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Hi, I recently installed anaconda in my computer, and now I cant catkin build or catkin_make_isolated (tried them in different ws) I use ubuntu 16.04 and ros kinetic

When running catkin build i get this;

Errors     << catkin_tools_prebuild:cmake /home/daniel/catkin_ws/logs/catkin_tools_prebuild/build.cmake.000.log          
ImportError: "from catkin_pkg.package import parse_package" failed: No module named 'catkin_pkg'
Make sure that you have installed "catkin_pkg", it is up to date and on the PYTHONPATH.

CMake Error at /opt/ros/kinetic/share/catkin/cmake/safe_execute_process.cmake:11 (message):
  execute_process(/home/daniel/anaconda3/bin/python
  "/opt/ros/kinetic/share/catkin/cmake/parse_package_xml.py"
  "/opt/ros/kinetic/share/catkin/cmake/../package.xml"
  "/home/daniel/catkin_ws/build/catkin_tools_prebuild/catkin/catkin_generated/version/package.cmake")
  returned error code 1
Call Stack (most recent call first):
  /opt/ros/kinetic/share/catkin/cmake/catkin_package_xml.cmake:63 (safe_execute_process)
  /opt/ros/kinetic/share/catkin/cmake/all.cmake:151 (_catkin_package_xml)
  /opt/ros/kinetic/share/catkin/cmake/catkinConfig.cmake:20 (include)
  CMakeLists.txt:4 (find_package)

When running catkin_make_isolated:

-- Using CATKIN_DEVEL_PREFIX: /home/daniel/catkin_ws2/devel_isolated/cartographer_ros_msgs
-- Using CMAKE_PREFIX_PATH: /home/daniel/catkin_ws2/install_isolated;/home/daniel/catkin_ws/devel;/opt/ros/kinetic
-- This workspace overlays: /home/daniel/catkin_ws/devel;/opt/ros/kinetic
-- Using PYTHON_EXECUTABLE: /home/daniel/anaconda3/bin/python
-- Using Debian Python package layout
-- Using empy: /usr/bin/empy
-- Using CATKIN_ENABLE_TESTING: ON
-- Call enable_testing()
-- Using CATKIN_TEST_RESULTS_DIR: /home/daniel/catkin_ws2/build_isolated/cartographer_ros_msgs/test_results
-- Found gtest sources under '/usr/src/gtest': gtests will be built
-- Using Python nosetests: /home/daniel/anaconda3/bin/nosetests
ImportError: "from catkin_pkg.package import parse_package" failed: No module named 'catkin_pkg'
Make sure that you have installed "catkin_pkg", it is up to date and on the PYTHONPATH.
CMake Error at /opt/ros/kinetic/share/catkin/cmake/safe_execute_process.cmake:11 (message):
  execute_process(/home/daniel/anaconda3/bin/python
  "/opt/ros/kinetic/share/catkin/cmake/parse_package_xml.py"
  "/opt/ros/kinetic/share/catkin/cmake/../package.xml"
  "/home/daniel/catkin_ws2/build_isolated/cartographer_ros_msgs/catkin/catkin_generated/version/package.cmake")
  returned error code 1
Call Stack (most recent call first):
  /opt/ros/kinetic/share/catkin/cmake/catkin_package_xml.cmake:63 (safe_execute_process)
  /opt/ros/kinetic/share/catkin/cmake/all.cmake:151 (_catkin_package_xml)
  /opt/ros/kinetic/share/catkin/cmake/catkinConfig.cmake:20 (include)
  CMakeLists.txt:27 (find_package)

The problem I think it is that it is getting anaconda python path. I have tried: sudo apt-get install --reinstall python-rospkg python-rosdep python-catkin-pkg python-rosinstall python-vcstools I will list you some commands I have seen in other questions, that might be useful:

echo $PYTHONPATH 
/home/daniel/catkin_ws/devel/lib/python2.7/dist-packages:/opt/ros/kinetic/lib/python2.7/dist-packages
dpkg -L python-catkin-pkg
/.
/usr
/usr/share
/usr/share/doc
/usr/share/doc/python-catkin-pkg
/usr/share/doc/python-catkin-pkg/changelog.Debian.gz
/usr/bin
/usr/bin/catkin_generate_changelog
/usr/bin/catkin_tag_changelog
/usr/bin/catkin_create_pkg
/usr/bin/catkin_test_changelog
/usr/bin/catkin_find_pkg
/usr/lib
/usr/lib/python2.7
/usr/lib/python2.7/dist-packages
/usr/lib/python2.7/dist-packages/catkin_pkg-0.3.1.egg-info
/usr/lib/python2.7/dist-packages/catkin_pkg-0.3.1.egg-info/top_level.txt
/usr/lib/python2.7/dist-packages/catkin_pkg-0.3.1.egg-info/dependency_links.txt
/usr/lib/python2.7/dist-packages/catkin_pkg-0.3.1.egg-info/requires.txt
/usr/lib/python2.7/dist-packages/catkin_pkg-0.3.1.egg-info/entry_points.txt
/usr/lib/python2.7/dist-packages/catkin_pkg-0.3.1.egg-info/PKG-INFO

which python
/home/daniel/anaconda3/bin/python

python -V
Python 3.6.0 :: Anaconda 4.3.0 (64-bit)

conda install -c auto catkin_pkg Fetching package metadata ........... Solving package specifications: .

