I am trying to install a Perl Module Bio::Tools::Run::Alignment::Muscle. I am using this docker image:

FROM ubuntu:16.04

RUN apt-get update && apt-get install -y software-properties-common
RUN apt-add-repository multiverse
RUN add-apt-repository restricted
    wget \
    unzip \
    sudo \
    make \
    gcc \
    libdb-dev \
    libgd-dev \
    zlib1g-dev \
    libxml2-dev \
    libexpat1-dev \
    pkg-config \
    graphviz \
    libssl-dev \

# Dependencies
RUN cpanm File::Sort Config::Any Bio::FeatureIO Bio::Cluster::SequenceFamily

# Install problematic ::Muscle
RUN cpanm Net::SSLeay LWP::Protocol::https Bio::Tools::Eponine
RUN cpanm Bio::DB::EUtilities # Ensembl requirement

When I try to install with cpanm by entering the container and typing "cpanm Bio::Tools::Run::Alignment::Muscle", I get the following error:

    Test Summary Report
    t/Eponine.t                 (Wstat: 65280 Tests: 2 Failed: 0)
      Non-zero exit status: 255
      Parse errors: Bad plan.  You planned 7 tests but ran 2.
    Files=70, Tests=2068, 15 wallclock secs ( 0.32 usr  0.09 sys + 12.22 cusr  1.33 csys = 13.96 CPU)
    Result: FAIL
    Failed 1/70 test programs. 0/2068 subtests failed.
-> FAIL Installing Bio::Tools::Run::Alignment::Muscle failed. See /root/.cpanm/work/1552304305.41131/build.log for details. Retry with --force to force install it.

Is there a way to debug this, and check if this is safe to ignore?

  • What does the mentioned log contain? – choroba Mar 11 at 12:15
  • The error message I posted is from the log. The installation itself is not verbose. – Cindy Almighty Mar 11 at 12:51

You need to install Java for a successful t/Eponine.t test.

There is an error in line:

open(my $PIPE,"java -version 2>&1 |") || exit;

If Java not installed the test just exits and the test plan fails.

  • Works perfectly. Can you teach me to fish - how did you find which line causes error? – Cindy Almighty Mar 12 at 14:04

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