I too receive the same warning message when applying the perspective effect. However, when I click the Ok box, the effect completes correctly.
Here are the steps I use to achieve a successful perspective transformation, using Ubuntu 9.04/Inkscape .46:
1. Use

to create some text.
2. Convert the text to a path [Path>Object to Path(Shift+Ctrl+C)].
3. Starting with the bottom left corner, draw a box with the

with exactly 4 nodes.
4. Select the text, press shift and select the box.
The order you select the text and the perspective box is important. Make sure you select the text first.5. Then apply the perspective, Effects->Modify Path-> Perspective
The warning message box will pop up, press ok.
Code: Select all
/usr/share/inkscape/extensions/perspective.py:71: DeprecationWarning: os.popen3 is deprecated. Use the subprocess module.
_,f,err = os.popen3("inkscape --query-%s --query-id=%s %s" % (query,id,file))
First post, hope this helps everybody.