How to suppress warnings when plotting with ggplot

You need to suppressWarnings() around the print() call, not the creation of the ggplot() object:

R> suppressWarnings(print(
+ ggplot(mydf, aes(x = species)) + 
+    stat_bin() + 
+    geom_text(data = labs, aes(x = species, y = value, 
+                               label = value, vjust = -0.5)) +
+    facet_wrap(~ lvl)))
R> 

It might be easier to assign the final plot to an object and then print().

plt <- ggplot(mydf, aes(x = species)) + 
   stat_bin() + 
   geom_text(data = labs, aes(x = species, y = value,
                              label = value, vjust = -0.5)) +
   facet_wrap(~ lvl)


R> suppressWarnings(print(plt))
R> 

The reason for the behaviour is that the warnings are only generated when the plot is actually drawn, not when the object representing the plot is created. R will auto print during interactive usage, so whilst

R> suppressWarnings(plt)
Warning message:
Removed 1 rows containing missing values (geom_text).

doesn't work because, in effect, you are calling print(suppressWarnings(plt)), whereas

R> suppressWarnings(print(plt))
R>

does work because suppressWarnings() can capture the warnings arising from the print() call.

A more targeted plot-by-plot approach would be to add na.rm=TRUE to your plot calls. E.g.:

  ggplot(mydf, aes(x = species)) + 
      stat_bin() + 
      geom_text(data = labs, aes(x = species, y = value, 
                                 label = value, vjust = -0.5), na.rm=TRUE) +
      facet_wrap(~ lvl)