TIMA fails to download libraries in Docker mode

[mmzdouc]

Describe the bug
I am trying to run tima using the docker image. Installation works, startup works, setting and saving parameters works.

However, when I launch a job, the app freezes. This happens both in tima-user (docker run --user tima-user -v "$(pwd)/.tima/data:/home/tima-user/.tima/data" -p 3838:3838 adafede/tima-r Rscript -e "tima::run_app()") and root (docker run -v "$(pwd)/.tima/data:/home/tima-user/.tima/data" -p 3838:3838 adafede/tima-r Rscript -e "tima::run_app()") modes.

This is the output observed in the console (only for root mode)

[2025-11-09 09:50:25.371 ] [DEBUG] Created directory: data/source
+ par_def_ann_spe dispatched
✔ par_def_ann_spe completed [39ms, 2.14 kB]
+ par_def_wei_ann dispatched
✔ par_def_wei_ann completed [1ms, 5.27 kB]
+ par_def_pre_ann_gnp dispatched
✔ par_def_pre_ann_gnp completed [1ms, 1.42 kB]
+ par_def_pre_lib_sop_mer dispatched
✔ par_def_pre_lib_sop_mer completed [1ms, 3.40 kB]
+ yaml_paths dispatched
✔ yaml_paths completed [1ms, 11.52 kB]
+ par_def_pre_lib_sop_lot dispatched
✔ par_def_pre_lib_sop_lot completed [1ms, 494 B]
+ par_def_ann_mas dispatched
✔ par_def_ann_mas completed [1ms, 6.09 kB]
+ par_def_pre_lib_sop_hmd dispatched
✔ par_def_pre_lib_sop_hmd completed [1ms, 492 B]
+ par_def_fil_ann dispatched
✔ par_def_fil_ann completed [1ms, 1.34 kB]
+ par_def_pre_lib_sop_clo dispatched
✔ par_def_pre_lib_sop_clo completed [1ms, 523 B]
+ par_def_pre_lib_spe dispatched
✔ par_def_pre_lib_spe completed [1ms, 1.57 kB]
+ par_def_pre_fea_com dispatched
✔ par_def_pre_fea_com completed [1ms, 358 B]
+ par_def_cre_com dispatched
✔ par_def_cre_com completed [1ms, 375 B]
+ par_def_cre_edg_spe dispatched
✔ par_def_cre_edg_spe completed [1ms, 1.42 kB]
+ par_def_pre_fea_edg dispatched
✔ par_def_pre_fea_edg completed [1ms, 706 B]
+ par_def_pre_fea_tab dispatched
✔ par_def_pre_fea_tab completed [1ms, 860 B]
+ par_def_pre_lib_rt dispatched
✔ par_def_pre_lib_rt completed [1ms, 2.05 kB]
+ par_def_pre_ann_spe dispatched
✔ par_def_pre_ann_spe completed [0ms, 1.46 kB]
+ par_def_pre_ann_sir dispatched
✔ par_def_pre_ann_sir completed [1ms, 1.93 kB]
+ par_def_pre_tax dispatched
✔ par_def_pre_tax completed [1ms, 1.51 kB]
+ par_def_pre_lib_sop_ecm dispatched
✔ par_def_pre_lib_sop_ecm completed [1ms, 492 B]
+ paths dispatched
✔ paths completed [2ms, 2.52 kB]
+ lib_spe_exp_gnp_pre_sop dispatched
[2025-11-09 09:50:40.571 ] [INFO ] Downloading file from: https://github.com/Adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/sop/gnps_11566051_prepared.tsv.gz
[2025-11-09 09:50:40.573 ] [DEBUG] Timeout limit: 3600 seconds
[2025-11-09 09:50:40.575 ] [DEBUG] Created directory: data/interim/libraries/sop
[2025-11-09 09:50:40.576 ] [DEBUG] Download attempt 1/3
[2025-11-09 09:50:40.648 ] [WARN ] Download attempt 1 failed: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Failed to open file data/interim/libraries/sop/gnps_11566051_prepared.tsv.gz.
[2025-11-09 09:50:40.653 ] [DEBUG] Waiting 2 seconds before retry...
[2025-11-09 09:50:42.657 ] [DEBUG] Download attempt 2/3
[2025-11-09 09:50:42.685 ] [WARN ] Download attempt 2 failed: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Failed to open file data/interim/libraries/sop/gnps_11566051_prepared.tsv.gz.
[2025-11-09 09:50:42.697 ] [DEBUG] Waiting 4 seconds before retry...
[2025-11-09 09:50:46.702 ] [DEBUG] Download attempt 3/3
[2025-11-09 09:50:46.732 ] [WARN ] Download attempt 3 failed: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Failed to open file data/interim/libraries/sop/gnps_11566051_prepared.tsv.gz.
[2025-11-09 09:50:46.745 ] [ERROR] Failed to download file after multiple attempts
✖ lib_spe_exp_gnp_pre_sop errored
✖ errored pipeline [13.5s, 22 completed, 0 skipped]
Warning: Error in : Error in tar_make():
  Failed to download file after multiple attempts: https://github.com/Adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/sop/gnps_11566051_prepared.tsv.gz
  See https://books.ropensci.org/targets/debugging.html
  92: <Anonymous>
  91: signalCondition
  90: signal_abort
  89: rlang::abort
  88: tar_error
  87: tar_throw_run
  86: callr_error
  84: callr_outer
  83: targets::tar_make
  82: observe [/home/tima-user/Library/Frameworks/R.framework/Resources/site-library/tima/app.R#2670]
  81: <observer:observeEvent(input$launch)>
   2: shiny::runApp
   1: tima::run_app

This is possibly related to Bioconductor/BiocFileCache#66.

Please let me know if there is any additional info you may need to resolve the issue!

Kind regards,

Mitja

Desktop (please complete the following information):

• OS: Ubuntu Linux 22.04
• Browser: Firefox
• Version 144.0

[Adafede]

Hey @mmzdouc I tried something... can you try again see if it still fails?