satijalab / seurat-data

Dataset distribution for Seurat
GNU General Public License v3.0
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Update SeuratData to be compatible with Rv4.4 #93

Closed emily-grantham closed 5 months ago

emily-grantham commented 5 months ago
> install.packages("SeuratData")
Warning in install.packages :
  package ‘SeuratData’ is not available for this version of R

> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS Ventura 13.6.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/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: America/Chicago
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] patchwork_1.2.0    loupeR_1.1.1       Seurat_5.1.0       SeuratObject_5.0.2
[5] sp_2.1-4          

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3      rstudioapi_0.16.0       jsonlite_1.8.8         
  [4] magrittr_2.0.3          spatstat.utils_3.0-5    fs_1.6.4               
  [7] zlibbioc_1.50.0         vctrs_0.6.5             ROCR_1.0-11            
 [10] memoise_2.0.1           spatstat.explore_3.2-7  usethis_2.2.3          
 [13] htmltools_0.5.8.1       sctransform_0.4.1       parallelly_1.37.1      
 [16] KernSmooth_2.23-24      htmlwidgets_1.6.4       ica_1.0-3              
 [19] plyr_1.8.9              plotly_4.10.4           zoo_1.8-12             
 [22] cachem_1.1.0            igraph_2.0.3            mime_0.12              
 [25] lifecycle_1.0.4         pkgconfig_2.0.3         Matrix_1.7-0           
 [28] R6_2.5.1                fastmap_1.2.0           GenomeInfoDbData_1.2.12
 [31] fitdistrplus_1.1-11     future_1.33.2           shiny_1.8.1.1          
 [34] digest_0.6.36           colorspace_2.1-0        AnnotationDbi_1.66.0   
 [37] S4Vectors_0.42.0        tensor_1.5              RSpectra_0.16-1        
 [40] irlba_2.3.5.1           pkgload_1.3.4           RSQLite_2.3.7          
 [43] progressr_0.14.0        fansi_1.0.6             spatstat.sparse_3.1-0  
 [46] httr_1.4.7              polyclip_1.10-6         abind_1.4-5            
 [49] compiler_4.4.1          remotes_2.5.0           bit64_4.0.5            
 [52] DBI_1.2.3               fastDummies_1.7.3       pkgbuild_1.4.4         
 [55] MASS_7.3-61             sessioninfo_1.2.2       tools_4.4.1            
 [58] lmtest_0.9-40           httpuv_1.6.15           future.apply_1.11.2    
 [61] goftest_1.2-3           glue_1.7.0              nlme_3.1-165           
 [64] promises_1.3.0          grid_4.4.1              Rtsne_0.17             
 [67] cluster_2.1.6           reshape2_1.4.4          generics_0.1.3         
 [70] hdf5r_1.3.10            gtable_0.3.5            spatstat.data_3.1-2    
 [73] tzdb_0.4.0              tidyr_1.3.1             data.table_1.15.4      
 [76] XVector_0.44.0          utf8_1.2.4              BiocGenerics_0.50.0    
 [79] spatstat.geom_3.2-9     RcppAnnoy_0.0.22        ggrepel_0.9.5          
 [82] RANN_2.6.1              pillar_1.9.0            stringr_1.5.1          
 [85] vroom_1.6.5             spam_2.10-0             RcppHNSW_0.6.0         
 [88] later_1.3.2             splines_4.4.1           dplyr_1.1.4            
 [91] lattice_0.22-6          survival_3.7-0          bit_4.0.5              
 [94] deldir_2.0-4            tidyselect_1.2.1        Biostrings_2.72.1      
 [97] miniUI_0.1.1.1          pbapply_1.7-2           gridExtra_2.3          
[100] IRanges_2.38.0          scattermore_1.2         stats4_4.4.1           
[103] Biobase_2.64.0          devtools_2.4.5          matrixStats_1.3.0      
[106] UCSC.utils_1.0.0        stringi_1.8.4           lazyeval_0.2.2         
[109] codetools_0.2-20        tibble_3.2.1            BiocManager_1.30.23    
[112] cli_3.6.3               uwot_0.2.2              xtable_1.8-4           
[115] reticulate_1.38.0       munsell_0.5.1           GenomeInfoDb_1.40.1    
[118] Rcpp_1.0.12             globals_0.16.3          spatstat.random_3.2-3  
[121] png_0.1-8               parallel_4.4.1          ellipsis_0.3.2         
[124] ggplot2_3.5.1           blob_1.2.4              dotCall64_1.1-1        
[127] profvis_0.3.8           urlchecker_1.0.1        listenv_0.9.1          
[130] viridisLite_0.4.2       scales_1.3.0            ggridges_0.5.6         
[133] crayon_1.5.3            leiden_0.4.3.1          purrr_1.0.2            
[136] rlang_1.1.4             cowplot_1.1.3           KEGGREST_1.44.1    
mojaveazure commented 5 months ago

SeuratData is not available on CRAN; to install, please use

remotes::install_github("satijalab/seurat-data")