Re: [Rdkit-discuss] Building RDKit from source under Ubuntu VM, ctest 87 tests failed out of 165. Any advice much appreciated.

2020-03-13 Thread Earl Higgins 
Paolo,

Thank you for your rapid reply. It's a great suggestion, we are getting 
somewhere. I ran the first Python test with the "-V" (verbose?) option and, as 
you can see from the output below, Python is having a problem finding the rdkit 
module. Do you have any suggestions on how to fix this? Thank you so much.

Earl Higgins

$ RDBASE=~/conda-rdkit/rdkit ctest -I 2,2 -V
UpdateCTestConfiguration  from 
:/home/deep/conda-rdkit/rdkit/build/DartConfiguration.tcl
Parse Config file:/home/deep/conda-rdkit/rdkit/build/DartConfiguration.tcl
Add coverage exclude regular expressions.
SetCTestConfiguration:CMakeCommand:/home/deep/anaconda3/bin/cmake
UpdateCTestConfiguration  from 
:/home/deep/conda-rdkit/rdkit/build/DartConfiguration.tcl
Parse Config file:/home/deep/conda-rdkit/rdkit/build/DartConfiguration.tcl
Test project /home/deep/conda-rdkit/rdkit/build
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 2
Start 2: pyCoordGen

2: Test command: /home/deep/anaconda3/bin/python 
"/home/deep/conda-rdkit/rdkit/External/CoordGen/Wrap/testCoordGen.py"
2: Test timeout computed to be: 1500
2: Traceback (most recent call last):
2:   File 
"/home/deep/conda-rdkit/rdkit/External/CoordGen/Wrap/testCoordGen.py", line 13, 
in 
2: from rdkit.Chem import rdCoordGen, rdMolAlign
2: ModuleNotFoundError: No module named 'rdkit'
1/1 Test #2: pyCoordGen ...***Failed0.07 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) =   0.09 sec

The following tests FAILED:
  2 - pyCoordGen (Failed)
Errors while running CTest

From: Paolo Tosco 

Dear Earl,

given that all Python tests are failing my guess is that you might be running 
the tests with a Python interpreter different from the one you have built RDKit 
against. Re-run one of the failing tests with -V

ctest -I 2,2 -V

to get some more information.

Cheers,
p.
On 13/03/2020 15:56, Earl Higgins wrote:

I am new to RDKit, and my goal is to be able to build it from source ... and 
I'm surprised at 87/165 test case failures right out of the box ... Any 
guidance anyone could offer in this area would be most appreciated. Thank you 
in advance...





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Re: [Rdkit-discuss] Building RDKit from source under Ubuntu VM, ctest 87 tests failed out of 165. Any advice much appreciated.

2020-03-13 Thread Paolo Tosco 

Dear Earl,

it looks like you might only need to add $RDBASE to your PYTHONPATH.

p.

On 13/03/2020 16:38, Earl Higgins wrote:


Paolo,

Thank you for your rapid reply. It's a great suggestion, we are 
getting somewhere. I ran the first Python test with the "-V" 
(verbose?) option and, as you can see from the output below, Python is 
having a problem finding the rdkit module. Do you have any suggestions 
on how to fix this? Thank you so much.


Earl Higgins

$ RDBASE=~/conda-rdkit/rdkit ctest -I 2,2 -V

UpdateCTestConfiguration  from 
:/home/deep/conda-rdkit/rdkit/build/DartConfiguration.tcl


Parse Config file:/home/deep/conda-rdkit/rdkit/build/DartConfiguration.tcl

Add coverage exclude regular expressions.

SetCTestConfiguration:CMakeCommand:/home/deep/anaconda3/bin/cmake

UpdateCTestConfiguration  from 
:/home/deep/conda-rdkit/rdkit/build/DartConfiguration.tcl


Parse Config file:/home/deep/conda-rdkit/rdkit/build/DartConfiguration.tcl

Test project /home/deep/conda-rdkit/rdkit/build

Constructing a list of tests

Done constructing a list of tests

Updating test list for fixtures

Added 0 tests to meet fixture requirements

Checking test dependency graph...

Checking test dependency graph end

test 2

    Start 2: pyCoordGen

2: Test command: /home/deep/anaconda3/bin/python 
"/home/deep/conda-rdkit/rdkit/External/CoordGen/Wrap/testCoordGen.py"


2: Test timeout computed to be: 1500

2: Traceback (most recent call last):

2:   File 
"/home/deep/conda-rdkit/rdkit/External/CoordGen/Wrap/testCoordGen.py", 
line 13, in 


2: from rdkit.Chem import rdCoordGen, rdMolAlign

2: ModuleNotFoundError: No module named 'rdkit'

1/1 Test #2: pyCoordGen ...***Failed    0.07 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) =   0.09 sec

The following tests FAILED:

      2 - pyCoordGen (Failed)

Errors while running CTest

*From:* Paolo Tosco 

Dear Earl,

given that all Python tests are failing my guess is that you might be 
running the tests with a Python interpreter different from the one you 
have built RDKit against. Re-run one of the failing tests with -V


ctest -I 2,2 -V

to get some more information.

