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Fix sagemath_doc_html build failure on Cygwin #33139

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slel opened this issue Jan 10, 2022 · 35 comments
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Fix sagemath_doc_html build failure on Cygwin #33139

slel opened this issue Jan 10, 2022 · 35 comments
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c: packages: standard c: porting: cygwin p: critical / 2 t: bug
Milestone
sage-9.6

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@slel
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slel commented Jan 10, 2022

On sage-release, report on a failure in Cygwin
(from a fresh git clone):

Also observed on Linux, where make distclean fixed it:

Let us deal with the Cygwin failure here,
and with the Linux failure at #33488.

CC: @fchapoton @mkoeppe @seblabbe @slel

Component: packages: standard

Author: Tobias Diez

Branch/Commit: 3aa3f09

Reviewer: Ethan Lin

Issue created by migration from https://trac.sagemath.org/ticket/33139
@slel slel added this to the sage-9.5 milestone Jan 10, 2022
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slel commented Jan 10, 2022

comment:1

Also observed on Linux, where make distclean fixed it.

So this ticket's component is not "porting: Cygwin".

Maybe "build" or "documentation" or "packages: standard"?

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slel commented Jan 10, 2022

comment:2

See also #33142 comment:4 and patchbot reports for #33142:

@slel slel changed the title Fix sagemath_doc_html-none build failure on Cygwin Fix sagemath_doc_html-none build failure Jan 10, 2022
@mkoeppe
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mkoeppe commented Jan 12, 2022

comment:3

I think this is "only" an incremental docbuild failure, probably nothing to be fixed here

From-scratch build of Sage on Cygwin on GH Actions succeeded in https://github.com/sagemath/sage/runs/4768915824?check_suite_focus=true - including documentation

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slel commented Jan 12, 2022

comment:4

In my case it was a fresh git clone. I'll try again.

@fchapoton
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comment:5

There are persistent problems with patchbots. Somebody needs to fix them. Maybe the people that introduced "make doc-uninstall" can pick up the task ?

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slel commented Jan 15, 2022

comment:6

New report on sage-release for Sage 9.5.rc1:

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slel commented Jan 22, 2022

comment:7

Happened again on Cygwin and Debian as reported at

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slel commented Jan 26, 2022

comment:8

This failed on Cygwin for all releases from
Sage 9.5.beta7 to Sage 9.5.rc4 for me.

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@slel slel changed the title Fix sagemath_doc_html-none build failure Fix sagemath_doc_html build failure Jan 26, 2022
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slel commented Jan 27, 2022

comment:10

A link with #32789 was initially suspected, but then ruled out, see:

For Sage 9.5.rc4, the file logs/pkgs/sagemath_doc_html-none.log
is as follows, up to replacing:

