Re: [Rdkit-discuss] install error

[Yingfeng W. <ywa...@gm...>]

Jan,

Thanks. I just found the problem. The environment setting is in .bashrc,
which is not for sudo.

Now, I install everything in a local directory, and don't need sudo. Then
it works now.

Sorry about my confusing mistake.

Yingfeng


On Wed, Jun 5, 2013 at 11:22 AM, Jan Holst Jensen <ja...@bi...>wrote:

>  OK, that looks fine. And I assume you build directly in
> /opt/RDKit_latest/latest/, so 'make install' puts files in
> /opt/RDKit_latest/latest/lib/.
>
> The only other thing that comes to my mind is if your boost libraries are
> included in LD_LIBRARY_PATH.
>
> Cheers
> -- Jan
>
>
> On 2013-06-05 16:55, Yingfeng Wang wrote:
>
> Yes, I did.
>
>  export RDBASE=/opt/RDKit_latest/latest
> export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH
> export PYTHONPATH=$RDBASE:$PYTHONPATH
>
>  I put them on ~/.bashrc
>
>
> On Wed, Jun 5, 2013 at 10:53 AM, Jan Holst Jensen <ja...@bi...>wrote:
>
>>  Hi Yingfeng,
>>
>> Looks like what happened to me, when I had forgotten to set the
>> environment. Did you set LD_LIBRARY_PATH to $RDBASE/lib before running the
>> tests ?
>>
>> Kind regards
>> -- Jan Holst Jensen
>>
>>
>> On 2013-06-05 16:09, Yingfeng Wang wrote:
>>
>> Yes. I tried again. This time,
>>
>>  after run download-inchi.sh
>>
>>  I
>>  mkdir build
>> cd build
>> sudo cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON
>> sudo make
>> sudo make install
>>
>>  by far, no error reported.
>>
>>  but, when I run sudo ctest
>>
>>  I got
>>
>>  The following tests FAILED:
>>   1 - testInchi (OTHER_FAULT)
>>   3 - testDataStructs (OTHER_FAULT)
>>   4 - pyBV (Failed)
>>   5 - pyDiscreteValueVect (Failed)
>>   6 - pySparseIntVect (Failed)
>>   8 - testGrid (OTHER_FAULT)
>>   9 - testPyGeometry (Failed)
>>  12 - pyAlignment (Failed)
>>  16 - pyDistGeom (Failed)
>>  20 - graphmolMolOpsTest (SEGFAULT)
>>  22 - graphmoltestChirality (OTHER_FAULT)
>>  23 - graphmoltestPickler (OTHER_FAULT)
>>  25 - testDepictor (OTHER_FAULT)
>>  26 - pyDepictor (Failed)
>>  29 - fileParsersTest1 (OTHER_FAULT)
>>  30 - testMolSupplier (OTHER_FAULT)
>>  31 - testMolWriter (OTHER_FAULT)
>>  32 - testTplParser (OTHER_FAULT)
>>  33 - testMol2ToMol (OTHER_FAULT)
>>  35 - testReaction (OTHER_FAULT)
>>  36 - pyChemReactions (Failed)
>>  37 - testChemTransforms (OTHER_FAULT)
>>  40 - testFragCatalog (OTHER_FAULT)
>>  41 - pyFragCatalog (Failed)
>>  42 - testDescriptors (OTHER_FAULT)
>>  43 - pyMolDescriptors (Failed)
>>  44 - testFingerprints (OTHER_FAULT)
>>  45 - pyPartialCharges (Failed)
>>  46 - testMolTransforms (OTHER_FAULT)
>>  47 - pyMolTransforms (Failed)
>>  48 - testForceFieldHelpers (OTHER_FAULT)
>>  49 - pyForceFieldHelpers (Failed)
>>  50 - testDistGeomHelpers (OTHER_FAULT)
>>  51 - pyDistGeom (Failed)
>>  52 - testMolAlign (OTHER_FAULT)
>>  53 - pyMolAlign (Failed)
>>  54 - testFeatures (OTHER_FAULT)
>>  55 - pyChemicalFeatures (Failed)
>>  56 - testShapeHelpers (OTHER_FAULT)
>>  57 - pyShapeHelpers (Failed)
>>  59 - pyMolCatalog (Failed)
>>  61 - pySLNParse (Failed)
>>  62 - pyGraphMolWrap (Failed)
>>  63 - pyTestConformerWrap (Failed)
>>  66 - pyMatCalc (Failed)
>>  67 - pyCMIM (Failed)
>>  68 - pyRanker (Failed)
>>  70 - pyFeatures (Failed)
>>  71 - pythonTestDbCLI (Failed)
>>  72 - pythonTestDirML (Failed)
>>  77 - pythonTestDirChem (Failed)
>> Errors while running CTest
>>
>>  Thanks.
>>
>>
>>
>> On Wed, Jun 5, 2013 at 5:54 AM, JP <jea...@in...> wrote:
>>
>>> mmmm,
>>>
>>>  Before running cmake - have you
>>> run ./External/INCHI-API/download-inchi.sh ?
>>>
>>>
>>>
>>>
>>>   On 5 June 2013 04:13, Yingfeng Wang <ywa...@gm...> wrote:
>>>
>>>>  After getting the latest code by git, I install RDKit on my ubuntu
>>>> 12.04.
>>>>
>>>>  In the step of make install, I got
>>>>
>>>>  CMake Error at External/INCHI-API/cmake_install.cmake:124 (FILE):
>>>>
>>>>  It seems the file $RDBASE/lib/libRDInchiLib.so.1.2013.06.1pre can't
>>>> be found. Please note that I have turned on the flag of inchi.
>>>>
>>>>  Thanks.
>>>>
>>>>  Yingfeng
>>>>
>>>>
>>
>
>