Re: [Rdkit-discuss] windows10 Postgres :: RDKit

[Paolo Tosco]

Dear Mike,

there are instructions how to build and install the PostgreSQL RDKit 
cartridge under Windows in Code/PgSQL/rdkit/README.

Please do not hesitate to get back to me offline if you need help.

Best,
Paolo

On 11/29/2016 07:20 PM, Mike Mazanetz wrote:


Dear All,

Has anyone successfully setup the RDKit Cartridge in Postgres in 
Windows10.


If so can you give some pointers?

Thanks,

mike



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Re: [Rdkit-discuss] errors with windows10 RDKit installation using conda

[Brian Kelley]

Another point:

I had the same path length issues and eventually installed anacond3 into 

C:\a3

For building packages and they magically went away.  Super annoying.


Brian Kelley

> On Nov 29, 2016, at 8:11 AM, Mike Mazanetz  
> wrote:
> 
> Hi,
>  
> Thought I’d update my progress:
>  
> Steps to fix issue:
> change Admin permissions for Anaconda3
> ran these commands:
> conda update conda
> conda update -n root conda-build
> conda install -c rdkit rdkit=2016.09.2 
>  
> as RDKit it was change in the last 24 hours J
>  
> then found that this filename was too long, so just deleted it !
> C:\boost_1_59_0.zip\boost_1_59_0\libs\geometry\doc\html\geometry\reference\spatial_indexes\boost__geometry__index__rtree\rtree_parameters_type_const___.html
>  
> That fixed that problem.
>  
> then had to rename this file as it was named incorrectly in two places. – 
> probably didn’t need this file anyway !
> Appendix A An Introduction to Preprocessor Metaprogramming.html
>  
> got a little further down the road then encountered this:
> File not found - boost_*-mt-1_*.lib
> 0 File(s) copied
> File not found - boost_*-mt-1_*.dll
> 0 File(s) copied
> Command failed: cmd.exe /c bld.bat
>  
> So battling these issues now…
>  
> ./mike
>  
> From: Mike Mazanetz [mailto:mi...@novadatasolutions.co.uk] 
> Sent: 29 November 2016 12:33
> To: rdkit-discuss@lists.sourceforge.net
> Subject: Re: [Rdkit-discuss] errors with windows10 RDKit installation using 
> conda
>  
> Hello,
>  
> Further to my little exploratoin, I managed to do a few things:
> conda update conda
> conda update -n root conda-build
>  
> so I’ve got a little further, but I’ve run into a Windows nightmare – path 
> files are too long…  I can see the file in the cache:  boost_1_59_0.zip, but 
> the name is so long windows will not open it. 
>  
> Has anyone done a build in Windows10, can you please send me your build 
> routine?
>  
> Thanks,
> mike
>  
>  
> conda build boost
> BUILD START: boost-1.59.0-py35_3
> updating index in: C:\Program Files\Anaconda3\conda-bld\win-64
> updating index in: C:\Program Files\Anaconda3\conda-bld\noarch
>  
> The following NEW packages will be INSTALLED:
>  
> bzip2:  1.0.6-vc14_3  [vc14]
> pip:9.0.1-py35_0
> python: 3.5.2-0
> setuptools: 27.2.0-py35_1
> vs2015_runtime: 14.0.25123-0
> wheel:  0.29.0-py35_0
> zlib:   1.2.8-vc14_3  [vc14]
>  
> Source cache directory is: C:\Program Files\Anaconda3\conda-bld\src_cache
> Found source in cache: boost_1_59_0.zip
> Extracting download
> Traceback (most recent call last):
>   File "C:\Program Files\Anaconda3\Scripts\conda-build-script.py", line 5, in 
> 
> sys.exit(conda_build.cli.main_build.main())
>   File "C:\Program 
> Files\Anaconda3\lib\site-packages\conda_build\cli\main_build.py", line 244, 
> in main
> execute(sys.argv[1:])
>   File "C:\Program 
> Files\Anaconda3\lib\site-packages\conda_build\cli\main_build.py", line 236, 
> in execute
> already_built=None, config=config, noverify=args.no_verify)
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\api.py", 
> line 75, in build
> need_source_download=need_source_download, config=config)
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\build.py", 
> line 1227, in build_tree
> config=recipe_config)
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\build.py", 
> line 790, in build
> config=config)
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\render.py", 
> line 86, in parse_or_try_download
> source.provide(metadata.path, metadata.get_section('source'), 
> config=config)
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\source.py", 
> line 485, in provide
> unpack(meta, config=config)
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\source.py", 
> line 86, in unpack
> unzip(src_path, config.work_dir)
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\utils.py", 
> line 287, in unzip
> with open(path, 'wb') as fo:
> FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Program 
> Files\\Anaconda3\\conda-bld\\boost_1480420542489\\work\\boost_1_59_0\\libs\\geometry\\doc\\html\\geometry\\reference\\spatial_indexes\\boost__geometry__index__rtree\\rtree_parameters_type_constindexable_getter_constvalue_equal_constallocator_type_const___.html'
>  
>  
> From: Mike Mazanetz [mailto:mi...@novadatasolutions.co.uk] 
> Sent: 29 November 2016 11:13
> To: rdkit-discuss@lists.sourceforge.net
> Subject: [Rdkit-discuss] errors with windows10 RDKit installation using conda
>  
> Hello RDKit Forum,
>  
> I’ve been using RDkit to several years through KNIME and have found it 
> thoroughly useful.  I’ve taken the next step and decided to try the Postgres 
> Cartridge, but I’ve had issues building RDKit on Windows.
> Has anyone encountered had success using 

