I have files that use the imakeidx package that uses either the restricted/protected \write18 modern TeX system feature or the full unrestricted \write18 feature. My MacTeX installation is configured with the restricted/ptotected \write18 feature as all 2013 distributions should be by default; in facts the automatic index production works perfectly by running any of my files with TeXShop; On my Ubuntu and Windows virtual machines, with TeXlive 2013 the \write 18 feature works perfectly.
Om Mac with TeXstudio, on the opposite, I get the message:
sh: makeindex: command not found
Makeindex is a normal program belonging to any TeX distribution; in facts makeindex works well by clicking the Index entry in the Tool menu, but it is being run without options and it operates in an asynchropous way as it used to be since the old times.
Package imakeidx allows to send the operating system a line command with any valid option makeindex can accept; imakeidx has many more features, as, for example, prepare and typeset in synchronous mode several thematic indices, with different index styles, different headers, optional insertion in the toc, optional use (te)xindy in place of makeindex, and many other features. None of this functionality is available with TeXstudio that, evidently, does interferes in the wrong way with the shell escape feature (\write18) of modern TeXlive distributions. I tried to explicitly add the -shell-escape option to the TeXstudio pdflatex command, but with no visible effects.
I suggest to consider adjusting this TeXstudio "deficiency".
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