  • INVENTORY_REF: local/share/doc/sage/inventory/en/reference
  • DOCTREES_REF: local/share/doc/sage/doctrees/en/reference
  • SITE_PKGS: local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages
  • SRC_REF: src/doc/en/reference
[reference] building [inventory]: targets for 1 source files that are out of date
[reference] updating environment: [new config] 1 added, 0 changed, 0 removed
[reference] The inventory files are in INVENTORY_REF/references.
Build finished. The built documents can be found in INVENTORY_REF/references
[spkg     ] building [inventory]: targets for 354 source files that are out of date
[spkg     ] updating environment: [new config] 354 added, 0 changed, 0 removed
[spkg     ] The inventory files are in INVENTORY_REF/spkg.
Build finished. The built documents can be found in INVENTORY_REF/spkg
[manifolds] building [inventory]: targets for 84 source files that are out of date
[manifolds] updating environment: [new config] 84 added, 0 changed, 0 removed
[manifolds] The inventory files are in INVENTORY_REF/manifolds.
Build finished. The built documents can be found in INVENTORY_REF/manifolds
[polynomia] building [inventory]: targets for 62 source files that are out of date
[polynomia] updating environment: [new config] 62 added, 0 changed, 0 removed
[polynomia] The inventory files are in INVENTORY_REF/polynomial_rings.
Build finished. The built documents can be found in INVENTORY_REF/polynomial_rings
[repl     ] building [inventory]: targets for 36 source files that are out of date
[repl     ] updating environment: [new config] 36 added, 0 changed, 0 removed
[repl     ] The inventory files are in INVENTORY_REF/repl.
Build finished. The built documents can be found in INVENTORY_REF/repl
[algebras ] building [inventory]: targets for 99 source files that are out of date
[algebras ] updating environment: [new config] 99 added, 0 changed, 0 removed
[tensor_fr] building [inventory]: targets for 19 source files that are out of date
[tensor_fr] updating environment: [new config] 19 added, 0 changed, 0 removed
[tensor_fr] The inventory files are in INVENTORY_REF/tensor_free_modules.
Build finished. The built documents can be found in INVENTORY_REF/tensor_free_modules
[combinat ] building [inventory]: targets for 369 source files that are out of date
[combinat ] updating environment: [new config] 369 added, 0 changed, 0 removed
[dynamics ] building [inventory]: targets for 16 source files that are out of date
[dynamics ] updating environment: [new config] 16 added, 0 changed, 0 removed
[dynamics ] The inventory files are in INVENTORY_REF/dynamics.
Build finished. The built documents can be found in INVENTORY_REF/dynamics
[plot3d   ] building [inventory]: targets for 20 source files that are out of date
[plot3d   ] updating environment: [new config] 20 added, 0 changed, 0 removed
[plot3d   ] The inventory files are in INVENTORY_REF/plot3d.
Build finished. The built documents can be found in INVENTORY_REF/plot3d
...
[structure] building [inventory]: targets for 32 source files that are out of date
[structure] updating environment: [new config] 32 added, 0 changed, 0 removed
[structure] The inventory files are in INVENTORY_REF/structure.
Build finished. The built documents can be found in INVENTORY_REF/structure
[valuation] building [inventory]: targets for 14 source files that are out of date
[valuation] updating environment: [new config] 14 added, 0 changed, 0 removed
[valuation] The inventory files are in INVENTORY_REF/valuations.
Build finished. The built documents can be found in INVENTORY_REF/valuations
[reference] building [inventory]: targets for 1 source files that are out of date
[reference] updating environment: [new config] 1 added, 0 changed, 0 removed
[reference] Merging environment/index file
[reference]     algebras:
[reference]     arithgroup: 1 todos, 12 index, 0 citations, 11 modules
[reference]     arithmetic_curves: 12 todos, 59 index, 2 citations, 58 modules
[reference]     asymptotic: 6 todos, 8 index, 0 citations, 7 modules
[reference]     calculus: 2 todos, 38 index, 0 citations, 37 modules
[reference]     categories:
[reference]     coding:
[reference]     coercion: 0 todos, 8 index, 0 citations, 7 modules
[reference]     combinat:
[reference]     constants: 0 todos, 3 index, 0 citations, 2 modules
[reference]     cpython: 0 todos, 8 index, 0 citations, 7 modules
...
[reference]     tensor_free_modules: 2 todos, 19 index, 0 citations, 15 modules
[reference]     topology: 0 todos, 14 index, 0 citations, 13 modules
[reference]     valuations: 1 todos, 14 index, 0 citations, 13 modules
[reference] ... done (184 todos, 1670 index, 1434 citations, 1281 modules)
[reference] WARNING: Unable to fetch DOCTREES_REF/algebras/environment.pickle
[reference] WARNING: Unable to fetch DOCTREES_REF/categories/environment.pickle
[reference] WARNING: Unable to fetch DOCTREES_REF/coding/environment.pickle
[reference] WARNING: Unable to fetch DOCTREES_REF/combinat/environment.pickle
[reference] WARNING: Unable to fetch DOCTREES_REF/graphs/environment.pickle
[reference] WARNING: Unable to fetch DOCTREES_REF/groups/environment.pickle
[reference] WARNING: Unable to fetch DOCTREES_REF/knots/environment.pickle
[reference] WARNING: Unable to fetch DOCTREES_REF/libs/environment.pickle
[reference] preparing documents... skipping loading of indexes... done
[reference] SRC_REF/index.rst:35: WARNING: unknown document: categories/index
[reference] SRC_REF/index.rst:77: WARNING: unknown document: groups/index
[reference] SRC_REF/index.rst:80: WARNING: unknown document: algebras/index
[reference] SRC_REF/index.rst:85: WARNING: unknown document: combinat/index
[reference] SRC_REF/index.rst:86: WARNING: unknown document: graphs/index
[reference] SRC_REF/index.rst:90: WARNING: unknown document: coding/index
[reference] SRC_REF/index.rst:105: WARNING: unknown document: knots/index
[reference] SRC_REF/index.rst:156: WARNING: unknown document: libs/index
[reference] The inventory files are in INVENTORY_REF.
Error building the documentation.
Traceback (most recent call last):
  File "/usr/lib/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/usr/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "SITE_PKGS/sage_docbuild/__main__.py", line 2, in <module>
    main()
  File "SITE_PKGS/sage_docbuild/__init__.py", line 1729, in main
    builder()
  File "SITE_PKGS/sage_docbuild/__init__.py", line 137, in f
    runsphinx()
  File "SITE_PKGS/sage_docbuild/sphinxbuild.py", line 323, in runsphinx
    sys.stderr.raise_errors()
  File "SITE_PKGS/sage_docbuild/sphinxbuild.py", line 258, in raise_errors
    raise OSError(self._error)
OSError: WARNING: Unable to fetch DOCTREES_REF/algebras/environment.pickle 

    Note: incremental documentation builds sometimes cause spurious
    error messages. To be certain that these are real errors, run
    "make doc-clean doc-uninstall" first and try again.
make[6]: *** [Makefile:20: doc-inventory--reference_top] Error 1
make[5]: *** [Makefile:38: doc-inventory-reference] Error 2

What are the environment.pickle files
in local/share/doc/sage/doctrees/en/reference/*?

