A LaTeX document that compiled with pdflatex without errors on Windows using MikTeX was failing with this error on Ubuntu:
Package epstopdf Warning: Shell escape feature is not enabled. ! Package pdftex.def Error: File `foobar-eps-converted-to.pdf' not found.
The document used the epstopdf package to include EPS figures. A foobar.eps figure that is included in the document would be converted to a PDF file named foobar-eps-converted-to.pdf. The inclusion of foobar.eps in the document was giving this error on Ubuntu.
It turns out that epstopdf converts the included EPS document to PDF at compile time. This requires a feature of pdflatex called shell escape. This seems to be enabled in MikTeX on Windows, but disabled in Ubuntu. The error went away on enabling the shell escape feature manually while compiling the document:
$ pdflatex --shell-escape main.tex
Tried with: Ubuntu 12.04.2 LTS