[SRU] extractreads crashed with ImportError in main__: /usr/lib/python3/dist-packages/obitools/word/_readindex.cpython-312-x86_64-linux-gnu.so: undefined symbol: heapsort

[Sudip Mukherjee]

[ Impact ]

extractreads fails to run and crashes immediately with the error:

$ extractreads
Traceback (most recent call last):
  File "/usr/bin/extractreads", line 12, in <module>
    from obitools.word._readindex import ReadIndex,minword
ImportError: /usr/lib/python3/dist-packages/obitools/word/_readindex.cpython-312-x86_64-linux-gnu.so: undefined symbol: heapsort

[ Test Plan ]

install obitools.

Execute "extractreads --help"

If the package is not fixed, it will fail with the above error.

With the fixed package, it will print the help menu.

[ Where problems could occur ]

As mentioned in the Debian patch, this change can introduce a possible perforomace tradeoff and a probable increased stack memory consumption.

[ Other Info ]

This has been fixed in Debian and has synced with Oracular, so Oracular is now fixed.

[ Original Bug Description ]

extractreads fails to run with the error:

$ extractreads
Traceback (most recent call last):
  File "/usr/bin/extractreads", line 12, in <module>
    from obitools.word._readindex import ReadIndex,minword
ImportError: /usr/lib/python3/dist-packages/obitools/word/_readindex.cpython-312-x86_64-linux-gnu.so: undefined symbol: heapsort

ProblemType: Crash
DistroRelease: Ubuntu 24.04
Package: obitools 1.2.13+dfsg-7build1
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 22:03:44 2024
ExecutablePath: /usr/bin/extractreads
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: -- No entries --
ProcCmdline: /usr/bin/python3 /usr/bin/extractreads
Python3Details: /usr/bin/python3.12, Python 3.12.3, python3-minimal, 3.12.3-0ubuntu1
PythonArgs: ['/usr/bin/extractreads']
PythonDetails: N/A
SourcePackage: obitools
Title: extractreads crashed with ImportError in __main__: /usr/lib/python3/dist-packages/obitools/word/_readindex.cpython-312-x86_64-linux-gnu.so: undefined symbol: heapsort
Traceback:
 Traceback (most recent call last):
   File "/usr/bin/extractreads", line 12, in <module>
     from obitools.word._readindex import ReadIndex,minword
 ImportError: /usr/lib/python3/dist-packages/obitools/word/_readindex.cpython-312-x86_64-linux-gnu.so: undefined symbol: heapsort
UpgradeStatus: No upgrade log present (probably fresh install)
UserGroups: adm cdrom dip lpadmin plugdev sudo users

[Sudip Mukherjee (sudipmuk)]

The Debian fix has synced in Oracular.

[Timo Aaltonen (tjaalton)]

Hello Sudip, or anyone else affected,

Accepted obitools into noble-proposed. The package will build now and be available at https://launchpad.net/ubuntu/+source/obitools/1.2.13+dfsg-7ubuntu0.1 in a few hours, and then in the -proposed repository.

Please help us by testing this new package. See https://wiki.ubuntu.com/Testing/EnableProposed for documentation on how to enable and use -proposed. Your feedback will aid us getting this update out to other Ubuntu users.

If this package fixes the bug for you, please add a comment to this bug, mentioning the version of the package you tested, what testing has been performed on the package and change the tag from verification-needed-noble to verification-done-noble. If it does not fix the bug for you, please add a comment stating that, and change the tag to verification-failed-noble. In either case, without details of your testing we will not be able to proceed.

Further information regarding the verification process can be found at https://wiki.ubuntu.com/QATeam/PerformingSRUVerification . Thank you in advance for helping!

N.B. The updated package will be released to -updates after the bug(s) fixed by this package have been verified and the package has been in -proposed for a minimum of 7 days.

[Timo Aaltonen (tjaalton)]

An upload of obitools to mantic-proposed has been rejected from the upload queue for the following reason: "mantic will be EOL in six days".

[Timo Aaltonen (tjaalton)]

Hello Sudip, or anyone else affected,

Accepted obitools into jammy-proposed. The package will build now and be available at https://launchpad.net/ubuntu/+source/obitools/1.2.13+dfsg-4ubuntu0.1 in a few hours, and then in the -proposed repository.

Please help us by testing this new package. See https://wiki.ubuntu.com/Testing/EnableProposed for documentation on how to enable and use -proposed. Your feedback will aid us getting this update out to other Ubuntu users.

