## APOD_ARTICLE_ASSEMBLY\Figure_1_repaired\12_session_info\Figure1_sessionInfo.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] SeuratObject_5.4.0 sp_2.2-1          

loaded via a namespace (and not attached):
 [1] digest_0.6.39       progressr_1.0.0     dotCall64_1.2      
 [4] codetools_0.2-20    Matrix_1.7-4        lattice_0.22-7     
 [7] parallel_4.5.2      generics_0.1.4      lifecycle_1.0.5    
[10] cli_3.6.6           parallelly_1.48.0   future_1.70.0      
[13] grid_4.5.2          compiler_4.5.2      globals_0.19.1     
[16] tools_4.5.2         listenv_1.0.0       future.apply_1.20.2
[19] Rcpp_1.1.2          rlang_1.3.0         spam_2.11-4        



## APOD_ARTICLE_ASSEMBLY\Figure_1_repaired\12_session_info\sessionInfo_Figure1_editorial_repair.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] SeuratObject_5.4.0 sp_2.2-1          

loaded via a namespace (and not attached):
 [1] digest_0.6.39       progressr_1.0.0     qpdf_1.4.1         
 [4] dotCall64_1.2       codetools_0.2-20    Matrix_1.7-4       
 [7] lattice_0.22-7      parallel_4.5.2      png_0.1-9          
[10] generics_0.1.4      lifecycle_1.0.5     cli_3.6.6          
[13] askpass_1.2.1       parallelly_1.48.0   future_1.70.0      
[16] grid_4.5.2          compiler_4.5.2      globals_0.19.1     
[19] tools_4.5.2         listenv_1.0.0       future.apply_1.20.2
[22] Rcpp_1.1.2          pdftools_3.9.0      rlang_1.3.0        
[25] spam_2.11-4        



## APOD_ARTICLE_ASSEMBLY\Figure_2_repaired\12_session_info\sessionInfo_Figure2.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] msigdbr_26.1.0     fgsea_1.36.2       edgeR_4.8.2        limma_3.66.0      
[5] Matrix_1.7-4       SeuratObject_5.4.0 sp_2.2-1          

loaded via a namespace (and not attached):
  [1] deldir_2.0-4           pbapply_1.7-4          gridExtra_2.3         
  [4] rlang_1.3.0            magrittr_2.0.5         RcppAnnoy_0.0.22      
  [7] otel_0.2.0             spatstat.geom_3.6-1    matrixStats_1.5.0     
 [10] ggridges_0.5.7         compiler_4.5.2         png_0.1-9             
 [13] vctrs_0.7.3            reshape2_1.4.5         stringr_1.6.0         
 [16] pkgconfig_2.0.3        fastmap_1.2.0          promises_1.5.0        
 [19] purrr_1.2.0            jsonlite_2.0.0         goftest_1.2-3         
 [22] later_1.4.4            spatstat.utils_3.2-0   BiocParallel_1.44.0   
 [25] irlba_2.3.5.1          parallel_4.5.2         cluster_2.1.8.1       
 [28] R6_2.6.1               ica_1.0-3              spatstat.data_3.1-9   
 [31] stringi_1.8.7          RColorBrewer_1.1-3     reticulate_1.44.1     
 [34] spatstat.univar_3.1-5  parallelly_1.48.0      lmtest_0.9-40         
 [37] scattermore_1.2        Rcpp_1.1.2             assertthat_0.2.1      
 [40] tensor_1.5.1           future.apply_1.20.2    snow_0.4-4            
 [43] zoo_1.8-14             sctransform_0.4.2      httpuv_1.6.16         
 [46] splines_4.5.2          igraph_2.2.1           tidyselect_1.2.1      
 [49] abind_1.4-8            dichromat_2.0-0.1      spatstat.random_3.4-3 
 [52] spatstat.explore_3.6-0 codetools_0.2-20       miniUI_0.1.2          
 [55] curl_7.1.0             qpdf_1.4.1             listenv_1.0.0         
 [58] lattice_0.22-7         tibble_3.3.1           plyr_1.8.9            
 [61] withr_3.0.3            shiny_1.12.0           S7_0.2.2              
 [64] askpass_1.2.1          ROCR_1.0-11            Rtsne_0.17            
 [67] future_1.70.0          fastDummies_1.7.5      survival_3.8-3        
 [70] polyclip_1.10-7        fitdistrplus_1.2-4     pillar_1.11.1         
 [73] Seurat_5.3.1           KernSmooth_2.23-26     plotly_4.11.0         
 [76] generics_0.1.4         RcppHNSW_0.6.0         ggplot2_4.0.3         
 [79] scales_1.4.0           globals_0.19.1         xtable_1.8-4          
 [82] glue_1.8.1             lazyeval_0.2.2         tools_4.5.2           
 [85] data.table_1.18.4      RSpectra_0.16-2        locfit_1.5-9.12       
 [88] pdftools_3.9.0         babelgene_22.9         RANN_2.6.2            
 [91] dotCall64_1.2          fastmatch_1.1-8        cowplot_1.2.0         
 [94] grid_4.5.2             tidyr_1.3.2            nlme_3.1-168          
 [97] patchwork_1.3.2        cli_3.6.6              spatstat.sparse_3.1-0 
[100] spam_2.11-4            viridisLite_0.4.3      dplyr_1.2.1           
[103] uwot_0.2.4             gtable_0.3.6           digest_0.6.39         
[106] progressr_1.0.0        ggrepel_0.9.8          htmlwidgets_1.6.4     
[109] farver_2.1.2           htmltools_0.5.9        lifecycle_1.0.5       
[112] httr_1.4.7             statmod_1.5.2          mime_0.13             
[115] MASS_7.3-65           



## APOD_ARTICLE_ASSEMBLY\Figure_3\12_session_info\sessionInfo_Figure3.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
 [1] Cairo_1.7-0        pdftools_3.9.0     png_0.1-9          ggrepel_0.9.8     
 [5] cowplot_1.2.0      ggplot2_4.0.3      data.table_1.18.4  Matrix_1.7-4      
 [9] SeuratObject_5.4.0 sp_2.2-1          

loaded via a namespace (and not attached):
 [1] gtable_0.3.6        future.apply_1.20.2 qpdf_1.4.1         
 [4] dplyr_1.2.1         compiler_4.5.2      tidyselect_1.2.1   
 [7] Rcpp_1.1.2          parallel_4.5.2      textshaping_1.0.5  
[10] systemfonts_1.3.2   globals_0.19.1      scales_1.4.0       
[13] lattice_0.22-7      R6_2.6.1            labeling_0.4.3     
[16] generics_0.1.4      dotCall64_1.2       future_1.70.0      
[19] tibble_3.3.1        svglite_2.2.2       pillar_1.11.1      
[22] RColorBrewer_1.1-3  rlang_1.3.0         S7_0.2.2           
[25] cli_3.6.6           withr_3.0.3         magrittr_2.0.5     
[28] progressr_1.0.0     digest_0.6.39       grid_4.5.2         
[31] askpass_1.2.1       spam_2.11-4         lifecycle_1.0.5    
[34] vctrs_0.7.3         glue_1.8.1          farver_2.1.2       
[37] listenv_1.0.0       ragg_1.5.2          codetools_0.2-20   
[40] parallelly_1.48.0   tools_4.5.2         pkgconfig_2.0.3    



## APOD_ARTICLE_ASSEMBLY\Figure_4\12_session_info\sessionInfo_Figure4.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0      png_0.1-9         pdftools_3.9.0    Cairo_1.7-0      
[5] survival_3.8-3    cowplot_1.2.0     ggplot2_4.0.3     data.table_1.18.4

loaded via a namespace (and not attached):
 [1] vctrs_0.7.3        svglite_2.2.2      cli_3.6.6          rlang_1.3.0       
 [5] generics_0.1.4     textshaping_1.0.5  S7_0.2.2           labeling_0.4.3    
 [9] glue_1.8.1         askpass_1.2.1      qpdf_1.4.1         ragg_1.5.2        
[13] grid_4.5.2         tibble_3.3.1       lifecycle_1.0.5    compiler_4.5.2    
[17] dplyr_1.2.1        RColorBrewer_1.1-3 Rcpp_1.1.2         pkgconfig_2.0.3   
[21] systemfonts_1.3.2  farver_2.1.2       lattice_0.22-7     R6_2.6.1          
[25] tidyselect_1.2.1   pillar_1.11.1      splines_4.5.2      magrittr_2.0.5    
[29] Matrix_1.7-4       withr_3.0.3        tools_4.5.2        gtable_0.3.6      



## APOD_ARTICLE_ASSEMBLY\Figure_5_final\12_session_info\sessionInfo_Figure5_final.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0   png_0.1-9      pdftools_3.9.0 Cairo_1.7-0    survival_3.8-3
[6] cowplot_1.2.0  ggplot2_4.0.3 

loaded via a namespace (and not attached):
 [1] vctrs_0.7.3        cli_3.6.6          rlang_1.3.0        generics_0.1.4    
 [5] S7_0.2.2           labeling_0.4.3     glue_1.8.1         askpass_1.2.1     
 [9] qpdf_1.4.1         grid_4.5.2         tibble_3.3.1       lifecycle_1.0.5   
[13] compiler_4.5.2     dplyr_1.2.1        RColorBrewer_1.1-3 Rcpp_1.1.2        
[17] pkgconfig_2.0.3    farver_2.1.2       lattice_0.22-7     R6_2.6.1          
[21] tidyselect_1.2.1   pillar_1.11.1      splines_4.5.2      magrittr_2.0.5    
[25] Matrix_1.7-4       withr_3.0.3        tools_4.5.2        gtable_0.3.6      



## APOD_ARTICLE_ASSEMBLY\Figure_5_final\12_session_info\sessionInfo_Figure5_repaired.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0   png_0.1-9      pdftools_3.9.0 Cairo_1.7-0    survival_3.8-3
[6] cowplot_1.2.0  ggplot2_4.0.3 

loaded via a namespace (and not attached):
 [1] vctrs_0.7.3        cli_3.6.6          rlang_1.3.0        generics_0.1.4    
 [5] S7_0.2.2           labeling_0.4.3     glue_1.8.1         askpass_1.2.1     
 [9] qpdf_1.4.1         grid_4.5.2         tibble_3.3.1       lifecycle_1.0.5   
[13] compiler_4.5.2     dplyr_1.2.1        RColorBrewer_1.1-3 Rcpp_1.1.2        
[17] pkgconfig_2.0.3    farver_2.1.2       lattice_0.22-7     R6_2.6.1          
[21] tidyselect_1.2.1   pillar_1.11.1      splines_4.5.2      magrittr_2.0.5    
[25] Matrix_1.7-4       withr_3.0.3        tools_4.5.2        gtable_0.3.6      



