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Conda Docker build fails #50

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markussitzmann opened this issue May 14, 2017 · 2 comments
Open

Conda Docker build fails #50

markussitzmann opened this issue May 14, 2017 · 2 comments

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@markussitzmann
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Hi,

If I checkout and either use master or develop, the Docker build ("docker build .") breaks (Docker runs on Fedora):

[...]
[100%] Built target rdMolDescriptors
[100%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so
[100%] Built target rdChemReactions
[100%] Linking CXX executable testReaction
[100%] Built target testReaction
++ uname

Ran 4 tests in 0.031s

OK
......

Ran 6 tests in 0.031s

OK
....[16:07:34]

Pre-condition Violation
valence not defined for atoms not associated with molecules
Violation occurred on line 267 in file /home/rdkit/bld/rdkit_1494777495800/work/Code/GraphMol/Atom.cpp
Failed Expression: dp_mol

.

Ran 5 tests in 0.007s

OK
....

Ran 4 tests in 0.006s

OK
..

Ran 2 tests in 0.007s

OK
......................

Ran 22 tests in 0.025s

OK
.....s.................ss

Ran 25 tests in 0.102s

OK (skipped=3)
..s

Ran 3 tests in 0.125s

OK (skipped=1)
...................................

Ran 35 tests in 1.056s

OK
....

Ran 4 tests in 0.013s

OK
.

Ran 1 test in 0.007s

OK
......

Ran 6 tests in 0.025s

OK
...

Ran 3 tests in 0.045s

OK
.ss.ss.......

Ran 13 tests in 0.786s

OK (skipped=4)
...[16:07:38] WARNING: More than one matching pattern found - picking one
[16:07:38] WARNING: More than one matching pattern found - picking one
.[16:07:38] WARNING: More than one matching pattern found - picking one
..

Ran 6 tests in 0.061s

OK
........

Ran 8 tests in 0.084s

OK
.....

Ran 5 tests in 3.380s

OK
[16:07:42] WARNING: Omitted undefined stereo
[16:07:42] WARNING: Proton(s) added/removed
.....

Ran 5 tests in 8.343s

OK

InChI write Summary: 1164 identical, 0 suffix variance, 17 reasonable

InChI read Summary: 620 identical, 0 variance, 561 reasonable variance
....

Ran 4 tests in 2.088s

OK
......

Ran 6 tests in 0.286s

OK
Traceback (most recent call last):
File "UnitTestPandasTools.py", line 12, in
from rdkit.Chem import PandasTools
File "/home/rdkit/bld/rdkit_1494777495800/work/rdkit/Chem/PandasTools.py", line 154, in
from pandas.core import format as fmt # older versions
ImportError: cannot import name format
..

Ran 2 tests in 0.000s

OK
UnitTestDocTestsChem.py:5: DeprecationWarning: The rdkit.Chem.MCS module is deprecated; please use rdkit.Chem.rdFMCS instead.
from rdkit.Chem import MCS, FragmentMatcher, MACCSkeys, Descriptors, TemplateAlign
/home/rdkit/bld/rdkit_1494777495800/work/rdkit/Chem/MCS.py:1: DeprecationWarning: The rdkit.Chem.MCS module is deprecated; please use rdkit.Chem.rdFMCS instead.

This work was funded by Roche and generously donated to the free

.............[16:07:55] WARNING: More than one matching pattern found - picking one
[16:07:55] WARNING: More than one matching pattern found - picking one
........

Ran 21 tests in 0.731s

OK
..

Ran 2 tests in 0.061s

OK
..................

Ran 18 tests in 0.837s

OK
...

Ran 3 tests in 0.073s

OK
........

Ran 8 tests in 0.019s

OK
..

Ran 2 tests in 0.014s

OK
..

Ran 2 tests in 0.011s

OK
.

Ran 1 test in 0.056s

OK
........

Ran 8 tests in 0.001s

OK
...

