Error: Negative length vectors are not allowed about rawdiag HOT 2 CLOSED

Update: Seems to be a memory issue, quite a lot hits for the error. When I chunk the scans (5x1000 scans) it runs fine. So I guess the function does not scale well to ~ 5k MS1 scans (profile) or > 80k MS2 scans (these were testfiles that fail).

from rawdiag.

@dzolg pfff; this is massive ...
Can you try to apply a `Divide and Conquer' strategy?
Maybe you can extract the desired information before the merging step.

here is an example

system.time(scanDat <- lapply(idx, function(x){
  scan <- readScans(file, x)[[1]]; 
  i <- scan$intensity > 0;
  scan$mZ <- scan$mZ[i];
  scan$intensity <- scan$intensity[i];  
 scan}
))

the snippet seems to work on our 64 cores Linux box:

Q.E.D.

from rawdiag.