[ Started: 2024-03-15 13:13:55 CET ] [ OmnipathR v3.11.4 for BioC-3.18 from https://github.com/saezlab/OmnipathR@master ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.11.4’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘OmnipathR’ can be installed ... WARNING Found the following significant warnings: Warning: OmnipathR.Rd: docType ‘_PACKAGE’ is unrecognized See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/00install.out’ for details. * checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: doc 4.8Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking startup messages can be suppressed ... NOTE [2024-03-15 13:14:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:16] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:14:16] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-15 13:14:16] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:14:16] [TRACE] [OmnipathR] Contains 1 files. [2024-03-15 13:14:16] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-15 13:14:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:14:16] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-15 13:14:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-15 13:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-15 13:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-15 13:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-15 13:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:16] [TRACE] [OmnipathR] Cache locked: FALSE It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE [2024-03-15 13:14:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:23] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:14:23] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-15 13:14:23] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:14:23] [TRACE] [OmnipathR] Contains 1 files. [2024-03-15 13:14:23] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-15 13:14:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:14:23] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-15 13:14:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-15 13:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-15 13:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-15 13:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-15 13:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:23] [TRACE] [OmnipathR] Cache locked: FALSE oma_pairwise_genesymbols: no visible binding for global variable ‘id_organism_a’ oma_pairwise_genesymbols: no visible binding for global variable ‘id_organism_b’ Undefined global functions or variables: id_organism_a id_organism_b * checking Rd files ... WARNING prepare_Rd: OmnipathR.Rd: docType ‘_PACKAGE’ is unrecognized * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘OmnipathR-Ex.R’ failed The error most likely occurred in: > ### Name: annotated_network > ### Title: Network interactions with annotations > ### Aliases: annotated_network > > ### ** Examples > > signalink_with_pathways <- + annotated_network('SignaLink3', 'SignaLink_pathway') [2024-03-15 13:14:40] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-03-15 13:14:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:14:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:40] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-03-15 13:14:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:14:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:40] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-03-15 13:14:40] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-03-15 13:14:40] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-03-15 13:14:40] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-03-15 13:14:40] [TRACE] [OmnipathR] HTTP 200 [2024-03-15 13:14:40] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-03-15 13:14:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:14:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:40] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. Error in `map_int()`: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error in `UseMethod()`: ! no applicable method for 'html_table' applied to an object of class "xml_missing" Backtrace: ▆ 1. ├─OmnipathR::annotated_network("SignaLink3", "SignaLink_pathway") 2. │ └─... %>% assert_data_frame 3. ├─checkmate::assert_data_frame(.) 4. │ └─checkmate::checkDataFrame(...) 5. │ └─... %and% checkListTypes(x, types) 6. │ └─base::isTRUE(lhs) 7. ├─rlang::exec(import_omnipath_interactions, !!!., !!!network_args) 8. ├─OmnipathR (local) ``(resources = "SignaLink3") 9. │ └─OmnipathR:::import_omnipath(...) 10. │ └─OmnipathR:::omnipath_check_param(param) 11. │ └─param$organisms %<>% map_int(ncbi_taxid) 12. ├─purrr::map_int(., ncbi_taxid) 13. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 14. │ ├─purrr:::with_indexed_errors(...) 15. │ │ └─base::withCallingHandlers(...) 16. │ ├─purrr:::call_with_cleanup(...) 17. │ └─OmnipathR (local) .f(.x[[i]], ...) 18. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 19. ├─purrr::map_int(., taxon_name, "ncbi") 20. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 21. │ ├─purrr:::with_indexed_errors(...) 22. │ │ └─base::withCallingHandlers(...) 23. │ ├─purrr:::call_with_cleanup(...) 24. │ └─OmnipathR (local) .f(.x[[i]], ...) 25. │ ├─... %>% if_null_len0(NA) 26. │ └─OmnipathR::get_db("organisms") 27. │ └─OmnipathR::load_db(key, param = param) 28. │ ├─rlang::exec(loader, !!!param) 29. │ └─OmnipathR (local) ``() 30. │ ├─... %>% ... 31. │ └─OmnipathR::ensembl_organisms() 32. │ ├─... %>% ... 33. │ └─OmnipathR::ensembl_organisms_raw() 34. │ └─... %>% html_table() 35. ├─OmnipathR:::if_null_len0(., NA) 36. │ └─value1 %>% is_empty_2 %>% if (value2) value1 37. ├─OmnipathR:::is_empty_2(.) 38. │ └─value %>% ... 39. ├─dplyr::first(.) 40. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm) 41. │ └─vctrs::vec_size(x) 42. ├─dplyr::pull(., name_type) 43. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name)) 44. ├─dplyr::select(., -latin_name.x, -latin_name.y) 45. ├─dplyr::mutate(...) 46. ├─dplyr::full_join(...) 47. ├─dplyr::mutate(...) 48. ├─dplyr::select(...) 49. ├─rvest::html_table(.) 50. └─base::.handleSimpleError(...) 51. └─purrr (local) h(simpleError(msg, call)) 52. └─cli::cli_abort(...) 53. └─rlang::abort(...) Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Caused by error in `map_int()`: ℹ In index: 1. Caused by error in `UseMethod()`: ! no applicable method for 'html_table' applied to an object of class "xml_missing" Class: purrr_error_indexed/rlang_error/error/condition ── Error ('test_import.R:185:13'): (code run outside of `test_that()`) ───────── Error in `eval(code, test_env)`: object 'response' not found Backtrace: ▆ 1. ├─response %<>% separate_rows(sources, sep = ";") at test_import.R:185:13 2. └─tidyr::separate_rows(., sources, sep = ";") [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘bioc_workshop.Rmd’ using ‘UTF-8’... OK ‘db_manager.Rmd’ using ‘UTF-8’... OK ‘drug_targets.Rmd’ using ‘UTF-8’... OK ‘extra_attrs.Rmd’ using ‘UTF-8’... OK ‘nichenet.Rmd’ using ‘UTF-8’... OK ‘omnipath_intro.Rmd’ using ‘UTF-8’... OK ‘paths.