I have a bash script that calls another script containing a psql command, i want to stop executing when the psql command fails. The below psql call is to execute a postgres function.
In below script the echo $exitcode always returns 0 even if script calling postgres function returns a error. I want psql command to return right error code, so i can handle it properly in below script.
FirstScript:
list=`sh /opt/dbb_promo_list.sh -60 -30`
ID_LIST=`echo $list |sed 's/[a-z _-]*//g'|sed 's/(.*//g'`
exitcode=$?
echo $exitcode //always returns 0 both in successful and error case, i want it to return corresponding exit code for error, so i can handle it and stop the script.
if [ $exitcode -ne 0 ] ; then
echo "There seems to have errors while running script "
echo "Exit code is : "$exitcode
exit 1
fi
dbb_promo_list.sh : This script contains the following command
psql -U $DB_USERNAME -h $DB_HOST -p $DB_PORT -d $DATABASE -c "SELECT schema.${PROCEDURE}($day_begin,$day_end)"
Error thrown below when calling the above command. Since this error is thrown the psql command shouldnt return exit code 0 but its not the case, it returns 0 even if the postgres function works fine or returns a error like below. I am not sure if there a way to tweak in bash script to recognize a error is thrown
ERROR: function string_agg(numeric, unknown) does not exist
LINE 1: SELECT string_agg(pmotn_id, ',') FROM ppcapr.p...
^
HINT: No function matches the given name and argument types. You might need to add explicit type casts.
When the sql function fails. It then reports the error on the console, but continues to proceed with executing remainder of the script. But i want the script execution to terminate once the error occurs.
Any suggestions?
I have written the following code:
#!/bin/bash
#Simple array
array=(1 2 3 4 5)
echo ${array[*]}
And I am getting error:
array.sh: 3: array.sh: Syntax error: "(" unexpected
From what I came to know from Google, that this might be due to the fact that Ubuntu is now not taking "#!/bin/bash" by default... but then again I added the line but the error is still coming.
Also I have tried by executing bash array.sh but no luck! It prints blank.
My Ubuntu version is: Ubuntu 14.04
Given that script:
#!/bin/bash
#Simple array
array=(1 2 3 4 5)
echo ${array[*]}
and assuming:
It's in a file in your current directory named array.sh;
You've done chmod +x array.sh;
You have a sufficiently new version of bash installed in /bin/bash (you report that you have 4.3.8, which is certainly new enough); and
You execute it correctly
then that should work without any problem.
If you execute the script by typing
./array.sh
the system will pay attention to the #!/bin/bash line and execute the script using /bin/bash.
If you execute it by typing something like:
sh ./array.sh
then it will execute it using /bin/sh. On Ubuntu, /bin/sh is typically a symbolic link to /bin/dash, a Bourne-like shell that doesn't support arrays. That will give you exactly the error message that you report.
The shell used to execute a script is not affected by which shell you're currently using or by which shell is configured as your login shell in /etc/passwd or equivalent (unless you use the source or . command).
In your own answer, you say you fixed the problem by using chsh to change your default login shell to /bin/bash. That by itself should not have any effect. (And /bin/bash is the default login shell on Ubuntu anyway; had you changed it to something else previously?)
What must have happened is that you changed the command you use from sh ./array.sh to ./array.sh without realizing it.
Try running sh ./array.sh and see if you get the same error.
Instead of using sh to run the script,
try the following command:
bash ./array.sh
I solved the problem miraculously. In order to solve the issue, I found a link where it was described to be gone by using the following code. After executing them, the issue got resolved.
chsh -s /bin/bash adhikarisubir
grep ^adhikarisubir /etc/passwd
FYI, "adhikarisubir" is my username.
After executing these commands, bash array.sh produced the desired result.
I'm quite new to bash scripting and i've been working on a small bash file that can do a few things for me. First of all, i'm calling this from a C function using system() and i'd like the script to return a value (1 for error, 0 for OK). Is this possible?
int kinit() {
int err = system("/home/bluemoon/Desktop/GSSExample/kinitScript.sh");
}
Second, using Zenity, i managed to create a pop up window to insert user/password. Now, according to what the user does, multiple things should happen. If he closes the window or clicks "cancel", nothing should happen. If he clicks "OK", then i should check the input (for empty text boxes or something).
Assuming a correct input, i will use Expect to run a kinit program (it's a promt related with Kerberos) and log in. Now, if the password is correct, the prompt closes and the script should return 0. If it's not, the prompt will show something like "Kinit: user not found". I wanted to, in any case of error (closing window, clicking cancel or wrong credentials) return 1 in my script and return 0 on success.
#!/bin/bash
noText=""
ENTRY=`zenity --password --username`
case $? in
0)
USER=`echo $ENTRY | cut -d'|' -f1`
PW=`echo $ENTRY | cut -d'|' -f2`
if [ "$USER"!="$noText" -a "$PW"!="$noText" ]
then
/usr/bin/expect -c 'spawn kinit '`echo $USER`'; expect "Password for '`echo $USER`':" { send "'`echo $PW`'\r" }; interact'
fi
;;
1)
echo "Stop login.";;
-1)
echo "An unexpected error has occurred.";;
esac
My if isn't working properly, the expect command is always run. Cancelling or closing the Zenity window also always lead to case "0". I've also tried to return a variable but it says i can only return vars from inside functions?
Well, if anyone could give me some pointers, i'd appreciate it.
