2  Update

2.1 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 (1.0.13.1). 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## tidymass/tidymass is out of date...

##tidymass/massconverter is up-to-date devel version

##tidymass/massdataset is up-to-date devel version

## tidymass/massprocesser is out of date...

##tidymass/masscleaner is up-to-date devel version

## tidymass/massqc is out of date...

##tidymass/metid is up-to-date devel version

## tidymass/massstat is out of date...

##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      tidymass             1.0.8         2.0.10      FALSE
2 massprocesser            1.0.10         1.0.11      FALSE
3        massqc             1.0.6          1.0.7      FALSE
4      massstat             1.0.5          1.0.6      FALSE

This will list all the packages version and if there are some new versions can be updated.

2.2 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.

1. “github”

2. “gitee”

3. “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)

2.3 Session information

sessionInfo()

R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS 15.5

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] tibble_3.2.1                polyclip_1.10-7            
  [3] preprocessCore_1.66.0       XML_3.99-0.17              
  [5] rpart_4.1.23                fastDummies_1.7.4          
  [7] lifecycle_1.0.4             doParallel_1.0.17          
  [9] globals_0.16.3              lattice_0.22-6             
 [11] MASS_7.3-61                 MultiAssayExperiment_1.30.3
 [13] backports_1.5.0             magrittr_2.0.3             
 [15] openxlsx_4.2.7.1            limma_3.60.6               
 [17] Hmisc_5.2-0                 rmarkdown_2.29             
 [19] remotes_2.5.0               doRNG_1.8.6                
 [21] zip_2.3.1                   MsCoreUtils_1.16.1         
 [23] pbapply_1.7-2               DBI_1.2.3                  
 [25] metid_1.3.1                 RColorBrewer_1.1-3         
 [27] abind_1.4-8                 zlibbioc_1.50.0            
 [29] rvest_1.0.4                 GenomicRanges_1.56.2       
 [31] purrr_1.0.2                 ggraph_2.2.1               
 [33] AnnotationFilter_1.28.0     BiocGenerics_0.50.0        
 [35] itertools_0.1-3             nnet_7.3-19                
 [37] tweenr_2.0.3                massstat_1.0.5             
 [39] circlize_0.4.16             GenomeInfoDbData_1.2.12    
 [41] IRanges_2.38.1              S4Vectors_0.42.1           
 [43] ggrepel_0.9.6               listenv_0.9.1              
 [45] ellipse_0.5.0               masstools_1.0.15           
 [47] RSpectra_0.16-2             missForest_1.5             
 [49] parallelly_1.38.0           MSnbase_2.30.1             
 [51] ncdf4_1.23                  codetools_0.2-20           
 [53] DelayedArray_0.30.1         ggforce_0.4.2              
 [55] xml2_1.3.6                  tidyselect_1.2.1           
 [57] Spectra_1.14.1              shape_1.4.6.1              
 [59] UCSC.utils_1.0.0            farver_2.1.2               
 [61] viridis_0.6.5               massdataset_1.0.34         
 [63] matrixStats_1.4.1           stats4_4.4.1               
 [65] base64enc_0.1-3             massqc_1.0.6               
 [67] jsonlite_1.8.9              GetoptLong_1.0.5           
 [69] e1071_1.7-16                tidygraph_1.3.1            
 [71] Formula_1.2-5               iterators_1.0.14           
 [73] foreach_1.5.2               tools_4.4.1                
 [75] progress_1.2.3              Rcpp_1.0.13-1              
 [77] glue_1.8.0                  rARPACK_0.11-0             
 [79] gridExtra_2.3               SparseArray_1.4.8          
 [81] xfun_0.52                   mixOmics_6.28.0            
 [83] MatrixGenerics_1.16.0       ggfortify_0.4.17           
 [85] GenomeInfoDb_1.40.1         dplyr_1.1.4                
 [87] withr_3.0.2                 BiocManager_1.30.25        
 [89] fastmap_1.2.0               digest_0.6.37              
 [91] R6_2.5.1                    colorspace_2.1-1           
 [93] tidyr_1.3.1                 generics_0.1.3             
 [95] data.table_1.16.2           corpcor_1.6.10             
 [97] robustbase_0.99-4-1         class_7.3-22               
 [99] graphlayouts_1.2.0          prettyunits_1.2.0          
[101] PSMatch_1.8.0               httr_1.4.7                 
[103] htmlwidgets_1.6.4           S4Arrays_1.4.1             
[105] pkgconfig_2.0.3             gtable_0.3.6               
[107] robust_0.7-5                tidymass_1.0.8             
[109] ComplexHeatmap_2.20.0       impute_1.78.0              
[111] MassSpecWavelet_1.70.0      XVector_0.44.0             
[113] pcaPP_2.0-5                 furrr_0.3.1                
[115] htmltools_0.5.8.1           MALDIquant_1.22.3          
[117] ProtGenerics_1.36.0         clue_0.3-65                
[119] scales_1.3.0                Biobase_2.64.0             
[121] png_0.1-8                   knitr_1.49                 
[123] MetaboCoreUtils_1.12.0      rstudioapi_0.17.1          
[125] tzdb_0.4.0                  reshape2_1.4.4             
[127] rjson_0.2.23                checkmate_2.3.2            
[129] ggcorrplot_0.1.4.1          cachem_1.1.0               
[131] proxy_0.4-27                GlobalOptions_0.1.2        
[133] stringr_1.5.1               parallel_4.4.1             
[135] foreign_0.8-87              mzID_1.42.0                
[137] vsn_3.72.0                  pillar_1.11.0              
[139] grid_4.4.1                  vctrs_0.6.5                
[141] MsFeatures_1.12.0           pcaMethods_1.96.0          
[143] randomForest_4.7-1.2        cluster_2.1.6              
[145] htmlTable_2.4.3             evaluate_1.0.1             
[147] readr_2.1.5                 mvtnorm_1.3-2              
[149] cli_3.6.3                   compiler_4.4.1             
[151] rlang_1.1.4                 crayon_1.5.3               
[153] rngtools_1.5.2              Rdisop_1.64.0              
[155] rrcov_1.7-6                 QFeatures_1.14.2           
[157] affy_1.82.0                 plyr_1.8.9                 
[159] masscleaner_1.0.12          fs_1.6.5                   
[161] stringi_1.8.4               viridisLite_0.4.2          
[163] BiocParallel_1.38.0         Biostrings_2.72.1          
[165] munsell_0.5.1               fit.models_0.64            
[167] lazyeval_0.2.2              xcms_4.2.3                 
[169] massprocesser_1.0.10        Matrix_1.7-1               
[171] hms_1.1.3                   patchwork_1.3.0            
[173] future_1.34.0               MsExperiment_1.6.0         
[175] ggplot2_3.5.1               KEGGREST_1.44.1            
[177] statmod_1.5.0               SummarizedExperiment_1.34.0
[179] mzR_2.38.0                  memoise_2.0.1              
[181] igraph_2.1.1                affyio_1.74.0              
[183] DEoptimR_1.1-3              metpath_1.0.10