After running a new installation, a lot more tests have now passed but some
python features are still failing
91% tests passed, 7 tests failed out of 76
Total Test time (real) = 171.73 sec
The following tests FAILED:
3 - pyBV (Failed)
8 - testPyGeometry (Failed)
35 - pyChemReactions (Failed)
42 - pyMolDescriptors (Failed)
61 - pyGraphMolWrap (SEGFAULT)
69 - pyFeatures (Failed)
76 - pythonTestDirChem (Failed)
Errors while running CTest
________________________________
From: Greg Landrum <[email protected]>
To: stanley5101 <[email protected]>
Cc: "[email protected]" <[email protected]>
Sent: Friday, 31 August 2012, 18:22
Subject: Re: [Rdkit-discuss] rdkit on ubuntu 10.04 LTS 32 bit
The failing tests are all python-related
This is usually a sign that either your PYTHONPATH or LD_LIBRARY_PATH
are not set properly.
please carry out the steps at the end of my message here:
http://www.mail-archive.com/[email protected]/msg02606.html
and send the output
-greg
On Fri, Aug 31, 2012 at 7:09 PM, stanley5101 <[email protected]> wrote:
> duh, sorry - hadn't seen that. The installation now runs to completion with
> the newer version of flex but I get a high failure rate on running the test
>
> 3 - pvBV
> 4 - pyDiscreteValueVect
> 5 - pySparseIntVect
> 8 - testPyGeometry
> 11 - pyAlignment
> 25 - pyDepictor
> 35 - pyChemReactions
> 40 - pyFragCatalog
> 42 - pyMolDescriptors
>
>
> all failed and the list goes on to 76, pythonTestDirChem.
>
> ________________________________
> From: greg landrum <[email protected]>
> To: stanley5101 <[email protected]>
> Cc: "[email protected]"
> <[email protected]>
> Sent: Friday, 31 August 2012, 17:39
> Subject: Re: [Rdkit-discuss] rdkit on ubuntu 10.04 LTS 32 bit
>
> Hi Alan,
>
>
> On Aug 31, 2012, at 5:58 PM, stanley5101 <[email protected]> wrote:
>
> Hi,
> I'm now trying to build Rdkit (RDKit_2012_06_1) on a linux machine and
> things were going well until....
>
> [38%] [FLEX][SmartsL] Building scanner with flex /usr/bin/flex version 2.5.4
> "smarts.ll", line 1: unrecognised %option: reentrant
> "smarts.ll", line 2: unrecognised %option: bison-bridge
> make[2]: *** [../Code/GraphMol/SmilesParse/lex.yysmarts.cpp] Error 1
> make[1]: *** [Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all]
> Error 2
> make: *** [all] Error 2
>
>
> You need a more recent version of flex. This is definitely available for
> Ubuntu 10.04 (that was my standard Linux build machine up until recently). I
> don't remember if it's available pre-built or not, but there are some
> details here: http://code.google.com/p/rdkit/wiki/BuildingWithCmake
>
> -Greg
>
>
> It seems to be finding flex and if I type bison --help on the command line,
> stuff happens and options come up so I'm guessing this is OK. Both these
> were installed via the Synaptic package manager. I'd welcome any
> suggestions about solving this.
> thanks
> Alan
>
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