plot(srn),Error in rep(rtime(z), lns) : invalid 'times' argument

[YUANMENG-1]

Sorry to bother!

I encountered an issue while filtering the "mse" object. There seems to be a problem with the retention times (rt). However, I have verified that the rt range I used for filtering exists within the data.Maybe other problem with the "rtime()"function?

srn <- mse |>
filterRt(rt = c(620, 640)) |>
filterMzRange(mz = c(100.300,100.330))
Filter spectra
Filter spectra

This was succeed,but error when plot

plot(srn)
Error in rep(rtime(z), lns) : invalid 'times' argument

srn
Object of class MsExperiment
Spectra: MS1 (177) MS2 (1650)
Experiment data: 5 sample(s)
Sample data links:

• spectra: 5 sample(s) to 1827 element(s)

[jorainer]

thanks for reporting! I will check that.

[jorainer]

Can you please provide the version of the packages you were using? Ideally, the output of calling sessionInfo().

[jorainer]

This bug was fixed in xcms, but this fixed but did not make it into the current release version of xcms. I included now the fix also into the release version and it should become available in version 4.2.2 within a couple of days. As a workaround, you can filter the data set first to MS1 data:

srn <- mse |>
    filterMsLevel(1L) |>
    filterRt(rt = c(620, 640)) |>
    filterMzRange(mz = c(100.300,100.330))

plot(srn)

[YUANMENG-1]

Can you please provide the version of the packages you were using? Ideally, the output of calling sessionInfo().

sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

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

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] dplyr_1.1.4 Spectra_1.14.1 ProtGenerics_1.36.0
[4] QFeatures_1.14.1 MultiAssayExperiment_1.30.2 SummarizedExperiment_1.34.0
[7] Biobase_2.64.0 GenomicRanges_1.56.0 GenomeInfoDb_1.40.1
[10] IRanges_2.38.0 S4Vectors_0.42.0 BiocGenerics_0.50.0
[13] MatrixGenerics_1.16.0 matrixStats_1.3.0 MsFeatures_1.12.0
[16] RColorBrewer_1.1-3 xcms_4.2.1 BiocParallel_1.38.0

loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 lazyeval_0.2.2 MassSpecWavelet_1.70.0
[4] digest_0.6.35 XML_3.99-0.16.1 lifecycle_1.0.4
[7] cluster_2.1.6 statmod_1.5.0 magrittr_2.0.3
[10] compiler_4.4.0 progress_1.2.3 rlang_1.1.4
[13] tools_4.4.0 igraph_2.0.3 utf8_1.2.4
[16] prettyunits_1.2.0 S4Arrays_1.4.1 DelayedArray_0.30.1
[19] plyr_1.8.9 abind_1.4-5 purrr_1.0.2
[22] grid_4.4.0 preprocessCore_1.66.0 fansi_1.0.6
[25] colorspace_2.1-0 ggplot2_3.5.1 iterators_1.0.14
[28] scales_1.3.0 MASS_7.3-60.2 cli_3.6.2
[31] mzR_2.38.0 crayon_1.5.2 generics_0.1.3
[34] rstudioapi_0.16.0 httr_1.4.7 reshape2_1.4.4
[37] ncdf4_1.22 DBI_1.2.3 affy_1.82.0
[40] stringr_1.5.1 zlibbioc_1.50.0 parallel_4.4.0
[43] impute_1.78.0 AnnotationFilter_1.28.0 BiocManager_1.30.23
[46] XVector_0.44.0 vsn_3.72.0 vctrs_0.6.5
[49] Matrix_1.7-0 jsonlite_1.8.8 hms_1.1.3
[52] MsExperiment_1.6.0 MALDIquant_1.22.2 clue_0.3-65
[55] foreach_1.5.2 limma_3.60.2 tidyr_1.3.1
[58] affyio_1.74.0 glue_1.7.0 MSnbase_2.30.1
[61] codetools_0.2-20 stringi_1.8.4 gtable_0.3.5
[64] UCSC.utils_1.0.0 mzID_1.42.0 munsell_0.5.1
[67] tibble_3.2.1 pillar_1.9.0 pcaMethods_1.96.0
[70] GenomeInfoDbData_1.2.12 R6_2.5.1 doParallel_1.0.17
[73] lattice_0.22-6 MetaboCoreUtils_1.12.0 Rcpp_1.0.12
[76] PSMatch_1.8.0 SparseArray_1.4.8 MsCoreUtils_1.16.0
[79] fs_1.6.4 pkgconfig_2.0.3

[YUANMENG-1]

This bug was fixed in xcms, but this fixed but did not make it into the current release version of xcms. I included now the fix also into the release version and it should become available in version 4.2.2 within a couple of days. As a workaround, you can filter the data set first to MS1 data:

srn <- mse |>
    filterMsLevel(1L) |>
    filterRt(rt = c(620, 640)) |>
    filterMzRange(mz = c(100.300,100.330))

plot(srn)

I met the followings:
srn <- mse |>

• filterMsLevel(1L) |>
  

• filterRt(rt = c(620, 640)) |>
  

• filterMzRange(mz = c(100.300,100.330))
  

Filter spectra
Filter spectra
Filter spectra
Error in validObject(object) :
invalid class “Spectra” object: slots in class definition but not in object: "processingChunkSize"

[jorainer]

OK, so, I guess you saved the mse variable and then updated the Spectra package. True, with the recent version we added a new property/slot to the Spectra object, that your saved/restored object does not have. You should be able to fix this with:

mse@spectra <- updateObject(mse@spectra)