## APOD_ARTICLE_ASSEMBLY\Figure_6\12_session_info\sessionInfo_Figure6.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0   png_0.1-9      pdftools_3.9.0 Cairo_1.7-0    cowplot_1.2.0 
[6] ggplot2_4.0.3 

loaded via a namespace (and not attached):
 [1] vctrs_0.7.3        cli_3.6.6          rlang_1.3.0        generics_0.1.4    
 [5] S7_0.2.2           labeling_0.4.3     glue_1.8.1         askpass_1.2.1     
 [9] qpdf_1.4.1         tibble_3.3.1       lifecycle_1.0.5    compiler_4.5.2    
[13] dplyr_1.2.1        RColorBrewer_1.1-3 Rcpp_1.1.2         pkgconfig_2.0.3   
[17] farver_2.1.2       R6_2.6.1           tidyselect_1.2.1   pillar_1.11.1     
[21] magrittr_2.0.5     tools_4.5.2        withr_3.0.3        gtable_0.3.6      



## APOD_ARTICLE_ASSEMBLY\Figure_7\12_session_info\sessionInfo_Figure7.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0   png_0.1-9      pdftools_3.9.0 Cairo_1.7-0    cowplot_1.2.0 
[6] ggplot2_4.0.3 

loaded via a namespace (and not attached):
 [1] labeling_0.4.3     RColorBrewer_1.1-3 R6_2.6.1           qpdf_1.4.1        
 [5] farver_2.1.2       gtable_0.3.6       glue_1.8.1         lifecycle_1.0.5   
 [9] cli_3.6.6          S7_0.2.2           askpass_1.2.1      vctrs_0.7.3       
[13] withr_3.0.3        compiler_4.5.2     tools_4.5.2        Rcpp_1.1.2        
[17] rlang_1.3.0       



## APOD_ARTICLE_ASSEMBLY\Figure_8\12_session_info\sessionInfo_Figure8.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0  cowplot_1.2.0 ggplot2_4.0.3

loaded via a namespace (and not attached):
 [1] labeling_0.4.3     RColorBrewer_1.1-3 R6_2.6.1           qpdf_1.4.1        
 [5] farver_2.1.2       gtable_0.3.6       glue_1.8.1         png_0.1-9         
 [9] lifecycle_1.0.5    cli_3.6.6          S7_0.2.2           askpass_1.2.1     
[13] vctrs_0.7.3        withr_3.0.3        compiler_4.5.2     tools_4.5.2       
[17] Rcpp_1.1.2         pdftools_3.9.0     rlang_1.3.0       



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\01_SUBMISSION_READY\08_Source_Data\Figure_1\12_session_info\Figure1_sessionInfo.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] SeuratObject_5.4.0 sp_2.2-1          

loaded via a namespace (and not attached):
 [1] digest_0.6.39       progressr_1.0.0     dotCall64_1.2      
 [4] codetools_0.2-20    Matrix_1.7-4        lattice_0.22-7     
 [7] parallel_4.5.2      generics_0.1.4      lifecycle_1.0.5    
[10] cli_3.6.6           parallelly_1.48.0   future_1.70.0      
[13] grid_4.5.2          compiler_4.5.2      globals_0.19.1     
[16] tools_4.5.2         listenv_1.0.0       future.apply_1.20.2
[19] Rcpp_1.1.2          rlang_1.3.0         spam_2.11-4        



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\01_SUBMISSION_READY\08_Source_Data\Figure_1\12_session_info\sessionInfo_Figure1_editorial_repair.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] SeuratObject_5.4.0 sp_2.2-1          

loaded via a namespace (and not attached):
 [1] digest_0.6.39       progressr_1.0.0     qpdf_1.4.1         
 [4] dotCall64_1.2       codetools_0.2-20    Matrix_1.7-4       
 [7] lattice_0.22-7      parallel_4.5.2      png_0.1-9          
[10] generics_0.1.4      lifecycle_1.0.5     cli_3.6.6          
[13] askpass_1.2.1       parallelly_1.48.0   future_1.70.0      
[16] grid_4.5.2          compiler_4.5.2      globals_0.19.1     
[19] tools_4.5.2         listenv_1.0.0       future.apply_1.20.2
[22] Rcpp_1.1.2          pdftools_3.9.0      rlang_1.3.0        
[25] spam_2.11-4        



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\01_SUBMISSION_READY\08_Source_Data\Figure_2\12_session_info\sessionInfo_Figure2.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] msigdbr_26.1.0     fgsea_1.36.2       edgeR_4.8.2        limma_3.66.0      
[5] Matrix_1.7-4       SeuratObject_5.4.0 sp_2.2-1          

loaded via a namespace (and not attached):
  [1] deldir_2.0-4           pbapply_1.7-4          gridExtra_2.3         
  [4] rlang_1.3.0            magrittr_2.0.5         RcppAnnoy_0.0.22      
  [7] otel_0.2.0             spatstat.geom_3.6-1    matrixStats_1.5.0     
 [10] ggridges_0.5.7         compiler_4.5.2         png_0.1-9             
 [13] vctrs_0.7.3            reshape2_1.4.5         stringr_1.6.0         
 [16] pkgconfig_2.0.3        fastmap_1.2.0          promises_1.5.0        
 [19] purrr_1.2.0            jsonlite_2.0.0         goftest_1.2-3         
 [22] later_1.4.4            spatstat.utils_3.2-0   BiocParallel_1.44.0   
 [25] irlba_2.3.5.1          parallel_4.5.2         cluster_2.1.8.1       
 [28] R6_2.6.1               ica_1.0-3              spatstat.data_3.1-9   
 [31] stringi_1.8.7          RColorBrewer_1.1-3     reticulate_1.44.1     
 [34] spatstat.univar_3.1-5  parallelly_1.48.0      lmtest_0.9-40         
 [37] scattermore_1.2        Rcpp_1.1.2             assertthat_0.2.1      
 [40] tensor_1.5.1           future.apply_1.20.2    snow_0.4-4            
 [43] zoo_1.8-14             sctransform_0.4.2      httpuv_1.6.16         
 [46] splines_4.5.2          igraph_2.2.1           tidyselect_1.2.1      
 [49] abind_1.4-8            dichromat_2.0-0.1      spatstat.random_3.4-3 
 [52] spatstat.explore_3.6-0 codetools_0.2-20       miniUI_0.1.2          
 [55] curl_7.1.0             qpdf_1.4.1             listenv_1.0.0         
 [58] lattice_0.22-7         tibble_3.3.1           plyr_1.8.9            
 [61] withr_3.0.3            shiny_1.12.0           S7_0.2.2              
 [64] askpass_1.2.1          ROCR_1.0-11            Rtsne_0.17            
 [67] future_1.70.0          fastDummies_1.7.5      survival_3.8-3        
 [70] polyclip_1.10-7        fitdistrplus_1.2-4     pillar_1.11.1         
 [73] Seurat_5.3.1           KernSmooth_2.23-26     plotly_4.11.0         
 [76] generics_0.1.4         RcppHNSW_0.6.0         ggplot2_4.0.3         
 [79] scales_1.4.0           globals_0.19.1         xtable_1.8-4          
 [82] glue_1.8.1             lazyeval_0.2.2         tools_4.5.2           
 [85] data.table_1.18.4      RSpectra_0.16-2        locfit_1.5-9.12       
 [88] pdftools_3.9.0         babelgene_22.9         RANN_2.6.2            
 [91] dotCall64_1.2          fastmatch_1.1-8        cowplot_1.2.0         
 [94] grid_4.5.2             tidyr_1.3.2            nlme_3.1-168          
 [97] patchwork_1.3.2        cli_3.6.6              spatstat.sparse_3.1-0 
[100] spam_2.11-4            viridisLite_0.4.3      dplyr_1.2.1           
[103] uwot_0.2.4             gtable_0.3.6           digest_0.6.39         
[106] progressr_1.0.0        ggrepel_0.9.8          htmlwidgets_1.6.4     
[109] farver_2.1.2           htmltools_0.5.9        lifecycle_1.0.5       
[112] httr_1.4.7             statmod_1.5.2          mime_0.13             
[115] MASS_7.3-65           



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\01_SUBMISSION_READY\08_Source_Data\Figure_3\12_session_info\sessionInfo_Figure3.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
 [1] Cairo_1.7-0        pdftools_3.9.0     png_0.1-9          ggrepel_0.9.8     
 [5] cowplot_1.2.0      ggplot2_4.0.3      data.table_1.18.4  Matrix_1.7-4      
 [9] SeuratObject_5.4.0 sp_2.2-1          

loaded via a namespace (and not attached):
 [1] gtable_0.3.6        future.apply_1.20.2 qpdf_1.4.1         
 [4] dplyr_1.2.1         compiler_4.5.2      tidyselect_1.2.1   
 [7] Rcpp_1.1.2          parallel_4.5.2      textshaping_1.0.5  
[10] systemfonts_1.3.2   globals_0.19.1      scales_1.4.0       
[13] lattice_0.22-7      R6_2.6.1            labeling_0.4.3     
[16] generics_0.1.4      dotCall64_1.2       future_1.70.0      
[19] tibble_3.3.1        svglite_2.2.2       pillar_1.11.1      
[22] RColorBrewer_1.1-3  rlang_1.3.0         S7_0.2.2           
[25] cli_3.6.6           withr_3.0.3         magrittr_2.0.5     
[28] progressr_1.0.0     digest_0.6.39       grid_4.5.2         
[31] askpass_1.2.1       spam_2.11-4         lifecycle_1.0.5    
[34] vctrs_0.7.3         glue_1.8.1          farver_2.1.2       
[37] listenv_1.0.0       ragg_1.5.2          codetools_0.2-20   
[40] parallelly_1.48.0   tools_4.5.2         pkgconfig_2.0.3    



