I have gotten an error message when loading xcms.

mzR has been built against a different Rcpp version (1.0.6) than is installed on your system (1.0.7). This might lead to errors when loading mzR.

There now seem to be errors for me when the readMSData function calls mzR.

# input (file path and names previously specified)
raw_pos <- readMSData(files, mode = "onDisk")

# error
Error in object@backend$getAllScanHeaderInfo() : 
  [SpectrumList_mzXML::spectrum()] Error seeking to <scan>.

# sessionInfo( ) output:
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] SummarizedExperiment_1.22.0 GenomicRanges_1.44.0       
 [3] GenomeInfoDb_1.28.1         IRanges_2.26.0             
 [5] MatrixGenerics_1.4.2        matrixStats_0.60.0         
 [7] magrittr_2.0.1              xcms_3.14.1                
 [9] MSnbase_2.18.0              ProtGenerics_1.24.0        
[11] S4Vectors_0.30.0            mzR_2.26.1                 
[13] Rcpp_1.0.7                  Biobase_2.52.0             
[15] BiocGenerics_0.38.0         BiocParallel_1.26.1        

loaded via a namespace (and not attached):
 [1] lattice_0.20-44        colorspace_2.0-2       vctrs_0.3.8           
 [4] vsn_3.60.0             utf8_1.2.2             XML_3.99-0.6          
 [7] rlang_0.4.11           pillar_1.6.2           glue_1.4.2            
[10] affy_1.70.0            RColorBrewer_1.1-2     GenomeInfoDbData_1.2.6
[13] affyio_1.62.0          foreach_1.5.1          lifecycle_1.0.0       
[16] plyr_1.8.6             mzID_1.30.0            robustbase_0.93-8     
[19] zlibbioc_1.38.0        munsell_0.5.0          pcaMethods_1.84.0     
[22] gtable_0.3.0           codetools_0.2-18       doParallel_1.0.16     
[25] MassSpecWavelet_1.58.0 fansi_0.5.0            preprocessCore_1.54.0 
[28] DEoptimR_1.0-9         scales_1.1.1           BiocManager_1.30.16   
[31] DelayedArray_0.18.0    limma_3.48.3           XVector_0.32.0        
[34] MsCoreUtils_1.4.0      RANN_2.6.1             impute_1.66.0         
[37] ggplot2_3.3.5          digest_0.6.27          ncdf4_1.17            
[40] grid_4.1.1             clue_0.3-59            bitops_1.0-7          
[43] tools_4.1.1            RCurl_1.98-1.3         tibble_3.1.3          
[46] cluster_2.1.2          crayon_1.4.1           pkgconfig_2.0.3       
[49] Matrix_1.3-4           MASS_7.3-54            ellipsis_0.3.2        
[52] iterators_1.0.13       R6_2.5.0               MALDIquant_1.20       
[55] compiler_4.1.1

Thanks!

If you do

library(BiocManager)
valid()

Does it tell you that your version of Rcpp is outdated and that you should run BiocManager:::install() in order to update?

The message that you get when loading mzR is only a warning and isn't causing the error you see later.

What data are stored in the files vector? mzML files? How were they generated?