[BUG] pip install of cellxgene in a conda environment fails with tiledb "image not found"

Describe the bug

From: https://cziscience.slack.com/archives/C8ME9JMBP/p1604955568138000

Hi all, I’ve started a conda environment and pip-installed cellxgene. I am attempting to run through the example data:

cellxgene launch https://cellxgene-example-data.czi.technology/pbmc3k.h5ad

and i’ve run into an error:

OSError: dlopen(libtiledb.dylib, 6): image not found

txt file attached with the entire error message. Any insight? I see there has been some buzz surrounding tileDB on the github issues tab

error_message.txt 
Traceback (most recent call last):
  File "/Users/colephalen/cellxgene/lib/python3.7/site-packages/tiledb/__init__.py", line 20, in <module>
    from .libtiledb import Ctx
ImportError: dlopen(/Users/colephalen/cellxgene/lib/python3.7/site-packages/tiledb/libtiledb.cpython-37m-darwin.so, 2): Symbol not found: ____chkstk_darwin
  Referenced from: /Users/colephalen/cellxgene/lib/python3.7/site-packages/tiledb/.dylibs/libintl.8.dylib (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib
 in /Users/colephalen/cellxgene/lib/python3.7/site-packages/tiledb/.dylibs/libintl.8.dylib
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "/Users/colephalen/cellxgene/lib/python3.7/site-packages/tiledb/__init__.py", line 24, in <module>
    ctypes.CDLL(os.path.join(lib_dir, lib_name))
  File "/opt/miniconda3/lib/python3.7/ctypes/__init__.py", line 364, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: dlopen(/Users/colephalen/cellxgene/lib/python3.7/site-packages/tiledb/native/libtiledb.dylib, 6): image not found
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "/Users/colephalen/cellxgene/bin/cellxgene", line 11, in <module>
    load_entry_point('cellxgene==0.16.5', 'console_scripts', 'cellxgene')()
  File "/Users/colephalen/cellxgene/lib/python3.7/site-packages/pkg_resources/__init__.py", line 489, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/Users/colephalen/cellxgene/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2852, in load_entry_point
    return ep.load()
  File "/Users/colephalen/cellxgene/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2443, in load
    return self.resolve()
  File "/Users/colephalen/cellxgene/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2449, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/Users/colephalen/cellxgene/lib/python3.7/site-packages/server/cli/cli.py", line 3, in <module>
    from .convert_to_cxg import convert_to_cxg
  File "/Users/colephalen/cellxgene/lib/python3.7/site-packages/server/cli/convert_to_cxg.py", line 5, in <module>
    from server.converters.h5ad_data_file import H5ADDataFile
  File "/Users/colephalen/cellxgene/lib/python3.7/site-packages/server/converters/h5ad_data_file.py", line 7, in <module>
    import tiledb
  File "/Users/colephalen/cellxgene/lib/python3.7/site-packages/tiledb/__init__.py", line 27, in <module>
    ctypes.CDLL(lib_name)
  File "/opt/miniconda3/lib/python3.7/ctypes/__init__.py", line 364, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: dlopen(libtiledb.dylib, 6): image not found

[kruegert]

@bmccandless yes, that works! Thanks

[bmccandless]

Hello @kruegert, I’m taking a look at this today with the tiledb team.
It may help in our debugging if you could supply the output of conda list.