Details
I am getting a build failure of my read-the-docs that I don't understand. The assertion of "verbatim" in line 2151 of nbsphinx.py is causing the build failure. So the build fails when I try to include the Jupyter Notebook tutorials I created. I compared current versions of the tutorials to previous versions which had not caused the build to fail, and I can't find a difference that could account for the current failure.
Read the Docs project URL: lofti_gaia
Build URL: https://github.com/logan-pearce/lofti_gaia
Read the Docs username: logan-pearce
Expected Result
A passing build including *.ipynb files
Actual Result
Build failed at line 2151 of nbsphinx.py due to assertion of 'Verbatim' failing.
Terminal output:
Running Sphinx v4.1.2
loading translations [en]... done
making output directory... done
WARNING: html_static_path entry '_static' does not exist
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [latex]: all documents
updating environment: 0 added, 0 changed, 0 removed
looking for now-outdated files... none found
processing lofti_gaia.tex... index installation tutorials/QuickStart tutorials/Tutorial api lofti loftitools
resolving references...
done
writing... failed
Exception occurred:
File "/home/docs/checkouts/readthedocs.org/user_builds/lofti-gaia/conda/latest/lib/python3.7/site-packages/nbsphinx.py", line 2151, in depart_codearea_latex
assert 'Verbatim' in lines[0]
AssertionError
The full traceback has been saved in /tmp/sphinx-err-x1h83s3m.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!
According to the github issue 584 for nbsphinx (https://github.com/spatialaudio/nbsphinx/issues/584), this is due to a compatibility issue with sphinx 4.1.0. It can be gotten around by requiring sphinx version 4.0.2.
So in my requirements.txt file, I included sphinx==4.0.2, after which the build passes. So now my requirements.txt file looks like:
numpy
matplotlib
astropy>=4.0.1.post1
astroquery>=0.4
sphinx==4.0.2
ipython==7.19.0
nbsphinx>=0.8.6
and the build passes.
I have encountered the same issue. I did not solve it with .ipynb format, but converting the jupyter notebook to .rst format works.
May it helps
Related
I'm new to Julia and I want to use COBRA Package.
For adding COBRA I use command :
Pkg.add("COBRA")
But when running, I get these errors:
INFO: Building WinRPM
WARNING: skipping repodata/repomd.xml, not in cache -- call WinRPM.update() to download
WARNING: skipping repodata/repomd.xml, not in cache -- call WinRPM.update() to download
INFO: Downloading https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win32/openSUSE_Leap_42.2/repodata/repomd.xml
WARNING: Unknown download failure, error code: 2148270086
WARNING: Retry 1/5 downloading: https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win32/openSUSE_Leap_42.2/repodata/repomd.xml
until:
WARNING: Unknown download failure, error code: 2148270086
WARNING: Retry 5/5 downloading: https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win32/openSUSE_Leap_42.2/repodata/repomd.xml
WARNING: received error 0 while downloading
https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win32/openSUSE_Leap_42.2/repodata/repomd.xml
After these errors, I have checked the link and I've found out the source is not there, anymore.
So then I ran this command as said above:
WinRPM.update()
But it has thrown this error:
ERROR: UndefVarError: WinRPM not defined
Please Help me to add COBRA to Julia. I'm using version 0.6.4 because Cobra does not work on the next versions.(Windows 10)
Any help would be appreciated.
The problem, as you've mentioned, is that the original sources used by the package aren't valid URLs anymore. The proper way to solve this is to open a pull request with the package to change the URLs (which I've now done here ). As a stopgap measure, here's a hacky way to work around this issue for now:
Do a Pkg.add("WinRPM"). This might trigger the same warnings as above, ignore these.
Next, using WinRPM to load the package we added
Now, the source URLs are read from the sources.list file (linked above) into a global WinRPM.sources variable. We're going to edit this variable's contents to point to new working URLs. (This is generally a terrible idea, to directly poke into the internals of a module and change things.)
julia> WinRPM.sources[:] = replace.(WinRPM.sources, "Leap_42.3" => "Leap_15.3")
2-element Vector{String}:
"https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win32/openSUSE_Leap_15.3"
"https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win64/openSUSE_Leap_15.3"
A WinRPM.update() should now work, and download things into a local cache.
I'm using version 0.6.4 because Cobra does not work on the next versions.
I hope you mean Julia 1.6.4 here, or version 0.6.4 of something else in the stack. If you mean Julia version 0.6.4, you might face further problems down the road and find it hard to get support for such an old version.
I am trying to build PhantomJS 2.0 on Windows from the c:\fastio\phantomjs\phantomjs directory. For some reason, the build process fails after a while, with 2 errors (see error message below):
1) It tries to access "C:fastiophantomjsphantomjssrcqtqtbasebinmoc.exe". Obviously, the backslash characters between directory names are somehow getting stripped away deep in the build process - possibly a mismatch between Windows-style "\" and Linux-style "/" (but this is only a guess).
2) There's another error, "Failed to read names from file: C:/fastio/phantomjs/phantomjs/src/qt/qtwebkit/Source/WebCore/mathml/mathtags.in".
If I remove sh.exe from the PATH, the build still gets to this point, and only error #2 appears, leading me to think that error #2 is the real problem here.
