You can use the tidymass to check the version of all packages and update them.
Check version of tidymass
If you want to check if there are updates for tidymass and packages in it. Just check it like this.
tidymass::check_tidymass_version()
Update tidymass
The update_tidymass() function can be used to update tidymass and packages in it.
tidymass::update_tidymass(from = "github")
If the
from = "github"doesn’t work, try set it asfrom = "gitlab"orfrom = "gitee".
Session information
sessionInfo()
#> R version 4.1.2 (2021-11-01)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur 10.16
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] magrittr_2.0.2
#>
#> loaded via a namespace (and not attached):
#> [1] metpath_0.99.4 blogdown_1.7
#> [3] tidyr_1.2.0 missForest_1.4
#> [5] ggplot2_3.3.5 tidymass_0.99.6
#> [7] knitr_1.37 DelayedArray_0.20.0
#> [9] data.table_1.14.2 rpart_4.1.16
#> [11] KEGGREST_1.34.0 RCurl_1.98-1.5
#> [13] doParallel_1.0.17 generics_0.1.2
#> [15] snow_0.4-4 leaflet_2.1.0
#> [17] BiocGenerics_0.40.0 preprocessCore_1.56.0
#> [19] mixOmics_6.18.1 RANN_2.6.1
#> [21] proxy_0.4-26 future_1.23.0
#> [23] tzdb_0.2.0 xml2_1.3.3
#> [25] lubridate_1.8.0 ggsci_2.9
#> [27] SummarizedExperiment_1.24.0 assertthat_0.2.1
#> [29] tidyverse_1.3.1 viridis_0.6.2
#> [31] xfun_0.29 hms_1.1.1
#> [33] jquerylib_0.1.4 evaluate_0.15
#> [35] DEoptimR_1.0-10 fansi_1.0.2
#> [37] dbplyr_2.1.1 readxl_1.3.1
#> [39] igraph_1.2.11 DBI_1.1.2
#> [41] htmlwidgets_1.5.4 MsFeatures_1.3.0
#> [43] massprocesser_0.99.3 rARPACK_0.11-0
#> [45] stats4_4.1.2 purrr_0.3.4
#> [47] ellipsis_0.3.2 RSpectra_0.16-0
#> [49] crosstalk_1.2.0 dplyr_1.0.8
#> [51] backports_1.4.1 bookdown_0.24
#> [53] ggcorrplot_0.1.3 MatrixGenerics_1.6.0
#> [55] vctrs_0.3.8 Biobase_2.54.0
#> [57] remotes_2.4.2 here_1.0.1
#> [59] withr_2.4.3 ggforce_0.3.3
#> [61] itertools_0.1-3 robustbase_0.93-9
#> [63] checkmate_2.0.0 cluster_2.1.2
#> [65] lazyeval_0.2.2 crayon_1.5.0
#> [67] ellipse_0.4.2 pkgconfig_2.0.3
#> [69] tweenr_1.0.2 GenomeInfoDb_1.30.0
#> [71] ProtGenerics_1.26.0 nnet_7.3-17
#> [73] rlang_1.0.1 globals_0.14.0
#> [75] lifecycle_1.0.1 affyio_1.64.0
#> [77] extrafontdb_1.0 fastDummies_1.6.3
#> [79] MassSpecWavelet_1.60.0 modelr_0.1.8
#> [81] cellranger_1.1.0 randomForest_4.7-1
#> [83] rprojroot_2.0.2 polyclip_1.10-0
#> [85] matrixStats_0.61.0 Matrix_1.4-0
#> [87] reprex_2.0.1 base64enc_0.1-3
#> [89] GlobalOptions_0.1.2 png_0.1-7
#> [91] viridisLite_0.4.0 rjson_0.2.21
#> [93] mzR_2.28.0 clisymbols_1.2.0
#> [95] bitops_1.0-7 pander_0.6.4
#> [97] Biostrings_2.62.0 shape_1.4.6
#> [99] stringr_1.4.0 parallelly_1.30.0
#> [101] robust_0.7-0 readr_2.1.2
#> [103] jpeg_0.1-9 gridGraphics_0.5-1
#> [105] S4Vectors_0.32.3 scales_1.1.1
#> [107] plyr_1.8.6 zlibbioc_1.40.0
#> [109] compiler_4.1.2 RColorBrewer_1.1-2
#> [111] pcaMethods_1.86.0 clue_0.3-60
#> [113] rrcov_1.6-2 cli_3.2.0
#> [115] affy_1.72.0 XVector_0.34.0
#> [117] listenv_0.8.0 patchwork_1.1.1
#> [119] pbapply_1.5-0 htmlTable_2.4.0
#> [121] Formula_1.2-4 MASS_7.3-55
#> [123] tidyselect_1.1.1 vsn_3.62.0
#> [125] stringi_1.7.6 forcats_0.5.1.9000
#> [127] yaml_2.3.4 latticeExtra_0.6-29
#> [129] MALDIquant_1.21 ggrepel_0.9.1
#> [131] grid_4.1.2 sass_0.4.0
#> [133] xcms_3.16.1 metid_1.2.4
#> [135] tools_4.1.2 parallel_4.1.2
#> [137] circlize_0.4.14 rstudioapi_0.13
#> [139] MsCoreUtils_1.6.0 foreach_1.5.2
#> [141] foreign_0.8-82 masscleaner_0.99.7
#> [143] gridExtra_2.3 masstools_0.99.5
#> [145] farver_2.1.0 mzID_1.32.0
#> [147] ggraph_2.0.5 rvcheck_0.2.1
#> [149] digest_0.6.29 BiocManager_1.30.16
#> [151] Rcpp_1.0.8 GenomicRanges_1.46.1
#> [153] broom_0.7.12 ncdf4_1.19
#> [155] httr_1.4.2 MSnbase_2.20.4
#> [157] ComplexHeatmap_2.10.0 colorspace_2.0-2
#> [159] rvest_1.0.2 XML_3.99-0.8
#> [161] fs_1.5.2 IRanges_2.28.0
#> [163] splines_4.1.2 yulab.utils_0.0.4
#> [165] massdataset_0.99.20 graphlayouts_0.8.0
#> [167] ggplotify_0.1.0 plotly_4.10.0
#> [169] fit.models_0.64 jsonlite_1.7.3
#> [171] tidygraph_1.2.0 corpcor_1.6.10
#> [173] R6_2.5.1 Hmisc_4.6-0
#> [175] pillar_1.7.0 htmltools_0.5.2
#> [177] glue_1.6.1 fastmap_1.1.0
#> [179] massqc_0.99.7 BiocParallel_1.28.3
#> [181] class_7.3-20 codetools_0.2-18
#> [183] pcaPP_1.9-74 mvtnorm_1.1-3
#> [185] furrr_0.2.3 utf8_1.2.2
#> [187] lattice_0.20-45 bslib_0.3.1
#> [189] tibble_3.1.6 massstat_0.99.13
#> [191] ggfortify_0.4.14 zip_2.2.0
#> [193] openxlsx_4.2.5 Rttf2pt1_1.3.9
#> [195] survival_3.2-13 limma_3.50.0
#> [197] rmarkdown_2.11 munsell_0.5.0
#> [199] e1071_1.7-9 GetoptLong_1.0.5
#> [201] GenomeInfoDbData_1.2.7 iterators_1.0.14
#> [203] impute_1.68.0 haven_2.4.3
#> [205] reshape2_1.4.4 gtable_0.3.0
#> [207] extrafont_0.17