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I'm trying to install Vcf.pm from CPAN and am having no luck. Part of the problem is that I can't get cpanm to work.

This is where I started:

https://metacpan.org/pod/release/AJPAGE/Bio-Pipeline-Comparison-1.123050/lib/Vcf.pm

The Install Instructions (at the lower left if that page) gives 2 options:

cpanm Vcf

and 

perl -MCPAN -e shell
install Vcf

For the second option, the first line goes okay but the second line returns:

Warning: Cannot install Vcf, don't know what it is.

Trying the first option, I get:

-bash: cpanm: command not found

That is strange, because I already installed cpanminus and it seemed to go okay, and when I give this command:

cpan App:cpanminus

I get this:

App::cpanminus is up to date (1.7044).

Can anyone help me get one of the above 2 options working so I can get the module installed? I'm just a humble dilettante where computer programming is concerned, but my understanding is that cpan is supposed to make installing modules easy, so I can't believe I've managed to fail at this!

brian d foy
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mcrepeau
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  • Apparently the whole distribution has been deleted from CPAN. – melpomene Aug 21 '19 at 00:20
  • You might want to look at https://github.com/vcftools/vcftools. – melpomene Aug 21 '19 at 00:22
  • Perhaps you are looking for [VCF](https://metacpan.org/pod/VCF) (all capital letters). It installs without problems. – daxim Aug 21 '19 at 08:08
  • You guys were correct: the module is part of VCFtools, and it is actually called VCF.pm (capitals). Not sure why the legacy program I got refers to it as Vcf.pm. But CPAN found and installed VCF just fine and when I changed all references in the legacy code from Vcf to VCF the program compiled and ran. Hooray! – mcrepeau Aug 22 '19 at 17:50

1 Answers1

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It appears that the Bio::Pipeline::Comparison distribution is not indexed by PAUSE, so CPAN does not know how to install it. It's listed on MetaCPAN, but it was released seven years ago. The GitHub repository is missing and it's not in the author's CPAN directory. The module has disappeared. You might write to the author to ask where's it's gone if you are supporting legacy code. If you are doing new work, find something else to do the job.

As for the missing cpanm, it's probably installed but not in your PATH. You can force install it to and see where it ends up:

% cpan -f App::cpan minus
brian d foy
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  • MetaCPAN lists deleted distributions, which is why it can be seen there. While `cpan` and `cpanm` won't find it, you can still [download](https://cpan.metacpan.org/authors/id/A/AJ/AJPAGE/Bio-Pipeline-Comparison-1.123050.tar.gz) it from MetaCPAN (and from [the author's BackPAN page](http://backpan.cpantesters.org/authors/id/A/AJ/AJPAGE/)) and install it manually. – ikegami Aug 21 '19 at 07:27
  • Okay, cpan -f App::cpanminus worked. Now the command cpanm functions. Not sure why the install without -f failed to add the module to PATH. I have my Mac set to automatically start in a conda environment when I open a new terminal window. Could that have anything to do with it? Interesting about the defunct distributions still showing up in MetaCPAN. – mcrepeau Aug 22 '19 at 18:02