Ran 3 tests in 0.004s

OK
...

Ran 3 tests in 0.001s

OK
....

Ran 4 tests in 0.003s

OK
......

Ran 6 tests in 0.009s

OK
....

Ran 4 tests in 0.012s

OK
....

Ran 4 tests in 2.571s

OK
..........

Ran 10 tests in 0.037s

OK
.

Ran 1 test in 0.000s

OK
..........

Ran 10 tests in 0.004s

OK
.....

Ran 5 tests in 0.051s

OK
.....................

Ran 21 tests in 3.186s

OK
.

Ran 1 test in 0.000s

OK
...[16:08:05]

Pre-condition Violation
molecule has no conformers
Violation occurred on line 37 in file /home/rdkit/bld/rdkit_1494777495800/work/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp
Failed Expression: dp_mol->getNumConformers()

.

Ran 4 tests in 0.018s

OK
..

Ran 2 tests in 6.986s

OK
..

Ran 2 tests in 0.075s

OK
...

Ran 3 tests in 0.008s

OK
....

Ran 4 tests in 0.015s

OK
..........

Ran 10 tests in 0.278s

OK
ssssss...s.....

Ran 15 tests in 0.159s

OK (skipped=7)
s

Ran 1 test in 0.000s

OK (skipped=1)
..........

Ran 10 tests in 0.425s

OK
..[16:08:14] reaction has no reactants
[16:08:14] reaction has no products
[16:08:14] initialization failed
[16:08:14] reaction has no reactants
[16:08:14] reaction has no products
.

Ran 3 tests in 0.020s

OK
................[16:08:14] ERROR:
[16:08:14] ERROR:
.

Ran 17 tests in 0.026s

OK
!!! TEST FAILURE: python UnitTestPandasTools.py {}
Exception TypeError: "'NoneType' object is not callable" in <function _removeHandlerRef at 0x7f4b48a6b668> ignored

99% tests passed, 1 tests failed out of 118

Total Test time (real) = 115.91 sec

The following tests FAILED:
118 - pythonTestDirChem (Failed)
BUILD START: rdkit-conda_version-np111py27_1
(actual version deferred until further download or env creation)

The following NEW packages will be INSTALLED:

boost:           1.56.0-py27_3      local
bzip2:           1.0.6-3                 
cairo:           1.14.6-nox_0       local [nox]
cmake:           3.6.3-0                 
curl:            7.52.1-0                
eigen:           3.2.8-2            local
expat:           2.1.0-0                 
fontconfig:      2.11.1-6                
freetype:        2.5.5-2                 
jbig:            2.1-0                   
jpeg:            9b-0                    
libiconv:        1.14-0                  
libpng:          1.6.27-0                
libtiff:         4.0.6-3                 
libxml2:         2.9.4-0                 
mkl:             2017.0.1-0              
ncurses:         5.9-10                  
nox:             1.0-0              local
numpy:           1.11.3-py27_0           
olefile:         0.44-py27_0             
openssl:         1.0.2k-2                
pandas:          0.20.1-np111py27_0      
pillow:          4.1.1-py27_0            
pip:             9.0.1-py27_1            
pixman:          0.32.6-0                
pkg-config:      0.28-1                  
python:          2.7.13-0                
python-dateutil: 2.6.0-py27_0            
pytz:            2017.2-py27_0           
readline:        6.2-2                   
requests:        2.14.2-py27_0           
setuptools:      27.2.0-py27_0           
six:             1.10.0-py27_0           
sqlite:          3.13.0-0                
tk:              8.5.18-0                
wheel:           0.29.0-py27_0           
xz:              5.2.2-1                 
zlib:            1.2.8-3

