[Bioc-devel] xcms adjustRtime-obiwarp Error

Riccardo Romoli Thu, 27 Jul 2017 03:57:31 -0700

Dear xcms devel,
running the latest stable xcms version I get the following error:


> xod <- adjustRtime(xod, param = ObiwarpParam())
Sample number 3 used as center sample.
Aligning pl55_06h_01.mzXML against pl55_03h_01.mzXML ...
Error: BiocParallel errors
  element index: 1, 2, 3, 4, 5

first error: Dimensions of profile matrices of filespl55_03h_01.mzXML and pl4_01.mzXML do not match!



This is the traceback:

> traceback()
9: stop(.error_bplist(res))
8: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
7: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
6: bplapply(objL, function(z, cntr, cntrPr, parms) {
       message("Aligning ", basename(fileNames(z)), " against ",
           basename(fileNames(cntr)), " ... ", appendLF = FALSE)

suppressMessages(curP <- profMat(z, method = "bin", step =binSize(parms),

           returnBreaks = TRUE)[[1]])
       scantime1 <- unname(rtime(cntr))
       scantime2 <- unname(rtime(z))
       mstdiff <- median(c(diff(scantime1), diff(scantime2)))
       mst1 <- which(diff(scantime1) > 5 * mstdiff)[1]
       if (!is.na(mst1)) {
           scantime1 <- scantime1[seq_len((mst1 - 1))]
           message("Found gaps in scan times of the center sample: cut ",
               "scantime-vector at ", scantime1[mst1], " seconds.")
       }
       mst2 <- which(diff(scantime2) > 5 * mstdiff)[1]
       if (!is.na(mst2)) {
           scantime2 <- scantime2[seq_len((mst2 - 1))]

message("Found gaps in scan time of file ",basename(fileNames(z)),

               ": cut scantime-vector at ", scantime2[mst2], " seconds.")
       }

rtmaxdiff <- abs(diff(c(scantime1[length(scantime1)],scantime2[length(scantime2)])))

       if (rtmaxdiff > (5 * mstdiff)) {

rtmax <- min(scantime1[length(scantime1)],scantime2[length(scantime2)])

           scantime1 <- scantime1[scantime1 <= rtmax]
           scantime2 <- scantime2[scantime2 <= rtmax]
       }
       valscantime1 <- length(scantime1)
       valscantime2 <- length(scantime2)
       if (ncol(cntrPr$profMat) > valscantime1) {
           cntrPr$profMat <- cntrPr$profMat[, -c((valscantime1 +
               1):ncol(cntrPr$profMat))]
       }
       if (ncol(curP$profMat) > valscantime2) {

curP$profMat <- curP$profMat[, -c((valscantime2 +1):ncol(curP$profMat))]

       }
       mzr1 <- c(cntrPr$breaks[1], cntrPr$breaks[length(cntrPr$breaks) -
           1])
       mzr2 <- c(curP$breaks[1], curP$breaks[length(curP$breaks) -
           1])
       mzmin <- min(c(mzr1[1], mzr2[1]))
       mzmax <- max(c(mzr1[2], mzr2[2]))
       mzs <- seq(mzmin, mzmax, by = binSize(parms))
       if (mzmin < mzr1[1]) {
           tmp <- matrix(0, (length(seq(mzmin, mzr1[1], binSize(parms))) -
               1), ncol = ncol(cntrPr$profMat))
           cntrPr$profMat <- rbind(tmp, cntrPr$profMat)
       }
       if (mzmax > mzr1[2]) {
           tmp <- matrix(0, (length(seq(mzr1[2], mzmax, binSize(parms))) -
               1), ncol = ncol(cntrPr$profMat))
           cntrPr$profMat <- rbind(cntrPr$profMat, tmp)
       }
       if (mzmin < mzr2[1]) {
           tmp <- matrix(0, (length(seq(mzmin, mzr2[1], binSize(parms))) -
               1), ncol = ncol(curP$profMat))
           curP$profMat <- rbind(tmp, curP$profMat)
       }
       if (mzmax > mzr2[2]) {
           tmp <- matrix(0, (length(seq(mzr2[2], mzmax, binSize(parms))) -
               1), ncol = ncol(curP$profMat))
           curP$profMat <- rbind(curP$profMat, tmp)
       }
       mzvals <- length(mzs)
       cntrVals <- length(cntrPr$profMat)
       curVals <- length(curP$profMat)

if ((mzvals * valscantime1) != cntrVals | (mzvals *valscantime2) !=

           curVals | cntrVals != curVals)

stop("Dimensions of profile matrices of files ",basename(fileNames(cntr)),

               " and ", basename(fileNames(z)), " do not match!")
       rtadj <- .Call("R_set_from_xcms", valscantime1, scantime1,
           mzvals, mzs, cntrPr$profMat, valscantime2, scantime2,
           mzvals, mzs, curP$profMat, response(parms), distFun(parms),
           gapInit(parms), gapExtend(parms), factorDiag(parms),
           factorGap(parms), as.numeric(localAlignment(parms)),
           initPenalty(parms))
       if (length(rtime(z)) > valscantime2) {
           rtadj <- c(rtadj, rtime(z)[(valscantime2 + 1):length(rtime(z))])
           warning(basename(fileNames(z)), " :could only align up to a ",
               "retention time of ", rtime(z)[valscantime2], " seconds. ",
               "After that raw retention times are reported.")
       }
       message("OK")
       return(rtadj)
   }, cntr = centerObject, cntrPr = profCtr, parms = param)
5: bplapply(objL, function(z, cntr, cntrPr, parms) {
       message("Aligning ", basename(fileNames(z)), " against ",
           basename(fileNames(cntr)), " ... ", appendLF = FALSE)