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I run Arduino IDE on both my Mac and under Raspbian on a Raspberry Pi, both running the latest version of OS.

The Raspberry Pi has Arduino 2:1.0.5+dfsg2-4.1 and I am running the latest 1.8.4 on macOS. Debian is always somewhat behind the latest software, and this has not concerned me before, as I have never had issues before. (I know I could download the latest ARM32 build or compile from source, but this would probably generate a lot of dependencies.)

I have recently run into a couple of problems. Compiling a script which has #include <SdFat.h> generates an error, although the library is present in ~/sketchbook/libraries/SdFat/src/SdFat.h. This does not seem to be an issue on macOS.

I was also trying to program an Atmega using a Uno as ISP as in "Using an Arduino as an AVR ISP". I have done this in the past, but the instructions and the Arduino program seem to have changed; there is no longer "Upload Using Programmer" menu, but suggests the "Burn Bootloader" command. Does this upload both the Bootloader and Sketch?

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Debian is always somewhat behind the latest software

No, when it comes to the Arduino IDE Debian is frozen on an ancient version.

1.0.5 is considered to be too old to use. Many many things have changed since then - bug fixes, optimisations, new API components. And not least the implementation of the Board Manager for installing support for more boards, both by Arduino and other makers, and support for multi-arch libraries (which your SdFat library is with a src folder in it).

You should never install the Arduino IDE from the Debian repositories. Instead you should download the current version of the Arduino website (http://arduino.cc/download) as a tar.\z file and extract it into a folder and run it from there.

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Majenko answered why my sketch did not compile.

I decided to give it a try and downloaded arduino-1.8.4-linux32.tar.xz. I was somewhat concerned that there seemed to be no indication whether the Linux ARM supported ARM6, or ARM7.

The download itself contained absolutely no information, not even a README. I ran install.sh as outlined in https://www.arduino.cc/en/Guide/Linux and Arduino IDE installed alongside the existing Arduino IDE, and worked (at least on the PI3).

I also solved my issue using a Uno as ISP. The documentation on the Arduino site now describes "Use the Burn Bootloader command". I found the missing "Upload Using Programmer" menu under the Sketch menu.

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