Check tidymass version
You can use the tidymass to check the version of all packages and update them.
If you want to check if there are updates for tidymass and packages in it. Just check it like this.
tidymass::check_tidymass_version()
## Registered S3 method overwritten by 'Hmisc':
## method from
## vcov.default fit.models
## ##tidymass/tidymass is up-to-date devel version
## ##tidymass/massconverter is up-to-date devel version
## ##tidymass/massdataset is up-to-date devel version
## ##tidymass/massprocesser is up-to-date devel version
## ##tidymass/masscleaner is up-to-date devel version
## ##tidymass/metid is up-to-date devel version
## ##tidymass/massstat is up-to-date devel version
## ##tidymass/metpath is up-to-date devel version
## ##tidymass/masstools is up-to-date devel version
## Use update_tidymass() to update the following pacakges.
## package installed_version latest_version up_to_date
## 1 massqc 1.0.6 1.0.5 FALSE
This will list all the packages version and if there are some new versions can be updated.
Update tidymass
The update_tidymass() function can be used to update tidymass and packages within it.
tidymass::update_tidymass(from = "gitlab")
You can change the from argument if from = "gitlab" doesn’t work.
-
“github”
-
“gitee”
-
“tidymass.org”
If all the options of from don’t work, you can try to set fastgit as TRUE.
tidymass::update_tidymass(from = "gitlab",
fastgit = TRUE)
Session information
sessionInfo()
## R version 4.3.0 (2023-04-21)
## Platform: x86_64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.5.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/Los_Angeles
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## loaded via a namespace (and not attached):
## [1] splines_4.3.0 bitops_1.0-7
## [3] cellranger_1.1.0 tibble_3.2.1
## [5] polyclip_1.10-4 preprocessCore_1.62.1
## [7] XML_3.99-0.14 rpart_4.1.19
## [9] fastDummies_1.6.3 lifecycle_1.0.3
## [11] doParallel_1.0.17 globals_0.16.2
## [13] lattice_0.21-8 MASS_7.3-58.4
## [15] backports_1.4.1 magrittr_2.0.3
## [17] plotly_4.10.2 openxlsx_4.2.5.2
## [19] limma_3.56.2 Hmisc_5.1-0
## [21] sass_0.4.6 rmarkdown_2.22
## [23] jquerylib_0.1.4 yaml_2.3.7
## [25] remotes_2.4.2 doRNG_1.8.6
## [27] zip_2.3.0 MsCoreUtils_1.12.0
## [29] pbapply_1.7-0 metid_1.2.30
## [31] RColorBrewer_1.1-3 zlibbioc_1.46.0
## [33] GenomicRanges_1.52.0 purrr_1.0.1
## [35] ggraph_2.1.0 BiocGenerics_0.46.0
## [37] itertools_0.1-3 RCurl_1.98-1.12
## [39] nnet_7.3-18 tweenr_2.0.2
## [41] massstat_1.0.5 circlize_0.4.15
## [43] GenomeInfoDbData_1.2.10 IRanges_2.34.0
## [45] S4Vectors_0.38.1 ggrepel_0.9.3
## [47] listenv_0.9.0 ellipse_0.4.5
## [49] masstools_1.0.10 RSpectra_0.16-1
## [51] missForest_1.5 parallelly_1.36.0
## [53] MSnbase_2.26.0 ncdf4_1.21
## [55] codetools_0.2-19 DelayedArray_0.26.3
## [57] ggforce_0.4.1 tidyselect_1.2.0
## [59] shape_1.4.6 farver_2.1.1
## [61] viridis_0.6.3 massdataset_1.0.25
## [63] matrixStats_1.0.0 stats4_4.3.0
## [65] base64enc_0.1-3 massqc_1.0.6
## [67] jsonlite_1.8.5 GetoptLong_1.0.5
## [69] multtest_2.56.0 e1071_1.7-13
## [71] tidygraph_1.2.3 Formula_1.2-5
## [73] survival_3.5-5 iterators_1.0.14
## [75] foreach_1.5.2 progress_1.2.2
## [77] tools_4.3.0 Rcpp_1.0.10
## [79] glue_1.6.2 rARPACK_0.11-0
## [81] gridExtra_2.3 xfun_0.39
## [83] mixOmics_6.24.0 MatrixGenerics_1.12.2
## [85] ggfortify_0.4.16 GenomeInfoDb_1.36.0
## [87] dplyr_1.1.2 withr_2.5.0
## [89] BiocManager_1.30.21 fastmap_1.1.1
## [91] fansi_1.0.4 blogdown_1.18.1
## [93] digest_0.6.31 R6_2.5.1
## [95] colorspace_2.1-0 utf8_1.2.3
## [97] tidyr_1.3.0 generics_0.1.3
## [99] data.table_1.14.8 corpcor_1.6.10
## [101] robustbase_0.95-1 class_7.3-21
## [103] graphlayouts_1.0.0 prettyunits_1.1.1
## [105] httr_1.4.6 htmlwidgets_1.6.2
## [107] S4Arrays_1.0.4 pkgconfig_2.0.3
## [109] gtable_0.3.3 robust_0.7-1
## [111] tidymass_1.0.8 ComplexHeatmap_2.16.0
## [113] impute_1.74.1 MassSpecWavelet_1.66.0
## [115] XVector_0.40.0 furrr_0.3.1
## [117] pcaPP_2.0-3 htmltools_0.5.5
## [119] bookdown_0.34 MALDIquant_1.22.1
## [121] ProtGenerics_1.32.0 clue_0.3-64
## [123] scales_1.2.1 Biobase_2.60.0
## [125] png_0.1-8 knitr_1.43
## [127] rstudioapi_0.14 tzdb_0.4.0
## [129] reshape2_1.4.4 rjson_0.2.21
## [131] checkmate_2.2.0 ggcorrplot_0.1.4
## [133] proxy_0.4-27 cachem_1.0.8
## [135] GlobalOptions_0.1.2 stringr_1.5.0
## [137] parallel_4.3.0 foreign_0.8-84
## [139] mzID_1.38.0 vsn_3.68.0
## [141] pillar_1.9.0 grid_4.3.0
## [143] vctrs_0.6.2 MsFeatures_1.8.0
## [145] RANN_2.6.1 pcaMethods_1.92.0
## [147] randomForest_4.7-1.1 cluster_2.1.4
## [149] htmlTable_2.4.1 evaluate_0.21
## [151] readr_2.1.4 mvtnorm_1.2-2
## [153] cli_3.6.1 compiler_4.3.0
## [155] rlang_1.1.1 crayon_1.5.2
## [157] rngtools_1.5.2 Rdisop_1.60.0
## [159] rrcov_1.7-3 affy_1.78.0
## [161] plyr_1.8.8 masscleaner_1.0.11
## [163] stringi_1.7.12 viridisLite_0.4.2
## [165] BiocParallel_1.34.2 Biostrings_2.68.1
## [167] munsell_0.5.0 lazyeval_0.2.2
## [169] fit.models_0.64 xcms_3.22.0
## [171] massprocesser_1.0.10 Matrix_1.5-4
## [173] hms_1.1.3 patchwork_1.1.2
## [175] future_1.32.0 ggplot2_3.4.2
## [177] KEGGREST_1.40.0 SummarizedExperiment_1.30.2
## [179] mzR_2.34.0 igraph_1.4.3
## [181] affyio_1.70.0 bslib_0.5.0
## [183] DEoptimR_1.0-14 metpath_1.0.8
## [185] readxl_1.4.2