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osx perl-json-xs (and other packages) install perl-threaded #10100
On macOS, perl-json-xs (at least) depends on the deprecated perl-threaded, which is Perl 5.22.0. When perl-threaded is installed, it causes $CONDA_PREFIX/bin/perl to refer to its version of perl, causing problems when other perl modules that depend on the conda-forge 5.26.2 are installed (e.g., perl-perlio-gzip).
Pristine Miniconda3 installation w/ bioconda channels configured per http://bioconda.github.io/:
$CONDA_PREFIX/bin/perl (perl-threaded) can use the installed perl-json module, but not perl-perlio-gzip. Conversely, $CONDA_PREFIX/bin/perl5.26.2 can use perl-perlio-gzip, but not perl-json:
This affects at least some Linux packages as well; e.g., perl-perlio-gzip and perl-bioperl (the latter of which has a dependency on perl-threaded somewhere).
In this case, $CONDA_PREFIX/bin/perl is perl5.26.2, and there isn't an executable for Perl 5.22.0. So PerlIO::gzip can be used, but bioperl cannot...
No worries @bgruening. Yes, there are still perl packages that use it - for example, perl-xml-twig and perl-xml-path. I suspect what happened is some packages were added to the blacklist and so were never rebuilt with perl 5.26.2, but were still pulled in as dependencies for other packages, thus pulling in
I'd be hesitant to try anything too clever with the