Problem installing Pybel & OpenBabel 2.41. on Windows

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Problem installing Pybel & OpenBabel 2.41. on Windows

RichardMR
Hi,

I am trying to install OpenBabel 2.4.1 and Pybel 1.8 for Python 2.7.12 (32-bit) under Windows 7.

[Python was installed via the vanilla python-2.7.12.msi installer. This is on a 'clean' machine, so there is no relation to the problem with installing Pybel for Anaconda I reported last month: https://sourceforge.net/p/openbabel/mailman/message/35429073/]

I obtained the OpenBabel installer [OpenBabel-2.4.1-x86.exe] from here: https://sourceforge.net/projects/openbabel/files/openbabel/2.4.1/OpenBabel-2.4.1-x86.exe/download

I obtained the Pybel installer [openbabel-python-1.8.py27.exe] from here: http://sourceforge.net/projects/openbabel/files/openbabel-python/1.8/
At least when I run the cmd prompt in administrator mode (here, I should clarify that I need to specify another ADMIN account to install software), I can reproduce all of the expected output for Open Babel, as documented here:  https://openbabel.org/docs/dev/UseTheLibrary/PythonInstall.html

However, when I try and import pybel into Python in the same cmd prompt session, I get the following error:
-----------------------
C:\windows\system32>python
Python 2.7.12 (v2.7.12:d33e0cf91556, Jun 27 2016, 15:19:22) [MSC v.1500 32 bit (
Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybel
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Python27\lib\site-packages\pybel.py", line 52, in <module>
    import openbabel as ob
  File "C:\Python27\lib\site-packages\openbabel.py", line 37, in <module>
    _openbabel = swig_import_helper()
  File "C:\Python27\lib\site-packages\openbabel.py", line 33, in swig_import_hel
per
    _mod = imp.load_module('_openbabel', fp, pathname, description)
ImportError: DLL load failed: The specified procedure could not be found.
>>>
-----------------------------

Thank you in advance for any assistance you have time to provide.

Best regards,

Richard







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Re: Problem installing Pybel & OpenBabel 2.41. on Windows

RichardMR
Hi,

Just to provide an update here, I have now verified that the problem is specifically with Open Babel version 2.4.1.

After uninstalling OpenBabel and Pybel on the same machine, I was able to successfully install Open Babel 2.3.2 [ttp://sourceforge.net/projects/openbabel/files/openbabel/2.3.2/OpenBabel2.3.2a_Windows_Installer.exe/download] and then Pybel 1.8, using the same installer I mentioned previously.

[With regard to the need to elevate privileges with a separate ADMIN account, this did require me to manually update my SYSTEM path, locate C:\User\[ADMIN]\AppData\Roaming\OpenBabel-[version], move this to C:\User\[LOGIN ACCOUNT]\AppData\Roaming\OpenBabel-[version] and set a SYSTEM variable BABEL_DATADIR=C:\User\[LOGIN ACCOUNT]\AppData\Roaming\OpenBabel-[version]\data. This enabled use of obabel in a new [LOGIN ACCOUNT] command prompt but still generated the same import pybel error as before. So, although this is an added complication, it does not appear to be related to the problem importing pybel with OpenBabel-2.4.1 that I previously reported.]

I checked the software was correctly installed and working as expected as follows:

-------------------------------

C:\Users\prerlm>echo %BABEL_DATADIR%
C:\Users\prerlm\AppData\Roaming\OpenBabel-2.3.2\data
C:\Users\prerlm>obabel -V
Open Babel 2.3.2 -- Oct  5 2012 -- 10:00:48
C:\Users\prerlm>python
Python 2.7.12 (v2.7.12:d33e0cf91556, Jun 27 2016, 15:19:22) [MSC v.1500 32 bit (
Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybel
>>> mol = pybel.readstring('smi','CCCBr')
>>> mol.write('inchi')
'InChI=1S/C3H7Br/c1-2-3-4/h2-3H2,1H3\n'
>>> quit()
C:\Users\prerlm>dir %BABEL_DATADIR%\mr.txt
 Volume in drive C is OSDisk
 Volume Serial Number is ECFC-1FAD
 Directory of C:\Users\prerlm\AppData\Roaming\OpenBabel-2.3.2\data
03/10/2012  09:50             4,295 mr.txt
               1 File(s)          4,295 bytes
               0 Dir(s)  308,117,536,768 bytes free
C:\Users\prerlm>
---------------------------------------

Best regards,

Richard


On Fri, Nov 18, 2016 at 8:30 PM, Richard Marchese Robinson <[hidden email]> wrote:
Hi,

I am trying to install OpenBabel 2.4.1 and Pybel 1.8 for Python 2.7.12 (32-bit) under Windows 7.

