Hello.
I´m trying to follow the tutorial for the installation of Metaboanalyst R in Rstudio ( MetaboAnalyst ) but when I try the options available for installing packages dependencies and packages I get many errors. Some packages don´t install or commands are not recognised. It seems like the tutorial has not been updated and now things are not working properly….I´m not sure. I would like to use R instead of the web app because the web app sometimes crashes and lags.
I´m using R 4.6.0 and I have created a brand new R project with an renv.
Find attached the log of the console with the run commands and outputs.
Can anyone help please?
Cheers
Eduardo
sessionInfo()
R version 4.6.0 (2026-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)
Matrix products: default
LAPACK version 3.12.1
locale:
[1] LC_COLLATE=Portuguese_Brazil.utf8 LC_CTYPE=Portuguese_Brazil.utf8 LC_MONETARY=Portuguese_Brazil.utf8
[4] LC_NUMERIC=C LC_TIME=Portuguese_Brazil.utf8
time zone: America/Sao_Paulo
tzcode source: internal
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] MetaboAnalystR_4.3.0 devtools_2.5.2 usethis_3.2.2 pacman_0.5.1
loaded via a namespace (and not attached):
[1] DBI_1.3.0 bitops_1.1-0 pROC_1.19.1 remotes_2.5.0
[5] rlang_1.3.0 magrittr_2.0.5 scrime_1.3.7 otel_0.2.0
[9] compiler_4.6.0 RSQLite_3.53.3 reshape2_1.4.5 callr_3.8.0
[13] vctrs_0.7.3 stringr_1.6.0 pkgconfig_2.0.3 fastmap_1.2.0
[17] ellipsis_0.3.3 caTools_1.18.4 prodlim_2026.03.11 sessioninfo_1.2.4
[21] purrr_1.2.2 bit_4.6.0 xfun_0.62 cachem_1.1.0
[25] jsonlite_2.0.0 pak_0.11.1 recipes_1.4.0 blob_1.3.0
[29] BiocParallel_1.46.0 parallel_4.6.0 R6_2.6.1 stringi_1.8.9
[33] RColorBrewer_1.1-3 limma_3.68.5 parallelly_1.48.0 pkgload_1.5.3
[37] rpart_4.1.27 lubridate_1.9.5 Rcpp_1.1.2 iterators_1.0.14
[41] knitr_1.52 future.apply_1.21.0 timechange_0.4.0 Matrix_1.7-5
[45] splines_4.6.0 nnet_7.3-20 igraph_2.3.4 tidyselect_1.2.1
[49] rstudioapi_0.19.0 yaml_2.3.12 stringfish_0.19.2 siggenes_1.86.0
[53] timeDate_4052.112 gplots_3.3.0 codetools_0.2-20 curl_8.1.0
[57] processx_3.9.0 listenv_1.1.0 pkgbuild_1.4.8 lattice_0.22-9
[61] tibble_3.3.1 plyr_1.8.9 withr_3.0.3 Biobase_2.72.0
[65] S7_0.2.2 evaluate_1.0.5 future_1.80.0 desc_1.4.3
[69] survival_3.8-6 RcppParallel_6.2.1 pillar_1.11.1 BiocManager_1.30.27
[73] KernSmooth_2.23-26 renv_1.3.1 foreach_1.5.2 stats4_4.6.0
[77] plotly_4.12.1 generics_0.1.4 ggplot2_4.0.3 scales_1.4.0
[81] globals_0.20.0 gtools_3.9.5 qs2_0.3.1 class_7.3-23
[85] glue_1.8.1 tools_4.6.0 data.table_1.18.6.1 ModelMetrics_1.2.2.2
[89] fgsea_1.38.0 gower_1.0.2 locfit_1.5-9.12 fs_2.1.0
[93] fastmatch_1.1-8 cowplot_1.2.0 grid_4.6.0 Cairo_1.7-0
[97] impute_1.86.0 tidyr_1.3.2 ipred_0.9-16 edgeR_4.10.7
[101] nlme_3.1-169 crmn_0.0.22 cli_3.6.6 viridisLite_0.4.3
[105] lava_1.9.3 dplyr_1.2.1 glasso_1.11 pcaMethods_2.4.0
[109] gtable_0.3.6 digest_0.6.39 BiocGenerics_0.58.1 caret_7.0-1
[113] htmlwidgets_1.6.4 farver_2.1.2 htmltools_0.5.9 memoise_2.0.1
[117] multtest_2.68.0 lifecycle_1.0.5 httr_1.4.9 hardhat_1.4.3
[121] statmod_1.5.2 bit64_4.8.6 MASS_7.3-65
log.txt (73.8 KB)