rdkit: Anaconda rdkit fails to import on OS X

Within the last month, an installation of anaconda rdkit in a fresh environment on OS X began to fail to import on my machine. Previously, I had no issues. I have also tested it on Travis CI using a fresh install of Miniconda (albeit with more in the environment). Please see a minimal working example:

conda create -n test_rdkit -c rdkit python=3.6 rdkit
source activate test_rdkit
python

>>> import rdkit
Fatal Python error: PyThreadState_Get: no current thread

Abort trap: 6

Repeating the above for Python 3.5 produces a Segmentation Fault.

Here is a description of my environment.

$ conda list
# packages in environment at /Users/saxen/anaconda3/envs/test_rdkit:
#
boost                     1.56.0                   py36_3    rdkit
bzip2                     1.0.6                h92991f9_1  
ca-certificates           2017.08.26           ha1e5d58_0  
cairo                     1.14.10              h7d8fbd7_5  
certifi                   2017.7.27.1      py36hd973bb6_0  
fontconfig                2.12.4               hc5e92fd_0  
freetype                  2.8                  h143eb01_0  
gettext                   0.19.8.1             hb0f4f8b_2  
glib                      2.53.6               ha08cb78_1  
icu                       58.2                 hea21ae5_0  
jpeg                      9b                   haccd157_1  
libcxx                    4.0.1                h579ed51_0  
libcxxabi                 4.0.1                hebd6815_0  
libedit                   3.1                  hb4e282d_0  
libffi                    3.2.1                hd939716_3  
libiconv                  1.15                 h99df5da_5  
libpng                    1.6.32               hce72d48_2  
libtiff                   4.0.8                h8cd0352_9  
libxml2                   2.9.4                hbd0960b_5  
mkl                       2017.0.3                      0  
ncurses                   6.0                  ha932d30_1  
numpy                     1.11.3                   py36_0  
olefile                   0.44             py36ha08bf50_0  
openssl                   1.0.2l               h57f3a61_2  
pandas                    0.20.3           py36hd6655d8_2  
pcre                      8.41                 h29eefc5_0  
pillow                    4.2.1            py36h0263179_0  
pip                       9.0.1            py36hbd95645_3  
pixman                    0.34.0               hc036c1e_2  
python                    3.6.3                h6804ab2_0  
python-dateutil           2.6.1            py36h86d2abb_1  
pytz                      2017.2           py36h2e7dfbc_1  
rdkit                     2017.03.3           np111py36_1    rdkit
readline                  7.0                  h81b24a6_3  
setuptools                36.5.0           py36h2134326_0  
six                       1.10.0           py36h1d5bd22_1  
sqlite                    3.20.1               h900c3b0_1  
tk                        8.6.7                hcdce994_1  
wheel                     0.29.0           py36h3597b6d_1  
xz                        5.2.3                ha24016e_1  
zlib                      1.2.11               h60db283_1

About this issue

Original URL
State: open
Created 7 years ago
Comments: 23 (6 by maintainers)

Commits related to this issue

Use most recent version of conda Installing rdkit with recent conda versions seems to work fine. See rdkit/rdkit#1617 — committed to keiserlab/e3fp by sethaxen 6 years ago

Most upvoted comments

I don’t know if it’s related with issue or not, but I didn’t want to spawn duplicates.

When I do import rdkit on iOS, it actually has no problem, but doing from rdkit import Chem throws a: Segmentation fault: 11 and exits. Related?

j3mdamas on Jan 11, 2018

@pstjohn, well what do you know? With conda 4.3.34 on OS X, the above example no longer fails on my system. Unless anyone else replies with an issue, I’ll close it shortly.

sethaxen on May 11, 2018

These all sound like the same problem. Due to some breaking changes made by the anaconda team, the current RDKit builds do not work with recent versions of conda on the Mac. We’ve been working on the problem but have been unable to find a fix. Until we do, you (unfortunately) need to use older conda versions (as described above).

greglandrum on Jan 15, 2018

I’m still struggling to get the Mac builds to work with the most recent versions of conda. Hopefully it won’t be too much longer.

greglandrum on Dec 8, 2017

This is a problem with recent versions of conda and is, I believe, a conda bug. There’s a bit more info here: https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg07315.html

greglandrum on Oct 22, 2017