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This may come as a surprise, but LilyPond isn't perfect. Some notation elements can overlap. This is unfortunate, but (in most cases) is easily solved.
e4^\markup{ \italic ritenuto } g b e
The easiest solution is to increase the distance between the object
(in this case text, but it could easily be fingerings or dynamics
instead) and the note. In LilyPond, this is called the
padding
property; it is measured in staff spaces. For most
objects, this value is around 1.0 or less (it varies with each
object). We want to increase it, so let's try 1.5
\once \override TextScript #'padding = #1.5 e4^\markup{ \italic ritenuto } g b e
That looks better, but it isn't quite big enough. After experimenting with a few values, we think 2.3 is the best number in this case. However, this number is merely the result of experimentation and my personal taste in notation. Try the above example with 2.3... but also try higher (and lower) numbers. Which do you think looks the best?
Another solution gives us complete control over placing the object – we
can move it horizontally or vertically. This is done with the
extra-offset
property. It is slightly more complicated and can
cause other problems. When we move objects with extra-offset
,
the movement is done after LilyPond has placed all other objects. This means
that the result can overlap with other objects.
\once \override TextScript #'extra-offset = #'( 1.0 . -1.0 ) e4^\markup{ \italic ritenuto } g b e
With extra-offset
, the first number controls the horizontal
movement (left is negative); the second number controls the vertial
movement (up is positive). After a bit of experimenting, we decided
that these values look good
\once \override TextScript #'extra-offset = #'( -1.6 . 1.0 ) e4^\markup{ \italic ritenuto } g b e
Again, these numbers are simply the result of a few experiments and looking at the output. You might prefer the text to be slightly higher, or to the left, or whatever. Try it and look at the result!
This manual: The \override command, Common tweaks.
This page is for LilyPond-2.8.0 (stable-branch).