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\01_SUBMISSION_READY\08_Source_Data\Figure_4\12_session_info\sessionInfo_Figure4.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0      png_0.1-9         pdftools_3.9.0    Cairo_1.7-0      
[5] survival_3.8-3    cowplot_1.2.0     ggplot2_4.0.3     data.table_1.18.4

loaded via a namespace (and not attached):
 [1] vctrs_0.7.3        svglite_2.2.2      cli_3.6.6          rlang_1.3.0       
 [5] generics_0.1.4     textshaping_1.0.5  S7_0.2.2           labeling_0.4.3    
 [9] glue_1.8.1         askpass_1.2.1      qpdf_1.4.1         ragg_1.5.2        
[13] grid_4.5.2         tibble_3.3.1       lifecycle_1.0.5    compiler_4.5.2    
[17] dplyr_1.2.1        RColorBrewer_1.1-3 Rcpp_1.1.2         pkgconfig_2.0.3   
[21] systemfonts_1.3.2  farver_2.1.2       lattice_0.22-7     R6_2.6.1          
[25] tidyselect_1.2.1   pillar_1.11.1      splines_4.5.2      magrittr_2.0.5    
[29] Matrix_1.7-4       withr_3.0.3        tools_4.5.2        gtable_0.3.6      



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\01_SUBMISSION_READY\08_Source_Data\Figure_5\12_session_info\sessionInfo_Figure5_final.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0   png_0.1-9      pdftools_3.9.0 Cairo_1.7-0    survival_3.8-3
[6] cowplot_1.2.0  ggplot2_4.0.3 

loaded via a namespace (and not attached):
 [1] vctrs_0.7.3        cli_3.6.6          rlang_1.3.0        generics_0.1.4    
 [5] S7_0.2.2           labeling_0.4.3     glue_1.8.1         askpass_1.2.1     
 [9] qpdf_1.4.1         grid_4.5.2         tibble_3.3.1       lifecycle_1.0.5   
[13] compiler_4.5.2     dplyr_1.2.1        RColorBrewer_1.1-3 Rcpp_1.1.2        
[17] pkgconfig_2.0.3    farver_2.1.2       lattice_0.22-7     R6_2.6.1          
[21] tidyselect_1.2.1   pillar_1.11.1      splines_4.5.2      magrittr_2.0.5    
[25] Matrix_1.7-4       withr_3.0.3        tools_4.5.2        gtable_0.3.6      



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\01_SUBMISSION_READY\08_Source_Data\Figure_5\12_session_info\sessionInfo_Figure5_repaired.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0   png_0.1-9      pdftools_3.9.0 Cairo_1.7-0    survival_3.8-3
[6] cowplot_1.2.0  ggplot2_4.0.3 

loaded via a namespace (and not attached):
 [1] vctrs_0.7.3        cli_3.6.6          rlang_1.3.0        generics_0.1.4    
 [5] S7_0.2.2           labeling_0.4.3     glue_1.8.1         askpass_1.2.1     
 [9] qpdf_1.4.1         grid_4.5.2         tibble_3.3.1       lifecycle_1.0.5   
[13] compiler_4.5.2     dplyr_1.2.1        RColorBrewer_1.1-3 Rcpp_1.1.2        
[17] pkgconfig_2.0.3    farver_2.1.2       lattice_0.22-7     R6_2.6.1          
[21] tidyselect_1.2.1   pillar_1.11.1      splines_4.5.2      magrittr_2.0.5    
[25] Matrix_1.7-4       withr_3.0.3        tools_4.5.2        gtable_0.3.6      



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\01_SUBMISSION_READY\08_Source_Data\Figure_6\12_session_info\sessionInfo_Figure6.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0   png_0.1-9      pdftools_3.9.0 Cairo_1.7-0    cowplot_1.2.0 
[6] ggplot2_4.0.3 

loaded via a namespace (and not attached):
 [1] vctrs_0.7.3        cli_3.6.6          rlang_1.3.0        generics_0.1.4    
 [5] S7_0.2.2           labeling_0.4.3     glue_1.8.1         askpass_1.2.1     
 [9] qpdf_1.4.1         tibble_3.3.1       lifecycle_1.0.5    compiler_4.5.2    
[13] dplyr_1.2.1        RColorBrewer_1.1-3 Rcpp_1.1.2         pkgconfig_2.0.3   
[17] farver_2.1.2       R6_2.6.1           tidyselect_1.2.1   pillar_1.11.1     
[21] magrittr_2.0.5     tools_4.5.2        withr_3.0.3        gtable_0.3.6      



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\01_SUBMISSION_READY\08_Source_Data\Figure_7\12_session_info\sessionInfo_Figure7.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0   png_0.1-9      pdftools_3.9.0 Cairo_1.7-0    cowplot_1.2.0 
[6] ggplot2_4.0.3 

loaded via a namespace (and not attached):
 [1] labeling_0.4.3     RColorBrewer_1.1-3 R6_2.6.1           qpdf_1.4.1        
 [5] farver_2.1.2       gtable_0.3.6       glue_1.8.1         lifecycle_1.0.5   
 [9] cli_3.6.6          S7_0.2.2           askpass_1.2.1      vctrs_0.7.3       
[13] withr_3.0.3        compiler_4.5.2     tools_4.5.2        Rcpp_1.1.2        
[17] rlang_1.3.0       



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\01_SUBMISSION_READY\08_Source_Data\Figure_8\12_session_info\sessionInfo_Figure8.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0  cowplot_1.2.0 ggplot2_4.0.3

loaded via a namespace (and not attached):
 [1] labeling_0.4.3     RColorBrewer_1.1-3 R6_2.6.1           qpdf_1.4.1        
 [5] farver_2.1.2       gtable_0.3.6       glue_1.8.1         png_0.1-9         
 [9] lifecycle_1.0.5    cli_3.6.6          S7_0.2.2           askpass_1.2.1     
[13] vctrs_0.7.3        withr_3.0.3        compiler_4.5.2     tools_4.5.2       
[17] Rcpp_1.1.2         pdftools_3.9.0     rlang_1.3.0       



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\assembly_session_info.txt

Assembly completed 2026-07-15T23:05:37.379427
Python script: assemble_final_manuscript.py



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\Figure1_sessionInfo.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] SeuratObject_5.4.0 sp_2.2-1          

loaded via a namespace (and not attached):
 [1] digest_0.6.39       progressr_1.0.0     dotCall64_1.2      
 [4] codetools_0.2-20    Matrix_1.7-4        lattice_0.22-7     
 [7] parallel_4.5.2      generics_0.1.4      lifecycle_1.0.5    
[10] cli_3.6.6           parallelly_1.48.0   future_1.70.0      
[13] grid_4.5.2          compiler_4.5.2      globals_0.19.1     
[16] tools_4.5.2         listenv_1.0.0       future.apply_1.20.2
[19] Rcpp_1.1.2          rlang_1.3.0         spam_2.11-4        



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\last_repair_session_info.txt

APOD_FINAL_MANUSCRIPT_LAST_REPAIR
Completed: 2026-07-16T11:55:41.846668
Status: REFERENCE_LIBRARY_INCOMPLETE



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\reference_supplementary_polish_session_info.txt

Completed: 2026-07-16T12:25:55.331713
Status: COMPLETE_AFTER_REFERENCE_AND_RENDER_QA



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\repair_session_info.txt

python_script=APOD_TRUE_FINAL_METHODS_SUPPLEMENTARY_LAYOUT_REPAIR
seed=20260716



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\R_sessionInfo_FINAL.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] SeuratObject_5.4.0 sp_2.2-1          

loaded via a namespace (and not attached):
 [1] digest_0.6.39       progressr_1.0.0     dotCall64_1.2      
 [4] codetools_0.2-20    Matrix_1.7-4        lattice_0.22-7     
 [7] parallel_4.5.2      generics_0.1.4      lifecycle_1.0.5    
[10] cli_3.6.6           parallelly_1.48.0   future_1.70.0      
[13] grid_4.5.2          compiler_4.5.2      globals_0.19.1     
[16] tools_4.5.2         listenv_1.0.0       future.apply_1.20.2
[19] Rcpp_1.1.2          rlang_1.3.0         spam_2.11-4        



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_09FINAL.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

loaded via a namespace (and not attached):
[1] compiler_4.5.2 Matrix_1.7-4   survival_3.8-3 splines_4.5.2  grid_4.5.2    
[6] lattice_0.22-7



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_Figure1_editorial_repair.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] SeuratObject_5.4.0 sp_2.2-1          

loaded via a namespace (and not attached):
 [1] digest_0.6.39       progressr_1.0.0     qpdf_1.4.1         
 [4] dotCall64_1.2       codetools_0.2-20    Matrix_1.7-4       
 [7] lattice_0.22-7      parallel_4.5.2      png_0.1-9          
[10] generics_0.1.4      lifecycle_1.0.5     cli_3.6.6          
[13] askpass_1.2.1       parallelly_1.48.0   future_1.70.0      
[16] grid_4.5.2          compiler_4.5.2      globals_0.19.1     
[19] tools_4.5.2         listenv_1.0.0       future.apply_1.20.2
[22] Rcpp_1.1.2          pdftools_3.9.0      rlang_1.3.0        
[25] spam_2.11-4        



