I've also encountered this problem with the 2016.09.2 windows packages on the
rdkit conda channel. It looks like somehow the RDConfig patch in the conda
recipe hasn't been applied properly in the published packages.
The original lines in the rdkit are:
condaDir += ['share', 'RDKit']
_share = os.path.join(*condaDir)
The conda recipe has a Windows-specific patch to change this to:
condaDir += ['Library','share','RDKit']
_share = os.path.sep.join(condaDir)
Which looks fine (although the second line doesn't really need changing?). But
in the published packages it is:
condaDir += ['share', 'RDKit', 'RDKit']
_share = os.path.join(condaDir)
This causes the AttributeError because it incorrectly passes a list to
os.path.join, with no asterisk for unpacking the list into *args. The first
line is also incorrect.
I built the package myself from the recipe, and didn't see this issue.
Matt
On Dec 09, 2016, at 05:05 PM, Curt Fischer <[email protected]> wrote:
I'm not sure of the source of the problem with the conda 2016.09 release on my
Windows box, but I was able to revert to a 2016.03 release with a conda install
-c rmg rdkit=2016.03*
conda couldn't seem to solve the specifications automagically, but after I
uninstalled boost and did the above command, it identified the proper boost to
install along with the 2016.03 rdkit.
I now have a functioning rdkit again, but would still be interested in hearing
from anyone that experiences a similar problem.
On Thu, Dec 8, 2016 at 9:27 AM, Curt Fischer <[email protected]> wrote:
To update rdkit to the September release, I recently did a
conda install -f --channel https://conda.anaconda.org/rdkit rdkit
on my Windows box, and everything seemed to update fine.
However now, when I try from rdkit import Chem, I get the disturbing error
message below.
Is this a sign that my particular installation got borked somehow, and I maybe
I should reinstall everything again? Or is this perchance a known issue with
the 2016.09 release? If the latter, how do I roll back to the old release
using conda? I tried a conda install --channel
https://conda.anaconda.org/rdkit rdkit=2016.03.4 but that didn't seem to do it.
Thanks all for any help!
Curt
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-5-17d7acb427ab> in <module>()
----> 1 from rdkit import Chem
C:\Anaconda2\lib\site-packages\rdkit\Chem\__init__.py in <module>()
17 """
18 from rdkit import rdBase
---> 19 from rdkit import RDConfig
20
21 from rdkit import DataStructs
C:\Anaconda2\lib\site-packages\rdkit\RDConfig.py in <module>()
31 condaDir[0] = os.path.sep
32 condaDir += ['share', 'RDKit', 'RDKit']
---> 33 _share = os.path.join(condaDir)
34 RDDataDir = os.path.join(_share, 'Data')
35 RDDocsDir = os.path.join(_share, 'Docs')
C:\Anaconda2\lib\ntpath.pyc in join(path, *paths)
63 def join(path, *paths):
64 """Join two or more pathname components, inserting "\\" as needed."""
---> 65 result_drive, result_path = splitdrive(path)
66 for p in paths:
67 p_drive, p_path = splitdrive(p)
C:\Anaconda2\lib\ntpath.pyc in splitdrive(p)
114 """
115 if len(p) > 1:
--> 116 normp = p.replace(altsep, sep)
117 if (normp[0:2] == sep*2) and (normp[2:3] != sep):
118 # is a UNC path:
AttributeError: 'list' object has no attribute 'replace'
------------------------------------------------------------------------------
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