UnsatisfiableError: The following specifications were found to be in conflict:
  - catkin_pkg -> argparse -> python 2.7* -> openssl 1.0.1*
  - python 3.6*
Use "conda info <package>" to see the dependencies for each package.

But when I run this command i get the following error:

python -c "import catkin_pkg; print(catkin_pkg.__version__)"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'catkin_pkg'

Any help here? Thanks a lot !!


Originally posted by Kailegh on ROS Answers with karma: 146 on 2017-03-13

Post score: 0


Original comments

Comment by gvdhoorn on 2017-03-13:\

Any help here? Thanks a lot !!

easiest would be to remove anaconda3/bin from your PATH.

Comment by jayess on 2018-01-09:
Here's some help from the IDE entry in the wiki

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2 Answers 2

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From the output of which python, it seems that your default python is anaconda python. Also, since your anaconda python is python3, it would be better to use ROS with another version (some python2 version).

I suggest you to use virtualenv (or virtualenvwrapper) and that way control which python you're using explicitly. Another solution could be modifying your PATH variable (I would guess that now /home/daniel/anaconda3/bin comes before /usr/bin, which is a default python location)


Originally posted by gavran with karma: 526 on 2017-03-13

This answer was ACCEPTED on the original site

Post score: 1


Original comments

Comment by Kailegh on 2017-03-13:
where can i modify the PATH variable? do I have to change it each time I want to use python3?

Comment by gavran on 2017-03-14:
so, the most elegant way would be working with virtualenvwrapper. That would enable you tho change between different versions easily.

Comment by gavran on 2017-03-14:
If not, check your ~/.bashrc file. There should be a line that says sth like: export PATH=/home/daniel/anaconda3/bin:$PATH. remove this anaconda part and then - when you want to use anaconda, write explicitly /home/daniel/anaconda3/bin/python. don't forget to reopen terminal afterwards

Comment by gavran on 2017-03-14:
... for the changes to take place (alternatively, run source ~/.bashrc

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Gavran already explained the problem very well.

Here's just another way to solve the issue.
The easiest solutions like using the full path, exporting the path every time it's needed or creating a second user account for Anaconda aren't really convenient which is why I wrote this little script:

https://gist.github.com/StefanFabian/17fa715e783cd2be6a32cd5bbb98acd9

What it does
It basically scans the Anaconda binary folder and for each executable that isn't present on the system already, it creates an alias. Now, when you execute the command e.g. anaconda-navigator, it adds Anaconda to PATH, executes anaconda-navigator (which is now in PATH) and after anaconda-navigator terminated, it removes Anaconda from PATH again.
For more information and how to use it check the top of the script and the comment on GitHub below the script.

Disclaimer
I'm not very good at bash, so, if someone with more experience could take a look at the script, that'd be great.
For now view this script as beta, it works for me but it needs to be tested by more people.
I've tested it on Ubuntu 16.04 with ROS Kinetic but in theory it should work on any bash system.
Don't know about zsh, etc. though.

Here's a copy of the script at the time of writing for the unlikely event that the link goes dead

Update 1: The script now removes ROS from the PATH to prevent issues with ROS python stuff that is incompatible with the Anaconda environment python version. To make this functionality as general as possible, the python path is backed up when the script is sourced, therefore, the script has to be source before any ROS setup bash is sourced.

### This script wraps all executables in the anaconda bin folder so that they can be used without adding Anaconda
### to the path which would break some functionality of ROS (Robot Operating System)
###
### The commands e.g. jupyter notebook will cause the script to add anaconda to the path, start jupyter notebook
### and after jupyter notebook terminated remove anaconda from the path again
###
### Notable commands:
### * release-the-snake       Adds conda to the path and removes all aliases defined by this script
###                           Conda will stay in the PATH until the end of the session (terminal is closed) or
###                           until "cage-the-snake" is called
### * cage-the-snake          Removes conda from the path and redefines all aliases for anaconda executables
### * source activate [env]   Works just like with anaconda in the PATH, will activate the environment or (root) and
###                           Anaconda will stay in the PATH for the remaining session or until "source deactivate" is run
### * source deactivate       Deactivates the environment and if Anaconda wasn't released manually using release-the-snake
###                           Anaconda will be removed from the PATH again.