Re: [Rdkit-discuss] errors with windows10 RDKit installation using conda

[Brian Kelley]

I'm very close to having stable c# wrappers again.  The painful bit is writing 
all the tests, but if you would like to help out, I can send you the current 
builds.


Brian Kelley

> On Nov 29, 2016, at 3:06 PM, Michal Krompiec  
> wrote:
> 
> 
> 
>> On Tuesday, 29 November 2016, Greg Landrum  wrote:
>> 
>>> On Tue, Nov 29, 2016 at 5:17 PM, Bob Funchess  wrote:
>>>  
>>> PS: All I really need is the C# wrappers; if those could be included in the 
>>> binary distribution it would be extremely helpful for me.
>>> 
>> 
>> Building these hasn't been automated since there aren't really any tests 
>> available and distributing something that hasn't been tested at all makes me 
>> very nervous. Of course if someone in the community who knows some C# were 
>> to contribute a set of tests (or even just a port of the existing Java 
>> wrapper tests) that would make me feel a lot safer. hint hint. :-)
>>  
> 
> If stable C# wrappers were available one could make a COM interop library and 
> access RDKit from VBA in MS Excel. I guess most of you aren't fans of Excel, 
> but it is still the workhorse for the less-geeky chemists and no such add-in 
> is widely available. 
> 
> Best,
> 
> Michal
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Re: [Rdkit-discuss] errors with windows10 RDKit installation using conda

[Michal Krompiec]

On Tuesday, 29 November 2016, Greg Landrum  wrote:

>
> On Tue, Nov 29, 2016 at 5:17 PM, Bob Funchess  > wrote:
>
>
>> PS: All I really need is the C# wrappers; if those could be included in
>> the binary distribution it would be extremely helpful for me.
>>
>
> Building these hasn't been automated since there aren't really any tests
> available and distributing something that hasn't been tested at all makes
> me very nervous. Of course if someone in the community who knows some C#
> were to contribute a set of tests (or even just a port of the existing Java
> wrapper tests) that would make me feel a lot safer. hint hint. :-)
>
>

If stable C# wrappers were available one could make a COM interop library
and access RDKit from VBA in MS Excel. I guess most of you aren't fans of
Excel, but it is still the workhorse for the less-geeky chemists and no
such add-in is widely available.

Best,

Michal
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Re: [Rdkit-discuss] windows10 Postgres :: RDKit

[Mike Mazanetz]

Dear All,

 

Has anyone successfully setup the RDKit Cartridge in Postgres in Windows10.

If so can you give some pointers?

 

Thanks,

mike

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Re: [Rdkit-discuss] comparing two or more tables of molecules

[Dimitri Maziuk]

On 11/29/2016 11:56 AM, Chris Swain wrote:

> However I’ve found that the success is very much dependent on the
> fact 1 described by Greg, get all the structures standardised then comparison
using canonical SMILES or InChi seems to work fine.

+1. Essentially you need to get standardized representation of all the
properties you consider relevant and produce a unique hash of that.
Doesn't matter if it's a SHA-1 string or some graph-based magic or a
matrix voodoo. (String comparison is of course easier.)

-- 
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu



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Re: [Rdkit-discuss] comparing two or more tables of molecules

[Chris Swain]

Hi,

I’ve done this sort of comparison many times I actually use a SVL script within 
Moe and there is an example here 
(http://www.cambridgemedchemconsulting.com/resources/hit_identification/fragment_collection_profiles.html
 
)

However I’ve found that the success is very much dependent on the fact 1 
described by Greg, get all the structures standardised then comparison using 
canonical SMILES or InChi seems to work fine.