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_Figure2.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] msigdbr_26.1.0     fgsea_1.36.2       edgeR_4.8.2        limma_3.66.0      
[5] Matrix_1.7-4       SeuratObject_5.4.0 sp_2.2-1          

loaded via a namespace (and not attached):
  [1] deldir_2.0-4           pbapply_1.7-4          gridExtra_2.3         
  [4] rlang_1.3.0            magrittr_2.0.5         RcppAnnoy_0.0.22      
  [7] otel_0.2.0             spatstat.geom_3.6-1    matrixStats_1.5.0     
 [10] ggridges_0.5.7         compiler_4.5.2         png_0.1-9             
 [13] vctrs_0.7.3            reshape2_1.4.5         stringr_1.6.0         
 [16] pkgconfig_2.0.3        fastmap_1.2.0          promises_1.5.0        
 [19] purrr_1.2.0            jsonlite_2.0.0         goftest_1.2-3         
 [22] later_1.4.4            spatstat.utils_3.2-0   BiocParallel_1.44.0   
 [25] irlba_2.3.5.1          parallel_4.5.2         cluster_2.1.8.1       
 [28] R6_2.6.1               ica_1.0-3              spatstat.data_3.1-9   
 [31] stringi_1.8.7          RColorBrewer_1.1-3     reticulate_1.44.1     
 [34] spatstat.univar_3.1-5  parallelly_1.48.0      lmtest_0.9-40         
 [37] scattermore_1.2        Rcpp_1.1.2             assertthat_0.2.1      
 [40] tensor_1.5.1           future.apply_1.20.2    snow_0.4-4            
 [43] zoo_1.8-14             sctransform_0.4.2      httpuv_1.6.16         
 [46] splines_4.5.2          igraph_2.2.1           tidyselect_1.2.1      
 [49] abind_1.4-8            dichromat_2.0-0.1      spatstat.random_3.4-3 
 [52] spatstat.explore_3.6-0 codetools_0.2-20       miniUI_0.1.2          
 [55] curl_7.1.0             qpdf_1.4.1             listenv_1.0.0         
 [58] lattice_0.22-7         tibble_3.3.1           plyr_1.8.9            
 [61] withr_3.0.3            shiny_1.12.0           S7_0.2.2              
 [64] askpass_1.2.1          ROCR_1.0-11            Rtsne_0.17            
 [67] future_1.70.0          fastDummies_1.7.5      survival_3.8-3        
 [70] polyclip_1.10-7        fitdistrplus_1.2-4     pillar_1.11.1         
 [73] Seurat_5.3.1           KernSmooth_2.23-26     plotly_4.11.0         
 [76] generics_0.1.4         RcppHNSW_0.6.0         ggplot2_4.0.3         
 [79] scales_1.4.0           globals_0.19.1         xtable_1.8-4          
 [82] glue_1.8.1             lazyeval_0.2.2         tools_4.5.2           
 [85] data.table_1.18.4      RSpectra_0.16-2        locfit_1.5-9.12       
 [88] pdftools_3.9.0         babelgene_22.9         RANN_2.6.2            
 [91] dotCall64_1.2          fastmatch_1.1-8        cowplot_1.2.0         
 [94] grid_4.5.2             tidyr_1.3.2            nlme_3.1-168          
 [97] patchwork_1.3.2        cli_3.6.6              spatstat.sparse_3.1-0 
[100] spam_2.11-4            viridisLite_0.4.3      dplyr_1.2.1           
[103] uwot_0.2.4             gtable_0.3.6           digest_0.6.39         
[106] progressr_1.0.0        ggrepel_0.9.8          htmlwidgets_1.6.4     
[109] farver_2.1.2           htmltools_0.5.9        lifecycle_1.0.5       
[112] httr_1.4.7             statmod_1.5.2          mime_0.13             
[115] MASS_7.3-65           



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_Figure3.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
 [1] Cairo_1.7-0        pdftools_3.9.0     png_0.1-9          ggrepel_0.9.8     
 [5] cowplot_1.2.0      ggplot2_4.0.3      data.table_1.18.4  Matrix_1.7-4      
 [9] SeuratObject_5.4.0 sp_2.2-1          

loaded via a namespace (and not attached):
 [1] gtable_0.3.6        future.apply_1.20.2 qpdf_1.4.1         
 [4] dplyr_1.2.1         compiler_4.5.2      tidyselect_1.2.1   
 [7] Rcpp_1.1.2          parallel_4.5.2      textshaping_1.0.5  
[10] systemfonts_1.3.2   globals_0.19.1      scales_1.4.0       
[13] lattice_0.22-7      R6_2.6.1            labeling_0.4.3     
[16] generics_0.1.4      dotCall64_1.2       future_1.70.0      
[19] tibble_3.3.1        svglite_2.2.2       pillar_1.11.1      
[22] RColorBrewer_1.1-3  rlang_1.3.0         S7_0.2.2           
[25] cli_3.6.6           withr_3.0.3         magrittr_2.0.5     
[28] progressr_1.0.0     digest_0.6.39       grid_4.5.2         
[31] askpass_1.2.1       spam_2.11-4         lifecycle_1.0.5    
[34] vctrs_0.7.3         glue_1.8.1          farver_2.1.2       
[37] listenv_1.0.0       ragg_1.5.2          codetools_0.2-20   
[40] parallelly_1.48.0   tools_4.5.2         pkgconfig_2.0.3    



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_Figure4.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0      png_0.1-9         pdftools_3.9.0    Cairo_1.7-0      
[5] survival_3.8-3    cowplot_1.2.0     ggplot2_4.0.3     data.table_1.18.4

loaded via a namespace (and not attached):
 [1] vctrs_0.7.3        svglite_2.2.2      cli_3.6.6          rlang_1.3.0       
 [5] generics_0.1.4     textshaping_1.0.5  S7_0.2.2           labeling_0.4.3    
 [9] glue_1.8.1         askpass_1.2.1      qpdf_1.4.1         ragg_1.5.2        
[13] grid_4.5.2         tibble_3.3.1       lifecycle_1.0.5    compiler_4.5.2    
[17] dplyr_1.2.1        RColorBrewer_1.1-3 Rcpp_1.1.2         pkgconfig_2.0.3   
[21] systemfonts_1.3.2  farver_2.1.2       lattice_0.22-7     R6_2.6.1          
[25] tidyselect_1.2.1   pillar_1.11.1      splines_4.5.2      magrittr_2.0.5    
[29] Matrix_1.7-4       withr_3.0.3        tools_4.5.2        gtable_0.3.6      



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_Figure5.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0      png_0.1-9         pdftools_3.9.0    Cairo_1.7-0      
[5] survival_3.8-3    cowplot_1.2.0     ggplot2_4.0.3     data.table_1.18.4

loaded via a namespace (and not attached):
 [1] vctrs_0.7.3        cli_3.6.6          rlang_1.3.0        generics_0.1.4    
 [5] S7_0.2.2           labeling_0.4.3     glue_1.8.1         askpass_1.2.1     
 [9] qpdf_1.4.1         grid_4.5.2         tibble_3.3.1       lifecycle_1.0.5   
[13] compiler_4.5.2     dplyr_1.2.1        RColorBrewer_1.1-3 Rcpp_1.1.2        
[17] pkgconfig_2.0.3    farver_2.1.2       lattice_0.22-7     R6_2.6.1          
[21] tidyselect_1.2.1   pillar_1.11.1      splines_4.5.2      magrittr_2.0.5    
[25] Matrix_1.7-4       withr_3.0.3        tools_4.5.2        gtable_0.3.6      



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_Figure5_final.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0   png_0.1-9      pdftools_3.9.0 Cairo_1.7-0    survival_3.8-3
[6] cowplot_1.2.0  ggplot2_4.0.3 

loaded via a namespace (and not attached):
 [1] vctrs_0.7.3        cli_3.6.6          rlang_1.3.0        generics_0.1.4    
 [5] S7_0.2.2           labeling_0.4.3     glue_1.8.1         askpass_1.2.1     
 [9] qpdf_1.4.1         grid_4.5.2         tibble_3.3.1       lifecycle_1.0.5   
[13] compiler_4.5.2     dplyr_1.2.1        RColorBrewer_1.1-3 Rcpp_1.1.2        
[17] pkgconfig_2.0.3    farver_2.1.2       lattice_0.22-7     R6_2.6.1          
[21] tidyselect_1.2.1   pillar_1.11.1      splines_4.5.2      magrittr_2.0.5    
[25] Matrix_1.7-4       withr_3.0.3        tools_4.5.2        gtable_0.3.6      



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_Figure5_repaired.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0   png_0.1-9      pdftools_3.9.0 Cairo_1.7-0    survival_3.8-3
[6] cowplot_1.2.0  ggplot2_4.0.3 

loaded via a namespace (and not attached):
 [1] vctrs_0.7.3        cli_3.6.6          rlang_1.3.0        generics_0.1.4    
 [5] S7_0.2.2           labeling_0.4.3     glue_1.8.1         askpass_1.2.1     
 [9] qpdf_1.4.1         grid_4.5.2         tibble_3.3.1       lifecycle_1.0.5   
[13] compiler_4.5.2     dplyr_1.2.1        RColorBrewer_1.1-3 Rcpp_1.1.2        
[17] pkgconfig_2.0.3    farver_2.1.2       lattice_0.22-7     R6_2.6.1          
[21] tidyselect_1.2.1   pillar_1.11.1      splines_4.5.2      magrittr_2.0.5    
[25] Matrix_1.7-4       withr_3.0.3        tools_4.5.2        gtable_0.3.6      



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_Figure6.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0   png_0.1-9      pdftools_3.9.0 Cairo_1.7-0    cowplot_1.2.0 
[6] ggplot2_4.0.3 

loaded via a namespace (and not attached):
 [1] vctrs_0.7.3        cli_3.6.6          rlang_1.3.0        generics_0.1.4    
 [5] S7_0.2.2           labeling_0.4.3     glue_1.8.1         askpass_1.2.1     
 [9] qpdf_1.4.1         tibble_3.3.1       lifecycle_1.0.5    compiler_4.5.2    
[13] dplyr_1.2.1        RColorBrewer_1.1-3 Rcpp_1.1.2         pkgconfig_2.0.3   
[17] farver_2.1.2       R6_2.6.1           tidyselect_1.2.1   pillar_1.11.1     
[21] magrittr_2.0.5     tools_4.5.2        withr_3.0.3        gtable_0.3.6      



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_Figure7.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0   png_0.1-9      pdftools_3.9.0 Cairo_1.7-0    cowplot_1.2.0 
[6] ggplot2_4.0.3 

loaded via a namespace (and not attached):
 [1] labeling_0.4.3     RColorBrewer_1.1-3 R6_2.6.1           qpdf_1.4.1        
 [5] farver_2.1.2       gtable_0.3.6       glue_1.8.1         lifecycle_1.0.5   
 [9] cli_3.6.6          S7_0.2.2           askpass_1.2.1      vctrs_0.7.3       
[13] withr_3.0.3        compiler_4.5.2     tools_4.5.2        Rcpp_1.1.2        
[17] rlang_1.3.0       



