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When I updated MikTeX through the automatic update program, I could not compile afterwards. It could not find pdftex-def. I then uninstalled MiKTeX and reinstalled it again. Now it is working again. If I run the update program again, I can see that pdftex-def is obsolete and will be removed. Is that was caused the problem in the first place? Is this a bug?

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    there should be a package graphics-def that has pdftex.def and several other def files that you can install. This was supposed to be an "invisible" re-organisation of some files in the distribution (to fit with current maintainers) but it seems that the move from pdftex-def to graphics-def isn't always as automatic as we hoped:-) – David Carlisle Aug 2 '16 at 11:36
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    Let MiKTeX Updater remove it, and install via MiKTeX Package Manager (if not proposed by the Updater) graphics-def. – Bernard Aug 2 '16 at 11:40
  • Should I just update MiKTeX again, and not expect the same problem occurs again? graphics is being updated to 1.0s (15-jul-2016). – TobiasDK Aug 2 '16 at 11:42
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    When packages are reorganized you should synchronize your offline package database tex.stackexchange.com/a/108490/2388 – Ulrike Fischer Aug 2 '16 at 11:42
  • OK - I go ahead again and automatic update MikTeX, and after that, manual install graphics-def in PM. Will post the result here. – TobiasDK Aug 2 '16 at 11:45
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A clean install of MiKTeX solved the problem. Now I can run the automatic update via MiKTeX which automatic remove pdftex-deffrom MikTeX, without any problems.

Edit: as pointed out by Ulrike Fischer, I did not need to make a clean install of MikTeX, just find the missing package and install that in the package manager.

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    Reinstalling miktex is not necessary. You only need to run the standard administration tools, like synchronizing, checking for new packages in the package manager and running the update manager. I had a missing pdftex.def too after one of the last updates and it took me only 5 minutes to get it. – Ulrike Fischer Aug 2 '16 at 13:09

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