su: ignoring --preserve-environment, it's mutually exclusive with --login
Loading required namespace: usethis
Loading required namespace: devtools
Coco running mode: dev
Coco dev database: /databases/CircleRNADb
Warning in warn_if_app_dir_is_package(appDir) :
  Loading R/ subdirectory for Shiny application, but this directory appears to contain an R package. Sourcing files in R/ may cause unexpected behavior. See `?loadSupport` for more details.
ℹ Loading coco
Warning: replacing previous import ‘shinyWidgets::alert’ by ‘shinyjs::alert’ when loading ‘coco’
Warning: replacing previous import ‘shiny::runExample’ by ‘shinyjs::runExample’ when loading ‘coco’
You are using coco version 1.0.0
Cache path: ~/.coco_cache
Cache size: 20 GB

Listening on http://127.0.0.1:46019
Warning in dir.create(cache_dir, recursive = TRUE) :
  cannot create dir '/srv/shiny-server/TCCIA/app_cache', reason 'Permission denied'
Warning in value[[3L]](cond) :
  Error using cache directory at '/srv/shiny-server/TCCIA/app_cache/sass'. Using temp dir instead.
Warning in dir.create(cache_dir, recursive = TRUE) :
  cannot create dir '/srv/shiny-server/TCCIA/app_cache', reason 'Permission denied'
Warning in value[[3L]](cond) :
  Error using cache directory at '/srv/shiny-server/TCCIA/app_cache/sass'. Using temp dir instead.
Warning in dir.create(cache_dir, recursive = TRUE) :
  cannot create dir '/srv/shiny-server/TCCIA/app_cache', reason 'Permission denied'
Warning in value[[3L]](cond) :
  Error using cache directory at '/srv/shiny-server/TCCIA/app_cache/sass'. Using temp dir instead.
[2026-06-16 10:11:32 | INFO] Library path: /usr/local/lib/R/extra-library
Library path: /usr/local/lib/R/site-library
Library path: /usr/local/lib/R/library
[2026-06-16 10:11:32 | INFO] Cache path: ~/.coco_cache
[2026-06-16 10:11:32 | INFO] Init database with necessary summary data...
Warning in renderWidget(instance) :
  Ignoring explicitly provided widget ID "repo-search-table"; Shiny doesn't use them
[2026-06-16 10:11:38 | INFO] the cohort(s) selected in repository: EGAD00001003977
[2026-06-16 10:11:43 | INFO] selected ids for filter: 1:A2M, 2:, 3:
[2026-06-16 10:11:49 | INFO] Only selected circ unit will be kept: Count
[2026-06-16 10:11:49 | INFO] Only selected circ method will be kept: Ensemble
[2026-06-16 10:11:49 | INFO] Final dataset list EGAD00001003977_circRNA_Ensemble
[2026-06-16 10:11:49 | INFO] handling Y dataset with id EGAD00001003977_circRNA_Ensemble
[2026-06-16 10:11:49 | INFO] checking databases: /databases/CircleRNADb
[2026-06-16 10:11:49 | INFO] query row index data
[2026-06-16 10:11:49 | INFO] query column index data
[2026-06-16 10:11:49 | INFO] analysis with circRNA Host Gene selected
[2026-06-16 10:11:50 | INFO] handling X dataset with id EGAD00001003977_circRNA_Ensemble
[2026-06-16 10:11:50 | INFO] analysis with circRNA Host Gene selected
[2026-06-16 10:11:56 | INFO] all samples selected for analysis
[2026-06-16 10:11:56 | INFO] call with spearman: EGAD00001003977_circRNA_Ensemble ABCA11P Gene; EGAD00001003977_circRNA_Ensemble A2M Gene add_dist-FALSE
[2026-06-16 10:11:56 | INFO] checking databases: /databases/CircleRNADb
[2026-06-16 10:11:56 | INFO] load dataset
[2026-06-16 10:11:56 | INFO] only_IO is enabled
[2026-06-16 10:11:56 | INFO] temporarily add 'Treatment' to filter IO samples
[2026-06-16 10:11:56 | INFO] check signature from input
[2026-06-16 10:11:59 | INFO] collapse CircRNA IDs to associated gene
[2026-06-16 10:11:59 | INFO] merge phenotype data and CircRNA value data
[2026-06-16 10:11:59 | INFO] assign the data value dataset metadata
[2026-06-16 10:11:59 | INFO] done for loading ABCA11P
[2026-06-16 10:11:59 | INFO] checking databases: /databases/CircleRNADb
[2026-06-16 10:11:59 | INFO] load dataset
[2026-06-16 10:11:59 | INFO] only_IO is enabled
[2026-06-16 10:11:59 | INFO] temporarily add 'Treatment' to filter IO samples
[2026-06-16 10:11:59 | INFO] check signature from input
[2026-06-16 10:12:00 | INFO] collapse CircRNA IDs to associated gene
[2026-06-16 10:12:00 | INFO] merge phenotype data and CircRNA value data
[2026-06-16 10:12:00 | INFO] assign the data value dataset metadata
[2026-06-16 10:12:00 | INFO] done for loading A2M
[2026-06-16 10:12:00 | INFO] done for plotting
Warning: The dot-dot notation (`..method..`) was deprecated in ggplot2 3.4.0.
ℹ Please use `after_stat(method)` instead.
ℹ The deprecated feature was likely used in the ggpubr package.
  Please report the issue at <https://github.com/kassambara/ggpubr/issues>.