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘bioc_workshop.Rmd’ using rmarkdown [2024-03-15 13:14:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:14:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:47] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:14:47] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-15 13:14:47] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:14:47] [TRACE] [OmnipathR] Contains 2 files. [2024-03-15 13:14:47] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-15 13:14:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:14:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:14:47] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-15 13:14:47] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-15 13:14:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:47] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-15 13:14:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:47] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-15 13:14:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:47] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-15 13:14:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:47] [TRACE] [OmnipathR] Cache locked: FALSE [2024-03-15 13:14:47] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-03-15 13:14:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:14:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:47] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-03-15 13:14:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:14:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:47] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-03-15 13:14:47] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-03-15 13:14:47] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-03-15 13:14:47] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-03-15 13:14:47] [TRACE] [OmnipathR] HTTP 200 [2024-03-15 13:14:47] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-03-15 13:14:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:14:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:47] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. Quitting from lines 225-227 [network] (bioc_workshop.Rmd) Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error in `UseMethod()`: ! no applicable method for 'html_table' applied to an object of class "xml_missing" --- failed re-building ‘bioc_workshop.Rmd’ --- re-building ‘db_manager.Rmd’ using rmarkdown [2024-03-15 13:14:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:14:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:48] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:14:48] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-15 13:14:48] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:14:48] [TRACE] [OmnipathR] Contains 2 files. [2024-03-15 13:14:48] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-15 13:14:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:14:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:14:48] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-15 13:14:48] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-15 13:14:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:48] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-15 13:14:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:49] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-15 13:14:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:49] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-15 13:14:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:14:49] [TRACE] [OmnipathR] Cache locked: FALSE [2024-03-15 13:14:49] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: `(function (to, from = "accession", reviewed = TRUE, organism = 9606) `. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: `{`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` .slow_doctest()`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` From <- To <- NULL`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` strip_semicol <- function(v) {`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` sub(";$", "", v)`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` }`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` ids <- c(.nse_ensure_str(!!enquo(to)), .nse_ensure_str(!!enquo(from)))`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` reviewed <- if ("trembl" %in% ids) `. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` FALSE`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` else if ("swissprot" %in% ids) `. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` TRUE`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` else reviewed`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` to <- .nse_ensure_str(!!enquo(to)) %>% uniprot_id_type`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` from <- .nse_ensure_str(!!enquo(from)) %>% uniprot_id_type`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` reens <- "ENS[A-Z]+\\d+"`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` to_ens <- to == "xref_ensembl"`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` from_ens <- from == "xref_ensembl"`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` log_trace(paste0("Creating ID mapping table from `%s` to `%s`, ", `. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` "for organism %d (only reviewed: %s)"), from, to, organism, `. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` reviewed)`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` c(from, to) %>% all_uniprots(reviewed = reviewed, organism = organism) %>% `. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` rename(From = 1, To = 2) %>% mutate(From = strip_semicol(From), `. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` To = strip_semicol(To)) %>% separate_rows(From, sep = "[; ]") %>% `. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` separate_rows(To, sep = "[; ]") %>% filter(!is.na(From) & `. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` !is.na(To)) %>% {`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` if (from_ens) `. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` mutate(., From = str_extract(From, reens))`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` else .`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` } %>% {`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` if (to_ens) `. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` mutate(., To = str_extract(To, reens))`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` else .`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: ` } %>% trim_and_distinct`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] Bypassing call: `})(to = "genesymbol", organism = 9606L)`. [2024-03-15 13:14:49] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2024-03-15 13:14:49] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2024-03-15 13:15:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:01] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:15:01] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-15 13:15:01] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:15:01] [TRACE] [OmnipathR] Contains 1 files. [2024-03-15 13:15:01] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-15 13:15:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:15:01] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-15 13:15:01] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-15 13:15:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:01] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-15 13:15:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:01] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-15 13:15:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:01] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-15 13:15:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:01] [TRACE] [OmnipathR] Cache locked: FALSE [2024-03-15 13:15:01] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-03-15 13:15:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:01] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-03-15 