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[Bioc-devel] Python package dependency loading problem on malbec1 builder

2 messages · William Chen, Hervé Pagès

William Chen
# 
Hi all,

A package I maintain on Bioconductor ('phemd') has failed R CMD check on
two of three of the Bioconductor builders (tokay1 and malbec1) with the
following error message:

Error in py_module_import(module, convert = convert) :

  ImportError: No module named phate


It looks like this package (or one of its dependent packages) has an

unstated dependence on a standard package.  All dependencies must be

declared in DESCRIPTION.

See section ?The DESCRIPTION file? in the ?Writing R Extensions?

manual.

* checking whether the package can be unloaded cleanly ... WARNING

---- unloading

* checking whether the namespace can be loaded with stated dependencies ...
WARNING

Error in py_module_import(module, convert = convert) :

  ImportError: No module named phate


A namespace must be able to be loaded with just the base namespace

loaded: otherwise if the namespace gets loaded by a saved object, the

session will be unable to start.

I have been told that the 'phate' python module is unable to be installed
on tokay1 which uses Python2 (phate requires Python3) but that it has been
installed on the malbec1 builder such that the error should not be occuring
on that build. I have tried without avail to fix this / search for a
solution online (including the 'Writing R Extensions' manual). Any
recommendations on how to address this issue?

Link to build:
https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/phemd/

Thanks!
Will

?
Hervé Pagès
# 
Hi William,

I can confirm that the phate module is installed for Python 3 on malbec1:

biocbuild at malbec1:~$ python3
Python 3.6.9 (default, Nov  7 2019, 10:44:02)
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
 >>> import phate
 >>> phate.__version__
'0.4.5'

However please note that it is NOT installed for Python 2:

biocbuild at malbec1:~$ python
Python 2.7.17 (default, Nov  7 2019, 10:07:09)
[GCC 7.4.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
 >>> import phate
Traceback (most recent call last):
   File "<stdin>", line 1, in <module>
ImportError: No module named phate

So make sure you invoke Python 3.

Best,
H.
On 12/22/19 22:51, William Chen wrote: