"Error in read.table(decoder.file, header = TRUE, stringsAsFactors = FALSE) : no lines available in input"

Question

[sc@791]

Hi! I am using JunctionSeq first time and not very expert in R language. While running JunctionSeq analysis I am getting an error in reading decoder file. Here is the command and error:

"#Read the decoder:
decoder.file <- system.file("~/R/Splicejunction/annoFiles/decoder.bySample.txt",
package="JunctionSeq");
decoder <- read.table(decoder.file,
header=TRUE,
stringsAsFactors=FALSE)"

"Error in read.table(decoder.file, header = TRUE, stringsAsFactors = FALSE) :
no lines available in input
In addition: Warning message:
In file(file, "rt") :
file("") only supports open = "w+" and open = "w+b": using the former"

Any help is much appreciated.

Thanks CS

[coolliuteng]

Maybe problem is the file permission of decoder.file. Try 'chmod 755 ~/R/Splicejunction/annoFiles/decoder.bySample.txt', then run JunctionSeq command.