Running programmatically created Rscript call at command line

Question

I have the following script:

rstest

text=$1

cmd="Rscript -e \"a='$1'; print(a)\""
echo $cmd
$cmd

This is the output I get when I run it:

balter@spectre3:~$ bash rstest hello
Rscript -e "a='hello'; print(a)"
Error: unexpected end of input
Execution halted

However, if I run the echoed command directly, it runs fine:

balter@spectre3:~$ Rscript -e "a='hello'; print(a)"

[1] "hello"

I would like to understand why this is. I've tried various combinations of quoting the bash variables and adding eval. But that doesn't seem to be the issue.

EDIT

I tried the answer given below, but get a different result!

balter@spectre3:~$ cat rstest
text=$1

cmd="Rscript -e \"a=$1; print(a)\""
echo $cmd
eval $cmd

balter@spectre3:~$ bash rstest
Rscript -e "a=; print(a)"
Error in cat("pointing to conda env:", env_name, "and lib location", lib,  :
  argument "env_name" is missing, with no default
Calls: startCondaEnv -> cat
Execution halted

I think you want eval $cmd rather than just $cmd

MrFlick
– MrFlick

2019-05-15 01:28:53 +00:00
Commented May 15, 2019 at 1:28 — MrFlick
– MrFlick, Commented May 15, 2019 at 1:28
That did not change the behavior :(

abalter
– abalter

2019-05-15 01:59:19 +00:00
Commented May 15, 2019 at 1:59 — abalter
– abalter, Commented May 15, 2019 at 1:59

Hisham Al Kayed · Accepted Answer · 2019-05-15 02:24:09Z

1

Below script worked for me.

text=$1

cmd="Rscript -e \"a='$1'; print(a)\""
echo $cmd
eval $cmd

Removing eval gave the same error you posted.

Rscript -e "a='Hello'; print(a)"
Error: unexpected end of input
Execution halted

answered May 15, 2019 at 2:24

Hisham Al Kayed

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2 Comments

abalter Over a year ago

Welcome to Stackoverflow! I added to the original post trying to run what you gave. I get the same error! I'm running this in Ubuntu 18.10. You?

Hisham Al Kayed Over a year ago

Mint 19.1 and R 3.6.0; i think after you used eval you changed cmd and forget to add the apostrophe around $1.

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