Knitr chunk is importing a subset of the records from *.csv as same code in R

Rstudio version 0.96.331 and knitr version 0.8

I thought my problem had been solved with update of RStudio and libraries... however:

The following run in R gives me 940 unique Table.ID values. Run in a knitr chunk I get 228 unique values and the following warning:

"invalid input found on input connection ''

I don't understand why the distinction exists between the two methods.

Sequence <- read.csv("",


Works fine on Rstudio version 0.96.331 and knitr version 0.8

My .Rmd file:

        knitr test for length
        This should successfully return a length of 940

    Sequence <- read.csv("", 
fileEncoding = "iso8859-8", stringsAsFactors = FALSE)

Resulting in this:

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