Cheers,

Chris

> On 29 Nov 2016, at 17:24, rdkit-discuss-requ...@lists.sourceforge.net wrote:
> 
> fact 1: if the structures are coming from different sources, they need to
> be standardized/normalized before you compare them. This is true regardless
> of how you want to compare them. The details of the standardization process
> are not incredibly important, but it does need to take care of the things
> you care about when comparing molecules. For example, if you don't care
> about differences between salts, it should strip salts. If you don't care
> about differences between tautomers, it should normalize tautomers.

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Re: [Rdkit-discuss] errors with windows10 RDKit installation using conda

[Greg Landrum]

Mike,

One question I realized that I forgot to ask here: Do you actually need to
be able to build the RDKit from source? Couldn't you just "conda install
rdkit" and go? If we get the cartridge working on windows via conda, then
you'll be able to install this the same way.

Unless you're planning on working on/modifying the RDKit code itself, you
likely don't need to build it.

-greg


On Tue, Nov 29, 2016 at 12:13 PM, Mike Mazanetz <
mi...@novadatasolutions.co.uk> wrote:

> Hello RDKit Forum,
>
>
>
> I’ve been using RDkit to several years through KNIME and have found it
> thoroughly useful.  I’ve taken the next step and decided to try the
> Postgres Cartridge, but I’ve had issues building RDKit on Windows.
>
> Has anyone encountered had success using Anaconda3 to build RDKit?  I get
> this message – which I’ve not found sufficient answers for from the conda
> github:
>
>
>
> Directory of C:\NovaData\Software\RDKit\conda-rdkit-master
>
>
>
> 28/11/2016  20:48  .
>
> 28/11/2016  20:48  ..
>
> 28/11/2016  05:45 3 .gitignore
>
> 28/11/2016  05:45  boost
>
> 28/11/2016  05:45  cairocffi
>
> 28/11/2016  05:45  cairo_nox
>
> 28/11/2016  05:45  django-rdkit
>
> 28/11/2016  05:45 2,626 Dockerfile
>
> 28/11/2016  05:45  eigen
>
> 28/11/2016  05:45  ncurses
>
> 28/11/2016  05:45  nox
>
> 28/11/2016  05:45  pixman
>
> 28/11/2016  05:45  postgresql
>
> 28/11/2016  05:45  postgresql95
>
> 28/11/2016  05:45  rdkit
>
> 28/11/2016  05:45  rdkit-postgresql
>
> 28/11/2016  05:45  rdkit-postgresql95
>
> 28/11/2016  05:45 6,626 README.rst
>
>3 File(s)  9,255 bytes
>
>   15 Dir(s)  360,784,285,696 bytes free
>
>
>
> C:\NovaData\Software\RDKit\conda-rdkit-master>conda build boost
>
> BUILD START: boost-1.59.0-py35_3
>
> updating index in: C:\Users\NovaData\conda-bld\win-64
>
> updating index in: C:\Users\NovaData\conda-bld\noarch
>
>
>
> The following packages will be downloaded:
>
>
>
> package|build
>
> ---|-
>
> pip-9.0.1  |   py35_0 1.7 MB
>
>
>
> The following NEW packages will be INSTALLED:
>
>
>
> bzip2:  1.0.6-vc14_3  [vc14] (copy)
>
> pip:9.0.1-py35_0
>
> python: 3.5.2-0   (copy)
>
> setuptools: 27.2.0-py35_1 (copy)
>
> vs2015_runtime: 14.0.25123-0  (copy)
>
> wheel:  0.29.0-py35_0 (copy)
>
> zlib:   1.2.8-vc14_3  [vc14] (copy)
>
>
>
> WARNING conda.lock:touch(53): Failed to create lock, do not run conda in
> parallel processes [errno 13]
>
> Traceback (most recent call last):
>
>   File "C:\Program Files\Anaconda3\Scripts\conda-build-script.py", line
> 5, in 
>
> sys.exit(conda_build.cli.main_build.main())
>
>   File "C:\Program 
> Files\Anaconda3\lib\site-packages\conda_build\cli\main_build.py",
> line 246, in main
>
> execute(sys.argv[1:])
>
>   File "C:\Program 
> Files\Anaconda3\lib\site-packages\conda_build\cli\main_build.py",
> line 238, in execute
>
> already_built=None, config=config)
>
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\api.py",
> line 83, in build
>
> need_source_download=need_source_download, config=config)
>
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\build.py",
> line 1004, in build_tree
>
> config=recipe_config)
>
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\build.py",
> line 561, in build
>
> create_env(config.build_prefix, specs, config=config)
>
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\build.py",
> line 431, in create_env
>
> plan.execute_actions(actions, index, verbose=config.debug)
>
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda\plan.py", line
> 643, in execute_actions
>
> inst.execute_instructions(plan, index, verbose)
>
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda\instructions.py",
> line 134, in execute_instructions
>
> cmd(state, arg)
>
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda\instructions.py",
> line 58, in EXTRACT_CMD
>
> extract(arg)
>
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda\install.py",
> line 801, in extract
>
> t.extractall(path=temp_path)
>
>   File "C:\Program Files\Anaconda3\lib\tarfile.py", line 1996, in
> extractall
>
> numeric_owner=numeric_owner)
>
>   File "C:\Program Files\Anaconda3\lib\tarfile.py", line 2038, in extract
>
> numeric_owner=numeric_owner)
>
>   File "C:\Program Files\Anaconda3\lib\tarfile.py", line 2100, in
> _extract_member
>
> os.makedirs(upperdirs)
>
>   File "C:\Program Files\Anaconda3\lib\os.py", line 231, in makedirs
>
> makedirs(head, mode, exist_ok)
>
>   File "C:\Program 

