Conda Docker build fails

[markussitzmann]

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

• [[ Linux == \L\i\n\u\x ]]
• RDBASE=/home/rdkit/bld/rdkit_1494777495800/work
• LD_LIBRARY_PATH=/home/rdkit/bld/rdkit_1494777495800/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib:/home/rdkit/bld/rdkit_1494777495800/work/lib
• PYTHONPATH=/home/rdkit/bld/rdkit_1494777495800/work
• ctest -j4 --output-on-failure
  Test project /home/rdkit/bld/rdkit_1494777495800/work
  Start 1: testInchi
  Start 2: testAvalonLib1
  Start 3: pyAvalonTools
  Start 4: testDict
  1/118 Test conda and $RDBASE #3: pyAvalonTools ...................... Passed 0.19 sec
  Start 5: testRDValue
  2/118 Test Multithread support #5: testRDValue ........................ Passed 0.30 sec
  Start 6: testDataStructs
  3/118 Test Boost in conda anaconda channel not compatible with rdkit. #6: testDataStructs .................... Passed 0.20 sec
  Start 7: testFPB
  4/118 Test switch to using pillow instead of pil for all python versions #7: testFPB ............................ Passed 0.30 sec
  Start 8: testMultiFPB
  5/118 Test comment out empty build block #8: testMultiFPB ....................... Passed 0.01 sec
  Start 9: pyBV
  6/118 Test Get the boost build working with py35 #9: pyBV ............................... Passed 0.42 sec
  Start 10: pyDiscreteValueVect
  7/118 Test conda build support on the mac #4: testDict ........................... Passed 2.53 sec
  8/118 Test move the inchi library into a separate conda package #10: pyDiscreteValueVect ................ Passed 0.30 sec
  Start 11: pySparseIntVect
  Start 12: pyFPB
  9/118 Test updated Makefile patch for building the postgres cartridge #11: pySparseIntVect .................... Passed 0.20 sec
  Start 13: testTransforms
  10/118 Test Add a headless cairo build #12: pyFPB .............................. Passed 0.30 sec
  11/118 Test Moving builds over to bioconda #13: testTransforms ..................... Passed 0.20 sec
  Start 14: testGrid
  Start 15: testPyGeometry
  12/118 Test switch to ctest instead of 'make test' #14: testGrid ........................... Passed 0.11 sec
  13/118 Test Enable parallel builds #15: testPyGeometry ..................... Passed 0.12 sec
  Start 16: testMatrices
  Start 17: testAlignment
  14/118 Test update development branch to current rdkit release #17: testAlignment ...................... Passed 0.10 sec
  15/118 Test explicit avalon and inchi pulls no longer required; bump version #16: testMatrices ....................... Passed 0.20 sec
  Start 18: pyAlignment
  Start 19: testOptimizer
  16/118 Test update of the master branch for rel 2016.03.1 #19: testOptimizer ...................... Passed 0.10 sec
  17/118 Test remove the rdkit depictor patch #18: pyAlignment ........................ Passed 0.20 sec
  Start 20: testUFFForceField
  Start 21: testMMFFForceField
  18/118 Test chain commands to reduce the image layering #20: testUFFForceField .................. Passed 0.11 sec
  Start 22: pyForceFieldConstraints
  19/118 Test build fails on CentOS 6.4  #22: pyForceFieldConstraints ............ Passed 0.91 sec
  20/118 Test Patches for boost required to build on OS X #1: testInchi .......................... Passed 4.99 sec
  Start 23: testDistGeom
  Start 24: pyDistGeom
  21/118 Test update the rdkit-postgresql* patch files  #24: pyDistGeom ......................... Passed 0.10 sec
  22/118 Test update to 2016.03.3 #23: testDistGeom ....................... Passed 0.10 sec
  Start 25: graphmolTest1
  Start 26: graphmolcpTest
  23/118 Test switch to using conda postgresql #26: graphmolcpTest ..................... Passed 0.10 sec
  24/118 Test update to Release_2016_03_4 #25: graphmolTest1 ...................... Passed 0.10 sec
  Start 27: graphmolqueryTest
  Start 28: graphmolMolOpsTest
  25/118 Test postgressql95 #27: graphmolqueryTest .................. Passed 0.20 sec
  Start 29: graphmoltestCanon
  26/118 Test fix issue #27 (reprise) #29: graphmoltestCanon .................. Passed 0.20 sec
  Start 30: graphmoltestChirality
