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baliga-lab / cmonkey2

Python port of cMonkey, a machine-learning based method for clustering
GNU Lesser General Public License v3.0
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Python 2.7.x/pip Installation issue (was: I can't load.) #56

Closed jacobvalenzuela closed 7 years ago

jacobvalenzuela commented 8 years ago

palomino:Val_Tests jake$ pip install cmonkey2 Collecting cmonkey2 Downloading cmonkey2-1.2.0-py2.py3-none-any.whl (1.0MB) 100% |████████████████████████████████| 1.0MB 245kB/s Collecting biopython (from cmonkey2) Downloading biopython-1.67.tar.gz (14.3MB) 100% |████████████████████████████████| 14.3MB 18kB/s Requirement already satisfied (use --upgrade to upgrade): scipy in /Users/jake/anaconda/lib/python2.7/site-packages (from cmonkey2) Requirement already satisfied (use --upgrade to upgrade): pandas in /Users/jake/anaconda/lib/python2.7/site-packages (from cmonkey2) Requirement already satisfied (use --upgrade to upgrade): beautifulsoup4 in /Users/jake/anaconda/lib/python2.7/site-packages (from cmonkey2) Requirement already satisfied (use --upgrade to upgrade): numpy in /Users/jake/anaconda/lib/python2.7/site-packages (from cmonkey2) Collecting configparser (from cmonkey2) Downloading configparser-3.5.0.tar.gz Requirement already satisfied (use --upgrade to upgrade): jinja2 in /Users/jake/anaconda/lib/python2.7/site-packages (from cmonkey2) Collecting cherrypy (from cmonkey2) Downloading CherryPy-7.1.0.tar.gz (416kB) 100% |████████████████████████████████| 417kB 556kB/s Requirement already satisfied (use --upgrade to upgrade): lxml in /Users/jake/anaconda/lib/python2.7/site-packages (from cmonkey2) Collecting routes (from cmonkey2) Downloading Routes-2.3.1.tar.gz (181kB) 100% |████████████████████████████████| 184kB 852kB/s Collecting rpy2 (from cmonkey2) Downloading rpy2-2.8.2.tar.gz (186kB) 100% |████████████████████████████████| 188kB 1.3MB/s Complete output from command python setup.py egg_info: Warning: Tried to guess R's HOME but no command (R) in the PATH.

----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/ch/v4y76w5s71v49lgcgtl_dwj40000gt/T/pip-build-LyPIgo/rpy2 You are using pip version 7.1.2, however version 8.1.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

weiju commented 8 years ago

It looks like you don't have R in your path, and the problem is when you try to install rpy2, could you try to install rpy2 separately ? Looks like you are anaconda, which should not be a problem, but I haven't tried it yet, are you on a Mac, Windows or Linux ?

jacobvalenzuela commented 8 years ago

mac

Jacob J. Valenzuela, Ph.D. Institute for Systems Biology 401 Terry Ave N Seattle WA 98109 (206)-732-1496 https://www.systemsbiology.org Jake.Valenzuela@systemsbiology.org

On Mon, Aug 15, 2016 at 2:24 PM, Wei-ju Wu notifications@github.com wrote:

It looks like you don't have R in your path, and the problem is when you try to install rpy2, could you try to install rpy2 separately ? Looks like you are anaconda, which should not be a problem, but I haven't tried it yet, are you on a Mac, Windows or Linux ?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/baliga-lab/cmonkey2/issues/56#issuecomment-239933649, or mute the thread https://github.com/notifications/unsubscribe-auth/AOgAMZSwqhuCb71SQUUluKZmEJsyn1vRks5qgNj0gaJpZM4JkyG8 .

jacobvalenzuela commented 8 years ago

I got this error when installing rpy2

palomino:~ jake$ pip install rpy2

Collecting rpy2

Using cached rpy2-2.8.2.tar.gz

Complete output from command python setup.py egg_info:

Warning: Tried to guess R's HOME but no command (R) in the PATH.

----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/ch/v4y76w5s71v49lgcgtl_dwj40000gt/T/pip-build-wR0bki/rpy2/

Jacob J. Valenzuela, Ph.D. Institute for Systems Biology 401 Terry Ave N Seattle WA 98109 (206)-732-1496 https://www.systemsbiology.org Jake.Valenzuela@systemsbiology.org

On Mon, Aug 15, 2016 at 2:32 PM, Jake Valenzuela < Jake.Valenzuela@systemsbiology.org> wrote:

mac

Jacob J. Valenzuela, Ph.D. Institute for Systems Biology 401 Terry Ave N Seattle WA 98109 (206)-732-1496 https://www.systemsbiology.org Jake.Valenzuela@systemsbiology.org

On Mon, Aug 15, 2016 at 2:24 PM, Wei-ju Wu notifications@github.com wrote:

It looks like you don't have R in your path, and the problem is when you try to install rpy2, could you try to install rpy2 separately ? Looks like you are anaconda, which should not be a problem, but I haven't tried it yet, are you on a Mac, Windows or Linux ?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/baliga-lab/cmonkey2/issues/56#issuecomment-239933649, or mute the thread https://github.com/notifications/unsubscribe-auth/AOgAMZSwqhuCb71SQUUluKZmEJsyn1vRks5qgNj0gaJpZM4JkyG8 .

weiju commented 8 years ago

so it seems that your R is installed in a way that it is not visible from the command line, maybe you are using RStudio as a Mac OS X app, or something like that ? For this to work, typically, you will have to install R in a way that it can be called from the command line, e.g. on the Mac that is typically done through Homebrew or Macports.

weiju commented 7 years ago

we have now solved this by using a centralized version on our ISB servers