检查 tidymass 版本
tidymass 包允许您检查所有包的版本并更新它们。要专门检查 tidymass 及其相关包的更新，可以使用以下代码。
tidymass::check_tidymass_version()
## Warning in fun(libname, pkgname): mzR has been built against a different Rcpp version (1.0.12)
## than is installed on your system (1.0.13). 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.
## Registered S3 method overwritten by 'Hmisc':
## method from
## vcov.default fit.models
## Warning: replacing previous import 'massdataset::check_mass_dataset' by
## 'metid::check_mass_dataset' when loading 'tidymass'
## Warning: replacing previous import 'masstools::remove_noise' by
## 'metid::remove_noise' when loading 'tidymass'
## ##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/massqc 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
## No package to update.
这将列出所有包的版本，并显示是否有可更新的新版本。
更新 tidymass
update_tidymass() 函数可以用于更新 tidymass 及其相关的包。
tidymass::update_tidymass(from = "gitlab")
如果 from = "gitlab" 不起作用，您可以更改 from 参数。
-
“github”
-
“gitee”
-
“tidymass.org”
如果所有 from 参数的选项都不起作用，您可以尝试将 fastgit 设置为 TRUE。
tidymass::update_tidymass(from = "gitlab",
fastgit = TRUE)
会话信息
sessionInfo()
## R version 4.4.1 (2024-06-14)
## Platform: aarch64-apple-darwin20
## Running under: macOS 15.0
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
##
## 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: Asia/Singapore
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-8 cellranger_1.1.0
## [3] tibble_3.2.1 polyclip_1.10-7
## [5] preprocessCore_1.66.0 fastDummies_1.7.4
## [7] XML_3.99-0.17 rpart_4.1.23
## [9] lifecycle_1.0.4 doParallel_1.0.17
## [11] globals_0.16.3 lattice_0.22-6
## [13] MASS_7.3-61 MultiAssayExperiment_1.30.3
## [15] backports_1.5.0 magrittr_2.0.3
## [17] plotly_4.10.4 openxlsx_4.2.7
## [19] limma_3.60.4 Hmisc_5.1-3
## [21] sass_0.4.9 rmarkdown_2.28
## [23] jquerylib_0.1.4 yaml_2.3.10
## [25] remotes_2.5.0 doRNG_1.8.6
## [27] zip_2.3.1 metid_1.2.34
## [29] MsCoreUtils_1.16.1 pbapply_1.7-2
## [31] DBI_1.2.3 RColorBrewer_1.1-3
## [33] abind_1.4-5 zlibbioc_1.50.0
## [35] GenomicRanges_1.56.1 purrr_1.0.2
## [37] ggraph_2.2.1 AnnotationFilter_1.28.0
## [39] BiocGenerics_0.50.0 itertools_0.1-3
## [41] RCurl_1.98-1.16 nnet_7.3-19
## [43] tweenr_2.0.3 massstat_1.0.6
## [45] circlize_0.4.16 GenomeInfoDbData_1.2.12
## [47] IRanges_2.38.1 S4Vectors_0.42.1
## [49] ggrepel_0.9.5 listenv_0.9.1
## [51] ellipse_0.5.0 masstools_1.0.13
## [53] RSpectra_0.16-2 missForest_1.5
## [55] parallelly_1.38.0 MSnbase_2.30.1
## [57] ncdf4_1.23 codetools_0.2-20
## [59] DelayedArray_0.30.1 ggforce_0.4.2
## [61] tidyselect_1.2.1 