I am trying to write a thesis following a template that has the following glossary items: Glossary, Abbreviations, Nomenclature and Symbols (some of them are part of the 'glossaries-extra' package). When I build the project normally, everything works fine, and these are the output files generated:

Files that are outputted normally (without using a sub-directory).

However, when I change the settings in Texmaker to use a sub-directory for the output files ("Options" -> "Configure Texmaker" -> "Commands" -> "Use a "build" subdirectory for output files"), some files aren't generated and I get an error message displayed on each page where the 4 glossary items should be:

Error message that shows up in the PDF document.

These are the files generated in the sub-directory and there are quite a few missing:

Files inside the "build" sub-directory.

There's also the following warning messages in Texmaker:

Warning messages inside the Texmaker window when running with "build" sub-directory enabled.

If I switch back to letting the output files go to the main folder, it runs again without any issues. It seems that the "build" sub-directory is causing the issue but I'm not sure why. Am I missing something?


For anyone who comes across this problem later, I managed to solve it using the solution to this question. I followed these steps:

  1. Install ActivePerl.
  2. Running perltex.exe to install the package with MiKTeX.
  3. Making the user command using makeglossaries as described in the solution.

Then, I am able to build the document normally, run makeglossaries and build the document again.

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