how to fix this error: duplicate 'row.names' are not allowed read.table

Question

[Reza]

Hello,

I’m a new to R. when I use this code in my computer:

library(MetaDE)
study.names<-c("S1","S2","S3")
BS.raw<-MetaDE.Read(study.names,skip=rep(1:3),via="csv",matched=T,log=F)

It is ok and read my data into R, but when I tried it in another computer it came back to this error:

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

I appreciate everyone could give me a hand.

[Arup Ghosh]

Is it just another computer or also another dataset?

[Reza]

all are same dataset.

GSM250883.CEL.gz    GSM250884.CEL.gz    GSM250889.CEL.gz    GSM250890.CEL.gz    GSM250895.CEL.gz    GSM250896.CEL.gz
label   0   1   0   1   0   1
AFFX-BioB-3_at  8.727673832 8.654787934 8.475718653 8.380745696 7.948503159 8.318558373
AFFX-BioB-5_at  8.6370538   8.627291389 8.30839749  8.3955828   7.767200367 8.069189015
AFFX-BioB-M_at  8.593500335 8.600487789 8.234365565 8.283075703 8.023524163 8.373746353

[ATpoint]

Please show data. It is difficult to debug without it. How does file look on the harddrive?

[Reza]

i added one of the files. the files are same. in my computer (windows) the error is encountered, but another computer (Ubuntu 16) shows this error.

is it because of missing some of packages!

[Reza]

same datasets

GSM250883.CEL.gz    GSM250884.CEL.gz    GSM250889.CEL.gz    GSM250890.CEL.gz    GSM250895.CEL.gz    GSM250896.CEL.gz
label   0   1   0   1   0   1
AFFX-BioB-3_at  8.727673832 8.654787934 8.475718653 8.380745696 7.948503159 8.318558373
AFFX-BioB-5_at  8.6370538   8.627291389 8.30839749  8.3955828   7.767200367 8.069189015
AFFX-BioB-M_at  8.593500335 8.600487789 8.234365565 8.283075703 8.023524163 8.373746353
AFFX-BioC-3_at  9.200566945 9.169073764 8.85702912  8.849328433 8.222657184 8.569707779
AFFX-BioC-5_at  9.338145273 9.321989731 9.0166683   8.998965599 8.580308916 8.876204458
AFFX-BioDn-3_at 11.67598393 11.61795021 11.5039667  11.43268323 11.52184582 11.70024537
AFFX-BioDn-5_at 9.882177138 9.750037383 9.481239248 9.566606189 9.074429355 9.44318762
AFFX-CreX-3_at  13.03818575 13.00502285 12.93526835 12.98489529 12.80020638 13.08603216
AFFX-CreX-5_at  12.23552789 12.22659733 12.15221451 12.26119906 12.02205343 12.42879065
AFFX-DapX-3_at  10.27224766 10.37595811 10.43981989 10.40807934 9.01409621  9.266227862
AFFX-DapX-5_at  9.294515889 9.334179156 9.411192837 9.527873208 7.376235467 7.539532067
AFFX-DapX-M_at  9.928373217 10.00482977 10.04899094 10.11004543 8.098506139 8.354794577

[russhh]

Do you know which of the files throws the error?

[Lemire]

1) you should have 3 files, yet you only pasted one

2) via="csv", yet the dataset you pasted is not comma-separated

3) skip=rep(1:3), yet from man page "skip: a vecter [sic] of size K (the number of data sets) composes [sic] of 1 or 2. see 'Details'." Just type rep(1:3) in R to see what I mean.

4) unclear from the documentation if the files are allowed to have a header line.

Note that the package has been removed from CRAN. That (and all the typos, indicating a lack of professionalism from the authors) is a sign you want to stay away from it.