Build time test issues for version 3.2.6 about pftools3 HOT 9 CLOSED

Hi

I think we got a similar issue with the Dockerfile. We started with a mini linux and something was missing. Never really found what is was, but moving to Ubuntu solves the issue.

So could you run manually the test_V3.sh script to see which step fails?

After the cmake step the script should be in the Tests/examples/ folder

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Hi,
I tried to run this command and attached the output. The strangest thing at the end of the log is the

test_V3.sh: 201: /build/pftools-3.2.6/src/Perl/make_iupac_cmp.pl: not found
 Error: Unexpected end of matrix file. Unable to find '..                              ' keyword.
Segmentation fault

I can confirm that

ls -l /build/pftools-3.2.6/src/Perl/make_iupac_cmp.pl
-rwxr-xr-x 1 pbuilder pbuilder 2278 Oct  8 10:56 /build/pftools-3.2.6/src/Perl/make_iupac_cmp.pl

exists. I think an issue is definitely

 $ /build/pftools-3.2.6/src/Perl/scramble_fasta.pl
 bash: /build/pftools-3.2.6/src/Perl/scramble_fasta.pl: /bin/env: bad interpreter: No such file or directory

On Debian it is

$ which env
/usr/bin/env

The interesting thing is that I tried to patch this script (to /usr/bin/perl as interpreter) but the exit code remained 1. :-(

Just let me know if I can provide more detailed information. Andreas.

test_V3.sh.output.zip

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I have harmonized the bin/env path in the master branch.

Is it better for you?

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Is this still for the execute_test_V3.sh and check_output_of_test_V3.sh tests?

Which Debian version do you use? I will try to reproduce the issue in a container with a controlled environment.

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I have built a container with debian:sid and the tests are successful on my side.

Like for our Dockerfile I have installed those packages before the compilation:

apt-get install -y --no-install-recommends \
      build-essential \
      libpcre++-dev \
      gfortran \
      libgfortran5 \
      ca-certificates \
      git \
      cmake \
      zlib1g-dev \
      libpng-dev \
      libfile-slurp-perl

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Great
Thanks

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