When using Rsubread v 1.28.1 it sucessfully parsed my input file names by removing the file path and just keeping the names. As of the current version, however, the names contain the entire file path, this makes for very long and ugly column names.

Example

Setup

files: /path/to/file/here/file1.bam; /path/to/file/here/file2.bam countData=featureCounts(.....)

1.28.1

colnames(countData$counts) [1] file1.bam
[2] file2.bam

1.34.0

colnames(countData$counts) [1] X.path.to.file.here.file1.bam [2] X.path.to.file.here.file2.bam

I guess the reason for the change was probably because file names without paths might not be unique. For example, we might have

files <- c("path1/file1.bam", "path2/file1.bam")

so that removing the paths would result in duplicate column names.

If you don't like it you can easily change the column names yourself by

colnames(countData$counts) <- basename(colnames(countData$counts))