Spectra_1.14.1
## [63] shape_1.4.6.1 farver_2.1.2
## [65] UCSC.utils_1.0.0 viridis_0.6.5
## [67] massdataset_1.0.34 matrixStats_1.3.0
## [69] stats4_4.4.1 base64enc_0.1-3
## [71] massqc_1.0.7 jsonlite_1.8.8
## [73] GetoptLong_1.0.5 e1071_1.7-14
## [75] tidygraph_1.3.1 Formula_1.2-5
## [77] iterators_1.0.14 foreach_1.5.2
## [79] tools_4.4.1 progress_1.2.3
## [81] rARPACK_0.11-0 Rcpp_1.0.13
## [83] glue_1.7.0 gridExtra_2.3
## [85] SparseArray_1.4.8 mixOmics_6.28.0
## [87] xfun_0.47 MatrixGenerics_1.16.0
## [89] ggfortify_0.4.17 GenomeInfoDb_1.40.1
## [91] dplyr_1.1.4 withr_3.0.1
## [93] BiocManager_1.30.25 fastmap_1.2.0
## [95] fansi_1.0.6 blogdown_1.19
## [97] digest_0.6.37 R6_2.5.1
## [99] colorspace_2.1-1 utf8_1.2.4
## [101] tidyr_1.3.1 generics_0.1.3
## [103] corpcor_1.6.10 data.table_1.16.0
## [105] robustbase_0.99-4 class_7.3-22
## [107] graphlayouts_1.1.1 htmlwidgets_1.6.4
## [109] prettyunits_1.2.0 PSMatch_1.8.0
## [111] httr_1.4.7 S4Arrays_1.4.1
## [113] pkgconfig_2.0.3 gtable_0.3.5
## [115] robust_0.7-5 tidymass_1.0.9
## [117] ComplexHeatmap_2.20.0 impute_1.78.0
## [119] MassSpecWavelet_1.70.0 XVector_0.44.0
## [121] furrr_0.3.1 pcaPP_2.0-5
## [123] htmltools_0.5.8.1 bookdown_0.40
## [125] MALDIquant_1.22.3 ProtGenerics_1.36.0
## [127] clue_0.3-65 scales_1.3.0
## [129] Biobase_2.64.0 png_0.1-8
## [131] knitr_1.48 MetaboCoreUtils_1.12.0
## [133] rstudioapi_0.16.0 tzdb_0.4.0
## [135] reshape2_1.4.4 rjson_0.2.22
## [137] checkmate_2.3.2 ggcorrplot_0.1.4.1
## [139] proxy_0.4-27 cachem_1.1.0
## [141] GlobalOptions_0.1.2 stringr_1.5.1
## [143] parallel_4.4.1 foreign_0.8-87
## [145] mzID_1.42.0 vsn_3.72.0
## [147] pillar_1.9.0 grid_4.4.1
## [149] vctrs_0.6.5 MsFeatures_1.12.0
## [151] pcaMethods_1.96.0 randomForest_4.7-1.1
## [153] cluster_2.1.6 htmlTable_2.4.3
## [155] evaluate_0.24.0 readr_2.1.5
## [157] mvtnorm_1.3-1 cli_3.6.3
## [159] compiler_4.4.1 rlang_1.1.4
## [161] crayon_1.5.3 rngtools_1.5.2
## [163] rrcov_1.7-6 QFeatures_1.14.2
## [165] affy_1.82.0 plyr_1.8.9
## [167] masscleaner_1.0.12 fs_1.6.4
## [169] stringi_1.8.4 viridisLite_0.4.2
## [171] BiocParallel_1.38.0 Biostrings_2.72.1
## [173] munsell_0.5.1 fit.models_0.64
## [175] lazyeval_0.2.2 xcms_4.2.3
## [177] massprocesser_1.0.10 Matrix_1.7-0
## [179] hms_1.1.3 patchwork_1.2.0
## [181] future_1.34.0 MsExperiment_1.6.0
## [183] ggplot2_3.5.1 KEGGREST_1.44.1
## [185] statmod_1.5.0 SummarizedExperiment_1.34.0
## [187] mzR_2.38.0 memoise_2.0.1
## [189] igraph_2.0.3 affyio_1.74.0
## [191] bslib_0.8.0 DEoptimR_1.1-3
## [193] metpath_1.0.8 readxl_1.4.3