Cheers,
p.

On 13/03/2020 15:56, Earl Higgins wrote:

I am new to RDKit, and my goal is to be able to build it from source … 
and I'm surprised at 87/165 test case failures right out of the box … 
Any guidance anyone could offer in this area would be most 
appreciated. Thank you in advance…


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recipient, you must not copy this message or attachment or disclose 
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transmission in error, please notify the sender immediately and delete 
the message and any attachment from your system. Merck KGaA, 
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for any omissions or errors in this message which may arise as a 
result of E-Mail-transmission or for damages resulting from any 
unauthorized changes of the content of this message and any attachment 
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Re: [Rdkit-discuss] Building RDKit from source under Ubuntu VM, ctest 87 tests failed out of 165. Any advice much appreciated.

2020-03-13 Thread Paolo Tosco 

Dear Earl,

given that all Python tests are failing my guess is that you might be 
running the tests with a Python interpreter different from the one you 
have built RDKit against. Re-run one of the failing tests with -V


ctest -I 2,2 -V

to get some more information.

Cheers,
p.

On 13/03/2020 15:56, Earl Higgins wrote:


I am new to RDKit, and my goal is to be able to build it from source 
under Ubuntu 18.04.4 LTS running in a VM using Oracle VirtualBox (host 
Windows 10). I need to be able to build from source because, as a 
developer, I am on a team which is looking at making some enhancements 
to the MOL file load support, possibly adding support for Opensmiles 
as a distinct dialect of SMILES.


So, following the Linux/Python 3 instructions at 
https://www.rdkit.org/docs/Install.html#how-to-build-from-source-with-conda 
, I am able to download and install everything fine until I get to the 
step to run ctest. I get:


$ ctest

CMake Error at /home/deep/conda-rdkit/rdkit/build/CTestCustom.ctest:3 
(MESSAGE):


  Please set your RDBASE env variable before running the tests.

Problem reading custom configuration: 
/home/deep/conda-rdkit/rdkit/build/CTestCustom.ctest


Test project /home/deep/conda-rdkit/rdkit/build

No tests were found!!!

$

So I run:

$ RDBASE=~/conda-rdkit/rdkit ctest

When I do that, I get:

$ RDBASE=~/conda-rdkit/rdkit ctest

Test project /home/deep/conda-rdkit/rdkit/build

    Start   1: testCoordGen

  1/165 Test   #1: testCoordGen ...   
Passed    0.37 sec


    Start   2: pyCoordGen

  2/165 Test   #2: pyCoordGen 
.***Failed    0.05 sec


    Start   3: testDict

  3/165 Test   #3: testDict ...   
Passed    0.63 sec


    Start   4: testRDValue

  4/165 Test   #4: testRDValue    
Passed    0.00 sec


    Start   5: testDataStructs

  5/165 Test   #5: testDataStructs    
Passed    0.01 sec


    Start   6: testFPB

  6/165 Test   #6: testFPB    
Passed    0.01 sec


    Start   7: testMultiFPB

  7/165 Test   #7: testMultiFPB ...   
Passed    0.04 sec


    Start   8: pyBV

  8/165 Test   #8: pyBV 
...***Failed    0.05 sec


    Start   9: pyDiscreteValueVect

  9/165 Test   #9: pyDiscreteValueVect 
***Failed    0.09 sec


    Start  10: pySparseIntVect

10/165 Test  #10: pySparseIntVect ***Failed    
0.06 sec


    Start  11: pyFPB

11/165 Test  #11: pyFPB ..***Failed    
0.05 sec


    Start  12: testTransforms

12/165 Test  #12: testTransforms .   Passed    
0.01 sec


    Start  13: testGrid

13/165 Test  #13: testGrid ...   Passed    
0.04 sec


    Start  14: geometryTestsCatch

(Lines omitted)

