[chimera-dev] About Chimera Extension Permission

Conrad Huang conrad at cgl.ucsf.edu
Mon Mar 25 10:19:04 PDT 2019


Hi, Yuhong.

Does this error still occur if you run the Chimera app after copying it 
to your local disk?

We never intended for Chimera to be run from the disk image because 
Python creates compiled modules in the same directory as the source 
Python modules.  Also, Apple has been tightening security around 
downloaded applications, so that also might contribute.  Notice that 
your error is "Operation not permitted", not "Permission denied", which 
is the more standard error (errno is 1 instead of 13) when file/folder 
permissions are involved.

Conrad

On 3/24/2019 8:22 PM, Yuhong Zha wrote:
> Dear Sir or Madam,
> 
> 
> This is Yuhong Zha from the Kihara Bioinformatics Laboratory. We are 
> currently developing a Chimera extension to implement our MAINMAST 
> algorithm. However, when I update my Chimera to the newest version, I 
> started to get permission errors. I'm using a Mac.
> 
> 
> In our extension, we have some code involving editing files like 
> "os.remove(filename)". However, after the update, the extension 
> receives error "Operation not permitted" when executing those lines.
> 
> 
> I think one possible reason might be improper updating steps. After the 
> update, I started Chimera directly from installer instead of drag the 
> icon to my folder. Then this error occurs. Later, even when I deleted 
> the Chimera by dragging it to trash and deleting trash, and then 
> re-download and install Chimera, the error still occurs.
> 
> 
> We have 2 Mac made the update but only one of them has this error. Do 
> you have any clue why this happens?
> 
> 
> Thank you in advance for your help and looking forward to your reply! If 
> there is any question regarding our extension, please let me know!
> 
> 
> Best,
> 
> Yuhong Zha,
> 
> Kihara Bioinformatics Laboratory,
> 
> Department of Biological & Computer Science at Purdue University
> 
> 
> 
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