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rvosa / bio-phylo

Bio::Phylo - Phyloinformatic analysis using Perl
http://search.cpan.org/dist/Bio-Phylo
GNU General Public License v3.0
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t/26-dom.t fails (with newest XML::LibXML?) #40

Closed eserte closed 7 years ago

eserte commented 7 years ago

On some of my smoker systems the test suite fails:

#   Failed test 'number of nex:nexml elements correct (0)'
#   at t/26-dom.t line 109.
#          got: '0'
#     expected: '1'
# Looks like you failed 1 test of 80.
t/26-dom.t .............. 
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/80 subtests 
    (less 6 skipped subtests: 73 okay)

This seems to happen if XML::LibXML 2.0131 (and probaly 2.0130) is installed. The test passes with XML::LibXML 2.0129 (@shlomif: FYI).

hlapp commented 7 years ago

FYI, this issue currently causes all rebuilds of the bioperl/bioperl Docker container to fail. Is there a plan for resolution? If not, I will probably need to remove Bio::Phylo from the container build, which would be unfortunate.

shlomif commented 7 years ago

On Sun, 29 Oct 2017 19:04:35 -0700 Hilmar Lapp notifications@github.com wrote:

FYI, this issue currently causes all rebuilds of the bioperl/bioperl Docker container to fail. Is there a plan for resolution? If not, I will probably need to remove Bio::Phylo from the container build, which would be unfortunate.

Please try it with XML-LibXML-2.0132 - it may be fixed there.

--

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rvosa commented 7 years ago

There seems to be an inconsistency in how XML::LibXML returns element names: in some versions these are NCNames (e.g. nexml), in others they have a prefix (e.g. nex:nexml). I think I will modify the unit test to deal with this (the test is a bit silly anyway).

hlapp commented 7 years ago

Please try it with XML-LibXML-2.0132 - it may be fixed there.

I saw you updated the release on CPAN, so I went ahead and rebuilt the bioperl-deps container, where XML::LibXML gets installed. The build succeeded, and if I install Bio::Phylo locally in that container it succeeds.

The bioperl-deps rebuild succeeding also triggered the bioperl/bioperl:latest and :stable containers to rebuild on Docker Hub, and both now succeeded. So I think we're good now.

shlomif commented 7 years ago

On Mon, 30 Oct 2017 14:36:12 +0000 (UTC) Hilmar Lapp notifications@github.com wrote:

Please try it with XML-LibXML-2.0132 - it may be fixed there.

I saw you updated the release on CPAN, so I went ahead and rebuilt the bioperl-deps container, where XML::LibXML gets installed. The build succeeded, and if I install Bio::Phylo locally in that container it succeeds.

The bioperl-deps rebuild succeeding also triggered the bioperl/bioperl:latest and :stable containers to rebuild on Docker Hub, and both now succeeded. So I think we're good now.

Great! Thanks for letting me know.

--

Shlomi Fish http://www.shlomifish.org/ List of Text Editors and IDEs - http://shlom.in/IDEs

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