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An extra staff appears

If contexts are not created explicitly with \new or \context, they will be silently created as soon as a command is encountered which cannot be applied to an existing context. In simple scores the automatic creation of contexts is useful, and most of the examples in the LilyPond manuals take advantage of this simplification. But occasionally the silent creation of contexts can give rise to unexpected new staves or scores. For example, it might be expected that the following code would cause all note heads within the following staff to be colored red, but in fact it results in two staves with the note heads remaining the default black in the lower staff.

\override Staff.NoteHead.color = #red
\new Staff { a' }

This is because a Staff context does not exist when the override is processed, so one is implicitly created and the override is applied to it, but then the \new Staff command creates another, separate, staff into which the notes are placed. The correct code to color all note heads red is

\new Staff {
  \override Staff.NoteHead.color = #red
  a'
}

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LilyPond Application Usage v2.25.14 (development-branch).