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Intermittent fails #3

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cjfields opened this issue Dec 2, 2019 · 6 comments
Closed

Intermittent fails #3

cjfields opened this issue Dec 2, 2019 · 6 comments

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@cjfields
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@cjfields cjfields commented Dec 2, 2019

Seems related to Module::Build (and maybe Bio::Root::Build?)

Example:

http://matrix.cpantesters.org/?dist=Bio-Procedural%201.7.4;os=linux;perl=5.28.0;reports=1

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@carandraug carandraug commented Dec 2, 2019

Last time this was because of trying to use the test_skip from Bio::Root::Test to decide whether network is available (I thought this was already fixed in the bioperl core distribution).

This should be replaced with Test::RequiresInternet (easier to put those in a separate test file as well).

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@eserte eserte commented Dec 5, 2019

The following backtrace appears when running the failing test with perl -d:

Can't find 'build_params' in _build at /usr/perl5.8.9/lib/site_perl/5.8.9/Module/Build/Base.pm line 1291.
 at /usr/perl5.8.9/lib/site_perl/5.8.9/Module/Build/Base.pm line 1291.
        Module::Build::Base::read_config(Module::Build=HASH(0x80697a5e0)) called at /usr/perl5.8.9/lib/site_perl/5.8.9/Module/Build/Base.pm line 78
        Module::Build::Base::resume("Module::Build") called at /usr/perl5.8.9/lib/site_perl/5.8.9/Module/Build/Base.pm line 137
        Module::Build::Base::current("Module::Build") called at /usr/perl5.8.9/lib/site_perl/5.8.9/Bio/Root/Test.pm line 359
        Bio::Root::Test::test_network() called at /usr/perl5.8.9/lib/site_perl/5.8.9/Bio/Root/Test.pm line 502
        Bio::Root::Test::_skip("-tests", 12, "-requires_networking", 1, "-requires_module", "LWP::UserAgent") called at /usr/perl5.8.9/lib/site_perl/5.8.9/Bio/Root/Test.pm line 274
        Bio::Root::Test::test_skip("-tests", 12, "-requires_networking", 1, "-requires_module", "LWP::UserAgent") called at t/Perl.t line 64
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@eserte eserte commented Dec 5, 2019

Module::Build->current is only valid if within a MB-based distribution --- but Bio-Procedural is using Makefile.PL:

$ perl5.8.9 -MModule::Build -e 'warn Module::Build->current()' 
Can't find 'build_params' in _build at /usr/perl5.8.9/lib/site_perl/5.8.9/Module/Build/Base.pm line 1291.
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@cjfields cjfields commented Dec 5, 2019

This looks like it may be from the dzil-generated Makefile. A Dist::Zilla bug? Or maybe our plugin?

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@cjfields cjfields commented Dec 5, 2019

Ah nevermind, it's not the Build but at the test level. I think @carandraug's recommended fix is best.

carandraug added a commit that referenced this issue Dec 5, 2019
The main issue is the use of test_skip to check for network connection
which was meant to be used when this was part of the core bioperl
distribution and it was using Module::Build.  This is no longer the
cases so its use was replaced with Test::RequiresInternet after moving
the associated tests to their own test files.

Also took the opportunity to sort the issue of high code duplication
and that the refseq for get_sequence block was actually connecting to
genbank (although even after changing it to refseq the test continues
to fail).
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@carandraug carandraug commented Dec 5, 2019

This is now fixed but the test to connect to refseq database fail on my end (the issue was already there before).

@carandraug carandraug closed this Dec 5, 2019
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