This has started happening since a few days ago with android GN builds (with internal android repo checked out if that matters):

% ninja -C out_android/Release/ chrome_apk
ninja: Entering directory `out_android/Release/'
ninja: warning: multiple rules generate libchrome.so. builds involving this target will not be correct; continuing anyway [-w dupbuild=warn]
ninja: warning: multiple rules generate libchrome.so.TOC. builds involving this target will not be correct; continuing anyway [-w dupbuild=warn]
ninja: warning: multiple rules generate lib.unstripped/libchrome.so. builds involving this target will not be correct; continuing anyway [-w dupbuild=warn]
ninja: warning: multiple rules generate libmonochrome.so. builds involving this target will not be correct; continuing anyway [-w dupbuild=warn]
ninja: warning: multiple rules generate libmonochrome.so.TOC. builds involving this target will not be correct; continuing anyway [-w dupbuild=warn]
ninja: warning: multiple rules generate lib.unstripped/libmonochrome.so. builds involving this target will not be correct; continuing anyway [-w dupbuild=warn]


I was getting this error instead but somehow bypassed that, I think by trying to build android_webview_apk once.

[1/1] Regenerating ninja files
FAILED: build.ninja 
/usr/local/google/home/danakj/s/c/src/buildtools/linux64/gn --root=/usr/local/google/home/danakj/s/c/src -q gen //out_android/Release/
ERROR at //chrome/android/BUILD.gn:441:1: Duplicate output file.
shared_library("chrome") {
^-------------------------
Two or more targets generate the same output:
  libchrome.so

This is can often be fixed by changing one of the target names, or by 
setting an output_name on one of them.

Collisions:
  //chrome/android:chrome
  //clank/native:libchrome

See //clank/native/BUILD.gn:48:1: Collision.
shared_library("libchrome") {
^----------------------------
ninja: error: rebuilding 'build.ninja': cannot make progress due to previous errors