  27/118 Test update to new release #30: graphmoltestChirality .............. Passed 0.20 sec
  Start 31: graphmoltestPickler
  28/118 Test Fix issue 27 #28: graphmolMolOpsTest ................. Passed 1.05 sec
  29/118 Test Fix postgres patch for 2016.09.1 #31: graphmoltestPickler ................ Passed 0.22 sec
  Start 32: graphmoltestPicklerGlobalSetting
  Start 33: graphmolIterTest
  30/118 Test fix the RDConfig patch in the rdkit recipe [win] #32: graphmoltestPicklerGlobalSetting ... Passed 0.10 sec
  31/118 Test Update to 2016 09 2 #33: graphmolIterTest ................... Passed 0.20 sec
  Start 34: hanoiTest
  Start 35: graphmolMemTest1
  32/118 Test Add own cairo #35: graphmolMemTest1 ................... Passed 0.20 sec
  Start 36: resMolSupplierTest
  33/118 Test relocate the conda build directory to fix the postgresql build. #36: resMolSupplierTest ................. Passed 1.11 sec
  Start 37: testDepictor
  34/118 Test 2016.09.2 rdkit build error on fedora 25 #37: testDepictor ....................... Passed 0.30 sec
  Start 38: pyDepictor
  35/118 Test use cmake to build the postgresql cartridge #38: pyDepictor ......................... Passed 0.60 sec
  Start 39: smiTest1
  36/118 Test conda build of Release_2016_09_2 on Kubuntu 16.10 64bit fails #39: smiTest1 ........................... Passed 0.30 sec
  Start 40: cxsmilesTest
  37/118 Test Lots of test failed on CentOS7 #40: cxsmilesTest ....................... Passed 0.20 sec
  Start 41: smaTest1
  38/118 Test Conda build fails on MacOS #41: smaTest1 ........................... Passed 1.11 sec
  Start 42: fileParsersTest1
  39/118 Test fix the rdkit-postgresql* recipes for Release_2016_03_2 #21: testMMFFForceField ................. Passed 8.44 sec
  Start 43: testMolSupplier
  40/118 Test sync 'development' branch with 'master' and update for 2016.09.3 #43: testMolSupplier .................... Passed 0.40 sec
  Start 44: testMolWriter
  41/118 Test consider porting to conda-forge? #44: testMolWriter ...................... Passed 0.40 sec
  Start 45: testTplParser
  42/118 Test update boost build to symlink python lib for all 3.x #45: testTplParser ...................... Passed 0.02 sec
  Start 46: testMol2ToMol
  43/118 Test Test in conda build rdkit fails in Ubuntu 14.04 #46: testMol2ToMol ...................... Passed 0.04 sec
  Start 47: testSequence
  44/118 Test RDKit for python 3.6 #47: testSequence ....................... Passed 0.05 sec
  Start 48: testSubstructMatch
  45/118 Test Correct link to miniconda website #2: testAvalonLib1 ..................... Passed 14.73 sec
  Start 49: testReaction
  46/118 Test Package not found on macOS: rdkit-postgresql #48: testSubstructMatch ................. Passed 0.71 sec
  47/118 Test conda build fails with latest anaconda on Windows 10 #49: testReaction ....................... Passed 0.41 sec
  Start 50: testReactionFingerprints
  Start 51: testEnumeration
  48/118 Test Conda Docker build fails #50: testReactionFingerprints ........... Passed 0.03 sec
  49/118 Test - enable conda-rdkit builds on all platforms #51: testEnumeration .................... Passed 0.23 sec
  Start 52: pyChemReactions
  Start 53: pyChemReactionEnumerations
  50/118 Test - added recipes for Windows PostgreSQL dependencies #52: pyChemReactions .................... Passed 0.30 sec
  Start 54: pyChemReactionSanitize
  51/118 Test merge development branch back over to master #54: pyChemReactionSanitize ............. Passed 0.16 sec
  Start 55: testChemTransforms
  52/118 Test review the dependency from ICU #55: testChemTransforms ................. Passed 0.31 sec
  Start 56: testSubgraphs1
  53/118 Test conda-build v3.0 breaks the rdkit recipes #53: pyChemReactionEnumerations ......... Passed 1.05 sec
  Start 57: testSubgraphs2
  54/118 Test RuntimeError when using numpy <1.13 #57: testSubgraphs2 ..................... Passed 0.01 sec
  55/118 Test Numerous updates  #56: testSubgraphs1 ..................... Passed 0.39 sec
  Start 58: filterCatalogTest
  Start 59: pyFilterCatalog
