nix doxy 3

Before I updated my default.nix with most of the restructuring in your example, I collected these from within nix-shell:

[nix-shell:~/.../doxygen/build]$ env | grep SQLITE3_INCLUDE_DIR
cmakeFlags=-DSQLITE3_INCLUDE_DIR=/nix/store/xxq4dfwhvv3b68zg0j1hff6bhydfrn26-sqlite-3.21.0-dev/include -Duse_sqlite3=ON -DICONV_INCLUDE_DIR=/nix/store/dwgxqvdv8mvckamsfz3zskay83w1xd02-glibc-iconv-2.25-123/include
[nix-shell:~/.../doxygen/build]$ cd src
[nix-shell:~/.../build/src]$ make
[  0%] Building CXX object src/CMakeFiles/_doxygen.dir/sqlite3gen.cpp.o
/home/myskran/work/doxygen/src/sqlite3gen.cpp:47:21: fatal error: sqlite3.h: No such file or directory
 #include <sqlite3.h>
                     ^
compilation terminated.
make[2]: *** [src/CMakeFiles/_doxygen.dir/build.make:1872: src/CMakeFiles/_doxygen.dir/sqlite3gen.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:255: src/CMakeFiles/_doxygen.dir/all] Error 2
make: *** [Makefile:163: all] Error 2

[nix-shell:~/.../build/src]$ ls /nix/store/xxq4dfwhvv3b68zg0j1hff6bhydfrn26-sqlite-3.21.0-dev/include
sqlite3ext.h  sqlite3.h


The I updated default.nix to:
with import <nixpkgs> {};
let
	doxygen = pkgs.doxygen.overrideDerivation (attrs: {
		name = "doxygen-1.8.13";
		src = ./.;
		buildInputs = attrs.buildInputs ++ [ pkgs.sqlite ];
		cmakeFlags = [ "-DSQLITE3_INCLUDE_DIR=${sqlite.dev}/include" "-Duse_sqlite3=ON"] ++ attrs.cmakeFlags;
});
in stdenv.mkDerivation {
	name = "env";
	buildInputs = [ doxygen pkgs.sqlite pkgs.python36 pkgs.python36Packages.pip pkgs.python36Packages.virtualenv ];
	shellHook = ''
		virtualenv --no-setuptools venv > /dev/null
	    export PATH=$PWD/venv/bin:$PATH > /dev/null
		pip install pcpp
	'';
}

moved doxygen/build to doxygen/build2, tried to run nix-shell...

[ 65%] Building CXX object src/CMakeFiles/_doxygen.dir/htmlgen.cpp.o
[ 65%] Building CXX object src/CMakeFiles/_doxygen.dir/htmlhelp.cpp.o
[ 66%] Building CXX object src/CMakeFiles/_doxygen.dir/image.cpp.o
[ 66%] Building CXX object src/CMakeFiles/_doxygen.dir/index.cpp.o
[ 67%] Building CXX object src/CMakeFiles/_doxygen.dir/language.cpp.o
[ 68%] Building CXX object src/CMakeFiles/_doxygen.dir/latexdocvisitor.cpp.o
[ 68%] Building CXX object src/CMakeFiles/_doxygen.dir/latexgen.cpp.o
[ 69%] Building CXX object src/CMakeFiles/_doxygen.dir/layout.cpp.o
[ 69%] Building CXX object src/CMakeFiles/_doxygen.dir/lodepng.cpp.o
[ 70%] Building CXX object src/CMakeFiles/_doxygen.dir/logos.cpp.o
[ 70%] Building CXX object src/CMakeFiles/_doxygen.dir/mandocvisitor.cpp.o
[ 71%] Building CXX object src/CMakeFiles/_doxygen.dir/mangen.cpp.o
[ 71%] Building CXX object src/CMakeFiles/_doxygen.dir/sqlite3gen.cpp.o
/tmp/nix-build-doxygen-1.8.13.drv-0/doxygen/src/sqlite3gen.cpp:47:21: fatal error: sqlite3.h: No such file or directory
 #include <sqlite3.h>
                     ^
compilation terminated.
make[2]: *** [src/CMakeFiles/_doxygen.dir/build.make:1872: src/CMakeFiles/_doxygen.dir/sqlite3gen.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:255: src/CMakeFiles/_doxygen.dir/all] Error 2
make: *** [Makefile:163: all] Error 2
builder for ‘/nix/store/figg7mybf1va9s8y5p6ivkflf6a9c653-doxygen-1.8.13.drv’ failed with exit code 2
error: build of ‘/nix/store/figg7mybf1va9s8y5p6ivkflf6a9c653-doxygen-1.8.13.drv’ failed
/run/current-system/sw/bin/nix-shell: failed to build all dependencies
[22:58:10] ~/work/doxygen[sqlite3_rebase*]$