after my inability to launch the new version of kiss2refgenome : this post, I encoutered another problem. For unrelated reasons, I needed R 4.0 (I was on 3.6). Therefore, I did the upgrade in the "dumb" way, by completely removing the previous install and ALL the packages (because I figured it was time do to a little cleanup), instead of installing it side to side.
My previous usage of KisSplice went great with the new version (2.5). This one use the count option at 2 by default (contrary to version 2.4, which use count = 0). So after kissplice2refgenome (1.2.3), with KissDE I was using the kissplice2counts function with the option counts = 2. Which worked perfectly.
myCounts <- kissplice2counts(k2rg_file, counts = 2, pairedEnd = TRUE, k2rg = TRUE)
But now that I have installed R 4.0.2, and only KissDE (with all the dependencies of course), nothing works anymore. I have tried the exact same output from kiss2refgenome, and the exact same command that worked when I was using R 3.6. This is the error and warnings I got :
Error in rep_len(0, nbcond) : incorrect 'length.out' value De plus : Warning messages: 1: In matrix(unlist(split2), nrow = 3) : data length  is not a divisor nor a multiple of the number of lines  2: In .countsSetk2rg(countsUp, counts, pairedEnd, order, exonicReads) : NAs introduced during automatic conversion 3: In .countsSetk2rg(countsUp, counts, pairedEnd, order, exonicReads) : NAs introduced during automatic conversion
(I had the silliest idea of setting the messages in French, so I hope I translated them right.)
I will try to revert to R 3.6, and see what will happen. It SHOULD works. If it works, then R 4.0, might be responsible.
Does anyone had this problem (considering R 4.0 is still kinda new, I guess not ?) ?
In anycase, I will update this when I'm done.
EDIT: So, I did exactly what I did for R 4.0.2 : I installed R 3.6.3, and only KissDE and its dependencies. Guess what ? KissDE is working again.
EDIT2: It works on a R 4.0 on a Windows computer...