Console vs RMD (pdf via Knit.) differs eg. train( Accuracy = 0.64 in Console and 0.76 in Rmd) everything is same

General
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modelN <-train(diagnosis~., data = smallDtrain, method = "glm")

Followed the exactly the same commands but get totally different results.

eg. train( Accuracy = 0.64 in Console and 0.76 in Rmd) everything is same

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