Dave
i'd like the script to return a value
Sure, just use exit in appropriate places
exit: exit [n]
Exit the shell.
Exits the shell with a status of N. If N is omitted, the exit status
is that of the last command executed.
My if isn't working properly, the expect command is always run.
if [ "$USER" != "$noText" -a "$PW" != "$noText" ]
# ^ ^ ^ ^
# | | | |
# \----- notice spaces ----/
When starting Catalina run, I get the following warning:
WARNING: ClearCaseRepository not working (missing binaries?):
Any idea, anyone?
Thanks, Avi
This is similar to this thread (I will adapt the following extract to your case):
As far as I can see from the code, this warning can only happen if the command "git --help" [in your case cleartool -version] exits with a non-zero exit code.
What do you see if you log in as the tomcat user, set the PATH like you do in startup.sh, and then execute following commands
cleartool -version
echo $?
Check the logs (catalina.out) after adding the following line to your Tomcat's conf/logging.properties:
org.opensolaris.opengrok.level=ALL
I want to redirect all console text to a file. Here is what I tried:
> sink("test.log", type=c("output", "message"))
> a <- "a"
> a
> How come I do not see this in log
Error: unexpected symbol in "How come"
Here is what I got in test.log:
[1] "a"
Here is what I want in test.log:
> a <- "a"
> a
[1] "a"
> How come I do not see this in log
Error: unexpected symbol in "How come"
What am I doing wrong? Thanks!
You have to sink "output" and "message" separately (the sink function only looks at the first element of type)
Now if you want the input to be logged too, then put it in a script:
script.R
1:5 + 1:3 # prints and gives a warning
stop("foo") # an error
And at the prompt:
con <- file("test.log")
sink(con, append=TRUE)
sink(con, append=TRUE, type="message")
# This will echo all input and not truncate 150+ character lines...
source("script.R", echo=TRUE, max.deparse.length=10000)
# Restore output to console
sink()
sink(type="message")
# And look at the log...
cat(readLines("test.log"), sep="\n")
If you have access to a command line, you might prefer running your script from the command line with R CMD BATCH.
== begin contents of script.R ==
a <- "a"
a
How come I do not see this in log
== end contents of script.R ==
At the command prompt ("$" in many un*x variants, "C:>" in windows), run
$ R CMD BATCH script.R &
The trailing "&" is optional and runs the command in the background.
The default name of the log file has "out" appended to the extension, i.e., script.Rout
== begin contents of script.Rout ==
R version 3.1.0 (2014-04-10) -- "Spring Dance"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: i686-pc-linux-gnu (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Previously saved workspace restored]
> a <- "a"
> a
[1] "a"
> How come I do not see this in log
Error: unexpected symbol in "How come"
Execution halted
== end contents of script.Rout ==
If you are able to use the bash shell, you can consider simply running the R code from within a bash script and piping the stdout and stderr streams to a file. Here is an example using a heredoc:
File: test.sh
#!/bin/bash
# this is a bash script
echo "Hello World, this is bash"
test1=$(echo "This is a test")
echo "Here is some R code:"
Rscript --slave --no-save --no-restore - "$test1" <<EOF
## R code
cat("\nHello World, this is R\n")
args <- commandArgs(TRUE)
bash_message<-args[1]
cat("\nThis is a message from bash:\n")
cat("\n",paste0(bash_message),"\n")
EOF
# end of script
Then when you run the script with both stderr and stdout piped to a log file:
$ chmod +x test.sh
$ ./test.sh
$ ./test.sh &>test.log
$ cat test.log
Hello World, this is bash
Here is some R code:
Hello World, this is R
This is a message from bash:
This is a test
Other things to look at for this would be to try simply pipping the stdout and stderr right from the R heredoc into a log file; I haven't tried this yet but it will probably work too.
You can't. At most you can save output with sink and input with savehistory separately. Or use external tool like script, screen or tmux.
Run R in emacs with ESS (Emacs Speaks Statistics) r-mode. I have one window open with my script and R code. Another has R running. Code is sent from the syntax window and evaluated. Commands, output, errors, and warnings all appear in the running R window session. At the end of some work period, I save all the output to a file. My own naming system is *.R for scripts and *.Rout for save output files.
Here's a screenshot with an example.
You can print to file and at the same time see progress having (or not) screen, while running a R script.
When not using screen, use R CMD BATCH yourscript.R & and step 4.
When using screen, in a terminal, start screen
screen
run your R script
R CMD BATCH yourscript.R
Go to another screen pressing CtrlA, then c
look at your output with (real-time):
tail -f yourscript.Rout
Switch among screens with CtrlA then n
To save text from the console: run the analysis and then choose (Windows) "File>Save to File".
Set your Rgui preferences for a large number of lines, then timestamp and save as file at suitable intervals.
If you want to get error messages saved in a file
zz <- file("Errors.txt", open="wt")
sink(zz, type="message")
the output will be:
Error in print(errr) : object 'errr' not found
Execution halted
This output will be saved in a file named Errors.txt
In case, you want printed values of console to a file you can use 'split' argument:
zz <- file("console.txt", open="wt")
sink(zz, split=TRUE)
print("cool")
print(errr)
output will be:
[1] "cool"
in console.txt file. So all your console output will be printed in a file named console.txt
This may not work for your needs, but one solution might be to run your code from within an Rmarkdown file. You could write both the code and console output to HTML/PDF/Word.