If this package fixes the bug for you, please add a comment to this bug, mentioning the version of the package you tested, what testing has been performed on the package and change the tag from verification-needed-jammy to verification-done-jammy. If it does not fix the bug for you, please add a comment stating that, and change the tag to verification-failed-jammy. In either case, without details of your testing we will not be able to proceed.

Further information regarding the verification process can be found at https://wiki.ubuntu.com/QATeam/PerformingSRUVerification . Thank you in advance for helping!

N.B. The updated package will be released to -updates after the bug(s) fixed by this package have been verified and the package has been in -proposed for a minimum of 7 days.

[Timo Aaltonen (tjaalton)]

Hello Sudip, or anyone else affected,

Accepted obitools into focal-proposed. The package will build now and be available at https://launchpad.net/ubuntu/+source/obitools/1.2.13+dfsg-3ubuntu0.1 in a few hours, and then in the -proposed repository.

Please help us by testing this new package. See https://wiki.ubuntu.com/Testing/EnableProposed for documentation on how to enable and use -proposed. Your feedback will aid us getting this update out to other Ubuntu users.

If this package fixes the bug for you, please add a comment to this bug, mentioning the version of the package you tested, what testing has been performed on the package and change the tag from verification-needed-focal to verification-done-focal. If it does not fix the bug for you, please add a comment stating that, and change the tag to verification-failed-focal. In either case, without details of your testing we will not be able to proceed.

Further information regarding the verification process can be found at https://wiki.ubuntu.com/QATeam/PerformingSRUVerification . Thank you in advance for helping!

N.B. The updated package will be released to -updates after the bug(s) fixed by this package have been verified and the package has been in -proposed for a minimum of 7 days.

[Sudip Mukherjee (sudipmuk)]

I can confirm that obitools from noble-proposed has fixed the bug for me.

Test done:

install obitools and try to execute "extractreads --help" and confirmed that it still fails.

Added noble-proposed to apt sources.
install obitools from noble-proposed.

execute "extractreads --help" and confirmed that it displays the help message.

Package tested:

$ apt-cache policy obitools
obitools:
  Installed: 1.2.13+dfsg-7ubuntu0.1
  Candidate: 1.2.13+dfsg-7ubuntu0.1
  Version table:
 *** 1.2.13+dfsg-7ubuntu0.1 100
        100 http://gb.archive.ubuntu.com/ubuntu noble-proposed/universe amd64 Packages
        100 /var/lib/dpkg/status
     1.2.13+dfsg-7build1 500
        500 http://gb.archive.ubuntu.com/ubuntu noble/universe amd64 Packages

[Sudip Mukherjee (sudipmuk)]

I can confirm that obitools from jammy-proposed has fixed the bug for me.

Test done:

install obitools and try to execute "extractreads --help" and confirmed that it still fails.

Added jammy-proposed to apt sources.
install obitools from jammy-proposed.

execute "extractreads --help" and confirmed that it displays the help message.

Package tested:

$ apt-cache policy obitools
obitools:
  Installed: 1.2.13+dfsg-4ubuntu0.1
  Candidate: 1.2.13+dfsg-4ubuntu0.1
  Version table:
 *** 1.2.13+dfsg-4ubuntu0.1 500
        500 http://gb.archive.ubuntu.com/ubuntu jammy-proposed/universe amd64 Packages
        100 /var/lib/dpkg/status
     1.2.13+dfsg-4build1 500
        500 http://gb.archive.ubuntu.com/ubuntu jammy/universe amd64 Packages

[Sudip Mukherjee (sudipmuk)]

I can confirm that obitools from focal-proposed has fixed the bug for me.

Test done:

install obitools and try to execute "extractreads --help" and confirmed that it still fails.

Added focal-proposed to apt sources.
install obitools from focal-proposed.

execute "extractreads --help" and confirmed that it displays the help message.

Package tested:

$ apt-cache policy obitools
obitools:
  Installed: 1.2.13+dfsg-3ubuntu0.1
  Candidate: 1.2.13+dfsg-3ubuntu0.1
  Version table:
 *** 1.2.13+dfsg-3ubuntu0.1 500
        500 http://gb.archive.ubuntu.com/ubuntu focal-proposed/universe amd64 Packages
        100 /var/lib/dpkg/status
     1.2.13+dfsg-3 500
        500 http://gb.archive.ubuntu.com/ubuntu focal/universe amd64 Packages