MacQIIME installed but cannot import commands from IPython.display or others

[jdoh...@umd.edu]

I just installed MacQIIME on my MacPro running El Capitan Version 10.11.1, and it seems to have successfully installed.  However, I cannot start MacQIIME by using the macqiime command, but I do not mind running 'source /macqiime/configs/bash_profile.txt to start it.  My main problem is that when I try running the commands to import commands from IPython.display, or os, or functools I get the following returned to me: "from: can't read /var/mail/IPython.display".  Did something get altered in the installation that is causing this error?

I can run print_qiime_config.py, as well as other scripts, but from what I can tell I need to be able to import commands such as FileLinks, FileLink, chdir, and partial to be able to utilize MacQIIME.  Does anyone know of a fix for this?  I have followed the MacQIIME installation procedures and have done the extra steps for working with the new security features of El Capitan.

Any help would be greatly appreciated.

Joe

[Sausage Mahoney]

Having the same problem here...ever resolve it on your end?

S

[Daniel McDonald]

Hello,

I'm reaching out to someone on this.

Best,

Daniel

[Jeff Werner]

Hi Joe,

That's odd and frustrating, sorry. Is it a qiime script in the bash terminal that is giving you the error message "can't read /var/mail/IPython.display"?  Or is this something you're doing in python rather than in the bash terminal? Could it be that something you're doing is mixing the default Mac OS X python install with the custom python install in macqiime (at /macqiime/anaconda/)? I haven't seen this error in the three El Capitan systems we're using, but I've only used QIIME directly from the bash terminal. It could be that I overlooked this usage and that you might need to (re)install something in the /macqiime/anaconda/ installation of python (e.g. you can use the conda command once you have macqiime sourced in the terminal)?  If there's a problem with IPython within the macqiime python install, updating with conda might help. 

And, on the side, when you run print_qiime_config.py -t in the terminal, it doesn't give any errors?

And, one other thing I always double-check: Updates to OS X will often break XQuartz, and reinstalling that has solved some confusing problems in the past (though I'm doubtful of whether that could be the problem in this case). 

Thanks, and sorry for the trouble.

Cheers,

Jeff