Re: [Rdkit-discuss] errors with windows10 RDKit installation using conda

[Greg Landrum]

On Tue, Nov 29, 2016 at 5:17 PM, Bob Funchess  wrote:

>
>
> I have been trying to build the RDKit under Windows WITHOUT using conda
> without success.  If you have working instructions for that (including,
> perhaps, a specific version of Boost and SWIG that are known to work) it
> would be helpful.  I figured out the Eigen3 problem I was having, but I’m
> still getting unresolved symbol errors when linking and a LOT of the tests
> fail; should I be trying to use Win64 Boost libs or do I have to use the
> x86 version?
>

The nice thing about the conda stuff is that it encapsulates the entire
build process (and a lot of the environment) in one place and more or less
automates it. I don't have the process automated for non-conda builds. I
can capture what I have in the current environment that I use to build the
Java wrappers for the KNIME nodes and see if I can make that
comprehensible. That's very old-school and command line and uses Visual
Studio 2010 (but that shouldn't be relevant thanks to how cmake works).


> PS: All I really need is the C# wrappers; if those could be included in
> the binary distribution it would be extremely helpful for me.
>

Building these hasn't been automated since there aren't really any tests
available and distributing something that hasn't been tested at all makes
me very nervous. Of course if someone in the community who knows some C#
were to contribute a set of tests (or even just a port of the existing Java
wrapper tests) that would make me feel a lot safer. hint hint. :-)

-greg
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Re: [Rdkit-discuss] comparing two or more tables of molecules

[Greg Landrum]

Wow, this is a great question and quite a fun thread.

It's hard to really make much of a contribution here without writing a
book/review article (something that I'm really not willing to do!), but I
have a few thoughts. Most of this is repeating/rephrasing things others
have already said.

I'm going to propose some things as facts. I think that these won't be
controversial:
fact 1: if the structures are coming from different sources, they need to
be standardized/normalized before you compare them. This is true regardless
of how you want to compare them. The details of the standardization process
are not incredibly important, but it does need to take care of the things
you care about when comparing molecules. For example, if you don't care
about differences between salts, it should strip salts. If you don't care
about differences between tautomers, it should normalize tautomers.
fact 2: The InChI algorithm includes a standardization step that normalizes
some tautomers, but does not remove salts.
fact 3: The InChI representation contain a number of layers defining the
structure in increasing detail (this isn't strictly true, because some of
the choices about how layers are ordered are arbitrary, but it's close).
fact 4: canonicalization, the way I define it, produces a canonical atom
numbering for a given structure, but it does *not* standardize
fact 5: the RDKit has essentially no well-documented standardization code

fact X: we don't have any standard, broadly accepted approach for
standardization, canonicalization or representation that is fool-proof or
that works for even all of organic chemistry, never mind organometallics.
InChI, useful as it is for some things, completely fails to handle things
like atropisomers (they are working on this kind of thing, but it's not out
yet).

Given all of this, if I wanted to have flexible duplicate checking *right*
now, I think I would use the AvalonTools struchk functionality that the
RDKit provides (the new pure-RDKit version still needs a bit more testing)
to handle basic standardization and salt stripping and then produce a table
that includes the InChI in a couple of different forms. I'd want to be able
to recognize molecules that differ only by stereochemistry, molecules that
differ only by location of tautomeric Hs, and molecules that differ only by
the location of isotopic labels. You can do this with various clever splits
of the InChI (how to do it is left as an exercise for the reader and/or a
future RDKit blog post).

