id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
4008	Unable to install bundle with mdtraj (source code package) dependency	jacknicoludis@…	Greg Couch	"{{{
This is not so much a bug, but help with an error when trying to install a
new bundle. I am working on a bundle to read .h5 trajectory files (based on
the example for loading .xyz files on the ChimeraX webpage). I have written
the bundle, built it, but when I try to install it I get the following (the
full message from the devel install step):

```
devel install /Users/jack.nicoludis/trjh5
running build
running build_py
running bdist_wheel
installing to build/bdist.macosx-10.13-x86_64/wheel
running install
running install_lib
creating build/bdist.macosx-10.13-x86_64/wheel
creating build/bdist.macosx-10.13-x86_64/wheel/chimerax
creating build/bdist.macosx-10.13-x86_64/wheel/chimerax/trjh5
copying build/lib/chimerax/trjh5/io.py ->
build/bdist.macosx-10.13-x86_64/wheel/chimerax/trjh5
copying build/lib/chimerax/trjh5/__init__.py ->
build/bdist.macosx-10.13-x86_64/wheel/chimerax/trjh5
running install_egg_info
running egg_info
writing ChimeraX_trjh5.egg-info/PKG-INFO
writing dependency_links to ChimeraX_trjh5.egg-info/dependency_links.txt
writing requirements to ChimeraX_trjh5.egg-info/requires.txt
writing top-level names to ChimeraX_trjh5.egg-info/top_level.txt
reading manifest file 'ChimeraX_trjh5.egg-info/SOURCES.txt'
writing manifest file 'ChimeraX_trjh5.egg-info/SOURCES.txt'
Copying ChimeraX_trjh5.egg-info to
build/bdist.macosx-10.13-x86_64/wheel/ChimeraX_trjh5-0.1-py3.7.egg-info
running install_scripts
creating
build/bdist.macosx-10.13-x86_64/wheel/ChimeraX_trjh5-0.1.dist-info/WHEEL
creating 'dist/ChimeraX_trjh5-0.1-py3-none-any.whl' and adding
'build/bdist.macosx-10.13-x86_64/wheel' to it
adding 'chimerax/trjh5/__init__.py'
adding 'chimerax/trjh5/io.py'
adding 'ChimeraX_trjh5-0.1.dist-info/METADATA'
adding 'ChimeraX_trjh5-0.1.dist-info/WHEEL'
adding 'ChimeraX_trjh5-0.1.dist-info/top_level.txt'
adding 'ChimeraX_trjh5-0.1.dist-info/RECORD'
removing build/bdist.macosx-10.13-x86_64/wheel
Distribution is in
/Users/jack.nicoludis/trjh5/dist/ChimeraX_trjh5-0.1-py3-none-any.whl
[toolshed install](help:user/commands/toolshed.html#install)
/Users/jack.nicoludis/trjh5/dist/ChimeraX_trjh5-0.1-py3-none-any.whl

[toolshed install
/Users/jack.nicoludis/trjh5/dist/ChimeraX_trjh5-0.1-py3-none-
any.whl](cxcmd:toolshed install
/Users/jack.nicoludis/trjh5/dist/ChimeraX_trjh5-0.1-py3-none-any.whl)

Traceback (most recent call last):
File
""/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/toolshed_utils/__init__.py"",
line 489, in _pip_install
results = _run_pip(command, logger)
File
""/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/toolshed_utils/__init__.py"",
line 540, in _run_pip
raise RuntimeError(s)
RuntimeError: Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing
/Users/jack.nicoludis/trjh5/dist/ChimeraX_trjh5-0.1-py3-none-any.whl
Requirement already satisfied: ChimeraX-Core~=1.1.1 in
/Applications/ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from
ChimeraX-trjh5==0.1) (1.1.1)
Requirement already satisfied: cython>=0.28 in
/Applications/ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from
ChimeraX-trjh5==0.1) (0.29.20)
Collecting mdtraj>=1.9.3
Using cached mdtraj-1.9.4.tar.gz (2.1 MB)
Installing build dependencies: started
Installing build dependencies: finished with status 'error'
WARNING: --use-feature=2020-resolver no longer has any effect, since it is
now the default dependency resolver in pip. This will become an error in
pip 21.0.
ERROR: Command errored out with exit status 70:
command: /Applications/ChimeraX-1.1.1.app/Contents/MacOS/ChimeraX
/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pip
install --ignore-installed --no-user --prefix
/private/var/folders/66/scl1xcmn6v9gncjw3wbp69qc0000gp/T/pip-build-env-37344ypk/overlay
--no-warn-script-location --no-binary :none: --only-binary :none: -i
https://pypi.org/simple --extra-index-url
https://cxtoolshed.rbvi.ucsf.edu/pypi/ -- setuptools wheel numpy
'Cython>0.28'
cwd: None
Complete output (0 lines):
----------------------------------------
ERROR: Command errored out with exit status 70:
/Applications/ChimeraX-1.1.1.app/Contents/MacOS/ChimeraX
/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pip
install --ignore-installed --no-user --prefix
/private/var/folders/66/scl1xcmn6v9gncjw3wbp69qc0000gp/T/pip-build-env-37344ypk/overlay
--no-warn-script-location --no-binary :none: --only-binary :none: -i
https://pypi.org/simple --extra-index-url
https://cxtoolshed.rbvi.ucsf.edu/pypi/ -- setuptools wheel numpy
'Cython>0.28' Check the logs for full command output.
```

The error indicates logs that might help figure out the issue but I don't
know where they are. I also do not know what exit status 70 refers to and
there's no documentation on this. Any suggestions?

Best,
Jack

}}}
"	defect	accepted	normal		Build System	1.1			chimera-programmers				all	ChimeraX