源代码无法在Shell脚本中运行

Question

We operate on a Linux server and I need to run an R script within anaconda.

How do I engage the anaconda environment via a shell script.

Via the command line:

$  source anaconda 
$  Rscript <file.R>

works just fine.

If anaconda is already engaged the following .sh works fine:

#!/bin/bash
PATH=$PATH:/usr/local/bin/anaconda
echo Rscript ./name.R

Is there a version of:

#!/bin/bash
PATH=$PATH:/usr/local/bin
echo source anaconda; Rscript ./name.R

That would open anconda and run the script?

My anaconda is located within ./anaconda. I've tried setting that as my initial path.

Thanks!

Answer 1

What we're missing is the contents of the anaconda file. I'm thinking it creates the Rscript command as an alias , since the shell by default does not expand aliases unless the shell is interactive. For example:

Interactive, all is well

$ cat > anaconda
alias Rscript='echo this is Rscript:'
$ source ./anaconda
$ Rscript foo bar
this is Rscript: foo bar

But in a script, I can reproduce your error

$ cat > test.sh
#!/bin/bash
source ./anaconda
Rscript foo bar
$ bash test.sh
test.sh: line 3: Rscript: command not found

Forcing bash to be interactive:

$ bash -i test.sh
this is Rscript: foo bar

Try this:

#!/bin/bash
shopt -s expand_aliases
source /path/to/anaconda
Rscript ./name.R