`summarise()` has grouped output by 'TenYearCHD'. You can override using the `.groups` argument.

[AvikGGU]

plot_sexCHD = heart%>%
group_by(TenYearCHD, male)%>%
summarise(cnt = n())%>%
mutate(pcnt = cnt/sum(cnt))%>%
ggplot(aes(x = as.factor(male), y = pcnt, fill = TenYearCHD))+
geom_bar(col = "white", position = "dodge", stat = "identity")+
labs(x = "Sex", y = "Percentage", title = 'Male Female Percentage of CHD')+
scale_fill_brewer(palette = "Blues")

str(heart)
'data.frame': 4238 obs. of 16 variables:
male : int 1 0 1 0 0 0 0 0 1 1 ... age : int 39 46 48 61 46 43 63 45 52 43 ...
education : int 4 2 1 3 3 2 1 2 1 1 ... currentSmoker : int 0 0 1 1 1 0 0 1 0 1 ...
cigsPerDay : int 0 0 20 30 23 0 0 20 0 30 ... BPMeds : int 0 0 0 0 0 0 0 0 0 0 ...
prevalentStroke: int 0 0 0 0 0 0 0 0 0 0 ... prevalentHyp : int 0 0 0 1 0 1 0 0 1 1 ...
diabetes : int 0 0 0 0 0 0 0 0 0 0 ... totChol : int 195 250 245 225 285 228 205 313 260 225 ...
sysBP : num 106 121 128 150 130 ... diaBP : num 70 81 80 95 84 110 71 71 89 107 ...
BMI : num 27 28.7 25.3 28.6 23.1 ... heartRate : int 80 95 75 65 85 77 60 79 76 93 ...
glucose : int 77 76 70 103 85 99 85 78 79 88 ... TenYearCHD : int 0 0 0 1 0 0 1 0 0 0 ...

[FJCC]

The message you quote in your title is normal and not a cause for concern. I get a similar message in the code below. Is there a problem with the result of your code?

library(dplyr)
DF <- data.frame(G = c("A", "A", "A", "A", "B", "B", "B", "B"),
                  G2 = c("X", "X", "Y", "Y", "X", "X", "Y", "Y"),
                  Val = 1:8)
DF |> group_by(G, G2) |> summarize(S = sum(Val))
`summarise()` has grouped output by 'G'. You can override using the `.groups` argument.
# A tibble: 4 x 3
# Groups:   G [2]
  G     G2        S
  <chr> <chr> <int>
1 A     X         3
2 A     Y         7
3 B     X        11
4 B     Y        15

[mikecrobp]

Most of the time you don't care that the result is grouped
It happens when you have more than one column in group_by
A while ago the option .groups = "drop" was added

I forget the circumstance (maybe when you try to select a few columns from the result) but R insists on adding back the grouped columns even though not in select.

I remember reading a comment that a better default would have been no grouping, but dplyr had been out there some time before v1.0.0 added the new options