if [ -z ${_ROS_CONDA_ADDED+x} ]
then
  _ROS_CONDA_PATH=~/anaconda3/bin
  _ROS_CONDA_ADDED=0
  _ROS_CONDA_ALIASES=''
  _ROS_CONDA_RELEASED_MANUALLY=0
  _ROS_CONDA_PYTHONPATH_WITHOUT_ROS=$PYTHONPATH
fi

function _ROS_CONDA_addAliases {
  if [[ $_ROS_CONDA_ALIASES != '' ]]
  then
    echo "ROS Conda Wrapper: Error! Aliases already defined!"
    _ROS_CONDA_removeAliases
  fi
  
  for file in $_ROS_CONDA_PATH/*
  do
    local name
    name=${file##*/}
    if ! [ -x "$(command -v $name)" ]
    then
      alias $name='_ROS_CONDA_runWithConda '$name' $@'
      _ROS_CONDA_ALIASES=$_ROS_CONDA_ALIASES" "$name
    fi
  done
}

function _ROS_CONDA_removeAliases {
  for cmd in $_ROS_CONDA_ALIASES
  do
    unalias $cmd
  done
  _ROS_CONDA_ALIASES=''
}

function _ROS_CONDA_runWithConda {
  _ROS_CONDA_ensureCondaInPath
  command $@
  _ROS_CONDA_removeCondaFromPath
}

function _ROS_CONDA_ensureCondaInPath {
  if [ $_ROS_CONDA_ADDED -eq 1 ]
  then
    return 1 # false
  fi
  _ROS_CONDA_ADDED=1

  # Check that the path doesn't start, end or contain the ros conda path
  if [[  $PATH != $_ROS_CONDA_PATH":"* && $PATH != *":"$_ROS_CONDA_PATH && $PATH != *":"$_ROS_CONDA_PATH":"* ]]
  then
    export PATH=$_ROS_CONDA_PATH:$PATH
    # Backup and clear python path to keep ros from checking ros directories for python modules
    _ROS_CONDA_PYTHONPATH_BACKUP=$PYTHONPATH
    export PYTHONPATH=$_ROS_CONDA_PYTHONPATH_WITHOUT_ROS

    # Unalias the stuff
    _ROS_CONDA_removeAliases

    return 0 # true
  fi
  return 1
}

function _ROS_CONDA_removeCondaFromPath {
  if [[ $PATH = $_ROS_CONDA_PATH":"* ]]
  then
    export PATH=${PATH#$_ROS_CONDA_PATH:}
  elif [[ $PATH = *":"$_ROS_CONDA_PATH ]]
  then
    export PATH=${PATH%:$_ROS_CONDA_PATH}
  elif [[ $PATH = *":"$_ROS_CONDA_PATH":"* ]]
  then
    export PATH=${PATH//:$_ROS_CONDA_PATH:/:}
  fi

  if [ $_ROS_CONDA_ADDED -eq 1 ]
  then
    # Restore ROS PYTHONPATH
    export PYTHONPATH=$_ROS_CONDA_PYTHONPATH_BACKUP
    _ROS_CONDA_addAliases
  fi

  _ROS_CONDA_ADDED=0
}

function _ROS_CONDA_sourceWrapper {
  if [ $1 == "activate" ]
  then
    _ROS_CONDA_ensureCondaInPath
    if [ $# == 1 ]
    then
    # If only source activate call source activate root.
    # Otherwise it will fail. Don't know why though
      command source activate
    else
      command source $@
    fi
  elif [ $1 == "deactivate" ]
  then
    command source deactivate
    if [ $_ROS_CONDA_RELEASED_MANUALLY -eq 0 ]
    then
      _ROS_CONDA_removeCondaFromPath
    fi
  else
    command source $@
  fi
}

if [ $_ROS_CONDA_ADDED -eq 0 ]
then
  if [[ $_ROS_CONDA_ALIASES != '' ]]
  then
    _ROS_CONDA_removeAliases
  fi
  _ROS_CONDA_addAliases
fi

alias source='_ROS_CONDA_sourceWrapper'
alias release-the-snake='_ROS_CONDA_RELEASED_MANUALLY=1; if _ROS_CONDA_ensureCondaInPath; then echo "All hail the snake!"; else echo "The snake is in another castle!
Jk, you released it already."; fi'
alias cage-the-snake='_ROS_CONDA_RELEASED_MANUALLY=0; _ROS_CONDA_removeCondaFromPath; echo "The snake has been caged if it wasn'"'"'t already."'

Originally posted by StefanFabian with karma: 46 on 2018-01-09

This answer was NOT ACCEPTED on the original site

Post score: 2

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