Here is the full error message (as far as I can tell this is happening while building WebKit):
sh: C:fastiophantomjsphantomjssrcqtqtbasebinmoc.exe: command not found
Failed to read names from file: C:/fastio/phantomjs/phantomjs/src/qt/qtwebkit/Source/WebCore/mathml/mathtags.in at C:/fastio/phantomjs/phantomjs/src/qt/qtwebkit/Source/WebCore/dom/make_names.pl line 315.
NMAKE : fatal error U1077: 'C:\Users\Eugene\AppData\Local\GitHub\PortableGit_c2ba306e536fdf878271f7fe636a147ff37326ad\bin\perl.EXE' : return code '0x7f'
Stop.
(By the way, I saw this question but I'm already past the issues described there, my error is happening later in the build process.)
How can I make this work?
Full logs below:
Console output:
http://pastebin.com/btMeNPz4
QT build log file build_qt_4-285-20-0859.log:
http://pastebin.com/LUEJz7E0
WebKit build log file build_webkit_4-285-20_0859.log:
http://pastebin.com/494TivXF
PhantomJS build log file build_phantomjs_4-285-20_0859.log:
Empty
Looks like I found the solution myself, here were my steps:
Remove as much as possible from the PATH leaving only the entries critical to the build process
Most importantly, remove all GitHub's git directories from the PATH
Install GIT separately (not from GitHub but from git-scm.com), add its cmd directory only (not its bin directory) to the PATH
Install ActivePerl separately, add it to the PATH
It's moving past the error I asked about with the steps above (still not sure if it will finish the build successfully, it's taking a while).
On "./configure" of an open source project I get:
user agent OS = Linux
./configure: line 13957: syntax error near unexpected token 0.9.3'
./configure: line 13957: GOBJECT_INTROSPECTION_CHECK(0.9.3)'
make: *** [config.status] Error 2
Ubuntu 12.04 package "gobject-introspection" and "libgirepository1.0-dev" are present. Removing the GOBJECT_INTROSPECTION_CHECK line allows configure to complete, but the project fails a dependency later.
How can I get past this configure step cleanly? Googling for this issue shows bugs filed against numerous OS projects for this same blocking issue, but the usual answer is "install gobject-introspection".
As the OP discovered on his own he had to install the gobject-introspection package to get the m4 macros that were being used.
The error message has the raw macro in it, as configure scripts are generated from configure.in/configure.ac files via m4/etc the fact that the raw macro is in the output file indicates that the macro did not get translated at generation time.
The gobject-introspection m4 files were apparently installed after autogen.sh (or equivalent) was run to generate the configure script. Re-running the autogen.sh script should regenerate the configure script and run the macro correctly.
I am trying to try out collective.examples.userdata (by adding collective.examples.userdata to the eggs section of my buildout) but it's giving an error:
Getting distribution for 'collective.examples.userdata'.
error: docs/HISTORY.txt: No such file or directory
I have looked at the git repo and there is a docs/HISTORY.txt, so I am not sure why this would happen.
Because the release is broken.
Often times due to the complexity of releasing a package, mistakes are made. To avoid errors like this one, release managers can use the check-manifest utility which matches files in the sdist to files in the MANIFEST.in file and reports the results.
I'm using Plone 4.1 and trying to run bin/buildout in a fresh directory, having just managed to get python bootstrap.py --distribute to work. bin/buildout runs along fine for a couple of minutes, downloading various distributions, then crashes with the following report:
Getting distribution for 'plone.recipe.zope2instance==4.1.7'.
Got plone.recipe.zope2instance 4.1.7.
... (many distributions omitted for brevity) ...
Getting distribution for 'zope.container==3.11.2'.
Got zope.container 3.11.2.
Getting distribution for 'zope.configuration==3.7.4'.
error: Not a recognized archive type: /Users/Jon/.buildout/downloads/dist/zope.configuration-3.7.4.zip
An error occured when trying to install zope.configuration 3.7.4. Look above this message for any errors that were output by easy_install.
While:
Installing.
Getting section instance.
Initializing section instance.
Installing recipe plone.recipe.zope2instance.
Getting distribution for 'zope.configuration==3.7.4'.
Error: Couldn't install: zope.configuration 3.7.4
It looks like the important error message is: Not a recognized archive type: /Users/Jon/.buildout/downloads/dist/zope.configuration-3.7.4.zip
Incidentally, I tried simply re-running bin/buildout and it picked up in a new place, starting with:
Getting distribution for 'zdaemon==2.0.4'.
Got zdaemon 2.0.4.
Getting distribution for 'pytz==2011g'.
Got pytz 2011g.
...and so on. Can I just keep retrying the script until it successfully get all the stuff that it needs?
Also, I tried running bin/buildout for version 4.2 in another directory, and that seemed to work okay.
EDIT The second time I ran bin/buildout it completed without crashing. However, I did a search of the output and it never once downloaded anything with "configuration" in it's name. So what is going on???
EDIT Just for good measure I tried running bin/buildout a third time and it exited quickly after printing the single line "Updating instance."
You're fine. I suspect you have a less than ideal network connection and/or that PyPI is having problems (one of your other posts was about network related issues as well, I think).
The error you saw is that it's tried to download a zip file that's been corrupted, and so it fails to extract the zip file. On your second attempt, it downloaded it successfully.