Re: [Rdkit-discuss] Fwd: conda / Windows update to 2016.09 release gives error

2017-01-05 Thread Curt Fischer 
This worked for me.  Thanks Greg.  CF

On Tue, Jan 3, 2017 at 8:03 PM, Greg Landrum  wrote:

> Curt,
>
> If you change lines 32 and 33 in /lib/site-
> packages\rdkit\RDConfig.py
> to:
>   condaDir += ['Library', 'share', 'RDKit']
>   _share = os.path.join(*condaDir)
>
> I think it should work.
>
> Sorry for the inconvenience here; we will fix it before running the next
> conda builds.
>
> -greg
>
>
> On Wed, Jan 4, 2017 at 1:44 AM, Curt Fischer 
> wrote:
>
>>
>> Thanks for writing in Matt!
>>
>> Do you or any other readers think there is any chance that a small manual
>> fix to RDConfig.py could fix the problem?  I have very little experience
>> with building anything from source and would like to use the newest version
>> of rdkit if possible.  Would it be as simple as adding the *.sep* to
>> */lib/site-packages\rdkit\RDConfig.py* ?
>> Curt
>>
>> On Wed, Dec 21, 2016 at 2:22 AM, Matthew Swain  wrote:
>>
>>> 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 
>>> 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 
>>> 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) in ()> 1 from rdkit import 
 Chem
 C:\Anaconda2\lib\site-packages\rdkit\Chem\__init__.py in () 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 () 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'


>>>

Re: [Rdkit-discuss] Fwd: conda / Windows update to 2016.09 release gives error

2017-01-03 Thread Greg Landrum 
Curt,

If you change lines 32 and 33
in /lib/site-packages\rdkit\RDConfig.py
to:
  condaDir += ['Library', 'share', 'RDKit']
  _share = os.path.join(*condaDir)

I think it should work.

Sorry for the inconvenience here; we will fix it before running the next
conda builds.

-greg


On Wed, Jan 4, 2017 at 1:44 AM, Curt Fischer 
wrote:

>
> Thanks for writing in Matt!
>
> Do you or any other readers think there is any chance that a small manual
> fix to RDConfig.py could fix the problem?  I have very little experience
> with building anything from source and would like to use the newest version
> of rdkit if possible.  Would it be as simple as adding the *.sep* to
> */lib/site-packages\rdkit\RDConfig.py* ?
> Curt
>
> On Wed, Dec 21, 2016 at 2:22 AM, Matthew Swain  wrote:
>
>> 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 
>> 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 
>> 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) in ()> 1 from rdkit import 
>>> Chem
>>> C:\Anaconda2\lib\site-packages\rdkit\Chem\__init__.py in () 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 () 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'
>>>
>>>
>> 
>> --
>> Developer Access Program for Intel Xeon Phi Processors
>> Access to Intel Xeon Phi processor-based developer platforms.
>> With one year of Intel Parallel Studio XE.
>> Training and support from Colfax.
>> Order your

[Rdkit-discuss] Fwd: conda / Windows update to 2016.09 release gives error

2017-01-03 Thread Curt Fischer 
Thanks for writing in Matt!

Do you or any other readers think there is any chance that a small manual
fix to RDConfig.py could fix the problem?  I have very little experience
with building anything from source and would like to use the newest version
of rdkit if possible.  Would it be as simple as adding the *.sep* to
*/lib/site-packages\rdkit\RDConfig.py* ?
Curt

On Wed, Dec 21, 2016 at 2:22 AM, Matthew Swain  wrote:

> 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 
> 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 
> 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) in ()> 1 from rdkit import 
>> Chem
>> C:\Anaconda2\lib\site-packages\rdkit\Chem\__init__.py in () 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 () 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'
>>
>>
> 
> --
> Developer Access Program for Intel Xeon Phi Processors
> Access to Intel Xeon Phi processor-based developer platforms.
> With one year of Intel Parallel Studio XE.
> Training and support from Colfax.
> Order your platform today.http://sdm.link/xeonphi
> ___
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