Applying patch: u'/home/rdkit/conda-rdkit/rdkit/rdpaths.patch'
Patch level ambiguous, selecting least deep
BUILD START (revised): rdkit-conda_version-np111py27_1
Package: rdkit-conda_version-np111py27_1
source tree in: /home/rdkit/bld/rdkit_1494777495800/work
Traceback (most recent call last):
File "/home/rdkit/miniconda/bin/conda-build", line 6, in
sys.exit(conda_build.cli.main_build.main())
File "/home/rdkit/miniconda/lib/python2.7/site-packages/conda_build/cli/main_build.py", line 334, in main
execute(sys.argv[1:])
File "/home/rdkit/miniconda/lib/python2.7/site-packages/conda_build/cli/main_build.py", line 325, in execute
noverify=args.no_verify)
File "/home/rdkit/miniconda/lib/python2.7/site-packages/conda_build/api.py", line 97, in build
need_source_download=need_source_download, config=config)
File "/home/rdkit/miniconda/lib/python2.7/site-packages/conda_build/build.py", line 1518, in build_tree
config=config)
File "/home/rdkit/miniconda/lib/python2.7/site-packages/conda_build/build.py", line 1143, in build
utils.check_call_env(cmd, env=env, cwd=src_dir)
File "/home/rdkit/miniconda/lib/python2.7/site-packages/conda_build/utils.py", line 628, in check_call_env
return _func_defaulting_env_to_os_environ(subprocess.check_call, *popenargs, **kwargs)
File "/home/rdkit/miniconda/lib/python2.7/site-packages/conda_build/utils.py", line 624, in _func_defaulting_env_to_os_environ
return func(_args, **kwargs)
File "/home/rdkit/miniconda/lib/python2.7/subprocess.py", line 186, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/bin/bash', '-x', '-e', '/home/rdkit/bld/rdkit_1494777495800/work/conda_build.sh']' returned non-zero exit status 8
The command '/bin/sh -c conda build boost --quiet --no-anaconda-upload && conda build nox --quiet --no-anaconda-upload && conda build cairo_nox --quiet --no-anaconda-upload && conda build cairocffi --quiet --no-anaconda-upload && conda build eigen --quiet --no-anaconda-upload && conda build rdkit --quiet --no-anaconda-upload && conda build ncurses --quiet --no-anaconda-upload && conda build postgresql --quiet --no-anaconda-upload && conda build rdkit-postgresql --quiet --no-anaconda-upload && conda build postgresql95 --quiet --no-anaconda-upload && conda build rdkit-postgresql95 --quiet --no-anaconda-upload && CONDA_PY=35 conda build boost --quiet --no-anaconda-upload && CONDA_PY=35 conda build nox --quiet --no-anaconda-upload && CONDA_PY=35 conda build cairo_nox --quiet --no-anaconda-upload && CONDA_PY=35 conda build cairocffi --quiet --no-anaconda-upload && CONDA_PY=35 conda build eigen --quiet --no-anaconda-upload && CONDA_PY=35 conda build rdkit --quiet --no-anaconda-upload && CONDA_PY=35 conda build postgresql --quiet --no-anaconda-upload && CONDA_PY=35 conda build rdkit-postgresql --quiet --no-anaconda-upload && CONDA_PY=35 conda build postgresql95 --quiet --no-anaconda-upload && CONDA_PY=35 conda build rdkit-postgresql95 --quiet --no-anaconda-upload && CONDA_NPY=110 conda build rdkit --quiet --no-anaconda-upload && CONDA_PY=35 CONDA_NPY=110 conda build rdkit --quiet --no-anaconda-upload' returned a non-zero code: 1
[sitzmann@green conda-rdkit]$
@greglandrum
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This is caused by backwards-incompatible changes that were made in v0.20 of pandas.
It's been fixed on master and will be part of the 2017_03_2 release, which will fix the conda builds.
In the meantime you could downgrade pandas to v0.19 (either manually or by specifying a version < 0.20 in rdkit/meta.yaml) and things should be fine.

@markussitzmann
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Thanks, Greg!

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@greglandrum @markussitzmann