  56/118 Test implemented alternative versioning mechanism to __conda_version__ (issue #53) #58: filterCatalogTest .................. Passed 0.40 sec
  Start 60: testFragCatalog
  57/118 Test Updates conda version to conda 3.0 compatible version #59: pyFilterCatalog .................... Passed 1.01 sec
  Start 61: pyFragCatalog
  58/118 Test Import error in jupyter and pycharm (Windows10) #60: testFragCatalog .................... Passed 0.50 sec
  59/118 Test rdkit build fail #61: pyFragCatalog ...................... Passed 0.20 sec
  Start 62: testDescriptors
  Start 63: testPBF
  60/118 Test Failure with conda build rdkit in Linux #63: testPBF ............................ Passed 0.30 sec
  Start 64: test3D
  61/118 Test Updates for the new conda #64: test3D ............................. Passed 0.92 sec
  Start 65: pyMolDescriptors
  62/118 Test update the rdkit-postgresql recipe for release 2018.03 #65: pyMolDescriptors ................... Passed 0.52 sec
  Start 66: testFingerprints
  63/118 Test rdkit builds fail because of sourceforge.net downloads? #62: testDescriptors .................... Passed 3.66 sec
  Start 67: testPartialCharges
  64/118 Test speed up postgresql builds #67: testPartialCharges ................. Passed 0.04 sec
  Start 68: pyPartialCharges
  65/118 Test remove the now obsolete rdkit-postgresql95 recipe #68: pyPartialCharges ................... Passed 0.32 sec
  Start 69: testMolTransforms
  66/118 Test Merge development branch onto master #69: testMolTransforms .................. Passed 0.04 sec
  Start 70: pyMolTransforms
  67/118 Test Update the boost version to 1.62 #42: fileParsersTest1 ................... Passed 12.46 sec
  Start 71: testMMFFForceFieldHelpers
  68/118 Test Adds travis-ci builds to conda-rdkit #70: pyMolTransforms .................... Passed 0.32 sec
  Start 72: testUFFForceFieldHelpers
  69/118 Test fix unix boost version to 1.65.1 #66: testFingerprints ................... Passed 8.58 sec
  Start 73: testCrystalForceField
  70/118 Test be less specific about the boost version #73: testCrystalForceField .............. Passed 0.05 sec
  Start 74: pyForceFieldHelpers
  71/118 Test is it expected that boost is pulled from conda3 main channel and not rdkit? #74: pyForceFieldHelpers ................ Passed 0.42 sec
  72/118 Test add --output-on-failure to ctest flags #34: hanoiTest .......................... Passed 23.39 sec
  Start 75: testDistGeomHelpers
  Start 76: pyDistGeom
  73/118 Test Fix runtime specification for boost #76: pyDistGeom ......................... Passed 5.56 sec
  Start 77: testMolAlign
  74/118 Test Need some way to lock the version of boost to what we build against #71: testMMFFForceFieldHelpers .......... Passed 17.79 sec
  Start 78: pyMolAlign
  75/118 Test pin the runtime dependency from the boost libraries #72: testUFFForceFieldHelpers ........... Passed 20.72 sec
  Start 79: testFeatures
  76/118 Test clean install of conda python 3.7 rdkit rdkit for postgres on ubuntu 18.04 has boost version issues #79: testFeatures ....................... Passed 0.20 sec
  Start 80: pyChemicalFeatures
  77/118 Test psql error #80: pyChemicalFeatures ................. Passed 0.25 sec
  Start 81: testShapeHelpers
  78/118 Test Error building conda-rdkit behind a firewall #81: testShapeHelpers ................... Passed 0.22 sec
  Start 82: pyShapeHelpers
  79/118 Test Cannot import rdEHTTools  #82: pyShapeHelpers ..................... Passed 0.29 sec
  Start 83: testMolCatalog
  80/118 Test mirror development over to master #83: testMolCatalog ..................... Passed 0.21 sec
  Start 84: pyMolCatalog
  81/118 Test Default rdkit from conda uses outdated version #84: pyMolCatalog ....................... Passed 0.29 sec
  Start 85: moldraw2DTest1
  82/118 Test Fixes broken PostgreSQL cartridge build on Windows #85: moldraw2DTest1 ..................... Passed 2.62 sec
  Start 86: pyMolDraw2D
  83/118 Test Fixes broken PostgreSQL cartridge build on Windows #86: pyMolDraw2D ........................ Passed 0.26 sec
  Start 87: testFMCS