I think there's something fun to be done here with SMILES variants,
borrowing heavily from some of the things that Roger has written about:
https://nextmovesoftware.com/blog/2013/04/25/finding-all-types-of-every-mer/
here's a more recent application of that from Noel:
https://nextmovesoftware.com/blog/2016/06/22/fishing-for-
matched-series-in-a-sea-of-structure-representations/

If I didn't really care about details and just wanted something that I
could explain easily to others, I'd skip all the complication and just use
InChIs (or InChI keys) to recognize duplicates. There would be times when
that would be the wrong answer, but it would be a broadly accepted kind of
wrong.[1]

Regardless of the approach, I would not, under most any circumstances,
discard the original input structures that I had. It's really good to be
able to figure out what the original data looked like later.

-greg
[1] I'm crying as I write this...




On Mon, Nov 28, 2016 at 5:25 PM, Stephen O'hagan 
wrote:

> Has anyone come up with fool-proof way of matching structurally equivalent
> molecules?
>
>
>
> Unique Smiles or InChI String comparisons don’t appear to work presumable
> because there are different but equivalent structures, e.g. explicit vs
> non-explicit H’s, Kekule vs Aromatic, isomeric forms vs non-isomeric form,
> tautomers etc.
>
>
>
> I also expect that comparing InChI strings might need something more than
> just a simple string comparison, such as masking off stereo information
> when you don’t care about stereo isomers.
>
>
>
> I assume there are suitable tools within RDKit that can do this?
>
>
>
> N.B. I need to collate tables from several sources that have a mix of
> smiles / InChI / sdf molecular representations.
>
>
>
> I usually use RDKit via Python and/or Knime.
>
>
>
> Cheers,
>
> Steve.
>
>
>
> 
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>
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Re: [Rdkit-discuss] comparing two or more tables of molecules

[Patrick Walters]

The Layered InChI (LyChi), developed by Trung Nguyen at NCATS was designed
to directly address the problem you describe.  I don't have any first hand
experience with this method (yet), but it looks intriguing.

https://github.com/ncats/lychi


Pat

On Mon, Nov 28, 2016 at 11:25 AM, Stephen O'hagan 
wrote:

> Has anyone come up with fool-proof way of matching structurally equivalent
> molecules?
>
>
>
> Unique Smiles or InChI String comparisons don’t appear to work presumable
> because there are different but equivalent structures, e.g. explicit vs
> non-explicit H’s, Kekule vs Aromatic, isomeric forms vs non-isomeric form,
> tautomers etc.
>
>
>
> I also expect that comparing InChI strings might need something more than
> just a simple string comparison, such as masking off stereo information
> when you don’t care about stereo isomers.
>
>
>
> I assume there are suitable tools within RDKit that can do this?
>
>
>
> N.B. I need to collate tables from several sources that have a mix of
> smiles / InChI / sdf molecular representations.
>
>
>
> I usually use RDKit via Python and/or Knime.
>
>
>
> Cheers,
>
> Steve.
>
>
>
> 
> --
>
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Re: [Rdkit-discuss] errors with windows10 RDKit installation using conda

[Greg Landrum]

Hi Mike,

Sorry this is so frustrating, but thanks for continuing to stick with it.
One quite unfortunate thing is going to happen when you do finally get the
RDKit itself building on windows: though that works (and is something we do
reasonably often), there are no build files for the cartridge under windows
(you can tell this from the lack of a bld.bat file here:
https://github.com/rdkit/conda-rdkit/tree/master/rdkit-postgresql). There's
a short thread about this here:
http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg05776.html

With respect to your problems with building the standard RDKit with conda:
that is something that we do reasonably frequently, but I guess most/all of
us do the build using a version of anaconda that is installed for the local
user (so that permissions are not a problem). This probably also has the
side effect of helping with some of the file path length problems.

I'm not in front of my windows machine right now, but when I get back to
it, I'll pull out exactly what I do in order to do a build and send it
along.

