I can't seem to find an answer to this issue. It has been flagged before but without a successful solution.
cwp <- CentWaveParam(peakwidth=c(5,20), ppm=15, snthresh=5, prefilter = c(0,0)) xod <- findChromPeaks(raw, param = cwp)
xod <- adjustRtime(xod, param = ObiwarpParam())
Sample number 6 used as center sample. Aligning SJ45.CDF against SJ50.CDF ... Error: BiocParallel errors element index: 1, 2, 3, 4, 5, 6, ... first error: Dimensions of profile matrices of files SJ50.CDF and SJ45.CDF do not match!
I also tried running adjustRtime on the raw data files, but without success.
Strangely enough, when I run the old XCMS pipeline with rector instead of adjustRtime it all works, but I'd really like to try the new functions!
R version 3.4.0 (2017-04-21) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)