when I used r3Cseq I ran into several cryptic error messages. After tracking down the problem I found out that this was due to the file names I used.
My file names started with numbers and contained "-" signs. In the r3Cseq pipeline the filenames are used to name the matrices and files that are created. By default R changed the file names by adding X in front of the numbers and replacing "-" by ".". As a result the r3Cseq package is not able to find the corresponding data, when it tries to look it up with the original filename. This results in error messages of missing data that are hard to track down because the package gives the confirmation that everything has been processed correctly before.
Looking into the help files I could not detect any provided conventions for naming the input files.
To prevent this problem in future I would recommend to check the used filenames if they are compatible with the standard naming of objects in R.