Hi Oliver,
On 18/11/15 15:46, Stolpe, Oliver wrote:
Hello list,
I have some homegrown recipes that are installing python modules. They
used to work with EasyBuild v2.1.0, but since the new releases of
EasyBuild they can't pass the sanity check.
In one of the releases since EasyBuild v2.1.0, we fixed an issue with
the sanity check not being properly performed, particularly for
extensions (like Python packages).
They search for a bin directory, but some python libs simply don't
have any. Right now, I am overriding it by setting
sanity_check_paths = {
'files': [],
'dirs': [('lib', 'lib64')]
}
Is there a more elegant way to do this?
I'm not sure what so non-elegant about this... Maybe you feel it's not
specific enough?
EasyBuild will already perform a sanity check in the sense that it will
check whether "python -c 'import foo'" works (with 'foo' being a module
name provided by that package).
You're right that we're not enforcing that sanity_check_paths is also
defined for Python packages, which was not the case before (which was
considered a bug, see
https://github.com/hpcugent/easybuild-framework/pull/1366.
If you find this really annoying, we can define a default
sanity_check_paths in the generic PythonPackage easyblock to only check
for lib or lib64 (not bin).
That makes sense, and can avoid that easyconfigs for Python packages
include a rather silly sanity_check_paths as the one you mentioned.
If sanity_check_paths are defined in the easyconfigs, they will still
take the upper hand, so this would be a backwards-compatible change.
regards,
Kenneth
Thanks,
Oliver
== 2015-11-18 13:09:33,267 runpy.PythonPackage INFO Using default
sanity check paths: {'files': [], 'dirs': ['bin', ('lib', 'lib64')]}
== 2015-11-18 13:09:33,267 runpy.PythonPackage INFO Using specified
sanity check commands: []
== 2015-11-18 13:09:33,267 runpy.PythonPackage WARNING Sanity check:
no (non-empty) directory of ('bin',) in
/tools/easybuild/software/pysam/0.8.3-foss-2015a-Python-2.7.9
== 2015-11-18 13:09:33,268 runpy.filetools INFO Creating directory
/tmp/eb-3586qK/tmpkQnTbE/all/pysam (parents: True, set_gid: False,
sticky: False)
== 2015-11-18 13:09:33,269 runpy.PythonPackage INFO Module file
/tmp/eb-3586qK/tmpkQnTbE/all/pysam/0.8.3-foss-2015a-Python-2.7.9
written: #%Module
[......]
== sanity checking...
== FAILED: Installation ended unsuccessfully (build directory:
/tools/easybuild/build/pysam/0.8.3/foss-2015a-Python-2.7.9): build
failed (first 300 chars): Sanity check failed: no (non-empty)
directory of ('bin',) in
/tools/easybuild/software/pysam/0.8.3-foss-2015a-Python-2.7.9
== Results of the build can be found in the log file
/tmp/eb-3586qK/easybuild-pysam-0.8.3-20151118.130659.LjfHr.log
ERROR: Build of
/tools/easybuild.local/easyconfigs/p/pysam/pysam-0.8.3-foss-2015a-Python-2.7.9.eb
failed (err: "build failed (first 300 chars): Sanity check failed: no
(non-empty) directory of ('bin',) in
/tools/easybuild/software/pysam/0.8.3-foss-2015a-Python-2.7.9")
--
Oliver Stolpe
Bioinformatics Core Unit
Berlin Institute of Health
Phone: +49 30 450 543605
Luisenstr. 56, 10117 Berlin, Germany
