Perplexing output from the system() command

I am running R2106b on a Macbook Pro OS X Yosemite.

In a Terminal window (using bash shell), if I type

which which

I get the expected output

/usr/bin/which

and similarly

which psql

yields

/usr/local/bin/psql

All is well and good so far. But if I issue these same command from within MATLAB, using the system() command, I get output that perplexes me. As expected, when I type

[status cmdout] = system('which which')

I get

status =

       0

cmdout =

      '/usr/bin/which
       '

But from

[status cmdout] = system('which psql')

I get

status =

       1

cmdout =

    0×0 empty char array

Finally, if I point directly to the known directory (which in my real application I would not know) ...

[status cmdout] = system('which /usr/local/bin/psql')

then the command is found

status =

       0

cmdout =

      '/usr/local/bin/psql
       '

Does anyone have some insight into what is happening here? I am not a Unix expert by any means. But the whole thing seems to be a bit of a shell game. ;-)

(I can add the why I am doing this if needed, but I won't burden folks just yet.)

[Lukas Krück]

Yeah, totally can sign this statement. Need an answer as well :(

[Walter Roberson]

The causes are described below: when you start MATLAB from the icon, that is not a login shell so your shell setup files are not run and so your PATH environment variable does not include everything you might be expecting.

[Jess Crawshaw]

Your answer below completely fixed my problems, thanks for this

Answer 1

[Walter Roberson]

psql is not on your PATH environment variable inside of MATLAB. When you enter the terminal then that would be a login shell and your bash profile would be executed, but when you start MATLAB from an icon then that is not a login shell and your bash profile would not be executed.

See http://stackoverflow.com/questions/22465332/setting-path-environmental-variables-in-osx-permanently

[the cyclist]

Thanks.

For the sake of others who may read this ...

The specific solution for me was to add /usr/local/bin to my MATLAB PATH environment variable. I did this by adding the line

setenv('PATH', [getenv('PATH') ':/usr/local/bin'])

to my startup file.

[Walter Roberson]

/etc/profile and ~/.bashrc and ~/.bash_profile and ~/.bash_login and ~/.profile are only executed for interactive shells.

/etc/bashrc (Red Hat) or /etc/bash.bashrc (Ubuntu) are executed for non-interactive shells.

Answer 2

[Nikunj Kothari]

Are you getting the same output if instead of using system(), you use the exclamation point? The following documentation link elaborates on how to properly run external commands and scripts:

http://www.mathworks.com/help/matlab/matlab_external/run-external-commands-scripts-and-programs.html