Unexpected token in primary type expression

[eserte]

On some of my smokers the test suite fails:

Unexpected token in primary type expression; got '=,D,H,I,M,N,P,S,X]]' at /opt/perl-5.26.2D/lib/site_perl/5.26.2/Type/Parser.pm line 280.
Compilation failed in require at t/basic.t line 4.
BEGIN failed--compilation aborted at t/basic.t line 4.
t/basic.t ............... 
Dubious, test returned 255 (wstat 65280, 0xff00)
No subtests run 

[eserte]

I did some experiments --- and it seems that the problem happens if a new version of Type::Parser is installed together with Type::Tiny::XS.

[ichobits]

I have the same error!

[ichobits]

ubuntu 20.04
perl 5.30

[ichobits]

conda create --name perl_env
conda activate perl_env
conda install -c bioconda biotradis=1.4.1
conda install -c bioconda perl-bio-cigar=1.01

after, cigar can be run in the perl_env

[xileF1337]

The problem is line 120 of lib/Bio/Cigar.pm:

    isa     => ArrayRef[ Tuple[ Int, Enum[split '', 'MIDNSHP=X'] ] ],

Here, the type of attribute ops is defined, and it seems as the Enum[ ] type does not support the = character as an enumeration member. Removing it makes the test compile and pass. Of course, this is no solution because a cigar string may contain the = character. So it is probably a bug in the Types::Standard module, which is contained in distribution Type::Tiny.

Solution: I had this problem with version 1.008001 of Type::Tiny, and updating (run cpanm Type::Tiny) to the current version 1.012005 fixed the issue for me.

[tsibley]

@xileF1337 Thanks for that info. It seems to be firmly an upstream issue in the Type-Tiny ecosystem, so I'm going to close this. But happy to re-open if there's a specific workaround Bio-Cigar could make to avoid this, such as 1) declaring a dep conflict with the known-bad versions of specific upstream versions or 2) adjusting the specific syntax used to declare the Enum with =.

[tsibley]

Ha, nevermind, turns out I don't actually still have maintainer on this repo so can't close the issue. (But I do have maint on CPAN, so can still make new releases with workarounds/fixes.)

[xileF1337]

@tsibley glad to help ;) Have you considered specifying the current version of Type::Tiny as a dependency of this module? This would trigger an update of the broken version first if people try to install Bio::Cigar.

[tsibley]

That would work, yes, but I'd prefer not to break out the big hammer of forcing a blanket upgrade. Those can cause conflicts with other software that have version maximums on the same module that exclude the latest version, for example.