Andreas Tille kirjoitti 12.1.2021 klo 23.08: > Hi, > > I confirm I can reproduce the issue in a minimal chroot while the > lumpyexpress command prints the help screen as expected. This smells > like a missing dependency but I do not have any idea which one. It > seems there is a similar known issue here > > > https://stackoverflow.com/questions/65028261/attributeerror-module-importlib-has-no-attribute-util-ii > > but there is no answer here. > > Any idea how to fix this? > > Kind regards > > Andreas.
It's a change made in debian/patches/lumpyexpress.config.patch. https://salsa.debian.org/med-team/lumpy-sv/-/commit/e64a65545fbf60c5c98965bc1d00d416b2f9582c#6864ced7557ec33a7ee70c7b0c75b076f84f4fac_24_30 - $PYTHON_TEST -c "import imp; imp.find_module('pysam')" - $PYTHON_TEST -c "import imp; imp.find_module('numpy')" + $PYTHON_TEST -c "import importlib; importlib.util.find_spec('pysam')" + $PYTHON_TEST -c "import importlib; importlib.util.find_spec('numpy')" It's not entirely correct even if it worked: the original causes a visible error message to alert if one of the required modules does not exist. The current patch will not cause error messages or the python check to exit non-zero. Because it's a Debian context we could rely on dpkg dependencies i.e. just don't perform this check and comment out the two lines. -- Juhani
