Issue in reading MRM files

[CaroPeltier]

Hello, I wanted to use MSnbase on MRM data (Waters) with several channels and I have converted the files as mzML with msconvert. However, I can not read the mzML with readMSData (nor readSMRData). I have the following error: Original error was: Error in pwizModule$open(filename): [IO::HandlerBinaryDataArray] Unknown binary data type. Could you help me ? Thanks a lot, Caroline

[jorainer]

Can you please provide the output from your sessionInfo()?

[CaroPeltier]

Hello, Here it is, Thank you very much, Caroline

R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C [5] LC_TIME=French_France.1252

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods [9] base

other attached packages: [1] MSnbase_2.14.2 ProtGenerics_1.20.0 S4Vectors_0.26.1 mzR_2.22.0 [5] Rcpp_1.0.7 Biobase_2.48.0 BiocGenerics_0.34.0

loaded via a namespace (and not attached): [1] lattice_0.20-41 assertthat_0.2.1 digest_0.6.27 [4] foreach_1.5.2 utf8_1.2.1 R6_2.5.1 [7] plyr_1.8.6 mzID_1.26.0 evaluate_0.18 [10] ggplot2_3.4.0 pillar_1.8.1 zlibbioc_1.34.0 [13] rlang_1.0.6 rstudioapi_0.14 preprocessCore_1.50.0 [16] rmarkdown_2.18 BiocParallel_1.22.0 munsell_0.5.0 [19] compiler_4.0.2 xfun_0.30 pkgconfig_2.0.3 [22] pcaMethods_1.80.0 htmltools_0.5.2 tidyselect_1.2.0 [25] tibble_3.1.8 IRanges_2.22.2 codetools_0.2-18 [28] XML_3.99-0.6 fansi_0.4.1 dplyr_1.0.10 [31] MASS_7.3-53 grid_4.0.2 gtable_0.3.1 [34] lifecycle_1.0.3 affy_1.66.0 DBI_1.1.3 [37] magrittr_2.0.1 scales_1.2.1 ncdf4_1.17 [40] zip_2.1.1 cli_3.2.0 stringi_1.5.3 [43] impute_1.62.0 affyio_1.58.0 doParallel_1.0.17 [46] limma_3.44.3 generics_0.1.3 vctrs_0.5.1 [49] openxlsx_4.2.3 iterators_1.0.14 tools_4.0.2 [52] glue_1.6.2 fastmap_1.1.0 yaml_2.3.5 [55] colorspace_1.4-1 BiocManager_1.30.19 vsn_3.56.0 [58] MALDIquant_1.19.3 knitr_1.39

De : Johannes Rainer @.> Envoyé : mercredi 26 avril 2023 11:07 À : lgatto/MSnbase @.> Cc : Caroline Peltier @.>; Author @.> Objet : Re: [lgatto/MSnbase] Issue in reading MRM files (Issue #591)

Can you please provide the output from your sessionInfo()?

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[lgatto]

Could you please update your R to version 4.3 or 4.2, update all your packages (for R 4.3, Bioconductor 3.17 will be released today, for R 4.2, it would be Bioconductor version 3.16). Your current R and Bioconductor package versions are seriously outdated and it is very possibly that the issue you see has been addressed in more recent versions.

[CaroPeltier]

Very nice, it is working ! (I have updated for R 4.3) Thank you very much for your response and your responsiveness, All the best, Caroline

De : Laurent Gatto @.> Envoyé : mercredi 26 avril 2023 15:51 À : lgatto/MSnbase @.> Cc : Caroline Peltier @.>; Author @.> Objet : Re: [lgatto/MSnbase] Issue in reading MRM files (Issue #591)

Could you please update your R to version 4.3 or 4.2, update all your packages (for R 4.3, Bioconductor 3.17 will be released today, for R 4.2, it would be Bioconductor version 3.16). Your current R and Bioconductor package versions are seriously outdated and it is very possibly that the issue you see has been addressed in more recent versions.

— Reply to this email directly, view it on GitHubhttps://github.com/lgatto/MSnbase/issues/591#issuecomment-1523460059, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARQUZ6YBXCKFM5G6W2O4JULXDER6DANCNFSM6AAAAAAXL7IVVE. You are receiving this because you authored the thread.Message ID: @.**@.>>