Check tidymass version
The tidymass package allows you to check the version of all packages and update them. To check for updates specifically for tidymass and its associated packages, you can use the following code.
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.
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 4.4.1 (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_1.2.33
## [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