Hello ! During the installation and lauching of MetaboAnalystR, i get these warning messages :

Warning messages: 
1: In fun(libname, pkgname) : mzR has been built against a different Rcpp version (1.0.2) than is installed on your system (1.0.3). 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. 
2: replacing previous import ‘xcms::plot’ by ‘graphics::plot’ when loading ‘CAMERA’ 
3: replacing previous import ‘CAMERA::annotate’ by ‘ggplot2::annotate’ when loading ‘MetaboAnalystR’ 
4: replacing previous import ‘MSnbase::normalize’ by ‘igraph::normalize’ when loading ‘MetaboAnalystR’ 
5: replacing previous import ‘reshape::recast’ by ‘reshape2::recast’ when loading ‘MetaboAnalystR’ 
6: replacing previous import ‘reshape::melt’ by ‘reshape2::melt’ when loading ‘MetaboAnalystR’ 
7: replacing previous import ‘reshape::colsplit’ by ‘reshape2::colsplit’ when loading ‘MetaboAnalystR’ 
8: replacing previous import ‘igraph::normalize’ by ‘xcms::normalize’ when loading ‘MetaboAnalystR’ 
9: replacing previous import ‘igraph::groups’ by ‘xcms::groups’ when loading ‘MetaboAnalystR’

I did a sessioninfo() has you expected :

R version 3.6.3 (2020-02-29) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 8.1 x64 (build 9600) 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] stats graphics grDevices utils datasets methods base other attached packages: [1] MetaboAnalystR_2.0.3 data.table_1.12.8 pls_2.7-2 [4] lattice_0.20-40 loaded via a namespace (and not attached): [1] backports_1.1.5 Hmisc_4.3-1 fastmatch_1.1-0 [4] sn_1.5-5 plyr_1.8.6 igraph_1.2.4.2 [7] lazyeval_0.2.2 CAMERA_1.42.0 splines_3.6.3 [10] BiocParallel_1.20.1 ggplot2_3.3.0 TH.data_1.0-10 [13] digest_0.6.25 foreach_1.4.8 htmltools_0.4.0 [16] gdata_2.18.0 magrittr_1.5 checkmate_2.0.0 [19] memoise_1.1.0 cluster_2.1.0 doParallel_1.0.15 [22] limma_3.42.2 recipes_0.1.9 gower_0.2.1 [25] sandwich_2.5-1 siggenes_1.60.0 jpeg_0.1-8.1 [28] colorspace_1.4-1 blob_1.2.1 xfun_0.12 [31] dplyr_0.8.4 jsonlite_1.6.1 crayon_1.3.4 [34] graph_1.64.0 impute_1.60.0 survival_3.1-11 [37] zoo_1.8-7 iterators_1.0.12 glue_1.3.1 [40] gtable_0.3.0 ipred_0.9-9 zlibbioc_1.32.0 [43] BiocGenerics_0.32.0 DEoptimR_1.0-8 scales_1.1.0 [46] vsn_3.54.0 mvtnorm_1.1-0 DBI_1.1.0 [49] bibtex_0.4.2.2 Rcpp_1.0.3 metap_1.3 [52] plotrix_3.7-7 mzR_2.20.0 viridisLite_0.3.0 [55] htmlTable_1.13.3 foreign_0.8-76 bit_1.1-15.2 [58] preprocessCore_1.48.0 Formula_1.2-3 stats4_3.6.3 [61] lava_1.6.7 prodlim_2019.11.13 httr_1.4.1 [64] htmlwidgets_1.5.1 fgsea_1.12.0 gplots_3.0.3 [67] RColorBrewer_1.1-2 acepack_1.4.1 TFisher_0.2.0 [70] pkgconfig_2.0.3 reshape_0.8.8 XML_3.99-0.3 [73] nnet_7.3-13 caret_6.0-85 tidyselect_1.0.0 [76] rlang_0.4.5 reshape2_1.4.3 munsell_0.5.0 [79] tools_3.6.3 generics_0.0.2 RSQLite_2.2.0 [82] stringr_1.4.0 mzID_1.24.0 ModelMetrics_1.2.2.1 [85] knitr_1.28 bit64_0.9-7 robustbase_0.93-5 [88] caTools_1.18.0 scrime_1.3.5 purrr_0.3.3 [91] RANN_2.6.1 ncdf4_1.17 RBGL_1.62.1 [94] nlme_3.1-145 compiler_3.6.3 rstudioapi_0.11 [97] plotly_4.9.2 png_0.1-7 affyio_1.56.0 [100] MassSpecWavelet_1.52.0 tibble_2.1.3 stringi_1.4.6 [103] MSnbase_2.12.0 ProtGenerics_1.18.0 Matrix_1.2-18 [106] multtest_2.42.0 vctrs_0.2.4 mutoss_0.1-12 [109] pillar_1.4.3 lifecycle_0.2.0 BiocManager_1.30.10 [112] Rdpack_0.11-1 MALDIquant_1.19.3 bitops_1.0-6 [115] gbRd_0.4-11 xcms_3.8.2 R6_2.4.1 [118] latticeExtra_0.6-29 pcaMethods_1.78.0 affy_1.64.0 [121] KernSmooth_2.23-16 gridExtra_2.3 IRanges_2.20.2 [124] codetools_0.2-16 MASS_7.3-51.5 gtools_3.8.1 [127] assertthat_0.2.1 withr_2.1.2 mnormt_1.5-6 [130] multcomp_1.4-12 S4Vectors_0.24.3 parallel_3.6.3 [133] grid_3.6.3 rpart_4.1-15 timeDate_3043.102 [136] tidyr_1.0.2 class_7.3-15 pROC_1.16.1 [139] numDeriv_2016.8-1.1 Biobase_2.46.0 lubridate_1.7.4 [142] base64enc_0.1-3

You can safely ignore the first warning (mzR has been built against a different Rcpp version ...).

As for the other ones, different packages define the same function/methods, and you'll need to make sure that it is the right method that is called.