Why are some of them missing?

@fchapoton
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comment:11

bump to 9.6

@fchapoton fchapoton modified the milestones: sage-9.5, sage-9.6 Jan 29, 2022
@slel
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slel commented Jan 29, 2022

comment:12

This breaks my development versions of Sage
on Cygwin, Debian, macOS, Ubuntu.

I agree Sage 9.5 needs to get out though,
and I have no clue on solving this failure.

@slel
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slel commented Jan 31, 2022

comment:13

This blocked merging a positively reviewed ticket,
see #32505 comment:83.

Oops, no it did not. Something else caused an error
in sagemath_doc_html there.

@tobiasdiez
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Branch: public/docs/pickled_env

@slel
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slel commented Mar 10, 2022

comment:15

Let us deal with the Cygwin failure here,
and with the Linux failure at #33488.

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@slel slel changed the title Fix sagemath_doc_html build failure Fix sagemath_doc_html build failure on Cygwin Mar 10, 2022
@tobiasdiez
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comment:16

It looks like #33488 is about a different error, though, or not?

What you think about the fix here in this ticket? It solves the issue for me also on Ubuntu.

@WindowsSystemAdmin
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comment:17

Can I be notified of this as well?

@WindowsSystemAdmin
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comment:18

So on the latest version of sage, 9.6.beta5, the sagemath_doc_html_none did successfully build :) and now I have a functioning version of sage!!

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Reviewer: gh-WindowsSystemAdmin

@tobiasdiez
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comment:21

Thanks for the review!

@mkoeppe
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mkoeppe commented Mar 21, 2022

comment:22

Full reviewer name please

@vbraun
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vbraun commented Mar 21, 2022

comment:23

Merge failure on top of:

6dbf093 Trac #30845: Fixes for the conda-for-Sage-developers installation method, add GH Actions workflow

95307a6 Trac #33522: pythran: Update to 0.11.0

3afe1c7 Trac #33440: sage.libs.singular: Do not fail if the Singular binary is not in PATH

3cc2873 Trac #33437: Add Lehrer-Solomon symmetric function

6e77b3f Trac #33416: Colormaps and contours for complex_plot

a636498 Trac #33407: sage -t --installed

ff2baed Trac #33396: removing some useless ...: in the doc

dce5f06 Trac #33233: sage -t --baseline-stats-path

f06a7f8 Trac #33170: Update doctests for compatibility with ipython 8.x

2fbf359 Trac #33156: fix wrong results & huge slowdown due to broken caching in .multiplication_by_m()

b8d91ac Trac #33141: Fix doctests in sage_setup and sage_docbuild for sage-on-distribution

f30a4c8 Trac #32942: Introduce align_latex option that allows latex displays aligned left or centered

39de62b Trac #32429: Typos

d79b00d Trac #30078: Check for duplicate hyperplanes in arrangements over any base ring

a633cce Trac #33532: Doctest failure when SAGE_LIB doesn't match .../site-packages

9873ee5 Trac #33361: configure: Handle the case of SAGE_LOCAL = a system directory with gcc better

dc311dc Trac #32975: Improve doctest interaction with pytest

0e4f121 Trac #33471: Add pictures to various 2d graphics manual pages

5b20998 Trac #33487: Package CyLP

df50acb Trac #33477: Conversion problem between multivariate Laurent polynomial ring and its field of fraction

3c80055 Trac #33475: deTeX document titles of sage documentation

5b872c9 Trac #30717: add "How to cite SageMath" to FAQ

a61c15e Trac #29631: spkg-configure.m4 for linbox

55a711e Updated SageMath version to 9.6.beta5

reviewer 'gh-WindowsSystemAdmin' does not look right

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comment:25

How do I change my username?

@slel
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slel commented Mar 25, 2022

comment:26

Your username is fine. Type in your real name
in the "Reviewers" field.

@WindowsSystemAdmin
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comment:27

k

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Changed reviewer from gh-WindowsSystemAdmin to Ethan Lin

@slel
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slel commented Mar 26, 2022

comment:29

Thank you. And now you can set to positive review!

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vbraun commented Apr 2, 2022

Changed branch from public/docs/pickled_env to 3aa3f09

@vbraun vbraun closed this as completed in d20cc49 Apr 2, 2022
@WindowsSystemAdmin WindowsSystemAdmin mentioned this issue Aug 2, 2022
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@vbraun vbraun mentioned this issue Mar 31, 2022
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