-greg




On Tue, Nov 29, 2016 at 2:11 PM, Mike Mazanetz <
mi...@novadatasolutions.co.uk> wrote:

> Hi,
>
>
>
> Thought I’d update my progress:
>
>
>
> Steps to fix issue:
>
> change Admin permissions for Anaconda3
>
> ran these commands:
>
> conda update conda
>
> conda update -n root conda-build
>
> conda install -c rdkit rdkit=2016.09.2
>
>
>
> as RDKit it was change in the last 24 hours J
>
>
>
> then found that this filename was too long, so just deleted it !
>
> C:\boost_1_59_0.zip\boost_1_59_0\libs\geometry\doc\html\
> geometry\reference\spatial_indexes\boost__geometry__
> index__rtree\rtree_parameters_type_const___.html
>
>
>
> That fixed that problem.
>
>
>
> then had to rename this file as it was named incorrectly in two places. –
> probably didn’t need this file anyway !
>
> Appendix A An Introduction to Preprocessor Metaprogramming.html
>
>
>
> got a little further down the road then encountered this:
>
> File not found - boost_*-mt-1_*.lib
>
> 0 File(s) copied
>
> File not found - boost_*-mt-1_*.dll
>
> 0 File(s) copied
>
> Command failed: cmd.exe /c bld.bat
>
>
>
> So battling these issues now…
>
>
>
> ./mike
>
>
>
> *From:* Mike Mazanetz [mailto:mi...@novadatasolutions.co.uk]
> *Sent:* 29 November 2016 12:33
> *To:* rdkit-discuss@lists.sourceforge.net
> *Subject:* Re: [Rdkit-discuss] errors with windows10 RDKit installation
> using conda
>
>
>
> Hello,
>
>
>
> Further to my little exploratoin, I managed to do a few things:
>
> conda update conda
>
> conda update -n root conda-build
>
>
>
> so I’ve got a little further, but I’ve run into a Windows nightmare – path
> files are too long…  I can see the file in the cache:  boost_1_59_0.zip,
> but the name is so long windows will not open it.
>
>
>
> Has anyone done a build in Windows10, can you please send me your build
> routine?
>
>
>
> Thanks,
>
> mike
>
>
>
>
>
> conda build boost
>
> BUILD START: boost-1.59.0-py35_3
>
> updating index in: C:\Program Files\Anaconda3\conda-bld\win-64
>
> updating index in: C:\Program Files\Anaconda3\conda-bld\noarch
>
>
>
> The following NEW packages will be INSTALLED:
>
>
>
> bzip2:  1.0.6-vc14_3  [vc14]
>
> pip:9.0.1-py35_0
>
> python: 3.5.2-0
>
> setuptools: 27.2.0-py35_1
>
> vs2015_runtime: 14.0.25123-0
>
> wheel:  0.29.0-py35_0
>
> zlib:   1.2.8-vc14_3  [vc14]
>
>
>
> Source cache directory is: C:\Program Files\Anaconda3\conda-bld\src_cache
>
> Found source in cache: boost_1_59_0.zip
>
> Extracting download
>
> Traceback (most recent call last):
>
>   File "C:\Program Files\Anaconda3\Scripts\conda-build-script.py", line
> 5, in 
>
> sys.exit(conda_build.cli.main_build.main())
>
>   File "C:\Program 
> Files\Anaconda3\lib\site-packages\conda_build\cli\main_build.py",
> line 244, in main
>
> execute(sys.argv[1:])
>
>   File "C:\Program 
> Files\Anaconda3\lib\site-packages\conda_build\cli\main_build.py",
> line 236, in execute
>
> already_built=None, config=config, noverify=args.no_verify)
>
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\api.py",
> line 75, in build
>
> need_source_download=need_source_download, config=config)
>
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\build.py",
> line 1227, in build_tree
>
> config=recipe_config)
>
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\build.py",
> line 790, in build
>
> config=config)
>
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\render.py",
> line 86, in parse_or_try_download
>
> source.provide(metadata.path, metadata.get_section('source'),
> config=config)
>
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\source.py",
> line 485, in provide
>
> unpack(meta, config=config)
>
>   File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\source.py",
> line 86, in unpack
>
> 

Re: [Rdkit-discuss] errors with windows10 RDKit installation using conda

[Mike Mazanetz]

Hi,

 

Thought I'd update my progress:

 

Steps to fix issue:

change Admin permissions for Anaconda3

ran these commands:

conda update conda

conda update -n root conda-build

conda install -c rdkit rdkit=2016.09.2  

 

as RDKit it was change in the last 24 hours :)

 

then found that this filename was too long, so just deleted it !

C:\boost_1_59_0.zip\boost_1_59_0\libs\geometry\doc\html\geometry\reference\s
patial_indexes\boost__geometry__index__rtree\rtree_parameters_type_const___*
***.html

 

That fixed that problem.

