Fix jmol permissions

[jhpalmieri]

This is a followup to #25026: the permissions of SAGE_ROOT/local/share/jmol/ are wrong:

  drwxr-xr-x 24 palmieri staff  768 Sep 12 00:11 info
  drwx------ 21 palmieri staff  672 Oct 12 10:28 jmol
  drwxr-xr-x 80 palmieri staff 2560 Oct 12 10:28 jsmol
  drwxr-xr-x  4 palmieri staff  128 Sep 12 00:11 jupyter

[jhpalmieri]

I can see two solutions: change jmol's spkg-install script so it sets the right permissions, or set the permissions differently for all packages. Here is a branch which does the second of these: after unpacking the tarball into src, run chmod +rx src. Is this a bad idea for some reason?

[jhpalmieri]

New commits:

​82e736b

trac 28596: change permissions on src after unpacking each package's tarball.

[jhpalmieri]

I want to do this for all packages to avoid similar situations in the future.

[chapoton]

This does not seem to fix the doc building issue.

[embray]

Replying to chapoton:

This does not seem to fix the doc building issue.

I don't know what doc building issue you're referencing.

[chapoton]

Here is the docbuild log where the problem appears:

​https://patchbot.sagemath.org/log/0/Ubuntu/16.04/x86_64/4.4.0-166-generic/atlas/2019-11-27%2010:02:21?plugin=docbuild

This prevents me from using this machine as a patchbot.

[embray]

This behavior originates from #24567, and would be different if we'd gone with Jeroen's suggestion of a less restricted mask on the files than I used.

I wrote at the time:

this should have no effect on the permissions applied when the files are installed, but I guess it depends in part on the installation mechanism

Which, incidentally was true at the time. But the part of "depends on the installation mechanism" was also true, and the installation mechanism did change after that, in such a way that this did have an effect on the installed files.

So I think the better option here might be to try Jeroen's original suggestion of a less restrictive permission mask on the source tarball's extraction location.

[embray]

This approach fixes the issue closer to the source. However, it would be good to test a full rebuild. I don't know for sure if there aren't some pathological packages that can break because of this (and if so those packages should probably be fixed...).

---

New commits:

​df58d4b	Trac #28596: Apply less restricted permission mask to extracted source
​87c694f	Add an spkg-legacy-uninstall for jmol.

[jhpalmieri]

All tests pass for me on OS X, with a build from scratch, and the permissions look okay.

[chapoton]

then it should be ok, no ?

[jhpalmieri]

Okay with me.

[embray]

I'm sure, if he were paying attention, Jeroen would be pleased to be vindicated :)