Maneage - Bugs: bug #61811, jinja2, extension-helpers,...
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bug #61811: jinja2, extension-helpers, pybind11 not found, even though installed; pyyaml error
Submitter: | Raul Infante-Sainz <infantesainz> | ||
Submitted: | Thu 13 Jan 2022 11:17:24 AM UTC | ||
Category: | Software | Severity: | 3 - Normal |
Item Group: | Crash | Status: | None |
Privacy: | Public | Assigned to: | None |
Open/Closed: | Open |
( Jump to the original submission )
Sat 24 Sep 2022 07:58:54 PM UTC, comment #9: |
Boud Roukema <boud>![]() |
Sat 24 Sep 2022 07:43:53 PM UTC, comment #8: Commit ab7303c [1], which is one commit beyond core maneage 4318670, works for me to solve compilation bugs for the python packages 'extension-helpers' (as mentioned in #61811 here), and 'packaging', which is mentioned in the #61811 discussion as a dependency. The solution is to add both 'setuptools' and 'setuptools_scm' as dependencies in 'python.mk'. This solves the bug for me on Debian 11 and CentOS 7 parallel machines.
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Boud Roukema <boud>![]() |
Wed 21 Sep 2022 06:48:35 PM UTC, comment #7: DESCRIPTION: Running commit 4318670 of core maneage, with the addition of pyyaml as a target:
leads to compilation errors of the C source code of pyyaml. Independently, in a research project package, the compilation error does not appear to block a full configure of python packages, with matplotlib selected in TARGETS.conf. Thus, this is a bug in principle, though not (so far) an obvious problem in practice. Nevertheless, it should be fixed, and seems to be included in bug #61811 [0], which is why I'm adding it here.
but the same error occurred.
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Boud Roukema <boud>![]() |
Wed 13 Jul 2022 10:40:08 AM UTC, comment #6: The same problem happens on another system (IAC's "darko" computer, run by a Maneage'd project of Zohreh Ghaffari), there is no problem with jinja2 and extension-helpers! However, an identical problem happens with 'pybind11' (as a dependency of Scipy!).
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Mohammad Akhlaghi <makhlaghi>![]() |
Wed 19 Jan 2022 10:33:06 AM UTC, comment #5: Indeed, a non-reproducible bug is the most annoying (showing that we still haven't understood it!).
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Mohammad Akhlaghi <makhlaghi>![]() |
Fri 14 Jan 2022 03:27:42 PM UTC, comment #4: In each case, I re-ran './project configure --existing-conf' without modifying either TARGETS.conf or python.mk.
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Boud Roukema <boud>![]() |
Fri 14 Jan 2022 08:50:00 AM UTC, comment #3: Thanks a lot for the help Boud.
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Raul Infante-Sainz <infantesainz>![]() |
Thu 13 Jan 2022 06:30:57 PM UTC, comment #2: I tried this in two separate builds (not completely from scratch, but partly from scratch, and both python and the python libraries were rebuilt from scratch). Both builds were on the same many-cpu machine.
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Boud Roukema <boud>![]() |
Thu 13 Jan 2022 04:03:38 PM UTC, comment #1: I wonder if this is due to the same bug as https://savannah.nongnu.org/bugs/?61271 - Python build bug with curses.h in commit 775fc03 .
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Boud Roukema <boud>![]() |
Thu 13 Jan 2022 11:17:24 AM UTC, original submission:
I am trying to run the installation of all software of Maneage from scratch. All basic software runs smoothly without any error.
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Raul Infante-Sainz <infantesainz>![]() |
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Follow 2 latest changes.
Date | Changed by | Updated Field | Previous Value | => | Replaced by |
---|---|---|---|---|---|
2022-09-21 | boud | Summary | jinja2, extension-helpers, pybind11 not found, even though installed | ![]() |
jinja2, extension-helpers, pybind11 not found, even though installed; pyyaml error |
2022-07-13 | makhlaghi | Summary | jinja2 and extension-helpers packages not found in Astropy installation | ![]() |
jinja2, extension-helpers, pybind11 not found, even though installed |
Commit 67daeee [0], which is one commit beyond core maneage 4318670, works for me to solve the 'pyyaml' compilation bug listed below here in bug #61811. The solution is to update from pyyaml-5.1 to pyyaml-6.0. (This seems to be independent from the other set of python bugs listed here.)
The cause of the problem is stated in the python documentation: Py_REFCNT changed in implementation to a function [1], so increasing its value with '++Py_REFCNT' is invalid, which is why the error message states 'lvalue required as increment operand'. An 'lvalue' is a 'left-hand value', i.e. that can be put in the left-hand part of an assignment operation, written '=' in C; the "value" of a function is (I guess) the address of the function in RAM, so augmenting the value of that address would be nonsense.
To see the problem for yourself, try compiling the standalone program
with a C compiler. You should obtain the same error as when installing pyyaml-5.1 with python-3.10.6. Grep your log file if you didn't notice the bug before.
Commit 67daeee also adds 'setuptools_scm' dependencies for the python build rules for 'soupsieve' and 'webencodings', since otherwise these builds may fail (depending on the speed and parallel nature of compiles; these did fail for me); see also bug #63054 [2].
Astropy (for example) has to be enabled in TARGETS.conf for 67daeee to be tested.
[0] https://codeberg.org/boud/maneage_dev/commit/67daeee967fafd44e6f8199748f5cae4dd7ad5d6
[1] https://docs.python.org/3/c-api/structures.html#c.Py_REFCNT
[2] https://savannah.nongnu.org/bugs/?63054