 

then had to rename this file as it was named incorrectly in two places. -
probably didn't need this file anyway !

Appendix A An Introduction to Preprocessor Metaprogramming.html

 

got a little further down the road then encountered this:

File not found - boost_*-mt-1_*.lib

0 File(s) copied

File not found - boost_*-mt-1_*.dll

0 File(s) copied

Command failed: cmd.exe /c bld.bat

 

So battling these issues now.

 

./mike

 

From: Mike Mazanetz [mailto:mi...@novadatasolutions.co.uk] 
Sent: 29 November 2016 12:33
To: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] errors with windows10 RDKit installation using
conda

 

Hello,

 

Further to my little exploratoin, I managed to do a few things:

conda update conda

conda update -n root conda-build

 

so I've got a little further, but I've run into a Windows nightmare - path
files are too long.  I can see the file in the cache:  boost_1_59_0.zip, but
the name is so long windows will not open it.  

 

Has anyone done a build in Windows10, can you please send me your build
routine?

 

Thanks,

mike

 

 

conda build boost

BUILD START: boost-1.59.0-py35_3

updating index in: C:\Program Files\Anaconda3\conda-bld\win-64

updating index in: C:\Program Files\Anaconda3\conda-bld\noarch

 

The following NEW packages will be INSTALLED:

 

bzip2:  1.0.6-vc14_3  [vc14]

pip:9.0.1-py35_0

python: 3.5.2-0

setuptools: 27.2.0-py35_1

vs2015_runtime: 14.0.25123-0

wheel:  0.29.0-py35_0

zlib:   1.2.8-vc14_3  [vc14]

 

Source cache directory is: C:\Program Files\Anaconda3\conda-bld\src_cache

Found source in cache: boost_1_59_0.zip

Extracting download

Traceback (most recent call last):

  File "C:\Program Files\Anaconda3\Scripts\conda-build-script.py", line 5,
in 

sys.exit(conda_build.cli.main_build.main())

  File "C:\Program
Files\Anaconda3\lib\site-packages\conda_build\cli\main_build.py", line 244,
in main

execute(sys.argv[1:])

  File "C:\Program
Files\Anaconda3\lib\site-packages\conda_build\cli\main_build.py", line 236,
in execute

already_built=None, config=config, noverify=args.no_verify)

  File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\api.py",
line 75, in build

need_source_download=need_source_download, config=config)

  File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\build.py",
line 1227, in build_tree

config=recipe_config)

  File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\build.py",
line 790, in build

config=config)

  File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\render.py",
line 86, in parse_or_try_download

source.provide(metadata.path, metadata.get_section('source'),
config=config)

  File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\source.py",
line 485, in provide

unpack(meta, config=config)

  File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\source.py",
line 86, in unpack

unzip(src_path, config.work_dir)

  File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\utils.py",
line 287, in unzip

with open(path, 'wb') as fo:

FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Program
Files\\Anaconda3\\conda-bld\\boost_1480420542489\\work\\boost_1_59_0\\libs\\
geometry\\doc\\html\\geometry\\reference\\spatial_indexes\\boost__geometry__
index__rtree\\rtree_parameters_type_constindexable_getter_constvalue
_equal_constallocator_type_const___.html'

 

 

From: Mike Mazanetz [mailto:mi...@novadatasolutions.co.uk] 
Sent: 29 November 2016 11:13
To: rdkit-discuss@lists.sourceforge.net
Subject: [Rdkit-discuss] errors with windows10 RDKit installation using
conda

 

Hello RDKit Forum,

 

I've been using RDkit to several years through KNIME and have found it
thoroughly useful.  I've taken the next step and decided to try the Postgres
Cartridge, but I've had issues building RDKit on Windows.

Has anyone encountered had success using Anaconda3 to build RDKit?  I get
this message - which I've not found sufficient answers for from the conda
github:

 

Directory of C:\NovaData\Software\RDKit\conda-rdkit-master

 

28/11/2016  20:48  .

28/11/2016  20:48  ..

28/11/2016  05:45 3 .gitignore

28/11/2016  05:45  boost

28/11/2016  05:45  cairocffi

28/11/2016  05:45  cairo_nox

28/11/2016  05:45 

Re: [Rdkit-discuss] errors with windows10 RDKit installation using conda

[Mike Mazanetz]

Hello,

 

Further to my little exploratoin, I managed to do a few things:

conda update conda

conda update -n root conda-build

 

so I've got a little further, but I've run into a Windows nightmare - path
files are too long.  I can see the file in the cache:  boost_1_59_0.zip, but
the name is so long windows will not open it.  

