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bioperl / bioperl-live

Core BioPerl 1.x code
http://bioperl.org
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Bio::Procedural won't install #354

Closed threepistons closed 3 years ago

threepistons commented 3 years ago

Given: Ubuntu 18.04 on Azure Lab Services and CPANm from https://cpanmin.us/. Output of cpanm --version follows:

student@ML-RefVm-558285:~$ cpanm --version
cpanm (App::cpanminus) version 1.7044 (/usr/local/bin/cpanm)
perl version 5.026001 (/usr/bin/perl)

  %Config:
    archname=x86_64-linux-gnu-thread-multi
    installsitelib=/usr/local/share/perl/5.26.1
    installsitebin=/usr/local/bin
    installman1dir=/usr/share/man/man1
    installman3dir=/usr/share/man/man3
    sitearchexp=/usr/local/lib/x86_64-linux-gnu/perl/5.26.1
    sitelibexp=/usr/local/share/perl/5.26.1
    vendorarch=/usr/lib/x86_64-linux-gnu/perl5/5.26
    vendorlibexp=/usr/share/perl5
    archlibexp=/usr/lib/x86_64-linux-gnu/perl/5.26
    privlibexp=/usr/share/perl/5.26
  %ENV:
  @INC:
    FatPacked::94794177631760=HASH(0x5636fd48d610)
    /etc/perl
    /usr/local/lib/x86_64-linux-gnu/perl/5.26.1
    /usr/local/share/perl/5.26.1
    /usr/lib/x86_64-linux-gnu/perl5/5.26
    /usr/share/perl5
    /usr/lib/x86_64-linux-gnu/perl/5.26
    /usr/share/perl/5.26
    /usr/local/lib/site_perl
    /usr/lib/x86_64-linux-gnu/perl-base

When I: run cpanm --sudo Bio::Perl

I get:

--> Working on Bio::Perl
Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-Procedural-1.7.4.tar.gz ... OK
Configuring Bio-Procedural-1.7.4 ... OK
Building and testing Bio-Procedural-1.7.4 ... FAIL
! Installing Bio::Perl failed. See /home/student/.cpanm/work/1610913441.21814/build.log for details. Retry with --force to force install it.

Running cpanm --sudo Bio::Procedural gives:

--> Working on Bio::Procedural
Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-Procedural-1.7.4.tar.gz ... OK
Configuring Bio-Procedural-1.7.4 ... OK
Building and testing Bio-Procedural-1.7.4 ... FAIL
! Installing Bio::Procedural failed. See /home/student/.cpanm/work/1610913458.21910/build.log for details. Retry with --force to force install it.

Attached contents of /home/student/.cpanm/work/1610913458.21910/build.log

I expected: Perl::Bio to install without issues.

threepistons commented 3 years ago

cpanm --sudo cpanm --sudo Module::Build updated Module::Build but didn't allow Bio::Procedural to install, I still get the same test failures.

threepistons commented 3 years ago

Workaround, assuming that the workaround is not by-design installation technique: cpanm --sudo BioPerl without double-colons. Then cpanm --sudo Bio::Procedural installs without any problems.

carandraug commented 3 years ago

I'm pretty sure the issue is that you had an old version of the "BioPerl" distribution (which was updated when you cpanm BioPerl).

  1. The Bio::Perl module is part of the "Bio-Procedural" distribution (it is not part of the "BioPerl" distribution). That is why when you cpanm Bio::Perl it installs "Bio-Procedural" (you ask to install a module so cpanm installs the distribution that includes the module)
  2. "Bio-Procedural" distribution is dependent on the "BioPerl" distribution but not any specific version of it. My guess is that you already had an older "BioPerl" installed.
  3. The version of BioPerl you have has the bug you found. That bug has already been fixed.
  4. When you manually installed the "BioPerl" distribution (with cpanm BioPerl) you upgraded it to the latest version which has the issue fixed.
  5. When you then installed the "Bio-Procedural" distribution it worked fine.
threepistons commented 3 years ago

I was following the instructions for installing Prokka, which don't work.