I want to do DSEQ2 in R. I have the following files

transcript Control_R1 Control_R2 Control_R3 Day1_R1 Day1_R2 Day1_R3 Day2_R1 Day2_R2 Day2_R3 Day3_R1 Day3_R2 Day3_R3 Day5_R1 Day5_R2 Day5_R3
TraesCS1A02G007700.1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
TraesCS1A02G007800.1 19 30 26 13 8 1 10 10 19.4163 21 17 16 27 32 18
TraesCS1A02G007900.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
TraesCS1A02G007934.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
TraesCS1A02G008000.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
TraesCS1A02G008100.1 28.8806 38.5978 26.63 13.2727 14.65 10.259 24.8453 18.6404 47.969 24.6252 30.2632 25.7821 38.0815 27.1873 21.4213
TraesCS1A02G008200.1 2.78727 1.53136 5.38526 0 3.47021 3.78439 3.49165 1.80285 1.06531 1.99845 0 1.51613 2.0538 1.42314 0

my condition file is

Control_R1 Control
Control_R2 Control
Control_R3 Control
Day1_R1 Day1
Day1_R2 Day1
Day1_R3 Day1
Day2_R1 Day2
Day2_R2 Day2
Day2_R3 Day2
Day3_R1 Day3
Day3_R2 Day3
Day3_R3 Day3
Day5_R1 Day5
Day5_R2 Day5
Day5_R3 Day5

whenever I try to read my file using this code:
just.raw.counts = read.delim("Raw_counts_input.txt", row.names=1)
head(just.raw.counts)

I get a

Error in read.table(file = file, header = header, sep = sep, quote = quote, :
duplicate 'row.names' are not allowed

however, for my condition file it doesn't give this error, and I have tried all possible means to resolve this

Please how can I resolve this?

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