Hello, I already have my environment variables ready :
==========================================================
jperaltac@baco:~/buildob$ env | grep babel
BABEL_DATADIR=/home/jperaltac/local/share/openbabel
BABEL_LIBDIR=/home/jperaltac/local/lib/openbabel/
LD_LIBARY_PATH=/home/jperaltac/local/share/openbabel:/usr/local/lib:/opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/intel64:/opt/intel/composer_xe_2011_sp1.10.319/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2011_sp1.10.319/ipp/lib/intel64:/opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/intel64:/opt/intel/composer_xe_2011_sp1.10.319/mkl/lib/intel64:/opt/intel/composer_xe_2011_sp1.10.319/tbb/lib/intel64//cc4.1.0_libc2.4_kernel2.6.16.21:/opt/intel/composer_xe_2011_sp1.10.319/debugger/lib/intel64:/opt/intel/composer_xe_2011_sp1.10.319/mpirt/lib/intel64
jperaltac@baco:~/buildob$ babel -V
Open Babel 2.3.2 -- Sep 14 2012 -- 17:07:39
jperaltac@baco:~/buildob$
===============================================================
They are in my bashrc file.
Yes, I'm trying to solve the segfault first, so I can try my plugin later.
An the output of the make test is :
================================================================
jperaltac@baco:~/buildob$ make test
Running tests...
Test project /home/jperaltac/buildob
Start 1: automorphism_Test
1/59 Test #1: automorphism_Test ................ Passed 2.98 sec
Start 2: builder_Test
2/59 Test #2: builder_Test ..................... Passed 22.01 sec
Start 3: canonconsistent_Test
3/59 Test #3: canonconsistent_Test ............. Passed 2.46 sec
Start 4: canonstable_Test
4/59 Test #4: canonstable_Test ................. Passed 96.57 sec
Start 5: cistrans_Test
5/59 Test #5: cistrans_Test .................... Passed 0.06 sec
Start 6: graphsym_Test
6/59 Test #6: graphsym_Test .................... Passed 0.48 sec
Start 7: implicitH_Test
7/59 Test #7: implicitH_Test ................... Passed 0.19 sec
Start 8: lssr_Test
8/59 Test #8: lssr_Test ........................ Passed 40.12 sec
Start 9: isomorphism_Test
9/59 Test #9: isomorphism_Test .................***Failed Error regular
expression found in output. Regex=[FAIL] 0.12 sec
Start 10: rotor_Test
10/59 Test #10: rotor_Test .......................***Failed Error regular
expression found in output. Regex=[FAIL] 0.05 sec
Start 11: shuffle_Test
11/59 Test #11: shuffle_Test ..................... Passed 12.61 sec
Start 12: smiles_Test
12/59 Test #12: smiles_Test ...................... Passed 0.19 sec
Start 13: spectrophore_Test
13/59 Test #13: spectrophore_Test ................ Passed 2.90 sec
Start 14: squareplanar_Test
14/59 Test #14: squareplanar_Test ................ Passed 0.01 sec
Start 15: stereo_Test
15/59 Test #15: stereo_Test ...................... Passed 2.47 sec
Start 16: stereoperception_Test
16/59 Test #16: stereoperception_Test ............ Passed 0.18 sec
Start 17: tautomer_Test
17/59 Test #17: tautomer_Test .................... Passed 0.20 sec
Start 18: tetrahedral_Test
18/59 Test #18: tetrahedral_Test ................. Passed 0.01 sec
Start 19: tetranonplanar_Test
19/59 Test #19: tetranonplanar_Test .............. Passed 0.01 sec
Start 20: tetraplanar_Test
20/59 Test #20: tetraplanar_Test ................. Passed 0.05 sec
Start 21: uniqueid_Test
21/59 Test #21: uniqueid_Test .................... Passed 0.01 sec
Start 22: inchiSamples.sdf_Test
22/59 Test #22: inchiSamples.sdf_Test ............ Passed 1.15 sec
Start 23: inchiSamplesTechMan.sdf_Test
23/59 Test #23: inchiSamplesTechMan.sdf_Test ..... Passed 0.27 sec
Start 24: inchiSteffen_PubChem.smi_Test
24/59 Test #24: inchiSteffen_PubChem.smi_Test .... Passed 0.30 sec
Start 25: aromatest_Test
25/59 Test #25: aromatest_Test ................... Passed 0.14 sec
Start 26: atom_Test
26/59 Test #26: atom_Test ........................ Passed 0.01 sec
Start 27: bond_Test
27/59 Test #27: bond_Test ........................ Passed 0.01 sec
Start 28: cansmi_Test
28/59 Test #28: cansmi_Test ...................... Passed 7.19 sec
Start 29: charge-mmff94_Test
29/59 Test #29: charge-mmff94_Test ............... Passed 0.98 sec
Start 30: charge-gasteiger_Test
30/59 Test #30: charge-gasteiger_Test ............ Passed 0.52 sec
