gff2gff.py crashed with ModuleNotFoundError in Noble

Bug #2062071 reported by Sudip Mukherjee
10
This bug affects 1 person
Affects Status Importance Assigned to Milestone
bcftools (Debian)
Fix Released
Unknown
bcftools (Ubuntu)
Confirmed
Undecided
Unassigned

Bug Description

gff2gff.py fails to run with the error:

$ gff2gff.py
Traceback (most recent call last):
  File "/usr/bin/gff2gff.py", line 13, in <module>
    import gffutils
ModuleNotFoundError: No module named 'gffutils'

ProblemType: Crash
DistroRelease: Ubuntu 24.04
Package: bcftools 1.19-1build2
ProcVersionSignature: Ubuntu 6.8.0-22.22-generic 6.8.1
Uname: Linux 6.8.0-22-generic x86_64
ApportVersion: 2.28.0-0ubuntu1
Architecture: amd64
CasperMD5CheckResult: pass
CurrentDesktop: ubuntu:GNOME
Date: Wed Apr 17 22:16:25 2024
ExecutablePath: /usr/bin/gff2gff.py
InstallationDate: Installed on 2024-04-10 (7 days ago)
InstallationMedia: Ubuntu 24.04 LTS "Noble Numbat" - Beta amd64 (20240410)
InterpreterPath: /usr/bin/python3.12
JournalErrors:
 Apr 17 22:16:19 hostname org.gnome.Characters[2202]: MESA: error: ZINK: failed to choose pdev
 Apr 17 22:16:19 hostname org.gnome.Characters[2202]: libEGL warning: egl: failed to create dri2 screen
ProcCmdline: python3 /usr/bin/gff2gff.py
Python3Details: /usr/bin/python3.12, Python 3.12.3, python3-minimal, 3.12.3-0ubuntu1
PythonArgs: ['/usr/bin/gff2gff.py']
PythonDetails: N/A
SourcePackage: bcftools
Title: gff2gff.py crashed with ModuleNotFoundError in __main__: No module named 'gffutils'
Traceback:
 Traceback (most recent call last):
   File "/usr/bin/gff2gff.py", line 13, in <module>
     import gffutils
 ModuleNotFoundError: No module named 'gffutils'
UpgradeStatus: No upgrade log present (probably fresh install)
UserGroups: adm cdrom dip lpadmin plugdev sudo users

Revision history for this message
Sudip Mukherjee (sudipmuk) wrote :
information type: Private → Public
Revision history for this message
Sudip Mukherjee (sudipmuk) wrote :

Adding that guess-ploidy.py also fails with the error:

$ guess-ploidy.py --help
Traceback (most recent call last):
  File "/usr/bin/guess-ploidy.py", line 29, in <module>
    import matplotlib as mpl
ModuleNotFoundError: No module named 'matplotlib'

Revision history for this message
Sudip Mukherjee (sudipmuk) wrote :

debdiff attached for Noble. The crash with "guess-ploidy.py" needs python3-matplotlib but thats already mentioned in "Suggests".

Changed in bcftools (Ubuntu):
status: New → Confirmed
Changed in bcftools (Debian):
status: Unknown → New
Changed in bcftools (Debian):
status: New → Fix Released
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