 

Has anyone done a build in Windows10, can you please send me your build
routine?

 

Thanks,

mike

 

 

conda build boost

BUILD START: boost-1.59.0-py35_3

updating index in: C:\Program Files\Anaconda3\conda-bld\win-64

updating index in: C:\Program Files\Anaconda3\conda-bld\noarch

 

The following NEW packages will be INSTALLED:

 

bzip2:  1.0.6-vc14_3  [vc14]

pip:9.0.1-py35_0

python: 3.5.2-0

setuptools: 27.2.0-py35_1

vs2015_runtime: 14.0.25123-0

wheel:  0.29.0-py35_0

zlib:   1.2.8-vc14_3  [vc14]

 

Source cache directory is: C:\Program Files\Anaconda3\conda-bld\src_cache

Found source in cache: boost_1_59_0.zip

Extracting download

Traceback (most recent call last):

  File "C:\Program Files\Anaconda3\Scripts\conda-build-script.py", line 5,
in 

sys.exit(conda_build.cli.main_build.main())

  File "C:\Program
Files\Anaconda3\lib\site-packages\conda_build\cli\main_build.py", line 244,
in main

execute(sys.argv[1:])

  File "C:\Program
Files\Anaconda3\lib\site-packages\conda_build\cli\main_build.py", line 236,
in execute

already_built=None, config=config, noverify=args.no_verify)

  File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\api.py",
line 75, in build

need_source_download=need_source_download, config=config)

  File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\build.py",
line 1227, in build_tree

config=recipe_config)

  File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\build.py",
line 790, in build

config=config)

  File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\render.py",
line 86, in parse_or_try_download

source.provide(metadata.path, metadata.get_section('source'),
config=config)

  File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\source.py",
line 485, in provide

unpack(meta, config=config)

  File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\source.py",
line 86, in unpack

unzip(src_path, config.work_dir)

  File "C:\Program Files\Anaconda3\lib\site-packages\conda_build\utils.py",
line 287, in unzip

with open(path, 'wb') as fo:

FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Program
Files\\Anaconda3\\conda-bld\\boost_1480420542489\\work\\boost_1_59_0\\libs\\
geometry\\doc\\html\\geometry\\reference\\spatial_indexes\\boost__geometry__
index__rtree\\rtree_parameters_type_constindexable_getter_constvalue
_equal_constallocator_type_const___.html'

 

 

From: Mike Mazanetz [mailto:mi...@novadatasolutions.co.uk] 
Sent: 29 November 2016 11:13
To: rdkit-discuss@lists.sourceforge.net
Subject: [Rdkit-discuss] errors with windows10 RDKit installation using
conda

 

Hello RDKit Forum,

 

I've been using RDkit to several years through KNIME and have found it
thoroughly useful.  I've taken the next step and decided to try the Postgres
Cartridge, but I've had issues building RDKit on Windows.

Has anyone encountered had success using Anaconda3 to build RDKit?  I get
this message - which I've not found sufficient answers for from the conda
github:

 

Directory of C:\NovaData\Software\RDKit\conda-rdkit-master

 

28/11/2016  20:48  .

28/11/2016  20:48  ..

28/11/2016  05:45 3 .gitignore

28/11/2016  05:45  boost

28/11/2016  05:45  cairocffi

28/11/2016  05:45  cairo_nox

28/11/2016  05:45  django-rdkit

28/11/2016  05:45 2,626 Dockerfile

28/11/2016  05:45  eigen

28/11/2016  05:45  ncurses

28/11/2016  05:45  nox

28/11/2016  05:45  pixman

28/11/2016  05:45  postgresql

28/11/2016  05:45  postgresql95

28/11/2016  05:45  rdkit

28/11/2016  05:45  rdkit-postgresql

28/11/2016  05:45  rdkit-postgresql95

28/11/2016  05:45 6,626 README.rst

   3 File(s)  9,255 bytes

  15 Dir(s)  360,784,285,696 bytes free

 

C:\NovaData\Software\RDKit\conda-rdkit-master>conda build boost

BUILD START: boost-1.59.0-py35_3

updating index in: C:\Users\NovaData\conda-bld\win-64

updating index in: C:\Users\NovaData\conda-bld\noarch

 

The following packages will be downloaded:

 

package|build

---|-

pip-9.0.1  |   py35_0 1.7 MB

 

The following NEW packages will be INSTALLED:

 

bzip2:  1.0.6-vc14_3  [vc14] (copy)

pip:9.0.1-py35_0

python: 3.5.2-0