Error Invalid cvParam accession "1003293"

Dear contributors,

I encountered an error while using XCMS to process a .mzML. This data file was converted from .wiff using MSconvert 3.0.23090-ce9ba2b (automated build). This appears to be related to previous issue. I checked the list of CV IDs here and 1003293 is in the list. Did someone have a solution about this ?

Here are some info of my (very basic) R script.

library(xcms)

dda_file <-'/home/remy/Gammars_data/Pool_GMF_zSWATH_3.mzML' 
dda_data <- readMSData(dda_file, mode = "onDisk")

(this code work well with .mzXML file)

Error information:

Original error was: Error: Invalid cvParam accession "1003293"

Traceback :

12: stop("Can not open file ", filename, "! Original error was: ", 
        e, call. = FALSE)
11: value[[3L]](cond)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
8: tryCatch(pwizModule$open(filename), error = function(e) {
       stop("Can not open file ", filename, "! Original error was: ", 
           e, call. = FALSE)
   })
7: mzR::openMSfile(x)
6: FUN(X[[i]], ...)
5: lapply(X = X, FUN = FUN, ...)
4: sapply(files, mzR:::.hasSpectra)
3: sapply(files, mzR:::.hasSpectra)
2: hasSpectra(files)
1: readMSData(dda_file, mode = "onDisk")

Session information :

R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C               LC_TIME=fr_FR.UTF-8       
 [4] LC_COLLATE=fr_FR.UTF-8     LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] xcms_3.20.0         MSnbase_2.24.2      ProtGenerics_1.30.0 S4Vectors_0.36.1   
[5] mzR_2.31.1          Rcpp_1.0.10         Biobase_2.58.0      BiocGenerics_0.44.0
[9] BiocParallel_1.32.5

loaded via a namespace (and not attached):
 [1] lattice_0.20-45             digest_0.6.31               foreach_1.5.2              
 [4] utf8_1.2.2                  R6_2.5.1                    GenomeInfoDb_1.34.6        
 [7] plyr_1.8.8                  mzID_1.36.0                 ggplot2_3.4.0              
[10] pillar_1.8.1                zlibbioc_1.44.0             rlang_1.0.6                
[13] rstudioapi_0.14             Matrix_1.5-3                preprocessCore_1.60.2      
[16] RCurl_1.98-1.9              munsell_0.5.0               DelayedArray_0.24.0        
[19] compiler_4.2.2              MsFeatures_1.6.0            pkgconfig_2.0.3            
[22] pcaMethods_1.90.0           tidyselect_1.2.0            SummarizedExperiment_1.28.0
[25] tibble_3.1.8                GenomeInfoDbData_1.2.9      RANN_2.6.1                 
[28] IRanges_2.32.0              codetools_0.2-19            matrixStats_0.63.0         
[31] XML_3.99-0.13               fansi_1.0.4                 dplyr_1.0.10               
[34] MASS_7.3-58.2               bitops_1.0-7                MassSpecWavelet_1.64.0     
[37] grid_4.2.2                  gtable_0.3.1                lifecycle_1.0.3            
[40] affy_1.76.0                 magrittr_2.0.3              MsCoreUtils_1.10.0         
[43] scales_1.2.1                ncdf4_1.21                  cli_3.6.0                  
[46] impute_1.72.3               XVector_0.38.0              affyio_1.68.0              
[49] doParallel_1.0.17           limma_3.54.0                robustbase_0.95-0          
[52] generics_0.1.3              vctrs_0.5.2                 RColorBrewer_1.1-3         
[55] iterators_1.0.14            tools_4.2.2                 glue_1.6.2                 
[58] DEoptimR_1.0-11             MatrixGenerics_1.10.0       parallel_4.2.2             
[61] clue_0.3-63                 colorspace_2.1-0            cluster_2.1.4              
[64] BiocManager_1.30.19         vsn_3.66.0                  GenomicRanges_1.50.2       
[67] MALDIquant_1.22

sneumann / xcms

Error Invalid cvParam accession "1003293" #670