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_Figure8.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0  cowplot_1.2.0 ggplot2_4.0.3

loaded via a namespace (and not attached):
 [1] labeling_0.4.3     RColorBrewer_1.1-3 R6_2.6.1           qpdf_1.4.1        
 [5] farver_2.1.2       gtable_0.3.6       glue_1.8.1         png_0.1-9         
 [9] lifecycle_1.0.5    cli_3.6.6          S7_0.2.2           askpass_1.2.1     
[13] vctrs_0.7.3        withr_3.0.3        compiler_4.5.2     tools_4.5.2       
[17] Rcpp_1.1.2         pdftools_3.9.0     rlang_1.3.0       



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_files.csv

"source_phase","relative_path","source_file_path","file_extension","analysis_module","plot_type","real_data_plot","summary_text_only","suitable_main_figure","suitable_supplementary","requires_replot","proposed_figure","proposed_panel","claim_safety_grade"
"02","02/08_session_info/sessionInfo_phase02.txt","F:/legacy_candidate_removed + GC-18SCI/02/08_session_info/sessionInfo_phase02.txt","txt","other","script_or_report",FALSE,FALSE,FALSE,TRUE,TRUE,"","","B/C"
"02","02/08_session_info/sessionInfo_phase02_final.txt","F:/legacy_candidate_removed + GC-18SCI/02/08_session_info/sessionInfo_phase02_final.txt","txt","other","script_or_report",FALSE,FALSE,FALSE,TRUE,TRUE,"","","B/C"
"03","03/08_session_info/sessionInfo_phase03.txt","F:/legacy_candidate_removed + GC-18SCI/03/08_session_info/sessionInfo_phase03.txt","txt","other","script_or_report",FALSE,FALSE,FALSE,TRUE,TRUE,"","","B/C"
"03","03/08_session_info/sessionInfo_phase03_final.txt","F:/legacy_candidate_removed + GC-18SCI/03/08_session_info/sessionInfo_phase03_final.txt","txt","other","script_or_report",FALSE,FALSE,FALSE,TRUE,TRUE,"","","B/C"
"04","04/08_session_info/sessionInfo_phase04_final.txt","F:/legacy_candidate_removed + GC-18SCI/04/08_session_info/sessionInfo_phase04_final.txt","txt","other","script_or_report",FALSE,FALSE,FALSE,TRUE,TRUE,"","","B/C"
"05","05/08_session_info/sessionInfo_phase05.txt","F:/legacy_candidate_removed + GC-18SCI/05/08_session_info/sessionInfo_phase05.txt","txt","other","script_or_report",FALSE,FALSE,FALSE,TRUE,TRUE,"","","B/C"
"05","05/08_session_info/sessionInfo_phase05_package_check.txt","F:/legacy_candidate_removed + GC-18SCI/05/08_session_info/sessionInfo_phase05_package_check.txt","txt","other","script_or_report",FALSE,FALSE,FALSE,TRUE,TRUE,"","","B/C"
"05B","05B/08_session_info/sessionInfo_phase05B.txt","F:/legacy_candidate_removed + GC-18SCI/05B/08_session_info/sessionInfo_phase05B.txt","txt","other","script_or_report",FALSE,FALSE,FALSE,TRUE,TRUE,"","","B/C"
"06A","06A/08_session_info/sessionInfo_phase06A.txt","F:/legacy_candidate_removed + GC-18SCI/06A/08_session_info/sessionInfo_phase06A.txt","txt","other","script_or_report",FALSE,FALSE,FALSE,TRUE,TRUE,"","","B/C"
"06B","06B/08_session_info/sessionInfo_phase06B.txt","F:/legacy_candidate_removed + GC-18SCI/06B/08_session_info/sessionInfo_phase06B.txt","txt","other","script_or_report",FALSE,FALSE,FALSE,TRUE,TRUE,"","","B/C"
"07","07/08_session_info/sessionInfo_phase07.txt","F:/legacy_candidate_removed + GC-18SCI/07/08_session_info/sessionInfo_phase07.txt","txt","other","script_or_report",FALSE,FALSE,FALSE,TRUE,TRUE,"","","B/C"
"08","08/08_session_info/sessionInfo_phase08.txt","F:/legacy_candidate_removed + GC-18SCI/08/08_session_info/sessionInfo_phase08.txt","txt","other","script_or_report",FALSE,FALSE,FALSE,TRUE,TRUE,"","","B/C"
"08","08/08_session_info/sessionInfo_phase08_full.txt","F:/legacy_candidate_removed + GC-18SCI/08/08_session_info/sessionInfo_phase08_full.txt","txt","other","script_or_report",FALSE,FALSE,FALSE,TRUE,TRUE,"","","B/C"
"09","09/08_session_info/sessionInfo_phase09.txt","F:/legacy_candidate_removed + GC-18SCI/09/08_session_info/sessionInfo_phase09.txt","txt","other","script_or_report",FALSE,FALSE,FALSE,TRUE,TRUE,"","","B/C"
"09B","09B/14_session_info/sessionInfo_phase09B.txt","F:/legacy_candidate_removed + GC-18SCI/09B/14_session_info/sessionInfo_phase09B.txt","txt","other","script_or_report",FALSE,FALSE,FALSE,TRUE,TRUE,"","","B/C"
"09C","09C/11_session_info/sessionInfo_phase09C_R.txt","F:/legacy_candidate_removed + GC-18SCI/09C/11_session_info/sessionInfo_phase09C_R.txt","txt","other","script_or_report",FALSE,FALSE,FALSE,TRUE,TRUE,"","","B/C"



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_FINAL_SOURCE_REBUILD.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

loaded via a namespace (and not attached):
[1] compiler_4.5.2 Matrix_1.7-4   survival_3.8-3 splines_4.5.2  grid_4.5.2    
[6] lattice_0.22-7



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_FINAL_SUBMISSION_GRADE_REBUILD.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

loaded via a namespace (and not attached):
[1] compiler_4.5.2



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_phase02.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] future_1.68.0               tibble_3.3.0               
 [3] stringr_1.6.0               scales_1.4.0               
 [5] viridis_0.6.5               viridisLite_0.4.2          
 [7] RColorBrewer_1.1-3          ggpubr_0.6.2               
 [9] cowplot_1.2.0               openxlsx_4.2.8.1           
[11] pheatmap_1.0.13             scran_1.38.1               
[13] scater_1.38.1               scuttle_1.20.0             
[15] SingleCellExperiment_1.32.0 SummarizedExperiment_1.40.0
[17] Biobase_2.70.0              GenomicRanges_1.62.0       
[19] Seqinfo_1.0.0               IRanges_2.44.0             
[21] S4Vectors_0.48.0            BiocGenerics_0.56.0        
[23] generics_0.1.4              MatrixGenerics_1.22.0      
[25] matrixStats_1.5.0           UCell_2.14.0               
[27] harmony_2.0.3               Rcpp_1.1.0                 
[29] patchwork_1.3.2             ggplot2_4.0.3              
[31] tidyr_1.3.2                 dplyr_1.2.1                
[33] data.table_1.18.4           Matrix_1.7-4               
[35] Seurat_5.3.1                SeuratObject_5.2.0         
[37] sp_2.2-0                   

loaded via a namespace (and not attached):
  [1] R.methodsS3_1.8.2         dichromat_2.0-0.1        
  [3] GSEABase_1.72.0           goftest_1.2-3            
  [5] Biostrings_2.78.0         HDF5Array_1.38.0         
  [7] vctrs_0.7.3               ggtangle_0.0.9           
  [9] spatstat.random_3.4-3     digest_0.6.39            
 [11] png_0.1-9                 shape_1.4.6.1            
 [13] gypsum_1.6.0              ggrepel_0.9.6            
 [15] deldir_2.0-4              parallelly_1.45.1        
 [17] fontLiberation_0.1.0      MASS_7.3-65              
 [19] reshape2_1.4.5            withr_3.0.2              
 [21] httpuv_1.6.16             foreach_1.5.2            
 [23] qvalue_2.42.0             ggfun_0.2.0              
 [25] survival_3.8-3            memoise_2.0.1            
 [27] ggbeeswarm_0.7.3          clustree_0.5.1           
 [29] gson_0.1.0                clusterProfiler_4.18.2   
 [31] systemfonts_1.3.1         tidytree_0.4.6           
 [33] zoo_1.8-14                GlobalOptions_0.1.3      
 [35] pbapply_1.7-4             R.oo_1.27.1              
 [37] Formula_1.2-5             KEGGREST_1.50.0          
 [39] promises_1.5.0            otel_0.2.0               
 [41] httr_1.4.7                restfulr_0.0.16          
 [43] rstatix_0.7.3             globals_0.18.0           
 [45] fitdistrplus_1.2-4        rhdf5filters_1.22.0      
 [47] rhdf5_2.54.0              UCSC.utils_1.6.1         
 [49] miniUI_0.1.2              DOSE_4.4.0               
 [51] fields_17.3               babelgene_22.9           
 [53] curl_7.0.0                ggraph_2.2.2             
 [55] ScaledMatrix_1.18.0       h5mread_1.2.1            
 [57] polyclip_1.10-7           ExperimentHub_3.0.0      
 [59] SparseArray_1.10.4        xtable_1.8-4             
 [61] doParallel_1.0.17         S4Arrays_1.10.1          
 [63] BiocFileCache_3.0.0       irlba_2.3.5.1            
 [65] colorspace_2.1-2          filelock_1.0.3           
 [67] ROCR_1.0-11               reticulate_1.44.1        
 [69] spatstat.data_3.1-9       magrittr_2.0.4           
 [71] lmtest_0.9-40             later_1.4.4              
 [73] ggtree_4.0.1              lattice_0.22-7           
 [75] spatstat.geom_3.6-1       future.apply_1.20.0      
 [77] scattermore_1.2 


## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_phase02_final.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
 [1] future_1.68.0      viridis_0.6.5      viridisLite_0.4.2  scales_1.4.0      
 [5] tibble_3.3.0       pheatmap_1.0.13    UCell_2.14.0       harmony_2.0.3     
 [9] Rcpp_1.1.0         patchwork_1.3.2    ggplot2_4.0.3      tidyr_1.3.2       
[13] dplyr_1.2.1        Matrix_1.7-4       Seurat_5.3.1       SeuratObject_5.2.0
[17] sp_2.2-0          

