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Bug 685094 - dev-python/nbconvert-5.5.0: missing dependency on defusedxml
Summary: dev-python/nbconvert-5.5.0: missing dependency on defusedxml
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Virgil Dupras (RETIRED)
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2019-05-05 10:51 UTC by Helmut Jarausch
Modified: 2019-05-09 15:30 UTC (History)
4 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
successful build log xz-compressed (spyder-4.0.0_beta1-r1.build.xz,14.73 KB, application/octet-stream)
2019-05-05 13:00 UTC, Helmut Jarausch
Details

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Description Helmut Jarausch 2019-05-05 10:51:47 UTC
Starting spyder I get the error messages
You have missing dependencies!

nbconvert >=4.0: None (NOK)


Please install them to avoid this message.

I have dev-python/nbconvert-5.5.0 installed here.
Comment 1 Andreas Sturmlechner gentoo-dev 2019-05-05 11:51:20 UTC
build.log missing.
Comment 2 Virgil Dupras (RETIRED) gentoo-dev 2019-05-05 12:07:39 UTC
This is very probably related to bug 685094.
Comment 3 Virgil Dupras (RETIRED) gentoo-dev 2019-05-05 12:09:43 UTC
Oops, sorry, bug 685040
Comment 4 Helmut Jarausch 2019-05-05 13:00:12 UTC
Created attachment 575306 [details]
successful build log xz-compressed
Comment 5 Virgil Dupras (RETIRED) gentoo-dev 2019-05-05 13:22:48 UTC
I'm a bit puzzled at how you managed to build spyder with python3_7 target when that target isn't in PYTHON_COMPAT.
Comment 6 Helmut Jarausch 2019-05-05 13:57:01 UTC
(In reply to Virgil Dupras from comment #5)
> I'm a bit puzzled at how you managed to build spyder with python3_7 target
> when that target isn't in PYTHON_COMPAT.

My whole system only uses Python2.7 or Python3.7.
So, I have a local overlay.

I cannot remember any package which is qualified for Python3.6 but breaks with Python3.7

Therefore I'd be surprised if the error wouldn't occur with Python3.6.

(I don't have Python versions 3.x with x < 7 installed here)
Comment 7 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2019-05-05 15:14:05 UTC
Do you have nbconvert built with py3.7 target?
Comment 8 Virgil Dupras (RETIRED) gentoo-dev 2019-05-05 16:44:18 UTC
It took a while for me to compile qt's webengine, but I can now confirm that spyder-4.0.0_beta1-r1 builds and runs fine under py3.6. My guess is that the problem is in your overlay.
Comment 9 Andrew Nowa Ammerlaan gentoo-dev 2019-05-09 15:10:50 UTC
I ran into this issue today as well, importing nbconvert manually gives me:

import nbconvert
Traceback (most recent call last):

  File "<ipython-input-1-6bb6e1863707>", line 1, in <module>
    import nbconvert

  File "/usr/lib64/python3.6/site-packages/nbconvert/__init__.py", line 4, in <module>
    from .exporters import *

  File "/usr/lib64/python3.6/site-packages/nbconvert/exporters/__init__.py", line 3, in <module>
    from .html import HTMLExporter

  File "/usr/lib64/python3.6/site-packages/nbconvert/exporters/html.py", line 13, in <module>
    from nbconvert.filters.highlight import Highlight2HTML

  File "/usr/lib64/python3.6/site-packages/nbconvert/filters/__init__.py", line 7, in <module>
    from .strings import *

  File "/usr/lib64/python3.6/site-packages/nbconvert/filters/strings.py", line 22, in <module>
    from defusedxml import cElementTree as ElementTree

ModuleNotFoundError: No module named 'defusedxml'

emerge -1 defusedxml solved this issue for me. Seems that nbconvert-5.5.0 should depend on defusedxml. (nbconvert-5.2.1 works fine without defusedxml, spyder does not give any error)
Comment 10 Andrew Nowa Ammerlaan gentoo-dev 2019-05-09 15:24:48 UTC
Looking at the changelog on github: https://github.com/jupyter/nbconvert/blob/master/docs/source/changelog.rst#id213 I can indeed confirm that nbconvert now should depend on defusedxml
Comment 11 Virgil Dupras (RETIRED) gentoo-dev 2019-05-09 15:25:56 UTC
I can reproduce this, thanks for the hint, fixing.
Comment 12 Larry the Git Cow gentoo-dev 2019-05-09 15:30:56 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5b0b17f3e282dd5f8595ebbb0d71bced2d2e5131

commit 5b0b17f3e282dd5f8595ebbb0d71bced2d2e5131
Author:     Virgil Dupras <vdupras@gentoo.org>
AuthorDate: 2019-05-09 15:30:16 +0000
Commit:     Virgil Dupras <vdupras@gentoo.org>
CommitDate: 2019-05-09 15:30:40 +0000

    dev-python/nbconvert: add missing dependency
    
    Closes: https://bugs.gentoo.org/685094
    Signed-off-by: Virgil Dupras <vdupras@gentoo.org>
    Package-Manager: Portage-2.3.62, Repoman-2.3.11

 dev-python/nbconvert/nbconvert-5.5.0.ebuild | 1 +
 1 file changed, 1 insertion(+)