synapser error in virtual environment built from Docker

Description

I'm trying to build a virtual environment leveraging a tool Binder (that is really cool for reproducing small bits of code).

build fail: https://mybinder.org/v2/gh/kelshmo/dummyDocker/master?urlpath=rstudio

Dockerfile

I have some different constraints that the use case addressed in the Using synapser with Docker vignette, though I tried to adapt the suggested Dockerfile.

/usr/local/lib/R/site-library/PythonEmbedInR/lib/python3.5/distutils/dist.py:261: UserWarning: Unknown distribution option: 'long_description_content_type'
warnings.warn(msg)

running install

Traceback (most recent call last):

File "<string>", line 1, in <module>

File "/tmp/RtmpPoEdYa/R.INSTALL3e90a0dcb24/synapser/inst/python/installPythonClient.py", line 78, in main

installPackage(packageName, url, archivePrefix, archiveSuffix, path, moduleInstallationPrefix)
File "/tmp/RtmpPoEdYa/R.INSTALL3e90a0dcb24/synapser/inst/python/installPythonClient.py", line 170, in installPackage

importlib.import_module("setup")
File "/usr/local/lib/R/site-library/PythonEmbedInR/lib/python3.5/importlib/_init_.py", line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 986, in _gcd_import

File "<frozen importlib._bootstrap>", line 969, in _find_and_load

File "<frozen importlib._bootstrap>", line 958, in _find_and_load_unlocked

File "<frozen importlib._bootstrap>", line 673, in _load_unlocked

File "<frozen importlib._bootstrap_external>", line 673, in exec_module

File "<frozen importlib._bootstrap>", line 222, in _call_with_frames_removed

File "./setup.py", line 73, in <module>

File "/usr/local/lib/R/site-library/PythonEmbedInR/lib/python3.5/distutils/core.py", line 148, in setup

dist.run_commands()
File "/usr/local/lib/R/site-library/PythonEmbedInR/lib/python3.5/distutils/dist.py", line 955, in run_commands

self.run_command(cmd)
File "/usr/local/lib/R/site-library/PythonEmbedInR/lib/python3.5/distutils/dist.py", line 974, in run_command

cmd_obj.run()
File "/srv/venv/share/python-wheels/setuptools-33.1.1-py2.py3-none-any.whl/setuptools/command/install.py", line 67, in run

File "/srv/venv/share/python-wheels/setuptools-33.1.1-py2.py3-none-any.whl/setuptools/command/install.py", line 103, in do_egg_install

File "/usr/local/lib/R/site-library/PythonEmbedInR/lib/python3.5/distutils/cmd.py", line 107, in ensure_finalized

self.finalize_options()
File "/srv/venv/share/python-wheels/setuptools-33.1.1-py2.py3-none-any.whl/setuptools/command/easy_install.py", line 305, in finalize_options

File "/usr/local/lib/R/site-library/PythonEmbedInR/lib/python3.5/distutils/cmd.py", line 287, in set_undefined_options

src_cmd_obj.ensure_finalized()
File "/usr/local/lib/R/site-library/PythonEmbedInR/lib/python3.5/distutils/cmd.py", line 107, in ensure_finalized

self.finalize_options()
File "/srv/venv/share/python-wheels/setuptools-33.1.1-py2.py3-none-any.whl/setuptools/command/install_lib.py", line 18, in finalize_options

File "/usr/local/lib/R/site-library/PythonEmbedInR/lib/python3.5/distutils/cmd.py", line 290, in set_undefined_options

setattr(self, dst_option, getattr(src_cmd_obj, src_option))
File "/usr/local/lib/R/site-library/PythonEmbedInR/lib/python3.5/distutils/cmd.py", line 103, in _getattr_

raise AttributeError(attr)
AttributeError
:
install_layout
Error in PythonEmbedInR:yExec(command) :
An error has occurred while executing Python code. See traceback above.
Execution halted
ERROR: configuration failed for package ‘synapser’

  • removing ‘/usr/local/lib/R/site-library/synapser’
    Error in i.p(...) :
    (converted from warning) installation of package ‘synapser’ had non-zero exit status
    Calls: <Anonymous> ... with_rprofile_user -> with_envvar -> force -> force -> i.p
    Execution halted

Environment

None

Status

Assignee

Unassigned

Reporter

Kelsey Montgomery

Labels

None

Validator

Bruce Hoff

Release Version History

None

Priority

Major
Configure