upgrade wstool will return error (looks like due to SIP in El Capitan) #81

wuhy08 · 2015-10-23T04:14:26Z

When upgrading wstool in OS X el capitan, it give the following error:

Command "/usr/bin/python -c "import setuptools, tokenize;__file__='/private/tmp/pip-build-cXwzbm/wstool/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-J_oWgn-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/tmp/pip-build-cXwzbm/wstool

The text was updated successfully, but these errors were encountered:

tkruse · 2015-10-23T08:59:50Z

If you can, please paste more context information (like the command you used), and if you used pip (like it seems), try also using a --verbose option.

jayyoung · 2015-10-23T10:38:33Z

Also getting a similar error myself on El Capitan when trying to install wstool via pip so I thought I'd pile on:

sudo pip install -U wstool

Gives the following output

Displacer:~ jxy$ sudo pip install -U wstool
Downloading/unpacking wstool
  Running setup.py egg_info for package wstool

Downloading/unpacking vcstools>=0.1.38 (from wstool)
  Running setup.py egg_info for package vcstools

Downloading/unpacking pyyaml (from wstool)
  Running setup.py egg_info for package pyyaml

Downloading/unpacking python-dateutil from https://pypi.python.org/packages/source/p/python-dateutil/python-dateutil-2.4.2.tar.gz#md5=4ef68e1c485b09e9f034e10473e5add2 (from vcstools>=0.1.38->wstool)
  Running setup.py egg_info for package python-dateutil

Downloading/unpacking six>=1.5 (from python-dateutil->vcstools>=0.1.38->wstool)
  Running setup.py egg_info for package six

    no previously-included directories found matching 'documentation/_build'
Installing collected packages: wstool, vcstools, pyyaml, python-dateutil, six
  Running setup.py install for wstool
    error: [Errno 1] Operation not permitted: '/usr/share/zsh/site-functions/_wstool'
    Complete output from command /usr/bin/python -c "import setuptools;__file__='/tmp/pip-build/wstool/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-0wQJiJ-record/install-record.txt --single-version-externally-managed:
    running install

running build

running build_py

running build_scripts

running install_lib

running install_data

copying completion/_wstool -> /usr/share/zsh/site-functions

error: [Errno 1] Operation not permitted: '/usr/share/zsh/site-functions/_wstool'

----------------------------------------
Command /usr/bin/python -c "import setuptools;__file__='/tmp/pip-build/wstool/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-0wQJiJ-record/install-record.txt --single-version-externally-managed failed with error code 1 in /tmp/pip-build/wstool
Storing complete log in /Users/jxy/Library/Logs/pip.log

tkruse · 2015-10-23T15:55:16Z

This seems to be related to installation of zsh completion. it seems strange that there should be a permission problem when sudo is being used, but maybe it's a missing directory or something. @jayyoung, do you have a /usr/share/zsh/site-functions/ directory on your system?

jayyoung · 2015-10-23T17:39:59Z

Yes I do, this directory is blank however. I have a Linux (Ubuntu 14.04) system here which has ROS Indigo installed all fine, and it also has that directory, but it contains two files named _wstool and wstool-completion.bash

tkruse · 2015-10-23T18:34:14Z

Then I have no clue. Does pip install -v ... provide more info about that operation?

jayyoung · 2015-10-25T12:04:50Z

Yes that does reveal some more information, specifically a python Exception trace.

Downloading/unpacking wstool
  Running setup.py egg_info for package wstool
    running egg_info
    writing requirements to pip-egg-info/wstool.egg-info/requires.txt
    writing pip-egg-info/wstool.egg-info/PKG-INFO
    writing top-level names to pip-egg-info/wstool.egg-info/top_level.txt
    writing dependency_links to pip-egg-info/wstool.egg-info/dependency_links.txt
    warning: manifest_maker: standard file '-c' not found

    reading manifest file 'pip-egg-info/wstool.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    writing manifest file 'pip-egg-info/wstool.egg-info/SOURCES.txt'
Downloading/unpacking vcstools>=0.1.38 (from wstool)
  Running setup.py egg_info for package vcstools
    running egg_info
    writing requirements to pip-egg-info/vcstools.egg-info/requires.txt
    writing pip-egg-info/vcstools.egg-info/PKG-INFO
    writing top-level names to pip-egg-info/vcstools.egg-info/top_level.txt
    writing dependency_links to pip-egg-info/vcstools.egg-info/dependency_links.txt
    warning: manifest_maker: standard file '-c' not found

