
then
open -a "Visual Studio Code"
else
local argPath="$1"
[[ $1 = /* ]] && argPath="$1" || argPath="$PWD/${1#./}"
open -a "Visual Studio Code" "$argPath"
fi
}
Thanks!
I'm a beginner for Python. My question might be basic, but I cannot figure it out. What I want to do is to run the following command 100 times in which the variable "num" runs from 0 through 99.
python test.py input_num.txt -i 5 --cor_file=output_num.txt
For example:
python test.py input_0.txt -i 5 --cor_file=output_0.txt
python test.py input_1.txt -i 5 --cor_file=output_1.txt
...
:::
python test.py input_99.txt -i 5 --cor_file=output_99.txt
I know that I have to write a script for running the loop, but cannot figure it out yet. If you have any recommendation, that would be very nice.
I tried to write a script called main.py containing the following commands, but it didn't work.
#!/usr/bin/env python
import test
ext_str = '.txt'
inp = 'input_'
out = 'output_'
for num in range(0,99):
inp += 'num'
inp_str = inp + ext_str
out += 'num'
out_str = out + ext_str
python test.py inp_str -i 5 --cor_file=out_str
Thank you very much.
Best,
Pim
In your case you need to call the python interpreter on various files, e.g. you need to call the "python" shell command, it means that you have to create a shell script (and not a python script, actually you could do it with some python code but it would be way too complicated in your case):
for i in {0..99}
do
python test.py input_$i.txt -i 5 --cor_file=output_$i.txt
done
put the above code in a ".sh" file then don't forget to "chmod +x the ", then run it with ./.sh (given that your are in the current directory).
N.B.: If you need some references on bash scripting : Linux Shell Scripting Tutorial
I am building a Qt GUI application via Jenkins. I added 3 build steps:
Building the test executable
Running the test executable
compiling a coverage report with gcovr
For some reason, the shell task for running the test executable stops after execution. Even a simple echo does not run after. The tests are written with Google Test and output xUnit XML files, which are analyzed after the build.
Some tests start the applications user interface, so I installed the jenkins xvnc plugin to get them to run.
The build tasks are as follows:
Build
cd $WORKSPACE/projectfiles/QMake
sh createbin.sh
Test
cd $WORKSPACE/bin
./Application --gtest_output=xml
Coverage Report
cd $WORKSPACE/projectfiles/QMake/out
gcovr -x -o coverage.xml
Now, an echo at the end of the first build task is correctly printed, but an echo at the end of the second is not. The third build task is therefore not even run, although the Google Test output is visible. I thought that maybe the problem is that some of the Google Tests fail, but why whould the script stop executing just because the tests fail?
Maybe someone can give me a hint on why the second task stops.
Edit
The console output looks like this:
Updating svn://repo/ to revision '2012-11-15T06:43:15.228 -0800'
At revision 2053
no change for svn://repo/ since the previous build
Starting xvnc
[VG5] $ vncserver :10
New 'ubuntu:10 (jenkins)' desktop is ubuntu:10
Starting applications specified in /var/lib/jenkins/.vnc/xstartup
Log file is /var/lib/jenkins/.vnc/ubuntu:10.log
[VG5] $ /bin/sh -xe /tmp/hudson7777833632767565513.sh
+ cd /var/lib/jenkins/workspace/projectfiles/QMake
+ sh createbin.sh
... Compiler output ...
+ echo Build Done
Build Done
[VG5] $ /bin/sh -xe /tmp/hudson4729703161621217344.sh
+ cd /var/lib/jenkins/workspace/VG5/bin
+ ./Application --gtest_output=xml
Xlib: extension "XInputExtension" missing on display ":10".
[==========] Running 29 tests from 8 test cases.
... Test output ...
3 FAILED TESTS
Build step 'Execute shell' marked build as failure
Terminating xvnc.
$ vncserver -kill :10
Killing Xvnc4 process ID 1953
Recording test results
Skipping Cobertura coverage report as build was not UNSTABLE or better ...
Finished: FAILURE
Generally, if one Build Step fails, the rest will not be executed.
Pay attention to this line from your log:
[VG5] $ /bin/sh -xe
The -x makes the shell print each command in console before execution.
The -e makes the shell exit with error if any of the commands failed.
A "fail" in this case, would be a return code of not 0 from any of the individual commands.
You can verify this by running this directly on the machine:
./Application --gtest_output=xml
echo $?
If the echo $? displays 0, it indicates successful completion of the previous command. If it displays anything else, it indicates an error code from the previous command (from ./Application), and Jenkins treats it as such.
Now, there are several things at play here. First is that your second Build Step (essentially a temporary shell script /tmp/hudson4729703161621217344.sh) is set to fail if one command fails (the default behaviour). When the Build Step fails, Jenkins will stop and fail the whole job.
You can fix this particular behaviour by adding set +e to the top of your second Build Step. This will not cause the script (Build Step) to fail due to individual command failure (it will display an error for the command, and continue).
However, the overall result of the script (Build Step) is the exit code of the last command. Since in your OP, you only have 2 commands in the script, and the last is failing, it will cause the whole script (Build Step) to be considered a failure, despite the +x that you've added. Note that if you add an echo as the 3rd command, this would actually work, since the last script command (echo) was successful, however this "workaround" is not what you need.
What you need is proper error handling added to your script. Consider this:
set +e
cd $WORKSPACE/bin && ./Application --gtest_output=xml
if ! [ $? -eq 0 ]; then
echo "Tests failed, however we are continuing"
else
echo "All tests passed"
fi
Three things are happening in the script:
First, we are telling shell not to exit on failure of individual commands
Then i've added basic error handling in the second line. The && means "execute ./Application if-and-only-if the previous cd was successful. You never know, maybe the bin folder is missing, or whatever else can happen. BTW, the && internally works on the same error code equals 0 principle
Lastly, there is now proper error handling for the result of ./Application. If the result is not 0, then we show that it had failed, else we show that it had passed. Note, this since the last command is not a (potentially) failing ./Application, but an echo from either of if-else possibilities, the overall result of the script (Built Step) will be a success (i.e 0), and the next Build Step will be executed.
BTW, you can as well put all 3 of your build steps into a single build step with proper error handling.
Yes... this answer may be a little longer than what's required, but i wanted you to understand how Jenkins and shell treat exit codes.
I am using cygwin on windows 7 env and it is unable to locate java, error message i get is that
ERROR: /cygdrive/c/Program
Files/Java/jdk1.6.0_22 does not exist!
wired path is if I do echo $JAVA_HOME then it shows me
$ echo $JAVA_HOME
/cygdrive/c/Program Files/Java/jdk1.6.0_22
not sure what is happening here, any suggestions?
The problem is that the pathname contains spaces. You need to escape the spaces as described here:
http://www.cygwin.com/faq/faq.using.html#faq.using.filename-spaces
Adding this line to your .bashrc should do it:
export JAVA_HOME='/cygdrive/c/Program Files/Java/jdk1.6.0_22'
Edit: You could try running this script which I found in this blog post:
case "`uname`" in
CYGWIN*) cygwin=true ;;
esac
# For Cygwin, switch paths to Windows format before running java
if $cygwin; then
JAVA_HOME=`cygpath --windows "$JAVA_HOME"`
CLASSPATH=`cygpath --windows --path "$CLASSPATH"`
fi
Use the old school way:
export JAVA_HOME=/cygdrive/c/Progra~1/Java/jdk1.6.0_22
It worked for me.