I'm trying to read in a mzXML file to R using the
xcms package and I keep on getting this error.
> mzxcms <- xcmsRaw("datafile.mzXML",profstep=0.01,profmethod="bin",profparam=list(),includeMSn=FALSE,mslevel=NULL, scanrange=NULL) Error in validObject(.Object) : invalid class “xcmsFileSource” object: superclass "characterORconnection" not defined in the environment of the object's class
I'm not sure if this has to do anything with the warnings I get when I load
xcms (I'm getting warning messages that I haven't seen before, and I'm worried if some of the packages I've updated for different things are colliding). These are the warnings I get when I call
> library(xcms) Warning messages: 1: package ‘BiocGenerics’ was built under R version 4.0.3 2: package ‘Biobase’ was built under R version 4.0.3 3: In fun(libname, pkgname) : mzR has been built against a different Rcpp version (22.214.171.124) than is installed on your system (1.0.5). This might lead to errors when loading mzR. If you encounter such issues, please send a report, including the output of sessionInfo() to the Bioc support forum at https://support.bioconductor.org/. For details see also https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue. 4: package ‘S4Vectors’ was built under R version 4.0.3 5: multiple methods tables found for ‘which’
And below is my
> sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale:  LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252 LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  stats4 parallel stats graphics grDevices utils datasets  methods base other attached packages:  xcms_3.10.2 MSnbase_2.14.2 ProtGenerics_1.20.0  S4Vectors_0.28.0 mzR_2.22.0 Rcpp_1.0.5  BiocParallel_1.22.0 Biobase_2.50.0 BiocGenerics_0.36.0 loaded via a namespace (and not attached):  SummarizedExperiment_1.18.2 tidyselect_1.1.0  purrr_0.3.4 lattice_0.20-41  colorspace_2.0-0 vctrs_0.3.4  generics_0.1.0 vsn_3.56.0  XML_3.99-0.5 rlang_0.4.8  pillar_1.4.6 glue_1.4.2  affy_1.66.0 RColorBrewer_1.1-2  matrixStats_0.57.0 GenomeInfoDbData_1.2.3  affyio_1.58.0 foreach_1.5.1  lifecycle_0.2.0 plyr_1.8.6  mzID_1.26.0 robustbase_0.93-6  zlibbioc_1.36.0 munsell_0.5.0  pcaMethods_1.80.0 gtable_0.3.0  codetools_0.2-16 IRanges_2.24.0  doParallel_1.0.16 GenomeInfoDb_1.24.2  MassSpecWavelet_1.54.0 preprocessCore_1.50.0  DEoptimR_1.0-8 scales_1.1.1  BiocManager_1.30.10 DelayedArray_0.14.1  limma_3.44.3 XVector_0.30.0  RANN_2.6.1 impute_1.62.0  ggplot2_3.3.2 digest_0.6.27  dplyr_1.0.2 ncdf4_1.17  GenomicRanges_1.40.0 grid_4.0.2  tools_4.0.2 bitops_1.0-6  magrittr_1.5 RCurl_1.98-1.2  tibble_3.0.4 crayon_1.3.4  pkgconfig_2.0.3 MASS_7.3-53  ellipsis_0.3.1 Matrix_1.2-18  rstudioapi_0.12 iterators_1.0.13  R6_2.5.0 MALDIquant_1.19.3  compiler_4.0.2
Can anyone give me suggestions on why I can't read my data files in?