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 <module> > > 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_const____indexable_getter_const____ > value_equal_const____allocator_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 <DIR> . > > 28/11/2016 20:48 <DIR> .. > > 28/11/2016 05:45 3 .gitignore > > 28/11/2016 05:45 <DIR> boost > > 28/11/2016 05:45 <DIR> cairocffi > > 28/11/2016 05:45 <DIR> cairo_nox > > 28/11/2016 05:45 <DIR> django-rdkit > > 28/11/2016 05:45 2,626 Dockerfile > > 28/11/2016 05:45 <DIR> eigen > > 28/11/2016 05:45 <DIR> ncurses > > 28/11/2016 05:45 <DIR> nox > > 28/11/2016 05:45 <DIR> pixman > > 28/11/2016 05:45 <DIR> postgresql > > 28/11/2016 05:45 <DIR> postgresql95 > > 28/11/2016 05:45 <DIR> rdkit > > 28/11/2016 05:45 <DIR> rdkit-postgresql > > 28/11/2016 05:45 <DIR> 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 <module> > > 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 Files\Anaconda3\lib\os.py", line 241, in makedirs > > mkdir(name, mode) > > PermissionError: [WinError 5] Access is denied: 'C:\\Program > Files\\Anaconda3\\pkgs\\vs2015_runtime-14.0.25123-0.tmp' > > > > > > I’m using Anaconda3 on Windows 10. > > Thanks for your help ! > > ./mike > > > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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