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3          jsonlite_2.0.0             
  [3] magrittr_2.0.4              ggbeeswarm_0.7.3           
  [5] spatstat.utils_3.2-0        farver_2.1.2               
  [7] vctrs_0.7.3                 ROCR_1.0-11                
  [9] spatstat.explore_3.6-0      htmltools_0.5.9            
 [11] S4Arrays_1.10.1             BiocNeighbors_2.4.0        
 [13] SparseArray_1.10.4          sctransform_0.4.2          
 [15] parallelly_1.45.1           KernSmooth_2.23-26         
 [17] htmlwidgets_1.6.4           ica_1.0-3                  
 [19] plyr_1.8.9                  plotly_4.11.0              
 [21] zoo_1.8-14                  igraph_2.2.1               
 [23] mime_0.13                   lifecycle_1.0.5            
 [25] pkgconfig_2.0.3             R6_2.6.1                   
 [27] fastmap_1.2.0               MatrixGenerics_1.22.0      
 [29] fitdistrplus_1.2-4          shiny_1.12.0               
 [31] digest_0.6.39               S4Vectors_0.48.0           
 [33] tensor_1.5.1                RSpectra_0.16-2            
 [35] irlba_2.3.5.1               GenomicRanges_1.62.0       
 [37] labeling_0.4.3              progressr_0.18.0           
 [39] spatstat.sparse_3.1-0       httr_1.4.7                 
 [41] polyclip_1.10-7             abind_1.4-8                
 [43] compiler_4.5.2              withr_3.0.2                
 [45] S7_0.2.1                    BiocParallel_1.44.0        
 [47] fastDummies_1.7.5           MASS_7.3-65                
 [49] DelayedArray_0.36.0         tools_4.5.2                
 [51] vipor_0.4.7                 lmtest_0.9-40              
 [53] otel_0.2.0                  beeswarm_0.4.0             
 [55] httpuv_1.6.16               future.apply_1.20.0        
 [57] goftest_1.2-3               glue_1.8.0                 
 [59] nlme_3.1-168                promises_1.5.0             
 [61] grid_4.5.2                  Rtsne_0.17                 
 [63] cluster_2.1.8.1             reshape2_1.4.5             
 [65] generics_0.1.4              gtable_0.3.6               
 [67] spatstat.data_3.1-9         data.table_1.18.4          
 [69] XVector_0.50.0              BiocGenerics_0.56.0        
 [71] spatstat.geom_3.6-1         RcppAnnoy_0.0.22           
 [73] ggrepel_0.9.6               RANN_2.6.2                 
 [75] pillar_1.11.1               stringr_1.6.0              
 [77] limma_3.66.0                spam_2.11-1                
 [79] RcppHNSW_0.6.0              later_1.4.4                
 [81] splines_4.5.2               lattice_0.22-7             
 [83] survival_3.8-3              deldir_2.0-4               
 [85] tidyselect_1.2.1            SingleCellExperiment_1.32.0
 [87] miniUI_0.1.2                pbapply_1.7-4              
 [89] gridExtra_2.3               IRanges_2.44.0             
 [91] Seqinfo_1.0.0               SummarizedExperiment_1.40.0
 [93] scattermore_1.2             RhpcBLASctl_0.23-42        
 [95] stats4_4.5.2                Biobase_2.70.0             
 [97] statmod_1.5.1               matrixStats_1


## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_phase03.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] tibble_3.3.0                stringr_1.6.0              
 [3] scales_1.4.0                viridis_0.6.5              
 [5] viridisLite_0.4.2           RColorBrewer_1.1-3         
 [7] ggpubr_0.6.2                cowplot_1.2.0              
 [9] future_1.68.0               pheatmap_1.0.13            
[11] scran_1.38.1                scater_1.38.1              
[13] scuttle_1.20.0              SingleCellExperiment_1.32.0
[15] SummarizedExperiment_1.40.0 Biobase_2.70.0             
[17] GenomicRanges_1.62.0        Seqinfo_1.0.0              
[19] IRanges_2.44.0              S4Vectors_0.48.0           
[21] BiocGenerics_0.56.0         generics_0.1.4             
[23] MatrixGenerics_1.22.0       matrixStats_1.5.0          
[25] UCell_2.14.0                harmony_2.0.3              
[27] Rcpp_1.1.0                  patchwork_1.3.2            
[29] ggplot2_4.0.3               tidyr_1.3.2                
[31] dplyr_1.2.1                 data.table_1.18.4          
[33] Matrix_1.7-4                Seurat_5.3.1               
[35] SeuratObject_5.2.0          sp_2.2-0                   

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22         splines_4.5.2            later_1.4.4             
  [4] BiocIO_1.20.0            fields_17.3              DoubletFinder_2.0.6     
  [7] bitops_1.0-9             polyclip_1.10-7          XML_3.99-0.20           
 [10] fastDummies_1.7.5        lifecycle_1.0.5          scDblFinder_1.24.10     
 [13] rstatix_0.7.3            edgeR_4.8.0              globals_0.18.0          
 [16] lattice_0.22-7           MASS_7.3-65              backports_1.5.0         
 [19] magrittr_2.0.4           openxlsx_4.2.8.1         limma_3.66.0            
 [22] plotly_4.11.0            yaml_2.3.11              metapod_1.18.0          
 [25] httpuv_1.6.16            otel_0.2.0               sctransform_0.4.2       
 [28] spam_2.11-1              zip_2.3.3                spatstat.sparse_3.1-0   
 [31] reticulate_1.44.1        pbapply_1.7-4            maps_3.4.3              
 [34] abind_1.4-8              Rtsne_0.17               purrr_1.2.0             
 [37] RCurl_1.98-1.19          ggrepel_0.9.6            irlba_2.3.5.1           
 [40] listenv_0.10.0           spatstat.utils_3.2-0     goftest_1.2-3           
 [43] RSpectra_0.16-2          spatstat.random_3.4-3    dqrng_0.4.1             
 [46] fitdistrplus_1.2-4       parallelly_1.45.1        codetools_0.2-20        
 [49] DelayedArray_0.36.0      tidyselect_1.2.1         UCSC.utils_1.6.1        
 [52] farver_2.1.2             ScaledMatrix_1.18.0      spatstat.explore_3.6-0  
 [55] GenomicAlignments_1.46.0 jsonlite_2.0.0           BiocNeighbors_2.4.0     
 [58] progressr_0.18.0         Formula_1.2-5            ggridges_0.5.7          
 [61] survival_3.8-3           tools_4.5.2              ica_1.0-3               
 [64] glue_1.8.0               gridExtra_2.3            SparseArray_1.10.4      
 [67] GenomeInfoDb_1.46.2      withr_3.0.2              BiocManager_1.30.27     
 [70] fastmap_1.2.0            bluster_1.20.0           digest_0.6.39           
 [73] rsvd_1.0.5               R6_2.6.1                 mime_0.13               
 [76] scattermore_1.2          tensor_1.5.1             dichromat_2.0-0.1       
 [79] spatstat.data_3.1-9      cigarillo_1.0.0          rtracklayer_1.70.1      
 [82] httr_1.4.7               htmlwidgets_1.6.4        S4Arrays_1.10.1 


## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_phase03_final.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
 [1] future_1.68.0      viridis_0.6.5      viridisLite_0.4.2  tibble_3.3.0      
 [5] pheatmap_1.0.13    UCell_2.14.0       harmony_2.0.3      Rcpp_1.1.0        
 [9] patchwork_1.3.2    ggplot2_4.0.3      tidyr_1.3.2        dplyr_1.2.1       
[13] Matrix_1.7-4       Seurat_5.3.1       SeuratObject_5.2.0 sp_2.2-0          

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3          jsonlite_2.0.0             
  [3] magrittr_2.0.4              spatstat.utils_3.2-0       
  [5] farver_2.1.2                vctrs_0.7.3                
  [7] ROCR_1.0-11                 spatstat.explore_3.6-0     
  [9] htmltools_0.5.9             S4Arrays_1.10.1            
 [11] BiocNeighbors_2.4.0         SparseArray_1.10.4         
 [13] sctransform_0.4.2           parallelly_1.45.1          
 [15] KernSmooth_2.23-26          htmlwidgets_1.6.4          
 [17] ica_1.0-3                   plyr_1.8.9                 
 [19] plotly_4.11.0               zoo_1.8-14                 
 [21] igraph_2.2.1                mime_0.13                  
 [23] lifecycle_1.0.5             pkgconfig_2.0.3            
 [25] R6_2.6.1                    fastmap_1.2.0              
 [27] MatrixGenerics_1.22.0       fitdistrplus_1.2-4         
 [29] shiny_1.12.0                digest_0.6.39              
 [31] S4Vectors_0.48.0            tensor_1.5.1               
 [33] RSpectra_0.16-2             irlba_2.3.5.1              
 [35] GenomicRanges_1.62.0        labeling_0.4.3             
 [37] progressr_0.18.0            spatstat.sparse_3.1-0      
 [39] mgcv_1.9-4                  httr_1.4.7                 
 [41] polyclip_1.10-7             abind_1.4-8                
 [43] compiler_4.5.2              withr_3.0.2                
 [45] S7_0.2.1                    BiocParallel_1.44.0        
 [47] fastDummies_1.7.5           MASS_7.3-65                
 [49] DelayedArray_0.36.0         tools_4.5.2                
 [51] lmtest_0.9-40               otel_0.2.0                 
 [53] httpuv_1.6.16               future.apply_1.20.0        
 [55] goftest_1.2-3               glue_1.8.0                 
 [57] nlme_3.1-168                promises_1.5.0             
 [59] grid_4.5.2                  Rtsne_0.17                 
 [61] cluster_2.1.8.1             reshape2_1.4.5             
 [63] generics_0.1.4              gtable_0.3.6               
 [65] spatstat.data_3.1-9         data.table_1.18.4          
 [67] XVector_0.50.0              BiocGenerics_0.56.0        
 [69] spatstat.geom_3.6-1         RcppAnnoy_0.0.22           
 [71] ggrepel_0.9.6               RANN_2.6.2                 
 [73] pillar_1.11.1               stringr_1.6.0              
 [75] spam_2.11-1                 RcppHNSW_0.6.0             
 [77] later_1.4.4                 splines_4.5.2              
 [79] lattice_0.22-7              survival_3.8-3             
 [81] deldir_2.0-4                tidyselect_1.2.1           
 [83] SingleCellExperiment_1.32.0 miniUI_0.1.2               
 [85] pbapply_1.7-4               gridExtra_2.3              
 [87] IRanges_2.44.0              Seqinfo_1.0.0              
 [89] SummarizedExperiment_1.40.0 scattermore_1.2            
 [91] RhpcBLASctl_0.23-42         stats4_4.5.2               
 [93] Biobase_2.70.0              matrixStats_1.5.0          
 [95] stringi_1.8.7               lazyeval_0.2.2             
 [97] codetools_0.2-20            cli_3.6.5                  
 [99] uwo


## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_phase04_final.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0       tidyr_1.3.2        dplyr_1.2.1        patchwork_1.3.2   
[5] ggplot2_4.0.3      Seurat_5.3.1       SeuratObject_5.2.0 sp_2.2-0          

loaded via a namespace (and not attached):
  [1] deldir_2.0-4           pbapply_1.7-4          gridExtra_2.3         
  [4] rlang_1.2.0            magrittr_2.0.4         RcppAnnoy_0.0.22      
  [7] otel_0.2.0             matrixStats_1.5.0      ggridges_0.5.7        
 [10] compiler_4.5.2         spatstat.geom_3.6-1    systemfonts_1.3.1     
 [13] png_0.1-9              vctrs_0.7.3            reshape2_1.4.5        
 [16] stringr_1.6.0          pkgconfig_2.0.3        fastmap_1.2.0         
 [19] labeling_0.4.3         promises_1.5.0         purrr_1.2.0           
 [22] jsonlite_2.0.0         goftest_1.2-3          later_1.4.4           
 [25] spatstat.utils_3.2-0   irlba_2.3.5.1          parallel_4.5.2        
 [28] cluster_2.1.8.1        R6_2.6.1               ica_1.0-3             
 [31] stringi_1.8.7          RColorBrewer_1.1-3     spatstat.data_3.1-9   
 [34] reticulate_1.44.1      parallelly_1.45.1      spatstat.univar_3.1-5 
 [37] lmtest_0.9-40          scattermore_1.2        Rcpp_1.1.0            
 [40] tensor_1.5.1           future.apply_1.20.0    zoo_1.8-14            
 [43] sctransform_0.4.2      httpuv_1.6.16          Matrix_1.7-4          
 [46] splines_4.5.2          igraph_2.2.1           tidyselect_1.2.1      
 [49] dichromat_2.0-0.1      abind_1.4-8            spatstat.random_3.4-3 
 [52] codetools_0.2-20       miniUI_0.1.2           spatstat.explore_3.6-0
 [55] listenv_0.10.0         lattice_0.22-7         tibble_3.3.0          
 [58] plyr_1.8.9             withr_3.0.2            shiny_1.12.0          
 [61] S7_0.2.1               ROCR_1.0-11            Rtsne_0.17            
 [64] future_1.68.0          fastDummies_1.7.5      survival_3.8-3        
 [67] polyclip_1.10-7        fitdistrplus_1.2-4     pillar_1.11.1         
 [70] KernSmooth_2.23-26     plotly_4.11.0          generics_0.1.4        
 [73] RcppHNSW_0.6.0         globals_0.18.0         xtable_1.8-4          
 [76] glue_1.8.0             lazyeval_0.2.2         tools_4.5.2           
 [79] data.table_1.18.4      RSpectra_0.16-2        RANN_2.6.2            
 [82] dotCall64_1.2          cowplot_1.2.0          grid_4.5.2            
 [85] nlme_3.1-168           cli_3.6.5              spatstat.sparse_3.1-0 
 [88] textshaping_1.0.4      spam_2.11-1            viridisLite_0.4.2     
 [91] svglite_2.2.2          uwot_0.2.4             gtable_0.3.6          
 [94] digest_0.6.39          progressr_0.18.0       ggrepel_0.9.6         
 [97] htmlwidgets_1.6.4      farver_2.1.2           htmltools_0.5.9       
[100] lifecycle_1.0.5        httr_1.4.7             mime_0.13             
[103] MASS_7.3-65           



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_phase05.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] scales_1.4.0      patchwork_1.3.2   ggplot2_4.0.3     tidyr_1.3.2      
[5] dplyr_1.2.1       data.table_1.18.4

loaded via a namespace (and not attached):
 [1] vctrs_0.7.3        svglite_2.2.2      cli_3.6.5          rlang_1.2.0       
 [5] purrr_1.2.0        generics_0.1.4     textshaping_1.0.4  S7_0.2.1          
 [9] glue_1.8.0         labeling_0.4.3     grid_4.5.2         tibble_3.3.0      
[13] lifecycle_1.0.5    compiler_4.5.2     RColorBrewer_1.1-3 pkgconfig_2.0.3   
[17] systemfonts_1.3.1  farver_2.1.2       viridisLite_0.4.2  R6_2.6.1          
[21] dichromat_2.0-0.1  tidyselect_1.2.1   pillar_1.11.1      magrittr_2.0.4    
[25] tools_4.5.2        withr_3.0.2        gtable_0.3.6      



## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_phase05B.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
 [1] scales_1.4.0       ranger_0.17.0      glmnet_4.1-10      meta_8.5-0        
 [5] metabook_0.2-0     survminer_0.5.2    ggpubr_0.6.2       survival_3.8-3    
 [9] patchwork_1.3.2    ggplot2_4.0.3      stringr_1.6.0      tidyr_1.3.2       
[13] dplyr_1.2.1        data.table_1.18.4  Matrix_1.7-4       Seurat_5.3.1      
[17] SeuratObject_5.2.0 sp_2.2-0          

loaded via a namespace (and not attached):
  [1] mathjaxr_2.0-0         RColorBrewer_1.1-3     shape_1.4.6.1         
  [4] jsonlite_2.0.0         magrittr_2.0.4         spatstat.utils_3.2-0  
  [7] farver_2.1.2           nloptr_2.2.1           vctrs_0.7.3           
 [10] ROCR_1.0-11            minqa_1.2.8            spatstat.explore_3.6-0
 [13] CompQuadForm_1.4.4     rstatix_0.7.3          htmltools_0.5.9       
 [16] broom_1.0.11           Formula_1.2-5          sctransform_0.4.2     
 [19] parallelly_1.45.1      KernSmooth_2.23-26     htmlwidgets_1.6.4     
 [22] ica_1.0-3              plyr_1.8.9             plotly_4.11.0         
 [25] zoo_1.8-14             igraph_2.2.1           iterators_1.0.14      
 [28] mime_0.13              lifecycle_1.0.5        pkgconfig_2.0.3       
 [31] R6_2.6.1               fastmap_1.2.0          rbibutils_2.4         
 [34] fitdistrplus_1.2-4     future_1.68.0          shiny_1.12.0          
 [37] numDeriv_2016.8-1.1    digest_0.6.39          tensor_1.5.1          
 [40] RSpectra_0.16-2        irlba_2.3.5.1          labeling_0.4.3        
 [43] metadat_1.6-0          progressr_0.18.0       spatstat.sparse_3.1-0 
 [46] httr_1.4.7             polyclip_1.10-7        abind_1.4-8           
 [49] compiler_4.5.2         withr_3.0.2            S7_0.2.1              
 [52] backports_1.5.0        metafor_5.0-1          viridis_0.6.5         
 [55] carData_3.0-5          fastDummies_1.7.5      ggsignif_0.6.4        
 [58] MASS_7.3-65            tools_4.5.2            lmtest_0.9-40         
 [61] otel_0.2.0             httpuv_1.6.16          future.apply_1.20.0   
 [64] goftest_1.2-3          glue_1.8.0             nlme_3.1-168          
 [67] promises_1.5.0         grid_4.5.2             Rtsne_0.17            
 [70] cluster_2.1.8.1        reshape2_1.4.5         generics_0.1.4        
 [73] gtable_0.3.6           spatstat.data_3.1-9    tzdb_0.5.0            
 [76] hms_1.1.4              xml2_1.5.1             car_3.1-3             
 [79] spatstat.geom_3.6-1    RcppAnnoy_0.0.22       foreach_1.5.2         
 [82] ggrepel_0.9.6          RANN_2.6.2             pillar_1.11.1         
 [85] spam_2.11-1            RcppHNSW_0.6.0         later_1.4.4           
 [88] splines_4.5.2          lattice_0.22-7         deldir_2.0-4          
 [91] tidyselect_1.2.1       miniUI_0.1.2           pbapply_1.7-4         
 [94] reformulas_0.4.2       gridExtra_2.3          scattermore_1.2       
 [97] matrixStats_1.5.0      stringi_1.8.7          lazyeval_0.2.2        
[100] boot_1.3-32            codetools_0.2-20       tibble_3.3.0          
[103] cli_3.6.5              uwot_0.2.4             xtable_1.8-4          
[106] reticulate_1.44.1      Rdpack_2.6.4           dichromat_2.0-0.1     
[109] Rcpp_1.1.0             globals_0.18.0         spatstat.random_3.4-3 
[112] png_0.1-9              spatstat.univar_3.1-5  parallel_4.5.2        
[115] readr_2.1.6            dotCall64_1.2          lme4_1.1-38           
[118] listenv_0.10.0         viridisLite_0.4.2      ggridges_0.5.7        
[121


## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_phase05_package_check.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

loaded via a namespace (and not attached):
  [1] igraph_2.2.1                            
  [2] graph_1.88.0                            
  [3] Formula_1.2-5                           
  [4] timeROC_0.4                             
  [5] tidyselect_1.2.1                        
  [6] rvest_1.0.5                             
  [7] bit_4.6.0                               
  [8] doParallel_1.0.17                       
  [9] clue_0.3-66                             
 [10] lattice_0.22-7                          
 [11] rjson_0.2.23                            
 [12] blob_1.2.4                              
 [13] stringr_1.6.0                           
 [14] S4Arrays_1.10.1                         
 [15] parallel_4.5.2                          
 [16] caret_7.0-1                             
 [17] oncoPredict_1.2                         
 [18] dichromat_2.0-0.1                       
 [19] Biobase_2.70.0                          
 [20] png_0.1-9                               
 [21] cli_3.6.5                               
 [22] ggplotify_0.1.3                         
 [23] BiocIO_1.20.0                           
 [24] purrr_1.2.0                             
 [25] Metrics_0.1.4                           
 [26] curl_7.0.0                              
 [27] evaluate_1.0.5                          
 [28] tidytree_0.4.6                          
 [29] ComplexHeatmap_2.26.0                   
 [30] stringi_1.8.7                           
 [31] pROC_1.19.0.1                           
 [32] backports_1.5.0                         
 [33] XML_3.99-0.20                           
 [34] lubridate_1.9.4                         
 [35] AnnotationDbi_1.72.0                    
 [36] magrittr_2.0.4                          
 [37] clusterProfiler_4.18.2                  
 [38] rappdirs_0.3.3                          
 [39] splines_4.5.2                           
 [40] prodlim_2025.04.28                      
 [41] rentrez_1.2.4                           
 [42] survminer_0.5.2                         
 [43] dplyr_1.2.1                             
 [44] org.Hs.eg.db_3.22.0                     
 [45] ridge_3.3                               
 [46] DBI_1.2.3                               
 [47] HDF5Array_1.38.0                        
 [48] genefilter_1.92.0                       
 [49] withr_3.0.2                             
 [50] reformulas_0.4.4                        
 [51] class_7.3-23                            
 [52] systemfonts_1.3.1                       
 [53] enrichplot_1.30.4                       
 [54] xgboost_3.2.1.1                         
 [55] lightgbm_4.6.0                          
 [56] ggnewscale_0.5.2                        
 [57] GSEABase_1.72.0                         
 [58] sva_3.58.0                              
 [59] rtracklayer_1.70.1                      
 [60] htmlwidgets_1.6.4                       
 [61] fs_1.6.6                                
 [62] S4Vectors_0.48.0                        
 [63] biomaRt_2.66.0                          
 [64] SingleCellExperiment_1.32.0             
 [65] ggrepel_0.9.6                           
 [66] tidyverse_2.0.0                         
 [67] SparseArray_1.10.4                      
 [68] DESeq2_1.50.2                           
 [69] ranger_0.17.0                           
 [70] MatrixGenerics_1.22.0                   
 [71] h5mread_1.2.1                           
 [72] annotate_1.88.0                         
 [73] zoo_1.8


## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_phase06A.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
 [1] viridis_0.6.5      viridisLite_0.4.2  scales_1.4.0       glmnet_4.1-10     
 [5] survival_3.8-3     patchwork_1.3.2    ggplot2_4.0.3      stringr_1.6.0     
 [9] tidyr_1.3.2        dplyr_1.2.1        data.table_1.18.4  Matrix_1.7-4      
[13] Seurat_5.3.1       SeuratObject_5.2.0 sp_2.2-0          

loaded via a namespace (and not attached):
  [1] matrixStats_1.5.0           GSVA_1.46.0                
  [3] spatstat.sparse_3.1-0       bitops_1.0-9               
  [5] httr_1.4.7                  RColorBrewer_1.1-3         
  [7] doParallel_1.0.17           numDeriv_2016.8-1.1        
  [9] tools_4.5.2                 sctransform_0.4.2          
 [11] backports_1.5.0             metafor_5.0-1              
 [13] R6_2.6.1                    HDF5Array_1.38.0           
 [15] mgcv_1.9-4                  lazyeval_0.2.2             
 [17] uwot_0.2.4                  rhdf5filters_1.22.0        
 [19] GetoptLong_1.1.0            withr_3.0.2                
 [21] gridExtra_2.3               progressr_0.18.0           
 [23] cli_3.6.5                   Biobase_2.70.0             
 [25] spatstat.explore_3.6-0      fastDummies_1.7.5          
 [27] mvtnorm_1.3-3               S7_0.2.1                   
 [29] spatstat.data_3.1-9         readr_2.1.6                
 [31] genefilter_1.92.0           ggridges_0.5.7             
 [33] pbapply_1.7-4               R.utils_2.13.0             
 [35] harmony_2.0.3               dichromat_2.0-0.1          
 [37] parallelly_1.45.1           limma_3.66.0               
 [39] RSQLite_2.4.5               generics_0.1.4             
 [41] shape_1.4.6.1               ica_1.0-3                  
 [43] spatstat.random_3.4-3       zip_2.3.3                  
 [45] car_3.1-3                   metadat_1.6-0              
 [47] S4Vectors_0.48.0            abind_1.4-8                
 [49] R.methodsS3_1.8.2           lifecycle_1.0.5            
 [51] edgeR_4.8.0                 CompQuadForm_1.4.4         
 [53] carData_3.0-5               mathjaxr_2.0-0             
 [55] SummarizedExperiment_1.40.0 rhdf5_2.54.0               
 [57] SparseArray_1.10.4          Rtsne_0.17                 
 [59] grid_4.5.2                  blob_1.2.4                 
 [61] promises_1.5.0              crayon_1.5.3               
 [63] miniUI_0.1.2                lattice_0.22-7             
 [65] beachmat_2.26.0             cowplot_1.2.0              
 [67] annotate_1.88.0             KEGGREST_1.50.0            
 [69] pillar_1.11.1               ComplexHeatmap_2.26.0      
 [71] GenomicRanges_1.62.0        boot_1.3-32                
 [73] rjson_0.2.23                future.apply_1.20.0        
 [75] codetools_0.2-20            glue_1.8.0                 
 [77] spatstat.univar_3.1-5       Rdpack_2.6.4               
 [79] vctrs_0.7.3                 png_0.1-9                  
 [81] spam_2.11-1                 gtable_0.3.6               
 [83] cachem_1.1.0                openxlsx_4.2.8.1           
 [85] rbibutils_2.4               S4Arrays_1.10.1            
 [87] mime_0.13                   prodlim_2025.04.28         
 [89] Seqinfo_1.0.0               reformulas_0.4.2           
 [91] pheatmap_1.0.13             SingleCellExperiment_1.32.0
 [93] iterators_1.0.14            metabook_0.2-0             
 [95] lava_1.8.2                  statmod_1.5.1              
 [97] fitdistrplus_1.2-4          ROCR_1.0-11                
 [99] nlme_3.1-168          


## APOD_ARTICLE_ASSEMBLY\3ditoubanben\02_FULL_ANALYSIS_ARCHIVE\06_Environment\sessionInfo_phase06B.txt

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
 [1] viridis_0.6.5     viridisLite_0.4.2 scales_1.4.0      glmnet_4.1-10    
 [5] Matrix_1.7-4      survival_3.8-3    patchwork_1.3.2   ggplot2_4.0.3    
 [9] stringr_1.6.0     tidyr_1.3.2       dplyr_1.2.1      

loaded via a namespace (and not attached):
  [1] cmprsk_2.2-12             matrixStats_1.5.0        
  [3] CoxBoost_1.5.1            rms_8.1-0                
  [5] lubridate_1.9.4           DiceDesign_1.10          
  [7] RColorBrewer_1.1-3        doParallel_1.0.17        
  [9] numDeriv_2016.8-1.1       tools_4.5.2              
 [11] backports_1.5.0           R6_2.6.1                 
 [13] vegan_2.7-2               metafor_5.0-1            
 [15] mgcv_1.9-4                yardstick_1.4.0          
 [17] GetoptLong_1.1.0          permute_0.9-8            
 [19] withr_3.0.2               gridExtra_2.3            
 [21] textshaping_1.0.4         quantreg_6.1             
 [23] cli_3.6.6                 iml_0.11.4               
 [25] network_1.19.0            sandwich_3.1-1           
 [27] mvtnorm_1.3-3             S7_0.2.1                 
 [29] polspline_1.1.25          readr_2.1.6              
 [31] randomForest_4.7-1.2      tune_2.1.0               
 [33] proxy_0.4-27              systemfonts_1.3.1        
 [35] foreign_0.8-90            svglite_2.2.2            
 [37] paradox_1.0.1             dichromat_2.0-0.1        
 [39] parallelly_1.45.1         DALEX_2.5.3              
 [41] maps_3.4.3                rstudioapi_0.19.0        
 [43] visNetwork_2.1.4          generics_0.1.4           
 [45] shape_1.4.6.1             risksetROC_1.0.4.1       
 [47] zip_2.3.3                 car_3.1-3                
 [49] lars_1.3                  metadat_1.6-0            
 [51] S4Vectors_0.48.0          abind_1.4-8              
 [53] lightgbm_4.6.0            lifecycle_1.0.5          
 [55] multcomp_1.4-29           CompQuadForm_1.4.4       
 [57] carData_3.0-5             mathjaxr_2.0-0           
 [59] recipes_1.3.3             grid_4.5.2               
 [61] crayon_1.5.3              lattice_0.22-7           
 [63] cowplot_1.2.0             sna_2.8                  
 [65] pillar_1.11.1             knitr_1.50               
 [67] ComplexHeatmap_2.26.0     rjson_0.2.23             
 [69] boot_1.3-32               xgboost_3.2.1.1          
 [71] future.apply_1.20.0       codetools_0.2-20         
 [73] glue_1.8.0                rsample_1.3.2            
 [75] data.table_1.18.4         workflowsets_1.1.1       
 [77] vctrs_0.7.3               png_0.1-9                
 [79] spam_2.11-1               Rdpack_2.6.4             
 [81] gtable_0.3.6              kernlab_0.9-33           
 [83] openxlsx_4.2.8.1          gower_1.0.2              
 [85] xfun_0.54                 rbibutils_2.4            
 [87] prodlim_2025.04.28        pracma_2.4.6             
 [89] coda_0.19-4.1             reformulas_0.4.2         
 [91] randomForestSRC_3.6.2     timeDate_4051.111        
 [93] pheatmap_1.0.13           iterators_1.0.14         
 [95] hardhat_1.4.3             metabook_0.2-0           
 [97] lava_1.8.2                fields_17.3              
 [99] DiagrammeR_1.0.11         TH.data_1.1-5            
[101] ROCR_1.0-11               ipred_0.9-15             
[103] modeldata_1.5.1           nlme_3.1-168             
[105] infer_1.1.0               SHAPforxgboost_0.2.0     
[107] data.tree_1.2.0           mlr3_1.7.1               
[109] rpart_4.1.24        