161/165 Test #161: pythonTestDirDbase 
.***Failed    0.03 sec


    Start 162: pythonTestDirSimDivFilters

162/165 Test #162: pythonTestDirSimDivFilters 
.***Failed    0.04 sec


    Start 163: pythonTestDirVLib

163/165 Test #163: pythonTestDirVLib 
..***Failed    0.04 sec


    Start 164: pythonTestDirChem

164/165 Test #164: pythonTestDirChem 
..***Failed    0.06 sec


    Start 165: pythonTestSping

165/165 Test #165: pythonTestSping 
***Failed    0.03 sec


47% tests passed, 87 tests failed out of 165

Total Test time (real) =  48.62 sec

The following tests FAILED:

      2 - pyCoordGen (Failed)

      8 - pyBV (Failed)

      9 - pyDiscreteValueVect (Failed)

    10 - pySparseIntVect (Failed)

    11 - pyFPB (Failed)

    15 - testPyGeometry (Failed)

    19 - pyAlignment (Failed)

    22 - testMMFFForceField (Child aborted)

    23 - pyForceFieldConstraints (Failed)

    25 - pyDistGeom (Failed)

    28 - graphmolqueryTest (Child aborted)

    29 - graphmolMolOpsTest (Child aborted)

    31 - graphmoltestPickler (Child aborted)

    34 - hanoiTest (Child aborted)

(Lines omitted)

    157 - pyFeatures (Failed)

    158 - pythonTestDbCLI (Failed)

    159 - pythonTestDirML (Failed)

    160 - pythonTestDirDataStructs (Failed)

    161 - pythonTestDirDbase (Failed)

    162 - pythonTestDirSimDivFilters (Failed)

    163 - pythonTestDirVLib (Failed)

    164 - pythonTestDirChem (Failed)

    165 - pythonTestSping (Failed)

Errors while running CTest

$

My impression is RDKit is quite robust, well tested and portable and 
I'm surprised at 87/165 test case failures right out of the box. I'm 
very

Re: [Rdkit-discuss] Building RDKit from source

2017-10-03 Thread Tyler Backman 
This might also be of interest, I have a Dockerfile here which builds
RDKit, including the postgresql cartridge:
https://github.com/JBEI/clusterCAD/blob/master/debian-cheminformatics/Dockerfile

Sincerely,
Tyler Backman

On Tue, Oct 3, 2017 at 2:45 AM, Greg Landrum  wrote:
> Thanks for sharing that Kovas.
> I'm sure this will be helpful for people who don't want to/can't use
> anaconda.
>
> Best,
> -greg
>
>
> On Mon, Oct 2, 2017 at 7:34 PM, Kovas Palunas 
> wrote:
>>
>> Hi all,
>>
>>
>> I thought I'd share a script I wrote to build RDKit and Boost together
>> which has worked for me on Linux (CentOS) and Mac machines so far.  I run
>> RDKit in a virtualenv Python environment (not in anaconda), so this may only
>> be helpful for a small group of RDKitters.  Hopefully some of you do find
>> this useful - it has personally saved me a lot of time getting RDKit
>> installed on multiple machines.
>>
>>
>> Note: please skim through the script to make sure you know what variables
>> inside it are set to what before running - there are multiple ways to
>> specify what code to build that may be useful for different purposes (and
>> some are commented out).
>>
>>
>> Make sure you pip install numpy before running (I should probably just add
>> this to the script).
>>
>>
>> Also, I have only tested this on RDKit 2016_09_3 and Boost 1_63_0.
>>
>>
>>  - Kovas
>>
>>
>>
>>
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Rdkit-discuss mailing list
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>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
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>



-- 
Tyler W. H. Backman
Postdoctoral Fellow
Lawrence Berkeley National Laboratory
Joint BioEnergy Institute
Agile BioFoundry

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Re: [Rdkit-discuss] Building RDKit from source

2017-10-03 Thread Greg Landrum 
Thanks for sharing that Kovas.
I'm sure this will be helpful for people who don't want to/can't use
anaconda.

Best,
-greg


On Mon, Oct 2, 2017 at 7:34 PM, Kovas Palunas 
wrote:

> Hi all,
>
>
> I thought I'd share a script I wrote to build RDKit and Boost together
> which has worked for me on Linux (CentOS) and Mac machines so far.  I run
> RDKit in a virtualenv Python environment (not in anaconda), so this may
> only be helpful for a small group of RDKitters.  Hopefully some of you
> do find this useful - it has personally saved me a lot of time getting
> RDKit installed on multiple machines.
>
>
> Note: please skim through the script to make sure you know what variables
> inside it are set to what before running - there are multiple ways to
> specify what code to build that may be useful for different purposes (and
> some are commented out).
>
>
> Make sure you pip install numpy before running (I should probably just add
> this to the script).
>
>
> Also, I have only tested this on RDKit 2016_09_3 and Boost 1_63_0.
>
>
>  - Kovas
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
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> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
--
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