#1115951 tombo: resquiggle.py breaks pypy3

Package:
tombo
Source:
tombo
Description:
identification of modified nucleotides from raw nanopore sequencing data
Submitter:
Patrice Duroux
Date:
2026-05-10 08:19:01 UTC
Severity:
normal
Tags:
#1115951#5
Date:
2025-09-22 12:03:25 UTC
From:
To:
Dear Maintainer,

Not sure if this have to be addressed to tombo or pypy3 but
here is what 'apt install pypy3' gives:

...
Paramétrage de pypy3 (7.3.19+dfsg-2) ...
running pypy3 rtupdate hooks for 7.3
Failed to byte-compile /usr/lib/python3/dist-packages/tombo/resquiggle.py:   File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 311
    global r
    ^^^^^^^^
SyntaxError: name 'r' is assigned to before global declaration

running pypy3 post-rtupdate hooks for 7.3
...


This is the only error shown among all the other python relatives installed on this system.

Regards,
Patrice

#1115951#10
Date:
2026-05-10 08:17:40 UTC
From:
To:
Hi Patrice,

thank you for the bug report.  I checked the situation and I can't
reproduce it on my system, neither do I think that any job on Salsa CI
like for instance autopkgtest[1] does show the problem.  Can you provide
a generic way in a chroot to reproduce the problem?

Kind regards
      Andreas.

[1] https://salsa.debian.org/med-team/tombo/-/jobs/9571662