Notebook sometimes fails to start up

[suchow]

I'm on OS X 10.9 running version 1.10 of the notebook. Sometimes, when I try to open the app, the program gives the following error:

Unable to launch iPython notebook
Server failed to start up

Other times, the notebook loads just fine.

I checked the system logs and there are many entries that show up at the time the notebook was loading:

12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny mach-lookup com.apple.ocspd
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny mach-lookup com.apple.ocspd
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny mach-lookup com.apple.ocspd
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny mach-lookup com.apple.ocspd
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny mach-lookup com.apple.ocspd
12/9/13 7:39:27.000 PM kernel[0]: Sandbox: appleeventsd(53) deny mach-lookup com.apple.ocspd
12/9/13 7:39:27.760 PM sandboxd[238]: ([53]) appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.889 PM sandboxd[238]: ([53]) appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.895 PM sandboxd[238]: ([53]) appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.935 PM sandboxd[238]: ([53]) appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.941 PM sandboxd[238]: ([53]) appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.945 PM sandboxd[238]: ([53]) appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.950 PM sandboxd[238]: ([53]) appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:27.954 PM sandboxd[238]: ([53]) appleeventsd(53) deny file-read-metadata /Library
12/9/13 7:39:28.464 PM IPython Notebook[4527]: Removing cache file /Users/admin/Library/Containers/ch.entropy.ipython-notebook/Data/.matplotlib/fontList.cache
12/9/13 7:39:43.000 PM kernel[0]: Sandbox: python(4532) deny file-read-data /opt/X11/share/fonts/TTF
12/9/13 7:39:43.000 PM kernel[0]: Sandbox: python(4532) deny file-read-data /opt/X11/share/fonts
12/9/13 7:39:45.000 PM kernel[0]: Sandbox: python(4532) deny file-read-data /opt/X11/share/fonts/TTF
12/9/13 7:39:45.000 PM kernel[0]: Sandbox: python(4532) deny file-read-data /opt/X11/share/fonts

[liyanage]

Thanks for the report. Do you see any occurrences of these log entries as well?

11/3/13 12:47:55.000 PM kernel[0]: exec of /Users/liyanage/Desktop/IPython Notebook.app/Contents/Resources/virtualenv/bin/python denied since it was quarantined by Safari.app and not approved by Gatekeeper, qtn-flags was 0x00000002
11/3/13 12:47:55.531 PM IPython Notebook[6471]: Couldn't posix_spawn: error 1

Also, how long does the spinner spin approximately before the sheet appears?

[suchow]

I see no occurrences of those log entries.

The spinner spins for about 15 s before the sheet appears. The arrival of the sheet comes at the same time that these messages are logged:

12/9/13 10:05:54.000 PM kernel[0]: Sandbox: python(4721) deny file-read-data /opt/X11/share/fonts/TTF
12/9/13 10:05:54.000 PM kernel[0]: Sandbox: python(4721) deny file-read-data /opt/X11/share/fonts

[suchow]

I restarted, opened iPython Notebook, and the error appeared in the same way as before, but there were three extra lines in the log:

12/9/13 10:33:16.839 PM com.apple.SecurityServer[26]: Killing auth hosts
12/9/13 10:33:16.839 PM com.apple.SecurityServer[26]: Session 100014 destroyed
12/9/13 10:33:16.841 PM com.apple.SecurityServer[26]: Session 100019 created

[liyanage]

Thanks for this additional information.

Could you run these commands and let me know what the output looks like on your system? This assumes that you have the app in /Applications, adjust accordingly if that's not the case:

xattr -p com.apple.quarantine /Applications/IPython\ Notebook.app
xattr -p com.apple.quarantine /Applications/IPython\ Notebook.app/Contents/Resources/virtualenv/bin/python
spctl --assess /Applications/IPython\ Notebook.app
spctl --assess /Applications/IPython\ Notebook.app/Contents/Resources/virtualenv/bin/python

and lastly, could you run this command and then try launching the app again:

xattr -dr com.apple.quarantine /Applications/IPython\ Notebook.app

[suchow]

➜  ~  xattr-2.7 -p com.apple.quarantine /Applications/IPython\ Notebook.app
xattr: /Applications/IPython Notebook.app: No such xattr: com.apple.quarantine
➜  ~  xattr-2.7 -p com.apple.quarantine /Applications/IPython\ Notebook.app/Contents/Resources/virtualenv/bin/python
xattr: /Applications/IPython Notebook.app/Contents/Resources/virtualenv/bin/python: No such xattr: com.apple.quarantine
➜  ~  spctl --assess /Applications/IPython\ Notebook.app
➜  ~  spctl --assess /Applications/IPython\ Notebook.app/Contents/Resources/virtualenv/bin/python
➜  ~  xattr-2.7 -dr com.apple.quarantine /Applications/IPython\ Notebook.app
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/.Python'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/include/python2.7'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/_abcoll.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/_weakrefset.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/abc.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/codecs.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/config'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/copy_reg.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/encodings'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/fnmatch.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/genericpath.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/lib-dynload'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/linecache.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/locale.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/ntpath.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/os.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/posixpath.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/re.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/sre.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/sre_compile.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/sre_constants.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/sre_parse.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/stat.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/types.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/UserDict.py'
xattr: [Errno 13] Permission denied: '/Applications/IPython Notebook.app/Contents/Resources/virtualenv/lib/python2.7/warnings.py'

[liyanage]

Thanks again. Given the output of the first commands it probably won't make a difference, but could you try re-running the last one with sudo?

sudo xattr -dr com.apple.quarantine /Applications/IPython\ Notebook.app

BTW, your snippet shows xattr-2.7 instead of just xattr. Is that how you ran it?

[suchow]

When I first ran xattr, I got the message:

python version 2.7.6 can't run /usr/bin/xattr.  Try the alternative(s):

/usr/bin/xattr-2.5 (uses python 2.5)
/usr/bin/xattr-2.6 (uses python 2.6)
/usr/bin/xattr-2.7 (uses python 2.7)

Run "man python" for more information about multiple version support in
Mac OS X.

which is why I switched to xattr-2.7.

When I now run the command you suggest (but with xattr-2.7), I get no output:

➜  ~  sudo xattr-2.7 -dr com.apple.quarantine /Applications/IPython\ Notebook.app
➜  ~