Start 31: conversion_Test
31/59 Test #31: conversion_Test .................. Passed 0.04 sec
Start 32: datatest_Test
32/59 Test #32: datatest_Test .................... Passed 0.02 sec
Start 33: ffgaff_Test
33/59 Test #33: ffgaff_Test ...................... Passed 3.68 sec
Start 34: ffghemical_Test
34/59 Test #34: ffghemical_Test .................. Passed 3.87 sec
Start 35: ffmmff94_Test
35/59 Test #35: ffmmff94_Test .................... Passed 3.49 sec
Start 36: ffuff_Test
36/59 Test #36: ffuff_Test ....................... Passed 3.54 sec
Start 37: formalcharge_Test
37/59 Test #37: formalcharge_Test ................ Passed 0.76 sec
Start 38: format_Test
38/59 Test #38: format_Test ...................... Passed 0.03 sec
Start 39: formula_Test
39/59 Test #39: formula_Test ..................... Passed 1.39 sec
Start 40: internalcoord_Test
40/59 Test #40: internalcoord_Test ............... Passed 0.02 sec
Start 41: invalidsmarts_Test
41/59 Test #41: invalidsmarts_Test ............... Passed 0.05 sec
Start 42: invalidsmiles_Test
42/59 Test #42: invalidsmiles_Test ............... Passed 0.04 sec
Start 43: iterators_Test
43/59 Test #43: iterators_Test ................... Passed 0.80 sec
Start 44: logp_psa_Test
44/59 Test #44: logp_psa_Test .................... Passed 0.13 sec
Start 45: math_Test
45/59 Test #45: math_Test ........................ Passed 0.18 sec
Start 46: mol_Test
46/59 Test #46: mol_Test ......................... Passed 0.08 sec
Start 47: phmodel_Test
47/59 Test #47: phmodel_Test ..................... Passed 0.22 sec
Start 48: residue_Test
48/59 Test #48: residue_Test ..................... Passed 0.10 sec
Start 49: ringtest_Test
49/59 Test #49: ringtest_Test .................... Passed 0.77 sec
Start 50: smartstest_Test
50/59 Test #50: smartstest_Test .................. Passed 1.24 sec
Start 51: smartsparse_Test
51/59 Test #51: smartsparse_Test ................. Passed 0.05 sec
Start 52: smilesmatch_Test
52/59 Test #52: smilesmatch_Test ................. Passed 4.33 sec
Start 53: unitcell_Test
53/59 Test #53: unitcell_Test .................... Passed 0.03 sec
Start 54: pytest_babel
54/59 Test #54: pytest_babel ..................... Passed 0.45 sec
Start 55: pytest_sym
55/59 Test #55: pytest_sym .......................***Failed Error regular
expression found in output. Regex=[FAIL] 7.97 sec
Start 56: pytest_smartssym
56/59 Test #56: pytest_smartssym ................. Passed 1.84 sec
Start 57: pytest_fastsearch
57/59 Test #57: pytest_fastsearch ................ Passed 0.27 sec
Start 58: pytest_unique
58/59 Test #58: pytest_unique .................... Passed 0.76 sec
Start 59: pytest_kekule
59/59 Test #59: pytest_kekule .................... Passed 0.98 sec
95% tests passed, 3 tests failed out of 59
Total Test time (real) = 231.61 sec
The following tests FAILED:
9 - isomorphism_Test (Failed)
10 - rotor_Test (Failed)
55 - pytest_sym (Failed)
Errors while running CTest
make: *** [test] Error 8
jperaltac@baco:~/buildob$
================================================================
Any suggestion is welcome.
All the best
Joaquin
On Fri, Sep 14, 2012 at 6:53 PM, My Th <rei4...@gmail.com> wrote:
> Pk, 2012-09-14 18:08 -0500, joaquin peralta rakstīja:
> > Hello,
> >
> >
> > Before I put all the text, just allow me to explain :
> >
> >
> > I'm not compiling with my plugin, it is just a clean svn version. I
> > tried with make clean and make and the problem still, I just set all
> > environment variables and the problem still.
>
> You can set environment variables in alias:
> $ alias obpath='LD_LIBRARY_PATH=/path/to/build_dir/lib/
> BABEL_LIBDIR=/path/to/build_dir/lib/
> BABEL_DATADIR=/path/to/source_dir/data/'
>
> Then from your build dir:
> $ obpath bin/babel -V
> Open Babel 2.3.2 -- Sep 15 2012 -- 02:48:52
>
> You already have issue without your plugin. Solve that first, it should
> not segfault. What is result of 'make test'?
>
>
> Reinis
>
>
>
--
Joaquín Peralta C.
Postdoctoral Research Associate
Materials Science and Engineering
Iowa State University
3326 Hoover Hall
Ames, IA 50011
Phone Lab: 515-294-9547
http://www.lpmd.cl/jperalta
http://www.gnm.cl
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