[Python was installed via the vanilla python-2.7.12.msi installer. This is on a 'clean' machine, so there is no relation to the problem with installing Pybel for Anaconda I reported last month: https://sourceforge.net/p/openbabel/mailman/message/35429073/]

I obtained the OpenBabel installer [OpenBabel-2.4.1-x86.exe] from here: https://sourceforge.net/projects/openbabel/files/openbabel/2.4.1/OpenBabel-2.4.1-x86.exe/download

I obtained the Pybel installer [openbabel-python-1.8.py27.exe] from here: http://sourceforge.net/projects/openbabel/files/openbabel-python/1.8/
At least when I run the cmd prompt in administrator mode (here, I should clarify that I need to specify another ADMIN account to install software), I can reproduce all of the expected output for Open Babel, as documented here:  https://openbabel.org/docs/dev/UseTheLibrary/PythonInstall.html

However, when I try and import pybel into Python in the same cmd prompt session, I get the following error:
-----------------------
C:\windows\system32>python
Python 2.7.12 (v2.7.12:d33e0cf91556, Jun 27 2016, 15:19:22) [MSC v.1500 32 bit (
Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybel
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Python27\lib\site-packages\pybel.py", line 52, in <module>
    import openbabel as ob
  File "C:\Python27\lib\site-packages\openbabel.py", line 37, in <module>
    _openbabel = swig_import_helper()
  File "C:\Python27\lib\site-packages\openbabel.py", line 33, in swig_import_hel
per
    _mod = imp.load_module('_openbabel', fp, pathname, description)
ImportError: DLL load failed: The specified procedure could not be found.
>>>
-----------------------------

Thank you in advance for any assistance you have time to provide.

Best regards,

Richard








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Re: Problem installing Pybel & OpenBabel 2.41. on Windows

Noel O'Boyle
Administrator
The Python bindings are to be installed via pip on Windows. Some of the docs are outdated I'm afraid.

On 2 Dec 2016 2:40 p.m., "Richard Marchese Robinson" <[hidden email]> wrote:
Hi,

Just to provide an update here, I have now verified that the problem is specifically with Open Babel version 2.4.1.

After uninstalling OpenBabel and Pybel on the same machine, I was able to successfully install Open Babel 2.3.2 [ttp://sourceforge.net/projects/openbabel/files/openbabel/2.3.2/OpenBabel2.3.2a_Windows_Installer.exe/download] and then Pybel 1.8, using the same installer I mentioned previously.

[With regard to the need to elevate privileges with a separate ADMIN account, this did require me to manually update my SYSTEM path, locate C:\User\[ADMIN]\AppData\Roaming\OpenBabel-[version], move this to C:\User\[LOGIN ACCOUNT]\AppData\Roaming\OpenBabel-[version] and set a SYSTEM variable BABEL_DATADIR=C:\User\[LOGIN ACCOUNT]\AppData\Roaming\OpenBabel-[version]\data. This enabled use of obabel in a new [LOGIN ACCOUNT] command prompt but still generated the same import pybel error as before. So, although this is an added complication, it does not appear to be related to the problem importing pybel with OpenBabel-2.4.1 that I previously reported.]

I checked the software was correctly installed and working as expected as follows:

-------------------------------

C:\Users\prerlm>echo %BABEL_DATADIR%
C:\Users\prerlm\AppData\Roaming\OpenBabel-2.3.2\data
C:\Users\prerlm>obabel -V
Open Babel 2.3.2 -- Oct  5 2012 -- 10:00:48
C:\Users\prerlm>python
Python 2.7.12 (v2.7.12:d33e0cf91556, Jun 27 2016, 15:19:22) [MSC v.1500 32 bit (
Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybel
>>> mol = pybel.readstring('smi','CCCBr')
>>> mol.write('inchi')
'InChI=1S/C3H7Br/c1-2-3-4/h2-3H2,1H3\n'
>>> quit()
C:\Users\prerlm>dir %BABEL_DATADIR%\mr.txt
 Volume in drive C is OSDisk
 Volume Serial Number is ECFC-1FAD
 Directory of C:\Users\prerlm\AppData\Roaming\OpenBabel-2.3.2\data
03/10/2012  09:50             4,295 mr.txt
               1 File(s)          4,295 bytes
               0 Dir(s)  308,117,536,768 bytes free
C:\Users\prerlm>
---------------------------------------

Best regards,

Richard


On Fri, Nov 18, 2016 at 8:30 PM, Richard Marchese Robinson <[hidden email]> wrote:
Hi,

I am trying to install OpenBabel 2.4.1 and Pybel 1.8 for Python 2.7.12 (32-bit) under Windows 7.

[Python was installed via the vanilla python-2.7.12.msi installer. This is on a 'clean' machine, so there is no relation to the problem with installing Pybel for Anaconda I reported last month: https://sourceforge.net/p/openbabel/mailman/message/35429073/]

I obtained the OpenBabel installer [OpenBabel-2.4.1-x86.exe] from here: https://sourceforge.net/projects/openbabel/files/openbabel/2.4.1/OpenBabel-2.4.1-x86.exe/download

I obtained the Pybel installer [openbabel-python-1.8.py27.exe] from here: http://sourceforge.net/projects/openbabel/files/openbabel-python/1.8/
At least when I run the cmd prompt in administrator mode (here, I should clarify that I need to specify another ADMIN account to install software), I can reproduce all of the expected output for Open Babel, as documented here:  https://openbabel.org/docs/dev/UseTheLibrary/PythonInstall.html

However, when I try and import pybel into Python in the same cmd prompt session, I get the following error:
-----------------------
C:\windows\system32>python
Python 2.7.12 (v2.7.12:d33e0cf91556, Jun 27 2016, 15:19:22) [MSC v.1500 32 bit (
Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybel
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Python27\lib\site-packages\pybel.py", line 52, in <module>
    import openbabel as ob
  File "C:\Python27\lib\site-packages\openbabel.py", line 37, in <module>
    _openbabel = swig_import_helper()
  File "C:\Python27\lib\site-packages\openbabel.py", line 33, in swig_import_hel
per
    _mod = imp.load_module('_openbabel', fp, pathname, description)
ImportError: DLL load failed: The specified procedure could not be found.
>>>
-----------------------------

Thank you in advance for any assistance you have time to provide.

Best regards,

Richard








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