[Debian-med-packaging] Bug#896931: fastqc: If the package libfindbin-libs-perl is not installed, fastqc exits with an error immediately.

[Robert Elshire]

Package: fastqc
Version: 0.11.5+dfsg-6
Severity: grave
Justification: renders package unusable

Dear Maintainer,

Working in a basic cloud environment, I install fastqc via apt and try
to run it. It exits with an error. See below for command line example.

debian at 40120a:~$ fastqc
Can't locate FindBin.pm in @INC (you may need to install the FindBin
module) (@INC contains: /etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.24.1 /usr/local/share/perl/5.24.1
/usr/lib/x86_64-linux-gnu/perl5/5.24 /usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.24 /usr/share/perl/5.24
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at
/usr/bin/fastqc line 4.
BEGIN failed--compilation aborted at /usr/bin/fastqc line 4.

After this happened, I installed the package libfindbin-libs-perl via
apt. When trying again, fastqc runs as expected.

Best regards,

Rob Elshire


-- System Information:
Debian Release: 9.4
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 4.9.0-4-amd64 (SMP w/1 CPU core)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages fastqc depends on:
ii  default-jre [java7-runtime]    2:1.8-58
ii  libcommons-math3-java          3.6.1-2
ii  libhtsjdk-java                 2.8.1+dfsg-1
ii  libjbzip2-java                 0.9.1-3
ii  openjdk-8-jre [java7-runtime]  8u162-b12-1~deb9u1

fastqc recommends no packages.

fastqc suggests no packages.

-- no debconf information