adjustRtime Errors

[jzhou19]

Hello,

adjustRtime gave me the following errors when attempting with xdata = adjustRtime(xdata, param = ObiwarpParam(binSize = 0.6))

Error in manager$availability[[as.character(result$node)]] <- TRUE : wrong args for environment subassignment
Error in serialize(data, node$con) : error writing to connection

I tried register(SerialParam()) as suggested in #766 but ended up with the "R session aborted" error.

Below are the steps I took prior to performing alignment:

## Load data
raw_data = readMsExperiment(spectraFiles = files, sampleData = phenodata)

## Subset based on retention time
raw_data = filterRt(raw_data, c(60, 1000))

## Perform chromatographic peak detection in this section
## Peak detection parameters
cwp = CentWaveParam(
  peakwidth       = c(16.25, 57.75), # expected approximate peak width in chromatographic space
  ppm             = 10,            # maximal tolerated m/z deviation
  noise           = 1000000,          # minimum intensity required for centroids to be considered
  snthresh        = 10,              # defining the signal to noise ratio cutoff
  mzdiff          = -0.0065,         # minimum difference in m/z dimension required for peaks with overlapping retention times
  prefilter       = c(3.7, 100),       # Mass traces are only retained if they contain at least 3 peaks with intensity >= 200
  mzCenterFun     = "wMean",         # function to calculate the m/z center of the chromatographic peak
  integrate       = 2,               # Integration method, for 2 the descent is done on the real data
  fitgauss        = TRUE,            # whether or not a Gaussian should be fitted to each peak
  verboseColumns  = FALSE)           # whether additional peak meta data columns should be returned

## Peak detection on the full data set
xdata = findChromPeaks(raw_data, param = cwp)

## Merge neighboring chromatographic peaks
mpp = MergeNeighboringPeaksParam(
  expandMz = 0.0005, 
  expandRt = 5, 
  ppm = 10) 
xdata = refineChromPeaks(xdata, mpp)

For your information, print(object.size(xdata), unit = "MB") reported 40.4 Mb

Session Info as follows:

R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] MsExperiment_1.8.0 ProtGenerics_1.38.0 SummarizedExperiment_1.36.0
[4] Biobase_2.64.0 GenomicRanges_1.56.2 GenomeInfoDb_1.42.0
[7] IRanges_2.38.1 S4Vectors_0.44.0 BiocGenerics_0.52.0
[10] MatrixGenerics_1.18.0 matrixStats_1.4.1 xcms_4.4.0
[13] BiocParallel_1.40.0

loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 dplyr_1.1.4 lazyeval_0.2.2
[4] MassSpecWavelet_1.70.0 digest_0.6.37 XML_3.99-0.17
[7] lifecycle_1.0.4 cluster_2.1.6 statmod_1.5.0
[10] magrittr_2.0.3 compiler_4.4.1 progress_1.2.3
[13] rlang_1.1.4 tools_4.4.1 igraph_2.1.1
[16] utf8_1.2.3 prettyunits_1.2.0 S4Arrays_1.6.0
[19] DelayedArray_0.32.0 plyr_1.8.9 RColorBrewer_1.1-3
[22] abind_1.4-8 purrr_1.0.2 grid_4.4.1
[25] preprocessCore_1.66.0 fansi_1.0.4 colorspace_2.1-1
[28] ggplot2_3.5.1 iterators_1.0.14 scales_1.3.0
[31] MASS_7.3-61 MultiAssayExperiment_1.32.0 cli_3.6.3
[34] mzR_2.38.0 crayon_1.5.3 generics_0.1.3
[37] rstudioapi_0.17.1 httr_1.4.7 reshape2_1.4.4
[40] ncdf4_1.23 DBI_1.2.3 affy_1.82.0
[43] stringr_1.5.1 zlibbioc_1.50.0 parallel_4.4.1
[46] impute_1.78.0 AnnotationFilter_1.30.0 BiocManager_1.30.25
[49] XVector_0.44.0 vsn_3.72.0 vctrs_0.6.5
[52] Matrix_1.7-1 jsonlite_1.8.9 hms_1.1.3
[55] MALDIquant_1.22.3 clue_0.3-65 foreach_1.5.2
[58] limma_3.60.6 tidyr_1.3.1 snow_0.4-4
[61] affyio_1.74.0 glue_1.7.0 MSnbase_2.30.1
[64] codetools_0.2-20 QFeatures_1.16.0 Spectra_1.16.0
[67] stringi_1.8.4 gtable_0.3.6 UCSC.utils_1.2.0
[70] mzID_1.44.0 munsell_0.5.1 tibble_3.2.1
[73] pillar_1.9.0 MsFeatures_1.14.0 pcaMethods_1.96.0
[76] GenomeInfoDbData_1.2.13 R6_2.5.1 doParallel_1.0.17
[79] lattice_0.22-6 MetaboCoreUtils_1.14.0 Rcpp_1.0.13-1
[82] PSMatch_1.10.0 SparseArray_1.6.0 fs_1.6.5
[85] MsCoreUtils_1.16.1 pkgconfig_2.0.3

[jorainer]

Thanks for the detailed error report. Do you repeatedly get this error, i.e. if you restart R and repeat the commands, do you get the same error? It is very puzzling that the R session gets aborted. Are you running this code within RStudio? Have you tried running the code just in R (not within RStudio)? Maybe also ensuring that all packages are up-to-date might help (using BiocManager::install()). Also, maybe force re-installation of xcms using BiocManager::install("xcms", force = TRUE).

[jzhou19]

Thank you for your reply.

Yes, I repeatedly get this error with new R sessions. I run the codes with RStudio.

I've now tried to update all packages, forced re-installation of xcms, and run the codes in R not RStudio but I still got the same errors. With register(SerialParam()), R just quit itself. This is not a part of the errors but I noticed that there was a message "value 5" printed before the progress bar for adjustRtime, not sure what that means.

[jzhou19]

I had no luck with obiwarp but peak groups alignment (PeaksGroupsParam), as mentioned in #668, worked for me.

[jorainer]

hm. this is the first time I hear such issues causing R to quit. that should not happen and I suspect there might be some problem with the R installation, settings or the compilation of the C code of obiwarp in xcms. Maybe forcing compilation of the code in xcms might help (i.e. running BiocManager::install("xcms", force = TRUE, type = "source"))?

From own experience, obiwarp never really worked great on our data sets - so we are also using mostly the PeakGroupsParam.