On Wed, Jan 13, 2021 at 12:04:08AM +0200, Juhani Numminen wrote: > 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
There's a discussion of the issue at https://stackoverflow.com/questions/39660934/error-when-using-importlib-util-to-check-for-library/39661116 To remove the error, - $PYTHON_TEST -c "import imp; imp.find_module('pysam')" - $PYTHON_TEST -c "import imp; imp.find_module('numpy')" + $PYTHON_TEST -c "from importlib import util; util.find_spec('pysam')" + $PYTHON_TEST -c "from importlib import util; util.find_spec('numpy')" To print an error message, perhaps the awkward-looking - $PYTHON_TEST -c "import imp; imp.find_module('pysam')" - $PYTHON_TEST -c "import imp; imp.find_module('numpy')" + $PYTHON_TEST -c "from importlib import util; print('pysam not found') if util.find_spec('pysam') is None else None" + $PYTHON_TEST -c "from importlib import util; print('numpy not found') if util.find_spec('numpy') is None else None" Ken