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I need help troubleshooting a problem using the Clip tool with QGIS 2.8.1 Wien.

When I try to use the tool, it just sits there idling and never finishes. I've let this run for hours and there hasn't been any change in the progress meter.

I've checked that all of the support libraries (numpy, gdal, python, etc) are up to date - they are - but it doesn't make any difference.

I've made sure that the CRS is the same for both layers.

I've reviewed the Console output on my mac but don't see any errors appearing (maybe there's another log file to check for QGIS?).

Here is a screen shot of what I'm seeing (note that the name for the "Output shapefile" disappears after I click the OK button): Screen shot of clip tool in QGIS

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    How big are the input files? Did you check if the feature geometries are valid? Can you share the data for debugging purposes?
    – underdark ♦
    Oct 19, 2015 at 21:46
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    The input layer contains a bit less than 80,000 polygons (almost 80MB in size) and the clip layer has one polygon (<25KB in size). I think the geometries are valid; I've been able to do other work the same layers. I can share the data, but it'd need to be a non-public repository. I can send you a PM on Twitter or an email since I don't think we can PM on StackExchange.
    – Twitch
    Oct 19, 2015 at 22:14
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    If you want to test if clipping works at all, start with simple layers with only a few hand-drawn objects with only a few vertices. If that works, try more complicated geometries.
    – AndreJ
    Oct 20, 2015 at 6:16

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I opened the log viewer in View > Panels > Log Messages and saw references to broken symlinks from a previous version of OS-X.

Ideally QGIS wouldn't silently drop errors and could let the user know when a problem occurs.

I don't know enough about QGIS to understand how to refresh, rebuild, or specify links to libraries, so I deleted QGIS from the Applications folder, re-installed the required libraries with HomeBrew, and re-installed QGIS.

Then I re-ran the Clip tool and everything worked fine.

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