[2026-06-16 10:12:04 | INFO] handling dataset with id EGAD00001003977_circRNA_Ensemble
[2026-06-16 10:12:04 | INFO] analysis with circRNA Host Gene selected
[2026-06-16 10:12:10 | INFO] handling dataset with id EGAD00001003977_circRNA_Ensemble
[2026-06-16 10:12:10 | INFO] analysis with circRNA Host Gene selected
[2026-06-16 10:12:10 | INFO] Querying row idx from dataset EGAD00001003977_circRNA_Ensemble
[2026-06-16 10:12:10 | INFO] query row index data
[2026-06-16 10:12:11 | INFO] query column index data
[2026-06-16 10:12:11 | INFO] 11838 ids found for the cohort(s) with head: A2M,A2ML1,AAAS,AACS,AADACL2-AS1,AADAT
[2026-06-16 10:12:14 | INFO] handling dataset with id EGAD00001003977_circRNA_Ensemble
[2026-06-16 10:12:14 | INFO] analysis with circRNA Host Gene selected
[2026-06-16 10:12:22 | INFO] handling dataset with id EGAD00001003977
Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.
ℹ The deprecated feature was likely used in the coco package.
  Please report the issue at <https://github.com/ShixiangWang/coco/issues>.
Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
ℹ The deprecated feature was likely used in the coco package.
  Please report the issue at <https://github.com/ShixiangWang/coco/issues>.
Warning in dir.create(cache_dir, recursive = TRUE) :
  cannot create dir '/srv/shiny-server/TCCIA/app_cache', reason 'Permission denied'
Warning in value[[3L]](cond) :
  Error using cache directory at '/srv/shiny-server/TCCIA/app_cache/sass'. Using temp dir instead.
Warning in dir.create(cache_dir, recursive = TRUE) :
  cannot create dir '/srv/shiny-server/TCCIA/app_cache', reason 'Permission denied'
Warning in value[[3L]](cond) :
  Error using cache directory at '/srv/shiny-server/TCCIA/app_cache/sass'. Using temp dir instead.
Warning in dir.create(cache_dir, recursive = TRUE) :
  cannot create dir '/srv/shiny-server/TCCIA/app_cache', reason 'Permission denied'
Warning in value[[3L]](cond) :
  Error using cache directory at '/srv/shiny-server/TCCIA/app_cache/sass'. Using temp dir instead.
[2026-06-16 10:18:46 | INFO] Library path: /usr/local/lib/R/extra-library
Library path: /usr/local/lib/R/site-library
Library path: /usr/local/lib/R/library
[2026-06-16 10:18:46 | INFO] Cache path: ~/.coco_cache
Warning in renderWidget(instance) :
  Ignoring explicitly provided widget ID "repo-search-table"; Shiny doesn't use them
[2026-06-16 10:18:52 | INFO] the cohort(s) selected in repository: EGAD00001003977
Warning in dir.create(cache_dir, recursive = TRUE) :
  cannot create dir '/srv/shiny-server/TCCIA/app_cache', reason 'Permission denied'
Warning in value[[3L]](cond) :
  Error using cache directory at '/srv/shiny-server/TCCIA/app_cache/sass'. Using temp dir instead.
Warning in dir.create(cache_dir, recursive = TRUE) :
  cannot create dir '/srv/shiny-server/TCCIA/app_cache', reason 'Permission denied'
Warning in value[[3L]](cond) :
  Error using cache directory at '/srv/shiny-server/TCCIA/app_cache/sass'. Using temp dir instead.
Warning in dir.create(cache_dir, recursive = TRUE) :
  cannot create dir '/srv/shiny-server/TCCIA/app_cache', reason 'Permission denied'
Warning in value[[3L]](cond) :
  Error using cache directory at '/srv/shiny-server/TCCIA/app_cache/sass'. Using temp dir instead.
[2026-06-16 10:18:58 | INFO] Library path: /usr/local/lib/R/extra-library
Library path: /usr/local/lib/R/site-library
Library path: /usr/local/lib/R/library
[2026-06-16 10:18:58 | INFO] Cache path: ~/.coco_cache
Warning in renderWidget(instance) :
  Ignoring explicitly provided widget ID "repo-search-table"; Shiny doesn't use them
[2026-06-16 10:19:02 | INFO] selected ids for filter: 1:A2M, 2:, 3:
[2026-06-16 10:19:04 | INFO] the cohort(s) selected in repository: EGAD00001003977
[2026-06-16 10:19:04 | INFO] handling Y dataset with id EGAD00001003977_circRNA_Ensemble
[2026-06-16 10:19:04 | INFO] analysis with circRNA Host Gene selected
[2026-06-16 10:19:04 | INFO] handling X dataset with id EGAD00001003977_circRNA_Ensemble
[2026-06-16 10:19:04 | INFO] analysis with circRNA Host Gene selected
[2026-06-16 10:19:05 | INFO] handling dataset with id EGAD00001003977_circRNA_Ensemble
[2026-06-16 10:19:05 | INFO] analysis with circRNA Host Gene selected
[2026-06-16 10:19:05 | INFO] Querying row idx from dataset EGAD00001003977_circRNA_Ensemble
[2026-06-16 10:19:05 | INFO] 11838 ids found for the cohort(s) with head: A2M,A2ML1,AAAS,AACS,AADACL2-AS1,AADAT
[2026-06-16 10:19:06 | INFO] handling dataset with id EGAD00001003977_circRNA_Ensemble
[2026-06-16 10:19:06 | INFO] analysis with circRNA Host Gene selected
Terminated