Rcpp mismatch? MzR problem
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@2c4da7d6
Last seen 11 weeks ago
United States

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!

mzR • 250 views
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@james-w-macdonald-5106
Last seen 2 days ago
United States

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?

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It tells me to update BiocManager from the website. I've tried doing it in R but that doesn't seem to have worked.

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Alas, updating to the newest BiocManager version has not resolved the issue.

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Updating BiocManager doesn't affect Rcpp. You are running Bioconductor 3.13, and 3.14 has been released, so you should probably just do

library(BiocManager)
install(version = "3.14")

which should upgrade Rcpp as part of the process.

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@laurent-gatto-5645
Last seen 2 days ago
Belgium

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?

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