OSError: [Errno 1] Operation not permitted

[yxliu-T]

Hi,
I am trying to install cryofit to phenix on Mac OS 10.15 Catalina. The installation failed when I use "libtbx.configure cryo_fit". In terminal, the error message is pasted as follows,
Traceback (most recent call last):
File "/Applications/phenix-1.17.1-3660/modules/cctbx_project/libtbx/env_config.py", line 2741, in
warm_start(sys.argv)
File "/Applications/phenix-1.17.1-3660/modules/cctbx_project/libtbx/env_config.py", line 2699, in warm_start
env.refresh()
File "/Applications/phenix-1.17.1-3660/modules/cctbx_project/libtbx/env_config.py", line 1816, in refresh
self.write_lib_dispatcher_head()
File "/Applications/phenix-1.17.1-3660/modules/cctbx_project/libtbx/env_config.py", line 1356, in write_lib_dispatcher_head
target_file=self.under_build(target_file, return_relocatable_path=True))
File "/Applications/phenix-1.17.1-3660/modules/cctbx_project/libtbx/env_config.py", line 1252, in write_bin_sh_dispatcher
target_file.chmod(0o755)
File "/Applications/phenix-1.17.1-3660/modules/cctbx_project/libtbx/path.py", line 283, in chmod
return os.chmod(abs(self), *args, **kwds)
OSError: [Errno 1] Operation not permitted: '/Applications/phenix-1.17.1-3660/build/dispatcher_head.sh'

I have set full disk access for terminal and have read&write permission for both the build and modules directories under phenix folder (as well as the dispatcher_head.sh file). I am not familiar with computer language and would be grateful if someone can help! Thank you.

[nwmoriarty]

Has anyone answered this question for you? Cheers Nigel

…

--- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

On Sat, Feb 13, 2021 at 8:29 AM yxliu-T ***@***.***> wrote: Hi, I am trying to install cryofit to phenix on Mac OS 10.15 Catalina. The installation failed when I use "libtbx.configure cryo_fit". In terminal, the error message is pasted as follows, Traceback (most recent call last): File "/Applications/phenix-1.17.1-3660/modules/cctbx_project/libtbx/env_config.py", line 2741, in warm_start(sys.argv) File "/Applications/phenix-1.17.1-3660/modules/cctbx_project/libtbx/env_config.py", line 2699, in warm_start env.refresh() File "/Applications/phenix-1.17.1-3660/modules/cctbx_project/libtbx/env_config.py", line 1816, in refresh self.write_lib_dispatcher_head() File "/Applications/phenix-1.17.1-3660/modules/cctbx_project/libtbx/env_config.py", line 1356, in write_lib_dispatcher_head target_file=self.under_build(target_file, return_relocatable_path=True)) File "/Applications/phenix-1.17.1-3660/modules/cctbx_project/libtbx/env_config.py", line 1252, in write_bin_sh_dispatcher target_file.chmod(0o755) File "/Applications/phenix-1.17.1-3660/modules/cctbx_project/libtbx/path.py", line 283, in chmod return os.chmod(abs(self), *args, **kwds) OSError: [Errno 1] Operation not permitted: '/Applications/phenix-1.17.1-3660/build/dispatcher_head.sh' I have set full disk access for terminal and have read&write permission for both the build and modules directories under phenix folder (as well as the dispatcher_head.sh file). I am not familiar with computer language and would be grateful if someone can help! Thank you. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHYQPGW2PR4XUEQBN763VDS62SHZANCNFSM4XSJDCQQ> .

[kimdn]

Hello,

I just did https://www.phenix-online.org/documentation/tutorials/cryo_fit_install.html#id3
which is about cloning cryo_fit and libtbx.configure cryo_fit (so that phenix can recognize cryo_fit).

It cloned well and linked well as

... Using /Users/kimd999/bin/phenix-1.19rc2-4022/conda_base/lib/python2.7/site-packages Finished processing dependencies for iota==1.4.20 Processing: "/Users/kimd999/bin/phenix-1.19rc2-4022/build/exe_dev" Done.

Currently, I use macOS 10.14.6.

Unfortunately, my employer doesn't allow me to upgrade my macbook's OS, so I can't reproduce your error in Mac OS 10.15 Catalina.

I've installed cryo_fit many times (>100) in various macOS and linux systems.
Mostly, it was fine.

My current hunch feeling is that Mac OS 10.15 Catalina changes some authority over
/Applications/....sh

Can you install phenix in non-Applications folder?
For example, as in
https://www.phenix-online.org/documentation/install-setup-run.html
just

tar xvf phenix-installer-<version>-<platform>.tar
cd phenix-installer-<version>
./install --prefix=<directory>  

here the "directory" could be for example, /Users/kimd999/bin

Even if you install phenix in non-Applications folder (like /Users/kimd999/bin),
all commandline and GUI functions will work. Sometimes macOS indexing of PHENIX GUI executables may take some time, but pretty soon it will allow you to access newly installed PHENIX gui automatically.

I think that if you reply to this github post, it will email me directly.
But if you prefer, you can email me as well ([email protected]).

Please let me know how it goes.
If the above method (alternative installation path) doesn't work, I will see what I can do (I may ask my IT support to lend me some new macbook. Additionally, my personal macbook will arrive in early March so I will check macOS of it).

best,
Doo Nam

[yxliu-T]

Thank you for your suggestions. The previous OSerror was indeed due to Mac OS 10.15 Catalina authority issue, which could be resolved using sudo. I also re-installed phenix as instructed under /Users/yixinliu/ and continued to install cryo_fit. The process went well until I do:
python /Users/yixinliu/phenix-1.19.1-4122/modules/cryo_fit/files_for_steps/0_install_cryo_fit/install_cryo_fit.py ~/Downloads/gromacs-4.5.5_cryo_fit.zip /Users/yixinliu/CryoFit

Several errors and warnings occurred and the installation wasn't successful. /cryo_fit/bin/ was not created in /cryo_fit/ directory. I copied here some problems that occurred. I can also copy the warnings and error messages here if it is helpful.

1. make command: make -j 3
   This did not return "Nothing to be done for `all-am'", but with inflating: __MACOSX/gromacs-4.5.5_cryo_fit/._src; inflating: __MACOSX/._gromacs-4.5.5_cryo_fit
2. In the end, it returned:
   make[2]: *** [md.o] Error 1
   make[1]: *** [install-recursive] Error 1
   make: *** [install-recursive] Error 1
3. Not successful installation because cryo_fit can't find /Users/yixinliu/CryoFit/cryo_fit/bin/mdrun