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Building XML-LibXML-2.0208, required for Bio::Tools::CodonTable, fails in (host) Ubuntu 20.04 LTS:
Building and testing XML-LibXML-2.0208 ... ! Installing XML::LibXML failed. See /root/.cpanm/work/1685495744.1/build.log for details. Retry with --force to force install it.
FAIL
The /root/.cpanm/work/1685495744.1/build.log file shows:
[...]
# Failed test 'exception thrown during parse'
# at t/35huge_mode.t line 58.
# got: ''
# expected: anything else
# Failed test 'exception refers to entity reference loop'
# at t/35huge_mode.t line 60.
# ''
# doesn't match '(?^si:entity.*loop)'
# Looks like you failed 2 tests of 5.
t/35huge_mode.t ....................................
Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/5 subtests
The error message suggests to add --force to the respective line in the Dockerfile, the old post also suggests skipping the test, and indeed substituting the line with, RUN cpanm --force --no-wget Bio::Tools::CodonTable
Allows to complete the image build, which seems to run fine.
The text was updated successfully, but these errors were encountered:
Building XML-LibXML-2.0208, required for Bio::Tools::CodonTable, fails in (host) Ubuntu 20.04 LTS:
The /root/.cpanm/work/1685495744.1/build.log file shows:
[...]
[...]
Old post from 2013 referring an issue with the same tests failing
The error message suggests to add --force to the respective line in the Dockerfile, the old post also suggests skipping the test, and indeed substituting the line with,
RUN cpanm --force --no-wget Bio::Tools::CodonTable
Allows to complete the image build, which seems to run fine.
The text was updated successfully, but these errors were encountered: