Thank you for the file.
There are different issues
(1) you compute the spectrum for a complete file with 471249 samples to that the fft is quite long (235624 samples) and produces some NA (I don't know why actually). This cannot not be handled by Q()
(2) Q() looks for the dominant frequency of the spectrum which is, in this case, a complete spectrum quite noisy. It is then better to use a smoothed spectrum, something you can obtain with meanspec()
(3) there is low frequency aircraft noise, you need to filter it, see fir()
(4) you should do the analysis syllable by syllable to get a Q value per syllable. The silence between the syllables can bias the results and the syllables do not all have the same dominant frequency.
library(tuneR)
library(seewave)
s <- readWave("Canto 3.wav")
s.fir <- fir(s, from=1000, bandpass=TRUE, output="Wave")
# for syllable 1, time start and end approximately estimated
Q(meanspec(s, dB="max0", from=0.38, to=0.78, plot=FALSE))
HTH
Jerome