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I installed the 32-bit version of the latest QGIS (2.18.16) and get this error message when loading restored plugins:

C:PROGRA~1\QGIS2~1.18\apps\saga-ltr\saga_cmd.exe is not a valid Win32 application.

Where do I remove the reference to this executable?

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I had the same problem and fixed it by:

  1. getting the win32 zip of SAGA-GIS v. 2.3.1 (not ltr, there is no reference of ltr there) from their sourceforge repository https://sourceforge.net/projects/saga-gis/files/SAGA%20-%202/SAGA%202.3.1/
  2. going to the \apps subfolder of the qgis installation folder (by default c:\Program Files\QGIS 2.18\apps) and renaming folder saga-ltr to something different, e.g. saga-ltrback
  3. unzipping the files from sourceforge there (as a subfolder of \apps) and renaming the created folder (in this case saga_2.3.1_win32) to saga-ltr.

This seems to work; there are no warning and I tried two geoalgorithms and they seemed to work as expected. I haven't done extended tests though.

Before that, I had tried:

  • to use osgeo4w setup (advanced mode) to download the saga-ltr package and replace as above--it was the same version (2.3.2) as the one that comes with qgis 2.18.16, and they were the exact same files and also didn't work

  • to use osgeo4w setup (advanced mode) to download the saga package and replace as above--it was version 2.1.2, it started as a standalone and qgis started without warnings, but there were no SAGA geoalgorithms in the qgis toolbox.

I hope this helps for the time being.

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