A few months ago, we published a new paper 1 (PDF).
For the 3 figures in the manuscript, we created some adjacency matrices that we wanted to be fully reproducible, so we decided to upload our code.
Because I had anticipated problems with .R files, I uploaded the syntax as a .txt file instead. A month or two later, when the manuscript appeared online, I found out that the copy editor had first taken screenshots of each page of code, and then put these screenshots into a word file that was available as supplementary material to our paper. You can find this piece of beauty for download here.
See below for the somewhat flabbergasted email I sent to the editor:
Flabberghasted, really? If someone really needs to use your code they can email you.
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