13:15:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:01] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-03-15 13:15:01] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-03-15 13:15:01] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-03-15 13:15:01] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-03-15 13:15:01] [TRACE] [OmnipathR] HTTP 200 [2024-03-15 13:15:01] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-03-15 13:15:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:01] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-03-15 13:15:01] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-03-15 13:15:01] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-03-15 13:15:01] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-03-15 13:15:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:02] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-03-15 13:15:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-15 13:15:02] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-03-15 13:15:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-03-15 13:15:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-15 13:15:02] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-03-15 13:15:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:02] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-03-15 13:15:02] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-03-15 13:15:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:15:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:15:02] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:15:02] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:15:02] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:15:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:15:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:15:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:15:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:05] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2024-03-15 13:15:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-03-15 13:15:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-03-15 13:15:05] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2024-03-15 13:15:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:05] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2024-03-15 13:15:08] [SUCCESS] [OmnipathR] Downloaded 81529 interactions. --- finished re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2024-03-15 13:15:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:12] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:15:12] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-15 13:15:12] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:15:12] [TRACE] [OmnipathR] Contains 4 files. [2024-03-15 13:15:12] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-15 13:15:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:15:12] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-15 13:15:12] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-15 13:15:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:12] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-15 13:15:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:13] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-15 13:15:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:13] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-15 13:15:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:13] [TRACE] [OmnipathR] Cache locked: FALSE [2024-03-15 13:15:13] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-03-15 13:15:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:13] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-03-15 13:15:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:13] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-03-15 13:15:13] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-03-15 13:15:13] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-03-15 13:15:13] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-03-15 13:15:14] [TRACE] [OmnipathR] HTTP 200 [2024-03-15 13:15:14] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-03-15 13:15:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:14] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-03-15 13:15:14] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-03-15 13:15:14] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-03-15 13:15:14] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-03-15 13:15:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:15] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-03-15 13:15:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-15 13:15:15] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-03-15 13:15:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-03-15 13:15:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-15 13:15:15] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-03-15 13:15:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:15] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-03-15 13:15:15] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-03-15 13:15:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-03-15 13:15:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-03-15 13:15:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-03-15 13:15:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-03-15 13:15:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-03-15 13:15:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-03-15 13:15:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-03-15 13:15:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-03-15 13:15:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:16] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`. [2024-03-15 13:15:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2024-03-15 13:15:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2024-03-15 13:15:16] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1] [2024-03-15 13:15:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:15:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:15:16] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`. [2024-03-15 13:15:16] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2024-03-15 13:15:23] [SUCCESS] [OmnipathR] Downloaded 134282 interactions. [2024-03-15 13:18:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:18:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2024-03-15 13:18:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2024-03-15 13:18:51] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2024-03-15 13:18:51] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2024-03-15 13:18:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2024-03-15 13:18:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2024-03-15 13:18:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2024-03-15 13:18:52] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2024-03-15 13:18:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:18:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:18:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:52] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`. [2024-03-15 13:18:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2024-03-15 13:18:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2024-03-15 13:18:52] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1] [2024-03-15 13:18:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:18:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:52] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`. [2024-03-15 