    reading manifest file 'pip-egg-info/vcstools.egg-info/SOURCES.txt'
    writing manifest file 'pip-egg-info/vcstools.egg-info/SOURCES.txt'
Downloading/unpacking pyyaml (from wstool)
  Running setup.py egg_info for package pyyaml
    running egg_info
    writing pip-egg-info/PyYAML.egg-info/PKG-INFO
    writing top-level names to pip-egg-info/PyYAML.egg-info/top_level.txt
    writing dependency_links to pip-egg-info/PyYAML.egg-info/dependency_links.txt
    warning: manifest_maker: standard file '-c' not found

    reading manifest file 'pip-egg-info/PyYAML.egg-info/SOURCES.txt'
    writing manifest file 'pip-egg-info/PyYAML.egg-info/SOURCES.txt'
Using version 2.4.2 (newest of versions: 2.4.2, 2.4.1.post1, 2.4.1.post1, 2.4.1, 2.4.0, 2.3, 2.2, 2.1, 2.0, 1.5, 1.5, 1.5, 1.4.1, 1.4.1, 1.4, 1.4, 1.3, 1.2, 1.1, 1.0)
Downloading/unpacking python-dateutil from https://pypi.python.org/packages/source/p/python-dateutil/python-dateutil-2.4.2.tar.gz#md5=4ef68e1c485b09e9f034e10473e5add2 (from vcstools>=0.1.38->wstool)
  Running setup.py egg_info for package python-dateutil
    running egg_info
    writing requirements to pip-egg-info/python_dateutil.egg-info/requires.txt
    writing pip-egg-info/python_dateutil.egg-info/PKG-INFO
    writing top-level names to pip-egg-info/python_dateutil.egg-info/top_level.txt
    writing dependency_links to pip-egg-info/python_dateutil.egg-info/dependency_links.txt
    warning: manifest_maker: standard file '-c' not found

    reading manifest file 'pip-egg-info/python_dateutil.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    writing manifest file 'pip-egg-info/python_dateutil.egg-info/SOURCES.txt'
Downloading/unpacking six>=1.5 (from python-dateutil->vcstools>=0.1.38->wstool)
  Running setup.py egg_info for package six
    running egg_info
    writing pip-egg-info/six.egg-info/PKG-INFO
    writing top-level names to pip-egg-info/six.egg-info/top_level.txt
    writing dependency_links to pip-egg-info/six.egg-info/dependency_links.txt
    warning: manifest_maker: standard file '-c' not found

    reading manifest file 'pip-egg-info/six.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    no previously-included directories found matching 'documentation/_build'
    writing manifest file 'pip-egg-info/six.egg-info/SOURCES.txt'
Installing collected packages: wstool, vcstools, pyyaml, python-dateutil, six
  Running setup.py install for wstool
    running install
    running build
    running build_py
    running build_scripts
    running install_lib
    running install_data
    copying completion/_wstool -> /usr/share/zsh/site-functions
    error: [Errno 1] Operation not permitted: '/usr/share/zsh/site-functions/_wstool'
    Complete output from command /usr/bin/python -c "import setuptools;__file__='/tmp/pip-build/wstool/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-sstNBJ-record/install-record.txt --single-version-externally-managed:
    running install

running build

running build_py

running build_scripts

running install_lib

running install_data

copying completion/_wstool -> /usr/share/zsh/site-functions

error: [Errno 1] Operation not permitted: '/usr/share/zsh/site-functions/_wstool'

