Bug 2125737 - sage cannot find nauty binaries
Summary: sage cannot find nauty binaries
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: sagemath
Version: 36
Hardware: x86_64
OS: Linux
unspecified
high
Target Milestone: ---
Assignee: Paulo Andrade
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks:
TreeView+ depends on / blocked
 
Reported: 2022-09-09 23:00 UTC by jsliacan
Modified: 2022-12-30 01:34 UTC (History)
1 user (show)

Fixed In Version: sagemath-9.6-7.fc37 sagemath-9.6-3.fc36
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2022-12-30 00:31:18 UTC
Type: Bug
Embargoed:


Attachments (Terms of Use)

Description jsliacan 2022-09-09 23:00:38 UTC
Description of problem:
Sage cannot find any nauty binaries where they're expected. When I query `rpm -ql nauty`, I get:

```
rpm -ql nauty
/usr/bin/dreadnaut
...
/usr/bin/nauty-geng
...
```

Version-Release number of selected component (if applicable):
SageMath version 9.6, Release Date: 2022-05-15


How reproducible:
100%

Steps to Reproduce:
1. From sage interpreter type e.g.:
```
sage: gen = graphs.nauty_geng("2")
sage: next(gen)
```

Actual results:
```
---------------------------------------------------------------------------
FeatureNotPresentError                    Traceback (most recent call last)
Input In [6], in <cell line: 1>()
----> 1 next(gen)

File /usr/lib64/python3.10/site-packages/sage/graphs/graph_generators.py:960, in GraphGenerators.nauty_geng(self, options, debug)
    958 import shlex
    959 from sage.features.nauty import NautyExecutable
--> 960 geng_path = NautyExecutable("geng").absolute_filename()
    961 sp = subprocess.Popen(shlex.quote(geng_path) + " {0}".format(options), shell=True,
    962                       stdin=subprocess.PIPE, stdout=subprocess.PIPE,
    963                       stderr=subprocess.PIPE, close_fds=True,
    964                       encoding='latin-1')
    965 msg = sp.stderr.readline()

File /usr/lib64/python3.10/site-packages/sage/features/__init__.py:619, in Executable.absolute_filename(self)
    617 if path is not None:
    618     return path
--> 619 raise FeatureNotPresentError(self,
    620                              reason="Executable {executable!r} not found on PATH.".format(executable=self.executable),
    621                              resolution=self.resolution())

FeatureNotPresentError: nauty_geng is not available.
Executable 'geng' not found on PATH.
No equivalent system packages for pip are known to Sage.
```

I asked on sage-devel forum, and it was suggested that packaging might be the problem. See [0].


[0] https://groups.google.com/g/sage-devel/c/XVMescQ1hJM

Comment 1 Fedora Update System 2022-12-21 16:01:21 UTC
FEDORA-2022-b6e7a17d24 has been submitted as an update to Fedora 37. https://bodhi.fedoraproject.org/updates/FEDORA-2022-b6e7a17d24

Comment 2 Fedora Update System 2022-12-21 16:01:23 UTC
FEDORA-2022-878f113400 has been submitted as an update to Fedora 36. https://bodhi.fedoraproject.org/updates/FEDORA-2022-878f113400

Comment 3 Fedora Update System 2022-12-22 01:17:10 UTC
FEDORA-2022-878f113400 has been pushed to the Fedora 36 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2022-878f113400`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2022-878f113400

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 4 Fedora Update System 2022-12-22 01:41:13 UTC
FEDORA-2022-b6e7a17d24 has been pushed to the Fedora 37 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2022-b6e7a17d24`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2022-b6e7a17d24

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 5 Fedora Update System 2022-12-30 00:31:18 UTC
FEDORA-2022-b6e7a17d24 has been pushed to the Fedora 37 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 6 Fedora Update System 2022-12-30 01:34:52 UTC
FEDORA-2022-878f113400 has been pushed to the Fedora 36 stable repository.
If problem still persists, please make note of it in this bug report.


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