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Using QGIS 2.14.3 on Ubuntu 16.04, I created a custom icon using inkscape for QGIS. You can find it here (Update: that icon is now fixed). In inkscape, in my filesystem, it displays as:
enter image description here

However in QGIS, it displays as

enter image description here

The colors are transparent. How can I fix this?

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I see the same issue. Took a look at this file in InkScape, and used Shift-Ctrl-F to bring up the Fill and Stroke properties.

I noticed that the fill on your green and blue areas were set to 'pattern fill', stripes 1:1.

Make a note of your blue and green colours first. Next, change to use 'Flat Color' on both the coloured areas, then reselect your colours manually.

Save as a new SVG, using "Plain SVG" (to be on the safe side), and you'll find it works...

Go from:-

enter image description here

to...

enter image description here

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  • Nail on the head. I fixed the pattern and was updating the question, but needed to also save it as a plain svg
    – raphael
    Jun 29 '16 at 19:35

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