----------------------------------------
Command /usr/bin/python -c "import setuptools;__file__='/tmp/pip-build/wstool/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-sstNBJ-record/install-record.txt --single-version-externally-managed failed with error code 1 in /tmp/pip-build/wstool
Exception information:
Traceback (most recent call last):
  File "/Library/Python/2.7/site-packages/pip-1.2.1-py2.7.egg/pip/basecommand.py", line 107, in main
    status = self.run(options, args)
  File "/Library/Python/2.7/site-packages/pip-1.2.1-py2.7.egg/pip/commands/install.py", line 261, in run
    requirement_set.install(install_options, global_options)
  File "/Library/Python/2.7/site-packages/pip-1.2.1-py2.7.egg/pip/req.py", line 1166, in install
    requirement.install(install_options, global_options)
  File "/Library/Python/2.7/site-packages/pip-1.2.1-py2.7.egg/pip/req.py", line 589, in install
    cwd=self.source_dir, filter_stdout=self._filter_install, show_stdout=False)
  File "/Library/Python/2.7/site-packages/pip-1.2.1-py2.7.egg/pip/util.py", line 612, in call_subprocess
    % (command_desc, proc.returncode, cwd))
InstallationError: Command /usr/bin/python -c "import setuptools;__file__='/tmp/pip-build/wstool/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-sstNBJ-record/install-record.txt --single-version-externally-managed failed with error code 1 in /tmp/pip-build/wstool

Storing complete log in /Users/jxy/Library/Logs/pip.log

tkruse · 2015-10-25T17:43:35Z

Still not very helpful information, but I found this:
http://stackoverflow.com/questions/31900008/oserror-errno-1-operation-not-permitted-when-installing-scrapy-in-osx-10-11
http://stackoverflow.com/questions/33004708/osx-el-capitan-sudo-pip-install-oserror-errno-1-operation-not-permitted

Does any of that help?

Not sure what should be done on our side to prevent any of this from failing the installation.

wuhy08 · 2015-10-25T18:44:28Z

I did an uninstallation of ROS and then a clean install and solve the problem. There were a lot of difficulties in the process thoug

jayyoung · 2015-10-25T22:22:49Z

@tkruse this is definitely the culprit, after disabling the System Integrity Protection as described here wstool installed just fine.

Seems there is little to be done on your end, but maybe a note in any installation instructions regarding this would avoid future questions, as the OS offers no info regarding why it happens. Thanks!

wjwwood · 2015-10-26T17:54:18Z

@wkentaro can you check to see if installing the completion scripts into /usr/local/share/zsh/... works? If so we should change it to install there, which would work around this system integrity protection issue.

wkentaro · 2015-10-26T19:31:00Z

@wjwwood Yes. If you install wstool without sudo, the completion script will be installed as /usr/local/share/zsh/site-functions/_wstool (and /usr/local/etc/share/bash_completion.d/wstool-completion.bash for bash).

Closes vcstools#81

wjwwood · 2015-10-26T20:07:02Z

@wkentaro but does that allow zsh completion to work out of the box?

wkentaro · 2015-10-26T20:10:03Z

@wjwwood What do you mean with "work out of the box"?

wjwwood · 2015-10-26T20:13:40Z

@wkentaro My understanding was that they needed to be installed to /usr so that the completion would be picked up automatically without changing any settings or environment variables.

wkentaro · 2015-10-26T20:17:13Z

@wjwwood That depends on how zsh is installed. If you are using default zsh, it does not work. (if installed via brew it does work).

wjwwood · 2015-10-26T20:18:53Z

@wkentaro ok, so maybe in addition to the pull request you opened, we need to add a note to the documentation saying that you need to add the directory /usr/local/share/zsh somehow to the system zsh's shell completion in order for it to work? I can try to add that now that I know that it is required.

garaemon · 2016-01-28T08:40:11Z

Could you release new version to avoid this issue?
pip install wstool does not work but pip install git+https://github.com/vcstools/wstool works.

wjwwood · 2016-01-31T21:57:45Z

It's on my list. I'll try to do it this week.

wkentaro added a commit to wkentaro/wstool that referenced this issue Oct 26, 2015

Install man & completion to outside of system to avoid SIP

10f45d9

Closes vcstools#81

wjwwood closed this as completed in e37ced2 Oct 26, 2015

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upgrade wstool will return error (looks like due to SIP in El Capitan) #81

upgrade wstool will return error (looks like due to SIP in El Capitan) #81

wuhy08 commented Oct 23, 2015

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wjwwood commented Jan 31, 2016

upgrade wstool will return error (looks like due to SIP in El Capitan) #81

upgrade wstool will return error (looks like due to SIP in El Capitan) #81

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wuhy08 commented Oct 23, 2015

tkruse commented Oct 23, 2015

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tkruse commented Oct 23, 2015

jayyoung commented Oct 23, 2015

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