Ok, continuing to try debug my own silly problems… I forgot about RDBASE,
PYTHONPATH, etc...
When I run the tests with:
PYTHONPATH=/home/sly/projects/rdkit/ RDBASE=/home/sly/projects/rdkit/
LD_LIBRARY_PATH=/home/sly/projects/rdkit/lib ctest
I get 64% of the tests passing. An improvement, but still not 100%. Is this to
be expected?
thanks,
Cyrus
> On Apr 3, 2015, at 3:51 PM, Cyrus Harmon <cy...@bobobeach.com> wrote:
>
> Hi Greg,
>
> Thanks for looking into this. Some time has gone by and I’m not sure if the
> changes you were referring to have been checked in yet, but I’m back to
> trying to get things running on both macos and linux.
>
> Unfortunately, things seem to be getting worse. While everything seems to
> build OK, when I run “make test” on macos, I get only 46% of tests passing.
> About half of the failures are seg faults, the other half are failures. Is
> this to be expected? On my linux box, it’s actually even worse, 38% of tests
> passing.
>
> I’m happy to send the list of failing tests, but I figured I’m probably doing
> something wrong and that I should get the basics working first before I try
> to figure out which specific tests are failing (much less solve my SVG
> problem). It’s quite possible that the twisty maze of multiple versions of
> python (not to mention python libraries), boost, etc… are rearing the ugly
> head and I’m not quite sure where to begin trying to fix things. Suggestions?
>
> thanks,
>
> Cyrus
>
>> On Mar 9, 2015, at 10:37 PM, Greg Landrum <greg.land...@gmail.com
>> <mailto:greg.land...@gmail.com>> wrote:
>>
>> Hi Cyrus,
>>
>> That's something we missed when we did the Python3 port of the RDKit.
>> It turns out that there are a few of these problems in the rdkit.sping
>> package that need to be brought up to date.
>>
>> I will get those fixed and checked in the next day or so.
>>
>> Thanks for reporting the problem,
>> -greg
>>
>>
>> On Tue, Mar 10, 2015 at 2:37 AM, Cyrus Harmon <cy...@bobobeach.com
>> <mailto:cy...@bobobeach.com>> wrote:
>> I’m trying to get a python program that uses rdkit running on macos and I
>> keep getting the following error:
>>
>> File "./rdkit-2d-draw.py", line 31, in <module>
>> Draw.MolToFile(mol,args.output,size=(500,500))
>> File "/usr/local/lib/python3.4/site-packages/rdkit/Chem/Draw/__init__.py",
>> line 167, in MolToFile
>> canvas = Canvas(size=size,name=fileName,imageType=imageType)
>> File
>> "/usr/local/lib/python3.4/site-packages/rdkit/Chem/Draw/spingCanvas.py",
>> line 33, in __init__
>> from rdkit.sping.SVG.pidSVG import SVGCanvas as _Canvas
>> File "/usr/local/lib/python3.4/site-packages/rdkit/sping/SVG/__init__.py",
>> line 3, in <module>
>> from pidSVG import *
>> ImportError: No module named 'pidSVG'
>>
>> It works for me on my unix box that uses the debian packaged rdkit, but
>> fails for me on MacOS. Surely I’m doing something wrong in configuring my
>> various python libraries, but I’m at a loss as to how to fix this.
>>
>> Any suggestions on how to make my program find the pidSVG stuff?
>>
>> thanks,
>>
>> Cyrus
>>
>>
>> ------------------------------------------------------------------------------
>> Dive into the World of Parallel Programming The Go Parallel Website,
>> sponsored
>> by Intel and developed in partnership with Slashdot Media, is your hub for
>> all
>> things parallel software development, from weekly thought leadership blogs to
>> news, videos, case studies, tutorials and more. Take a look and join the
>> conversation now. http://goparallel.sourceforge.net/
>> <http://goparallel.sourceforge.net/>
>> _______________________________________________
>> Rdkit-devel mailing list
>> Rdkit-devel@lists.sourceforge.net <mailto:Rdkit-devel@lists.sourceforge.net>
>> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>> <https://lists.sourceforge.net/lists/listinfo/rdkit-devel>
>>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website, sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for all
> things parallel software development, from weekly thought leadership blogs to
> news, videos, case studies, tutorials and more. Take a look and join the
> conversation now.
> http://goparallel.sourceforge.net/_______________________________________________
> Rdkit-devel mailing list
> Rdkit-devel@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Rdkit-devel mailing list
Rdkit-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-devel
