New warnings with perl 5.41.x

[eserte]

With perl 5.41.4 I see the following new (non-fatal) warnings while running the test suite:

Attempt to call undefined import method with arguments ("dumpValue") via package "Dumpvalue" (Perhaps you forgot to load the package?) at /home/cpansand/.cpan/build/2024101810/BioPerl-1.7.8-1/blib/lib/Bio/Tools/Alignment/Consed.pm line 114.
Attempt to call undefined import method with arguments ("new") via package "Bio::SearchIO" (Perhaps you forgot to load the package?) at bin/bp_find-blast-matches line 120.Attempt to call undefined import method with arguments ("new") via package "Bio::Seq" (Perhaps you forgot to load the package?) at bin/bp_find-blast-matches line 121.Attempt to call undefined import method with arguments ("new") via package "Bio::SeqIO" (Perhaps you forgot to load the package?) at bin/bp_find-blast-matches line 122. at t/00-compile.t line 596, <GEN1916> line 4.
t/00-compile.t ...................... ok

[cjfields]

Thx @eserte . Since this is a warning and from a perl developer release (odd-number versioning) it's not a huge issue at the moment, but worth noting.

[eserte]

I checked the test reports on my disk: the same warnings already happen in stable perl 5.40.0.
perl 5.38.x is not affected.

[cjfields]

Confirming this is being reported in CI as well:

Error: Attempt to call undefined import method with arguments ("dumpValue") via package "Dumpvalue" (Perhaps you forgot to load the package?) at /home/runner/work/bioperl-live/bioperl-live/blib/lib/Bio/Tools/Alignment/Consed.pm line 114.
Error: Attempt to call undefined import method with arguments ("new") via package "Bio::SearchIO" (Perhaps you forgot to load the package?) at bin/bp_find-blast-matches line 120.Attempt to call undefined import method with arguments ("new") via package "Bio::Seq" (Perhaps you forgot to load the package?) at bin/bp_find-blast-matches line 121.Attempt to call undefined import method with arguments ("new") via package "Bio::SeqIO" (Perhaps you forgot to load the package?) at bin/bp_find-blast-matches line 122. at t/00-compile.t line 596, <GEN1916> line 4.

#   Failed test 'no warnings found'
#   at t/00-compile.t line 604.
#          got: '4'
#     expected: '0'
# got warnings: [
#   'Attempt to call undefined import method with arguments ("dumpValue") via package "Dumpvalue" (Perhaps you forgot to load the package?) at /home/runner/work/bioperl-live/bioperl-live/blib/lib/Bio/Tools/Alignment/Consed.pm line 114.
# ',
#   'Attempt to call undefined import method with arguments ("new") via package "Bio::SearchIO" (Perhaps you forgot to load the package?) at bin/bp_find-blast-matches line 120.',
#   'Attempt to call undefined import method with arguments ("new") via package "Bio::Seq" (Perhaps you forgot to load the package?) at bin/bp_find-blast-matches line 121.',
#   'Attempt to call undefined import method with arguments ("new") via package "Bio::SeqIO" (Perhaps you forgot to load the package?) at bin/bp_find-blast-matches line 122.'
# ]
# Looks like you failed 1 test of 512.

I'm testing a fix for this with 01ba1a6.

[cjfields]

This now seems to be addressed. We'll leave open until a new release is pushed, aiming for sometime this week barring any issues.

[cjfields]

Just a small update, we have a few more tickets related to removing additional dependencies that we're working to resolve, so it may take a little longer.