Comments (9)
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.
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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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