sci-mathematics/sage-8.0 - QA Notice: Symbolic link /usr/share/jupyter/nbextensions/jsmol points to /usr/share/jsmol which does not exist.

[devurandom]

After building sci-mathematics/sage-8.0, emerge prints following QA notice:

QA Notice: Symbolic link /usr/share/jupyter/nbextensions/jsmol points to /usr/share/jsmol which does not exist.

The setup / use-flags are the same as reported in #490.

[kiwifb]

You don't have sage-jmol-bin installed I guess. Hum... I guess that symlink doesn't technically belong to this ebuild. I may have trouble convincing upstream that it doesn't belong where they've put it either.

[strogdon]

@kiwifb Perhaps sage-jmol-bin should be installed by default even when USE=-sagenb. The jupyter notebook stuff is installed by default and there are some things that won't work without jmol.

sage: show(sphere())
/storage/strogdon/gentoo-rap/usr/lib64/python2.7/site-packages/sage/repl/rich_output/display_manager.py:590: RichReprWarning: Exception in _rich_repr_ while displaying object: Jmol failed to create file '/storage/strogdon/gentoo-rap/.sage/temp/blitzen/13208/dir_LPpLbv/preview.png', see '/storage/strogdon/gentoo-rap/.sage/temp/blitzen/13208/tmp_hmX_aV.txt' for details
  RichReprWarning,
\newcommand{\Bold}[1]{\mathbf{#1}}\verb|Graphics3d|\phantom{\verb!x!}\verb|Object|

which also fails from the jupyter notebook. The contents of the .txt file is

Error: Unable to access jarfile /storage/strogdon/gentoo-rap/usr/share/sage-jmol-bin/lib/JmolData.jar

all of which is technically a Warning. I suppose

sage: show(sphere(), viewer='threejs', online=True)

will work, although I'm unable to test it properly.

[kiwifb]

Yes, I was thinking of making it a dependency to solve the problem. You are just giving me more arguments for it. I just wish jmol would go completely away. Do you have link problems on prefix for that? There are more links that should just be relative, and of course I have learned a new trick that I am eager to use :)

[strogdon]

After removing sage-jmol-bin and sage-notebook the only QA I have is the one reported above except relative to prefix

QA Notice: Symbolic link /storage/strogdon/gentoo-rap/usr/share/jupyter/nbextensions/jsmol points to /storage/strogdon/gentoo-rap/usr/share/jsmol which does not exist.

[kiwifb]

Ok, ready for testing. I am just worried that runtime dependency may not be enough.

[strogdon]

I have no QA Notice and show(sphere()) works from the sage prompt as well as from the sage -n jupyter, jupyter notebook. I usually build sage-9999 so I could have some needed runtime dependencies already installed, but I'm not aware of any. Have a nice time away!

[kiwifb]

Re-open if you find that the fix is not sufficient.