  84/118 Test ArgumentError: Python argument types in rdkit.Chem.rdMolDescriptors.CalcCrippenDescriptors(NoneType) did not match C++ signature: #87: testFMCS ........................... Passed 1.42 sec
  Start 88: pyFMCS
  85/118 Test remove things we never build #88: pyFMCS ............................. Passed 1.42 sec
  Start 89: FMCStest
  86/118 Test Changed CMake parameter to RDK_OPTIMIZE_POPCNT (see rdkit PR #2865) #89: FMCStest ........................... Passed 0.21 sec
  Start 90: testMolHash
  87/118 Test Issues with pandas on Ubuntu. #90: testMolHash ........................ Passed 0.21 sec
  Start 91: pyMolHash
  88/118 Test [WIP] Build RDKIT with python 3.8 #91: pyMolHash .......................... Passed 0.23 sec
  Start 92: testMMPA
  89/118 Test RDkit 2020.09.4 release issues with Conda-forge build and other modules (Python3-saml) #92: testMMPA ........................... Passed 0.21 sec
  Start 93: pyMMPA
  90/118 Test rdkit installs libboost 1.67.0 rdkit-postgresql wants 1.65.1 #78: pyMolAlign ......................... Passed 14.35 sec
  91/118 Test Explicit valence for atom # 1 O, 3, is greater than permitted #93: pyMMPA ............................. Passed 1.74 sec
  Start 94: testStructChecker
  Start 95: pyStructChecker
  92/118 Test #94: testStructChecker .................. Passed 0.10 sec
  93/118 Test #95: pyStructChecker .................... Passed 0.15 sec
  Start 96: testReducedGraphs
  Start 97: pyReducedGraphs
  94/118 Test #97: pyReducedGraphs .................... Passed 0.12 sec
  95/118 Test #96: testReducedGraphs .................. Passed 0.12 sec
  Start 98: trajectoryTest
  Start 99: testSLNParse
  96/118 Test #98: trajectoryTest ..................... Passed 0.16 sec
  97/118 Test #99: testSLNParse ....................... Passed 0.16 sec
  Start 100: pySLNParse
  Start 101: pyGraphMolWrap
  98/118 Test #100: pySLNParse ......................... Passed 0.20 sec
  Start 102: pyTestConformerWrap
  99/118 Test #102: pyTestConformerWrap ................ Passed 0.20 sec
  Start 103: pyTestTrajectory
  100/118 Test #103: pyTestTrajectory ................... Passed 0.60 sec
  Start 104: pyTestThreads
  101/118 Test #104: pyTestThreads ...................... Passed 1.45 sec
  Start 105: testQuery
  102/118 Test #105: testQuery .......................... Passed 0.30 sec
  Start 106: testMatCalc
  103/118 Test #106: testMatCalc ........................ Passed 0.21 sec
  Start 107: pyMatCalc
  104/118 Test #107: pyMatCalc .......................... Passed 0.50 sec
  Start 108: pySimDivPickers
  105/118 Test #108: pySimDivPickers .................... Passed 3.02 sec
  Start 109: pyRanker
  106/118 Test #109: pyRanker ........................... Passed 0.14 sec
  Start 110: testChemicalFeatures
  107/118 Test #110: testChemicalFeatures ............... Passed 0.30 sec
  Start 111: pyFeatures
  108/118 Test #111: pyFeatures ......................... Passed 0.30 sec
  Start 112: pythonTestDbCLI
  109/118 Test #101: pyGraphMolWrap ..................... Passed 8.75 sec
  Start 113: pythonTestDirML
  110/118 Test #113: pythonTestDirML .................... Passed 6.53 sec
  Start 114: pythonTestDirDataStructs
  111/118 Test #114: pythonTestDirDataStructs ........... Passed 0.91 sec
  Start 115: pythonTestDirDbase
  112/118 Test #115: pythonTestDirDbase ................. Passed 0.50 sec
  Start 116: pythonTestDirSimDivFilters
  113/118 Test #116: pythonTestDirSimDivFilters ......... Passed 0.19 sec
  Start 117: pythonTestDirVLib
  114/118 Test #117: pythonTestDirVLib .................. Passed 0.51 sec
  Start 118: pythonTestDirChem
  115/118 Test #112: pythonTestDbCLI .................... Passed 12.67 sec
  116/118 Test py-boost runtime should be = not >= #75: testDistGeomHelpers ................ Passed 52.92 sec
  117/118 Test Conda package rdkit-postgresql downgrades my rdkit conda package #77: testMolAlign ....................... Passed 78.98 sec
  118/118 Test #118: pythonTestDirChem ..................***Failed 40.60 sec
  Errors while running CTest
  ....

---

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]

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]

Thanks, Greg!