Hi everyone,

I am gettin this error (see below) with xcms whenever parallel computing is involved. I first noticed this issue during peak detection, but it also occurs when extracting chromatograms.

The weird thing is that the error is not reproducible. I.e., when calling the function multiple times in a row, the error will only occur in a fraction of the calls.

What I noticed is that the larger the computation (e.g. larger data set, higher mass resolution etc) the more likely the error, up to a point where it will fail 90% of the times.

When I run findChromPeaks with 'BPPARAM = SerialParam()', then it will always run fine (but much slower of course).

Is this a known issue with BiocParallel, and is there a known fix?

Thanks a lot!

findChromPeaks(msdata, param = MatchedFilterParam())

Sizes of mz and intensity arrays don't match. Error: BiocParallel errors element index: 6, 7 first error: dims [product 0] do not match the length of object [519]

###
> msdata
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 13.57 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 48384 
 MSn retention times: 2:0 - 20:1 minutes
- - - Processing information - - -
Data loaded [Sat Mar 20 20:50:39 2021] 
Filter: select retention time [120-1500] and MS level(s), 1 [Sat Mar 20 20:53:20 2021] 
 MSnbase version: 2.14.2 
- - - Meta data  - - -
phenoData
  rowNames: 1 2 ... 18 (18 total)
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  [1] r001.mzML...  [18] r018.mzML
  Use 'fileNames(.)' to see all files.
protocolData: none
featureData
  featureNames: F01.S0023 F01.S0024 ... F18.S2707 (48384 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'


####
sessionInfo( )

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] bayestestR_0.8.0    pspline_1.0-18      ggpubr_0.4.0        randomcoloR_1.1.0.1 RColorBrewer_1.1-2  zoo_1.8-8           doParallel_1.0.16   iterators_1.0.13    foreach_1.5.1      
[10] openxlsx_4.2.3      plotly_4.9.2.1      rlang_0.4.9         forcats_0.5.0       stringr_1.4.0       dplyr_1.0.2         purrr_0.3.4         readr_1.4.0         tidyr_1.1.2        
[19] tibble_3.0.4        ggplot2_3.3.2       tidyverse_1.3.0     CAMERA_1.44.0       xcms_3.10.2         BiocParallel_1.22.0 MSnbase_2.14.2      ProtGenerics_1.20.0 S4Vectors_0.28.1   
[28] mzR_2.22.0          Rcpp_1.0.5          Biobase_2.48.0      BiocGenerics_0.36.0

loaded via a namespace (and not attached):
  [1] snow_0.4-3                  readxl_1.3.1                backports_1.2.1             Hmisc_4.4-2                 plyr_1.8.6                  igraph_1.2.6               
  [7] lazyeval_0.2.2              splines_4.0.2               crosstalk_1.1.0.1           GenomeInfoDb_1.24.2         digest_0.6.27               htmltools_0.5.0            
 [13] fansi_0.4.1                 magrittr_2.0.1              checkmate_2.0.0             cluster_2.1.0               limma_3.44.3                modelr_0.1.8               
 [19] matrixStats_0.57.0          jpeg_0.1-8.1                colorspace_2.0-0            rvest_0.3.6                 haven_2.3.1                 xfun_0.19                  
 [25] crayon_1.3.4                RCurl_1.98-1.2              jsonlite_1.7.2              graph_1.66.0                impute_1.62.0               survival_3.2-7             
 [31] glue_1.4.2                  gtable_0.3.0                zlibbioc_1.34.0             XVector_0.28.0              DelayedArray_0.14.1         V8_3.4.0                   
 [37] car_3.0-10                  DEoptimR_1.0-8              abind_1.4-5                 scales_1.1.1                vsn_3.56.0                  DBI_1.1.0                  
 [43] rstatix_0.6.0               viridisLite_0.3.0           htmlTable_2.1.0             foreign_0.8-80              preprocessCore_1.50.0       Formula_1.2-4              
 [49] htmlwidgets_1.5.3           httr_1.4.2                  ellipsis_0.3.1              farver_2.0.3                pkgconfig_2.0.3             XML_3.99-0.5               
 [55] nnet_7.3-14                 dbplyr_2.0.0                labeling_0.4.2              tidyselect_1.1.0            munsell_0.5.0               cellranger_1.1.0           
 [61] tools_4.0.2                 cli_2.2.0                   generics_0.1.0              broom_0.7.2                 evaluate_0.14               mzID_1.26.0                
 [67] yaml_2.2.1                  knitr_1.30                  fs_1.5.0                    zip_2.1.1                   robustbase_0.93-6           RANN_2.6.1                 
 [73] ncdf4_1.17                  RBGL_1.64.0                 xml2_1.3.2                  compiler_4.0.2              rstudioapi_0.13             curl_4.3                   
 [79] png_0.1-7                   ggsignif_0.6.0              affyio_1.58.0               reprex_0.3.0                MassSpecWavelet_1.54.0      stringi_1.5.3              
 [85] lattice_0.20-41             Matrix_1.2-18               vctrs_0.3.5                 pillar_1.4.7                lifecycle_0.2.0             BiocManager_1.30.10        
 [91] MALDIquant_1.19.3           insight_0.11.1              data.table_1.13.4           bitops_1.0-6                GenomicRanges_1.40.0        R6_2.5.0                   
 [97] latticeExtra_0.6-29         pcaMethods_1.80.0           affy_1.66.0                 rio_0.5.16                  gridExtra_2.3               IRanges_2.24.0             
[103] codetools_0.2-18            MASS_7.3-53                 assertthat_0.2.1            SummarizedExperiment_1.18.2 withr_2.3.0                 GenomeInfoDbData_1.2.3     
[109] hms_0.5.3                   grid_4.0.2                  rpart_4.1-15                rmarkdown_2.5               carData_3.0-4               Rtsne_0.15                 
[115] lubridate_1.7.9.2           base64enc_0.1-3