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

[Pages, Herve]

Hi William,

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

biocbuild using 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 using 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:
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.10_bioc-2DLATEST_phemd_&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=F3I6u7a5ehHjXSCdocoJZt6QyxonF1Mr9yERW8nrkJg&s=0mydgs8zLKpjMbGeLEhBkhh8phXWfQi2pXPF431wR10&e=
> 
> Thanks!
> Will
> 
> ᐧ
> 
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> 
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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