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The source of this code is obtained by typing its name at the R prompt. The output is

function (x, thresh = 0) 
{
    pks <- which(diff(sign(diff(x, na.pad = FALSE)), na.pad = FALSE) < 
        0) + 2
    if (!missing(thresh)) {
        pks[x[pks - 1] - x[pks] > thresh]
    }
    else pks
}

The test pks[x[pks - 1] - x[pks] > thresh compares each peak value to the value immediately succeeding it in the series (not to the next trough in the series). It uses a (crude) estimate of the size of the slope of the function immediately after the peak and selects only those peaks where that slope exceeds thresh in size. In your case, only the first three peaks are sufficiently sharp to pass the test. You will detect all the peaks by using the default:

> p=findPeaks(cc)
[1]  3 22 41 59 78 96