No, QScintilla is useful when you want to use the shell in Visualea

(posted by T.Cokelaer on 27 August 2009)

When using python setup.py develop or python setup.py bdist_egg, I get : "unrecognized .svn/entries format; skipping ."

• Reason: you've updated SVN and setuptools is not compatible with it.
• Effect: when creating eggs, the tag corresponding to the release is always set to 0.
• Fix: wait for a new release of setuptools or apply this patch:

  in setuptools/command/egg_info.py:
  -            if data.startswith('8'):
  +            if data.startswith('8') or data.startswith('9'):

  in setuptools/command/sdist.py:
  -    if data.startswith('8'):    # subversion 1.4
  +    if data.startswith('8') or data.startswith('9'):  

This issue has been solved under Fedora Core 11 (Fedora re-packaged their own setuptools?).

During SVN checkout/update, you can have the following error:

  E000022: Can't convert string from 'UTF-8' to native encoding

You can fix it by doing:

  export LC_CTYPE=fr_FR.UTF-8
  locale-gen fr_FR.UTF-8
  

You can change langage (en_EN, fr_FR, ru_RU…). Then retry SVN checkout/update.

When you compile the sources (python setup.py install), you may get an error like:

   Exception: Qt4 command 'moc' not found. Tried: /usr/bin/moc-qt4 and /usr/bin/moc:

This mean that you do not have developments tools installed on your sytem. In the case above, you should install the development tools associated to Qt4. Search for your platform in the following link source_distribution and install the packages that are in the developers tools section.

If you got this kind of error message:

Traceback (most recent call last):
  File "ez_alea_setup.py", line 584, in <module>
    install_setuptools()
  File "ez_alea_setup.py", line 343, in install_setuptools
    main(sys.argv[1:])
  File "ez_alea_setup.py", line 213, in main
    pkg_resources.require(req)
  File "/usr/lib/python2.5/site-packages/pkg_resources.py", line 626, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/usr/lib/python2.5/site-packages/pkg_resources.py", line 524, in resolve
    raise DistributionNotFound(req)  # XXX put more info here
pkg_resources.DistributionNotFound: setuptools>=0.6c9

Reason: This is due to a setuptools conflict in the special file easy_install.pth. Solution: reinstall setuptools.

• Get the egg from the website:http://pypi.python.org/pypi/setuptools#files
• Follow the installation instructions: http://pypi.python.org/pypi/setuptools#id1 (e.g. under linux type *sh <filename.egg>*)

Installation with binary installer 1.1 and 1.2 may lead to unstabilities of the aplication on XP (unexpected crashes of visualea). In this case, you may use installer 1.0, available on gforge.

Windows Vista add security policy for environment variable modification that can make installation failed. In this case, you may have such message appearing:

The following directories contains shared library : C:\Python26\Lib\site-packages\shared_libs 

The following directories contains binaries : c:\python26\lib\site-packages\vplants.plantgl-2.9.4-py2.6-win32.egg\bin 

Unexpected error: <type 'exceptions.SystemExit'>
Please check you have permission to install package in the destination directory.

To solve this, you have to deactivate user account control. To do this, you have to do Open Configuration Panel; Choose User Accounts and Family Safety; Then Change security settings; Then unckeck the check box Use User Account Control (UAC) to help protect you computer. You will be ask to reboot. Once rebooted, you can open a shell and type

C:\Python26\Scripts\alea_config.exe

The environment variable should be updated. You can now reactivate the User Account Control by re checking the chek box Use User Account Control (UAC) … in Configuration Panel. Note that each time you install or update a new package, environment variables have to be updated. Thus you have to redo all this process.

With IE (Internet Explorer), when I click on the link ez_alea_setup.py (Step 2) I have a text beginning with: #!python ””“Bootstrap setuptools installation If you want to use setuptools in your package's setup.py, just include this file in the same …

⇒ You must download and execute the file

1. Right click on the link → save target as
2. When the download is finished, click on Open

nota : You can also use Firefox.

When I start Visualea or the OpenAlea installer, I have an error message like this:

Le point d'entrée de procedure _Z5qFreePv est introuvable dans la bibliothèque dynamique 
QtCore4.dll 

It means that there is a conflict between different QT4 versions

⇒ Check your PATH environment variable

⇒ For MikTex / Lyx Users : by default, the installation of Miktex add a directory in the PATH variable. This configuration is not mandatory. Remove it from the PATH variable and restart Visualea.

An error message related to matplotlib appears when trying to run a demo or dataflow that uses matplotlib. The error message complains about a missing DLL (DLL not loaded)

After a fresh install of openalea/visualea, some nodes and/or demos that use matplotlib interface fail with an error message that ends as follow:

from matplotlib._nstransforms import *
DLL load failed: Couldn't find one of the files of the library needed
to run this program.

Similarly in the python shell, you get an error message that is more specific and mention the missing DLL: msvcp71.dll.

This library is not part of your system. You need to install it manually. The easiest way is retrieve the library from a web site such as http://www.dll-files.com. Once done, copy the file msvcp71.dll to c:\windows\system (not system32!)

After a fresh installation, demos (such as fractalysis, adel) fail with an error message related to R/rpy2

Some nodes depend of R/rpy: you have to install compatible versions of R and rpy.

The rpy2 binaries shiped with Alinea installers curreently do not support R 3.xx

You must use an Rpy binary that corresponds to the version of R, and Python you have installed. For example, rpy-0.4.6-R-2.0.0-to-2.2.1-py25.win32.exe is for

• RPy version 0.4.6
• R versions 2.0.0 through 2.2.1
• Python version 2.5

If you have this error:

  from rpy import *
 
  File "C:\Python25\Lib\site-packages\rpy.py", line 134, in
    """ % RVERSION)
 
RuntimeError: No module named _rpy2080 RPy module can not be imported. 
Please check if your rpy installation supports R 2.8.0. 
If you have multiple R versions installed, you may need to set RHOME before importing rpy. 
For example: 
>>> from rpy_options import set_options 
>>> set_options(RHOME='c:/progra~1/r/rw2011/') 
>>> from rpy import *

this means that your R version is not compatible with RPy version.

Please install a compatible version of R, which can be downloaded from R download page. Follow the link “window”, “base”, “old” and the version of R that you want to install (e.g., 2.6.2).

If “universe” repository is not enable, you can fix it reading this.

When starting a demo, the following errors arises:

ImportError:libtinfo.so.5: cannot open shared object file: No such file or directory

Under Ubuntu, version 8.10, the entrypoints for libinfo are part of ncurses. The libtinfo.so functionality is built into the libncurses.so shared library.

For software that expects the libtinfo.so object, do the following:

sudo ln -s /usr/lib/libncurses.so.5 /usr/lib/libtinfo.so.5
sudo ln -s /usr/lib/libtinfo.so.5 /usr/lib/libtinfo.so

When starting a demo, the following errors arises:

ImportError:libboost_python.so.3: cannot open shared object file: 
No such file or directory

Under Ubuntu, version 8.10, the entrypoints for libboost_python may be different from those under which the egg where compiled. A solution can be to create a symbolic link to your libboost_python version

sudo ln -s /usr/lib/libboost_python-py25.so /usr/lib/libboost_python.so.3

Use ipython and its -q4thread option to enable Qt Gui Thread.

ipython --gui=qt
>>> ...

Note that since ipython 0.13, this option has been replaced by ipython –gui=qt.

If you get an error of type:

Library not loaded: QtGui.framework/Versions/4/QtGui

when you run :

sudo alea_install_gui

That is due to the environmental variables which are not set by the “sudo” (see man sudo). To resolve this matter, you have to specify the environmental variable as follows :

sudo DYLD_FRAMEWORK_PATH=/usr/local/lib alea_install_gui

problem : In the version 0.98.5.2 of matplotlib, there is a bug related to the legend. If a Collection of Lines is used, then calling the legend function raise this error:

AttributeError: 'Line2D' object has no attribute '_legmarker'

Solution: update to 0.99 or :

A temporary solution (that is apparently fixed in the matplotlib SVN) is to edit

C:\Python25\lib\site-packages\matplotlib\legend.py

and replace line 523 with

              if hasattr(handle, '_legmarker'):
                  handle._legmarker.set_ydata(ydata)

and line 627, add

  if hasattr(handle, "_legmarker"):

before

                  legline_marker = legline._legmarker
                  legline_marker.set_data(xdata_marker, ydata[:len(xdata_marker)])

Lets say that you have a dataflow in VisuAlea and that you want to execute it from an external python script without invoking the visualea environment.

The first solution is from the VisuAlea environment to export the dataflow into an independent application, as explained on the Wiki:

http://openalea.gforge.inria.fr/dokuwiki/doku.php?id=packages:core:visualea:manual&s[]=run#export_application

Second solution, as a python fan, you can go into a python shell and type the following commands:

  >>> from openalea.core.alea import run
  >>> from openalea.core.pkgmanager import PackageManager
  >>> pkg = PackageManager()
  >>> pkg.init()
  >>> run(('dataflow package', 'dataflow name'),{},pm=pkg)

where dataflow pacakge and dataflow name should be replaced by those of your application.

If your application is using X ouput like 3D plot, starts your python shell with ipython as follows:

  >>> ipython --gui=qt