13:18:52] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records. [2024-03-15 13:18:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2024-03-15 13:18:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2024-03-15 13:18:52] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2024-03-15 13:18:52] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2024-03-15 13:18:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2024-03-15 13:18:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2024-03-15 13:18:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2024-03-15 13:18:53] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2024-03-15 13:18:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:18:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:18:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:53] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`. [2024-03-15 13:18:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2024-03-15 13:18:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2024-03-15 13:18:53] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1] [2024-03-15 13:18:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:18:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:53] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`. [2024-03-15 13:18:53] [SUCCESS] [OmnipathR] Downloaded 70 enzyme-substrate relationships. --- finished re-building ‘extra_attrs.Rmd’ --- re-building ‘nichenet.Rmd’ using rmarkdown --- finished re-building ‘nichenet.Rmd’ --- re-building ‘omnipath_intro.Rmd’ using rmarkdown [2024-03-15 13:18:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:18:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:56] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:18:56] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-15 13:18:56] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:18:56] [TRACE] [OmnipathR] Contains 6 files. [2024-03-15 13:18:56] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-15 13:18:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:18:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:18:56] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-15 13:18:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-15 13:18:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-15 13:18:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-15 13:18:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-15 13:18:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:56] [TRACE] [OmnipathR] Cache locked: FALSE [2024-03-15 13:18:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:18:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:58] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-03-15 13:18:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:18:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:58] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-03-15 13:18:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:18:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:58] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-03-15 13:18:58] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-03-15 13:18:58] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-03-15 13:18:58] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-03-15 13:18:58] [TRACE] [OmnipathR] HTTP 200 [2024-03-15 13:18:58] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-03-15 13:18:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:18:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:58] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-03-15 13:18:58] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-03-15 13:18:58] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-03-15 13:18:58] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-03-15 13:18:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:18:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:18:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:58] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-03-15 13:18:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-15 13:18:58] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-03-15 13:18:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-03-15 13:18:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-15 13:18:58] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-03-15 13:18:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:18:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:58] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-03-15 13:18:58] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-03-15 13:18:59] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:18:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:18:59] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:18:59] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:18:59] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:18:59] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:18:59] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:18:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:18:59] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:18:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:18:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:18:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:59] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`. [2024-03-15 13:18:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2024-03-15 13:18:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2024-03-15 13:18:59] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1] [2024-03-15 13:18:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:18:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:18:59] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`. [2024-03-15 13:19:01] [SUCCESS] [OmnipathR] Downloaded 64485 interactions. [2024-03-15 13:19:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:19:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:06] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:06] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:06] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:06] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:06] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:06] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:06] [INFO] [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `unknown` to `started`. [2024-03-15 13:19:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`. [2024-03-15 13:19:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`. [2024-03-15 13:19:06] [INFO] [OmnipathR] Download ready [key=5ef52c90ffa996b5425a92df0ae5e7d825269078, version=1] [2024-03-15 13:19:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:06] [INFO] [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `started` to `ready`. [2024-03-15 13:19:06] [SUCCESS] [OmnipathR] Downloaded 1532 interactions. [2024-03-15 13:19:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:19:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:06] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:06] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:06] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:06] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:06] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:07] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`. [2024-03-15 13:19:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2024-03-15 13:19:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2024-03-15 13:19:07] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1] [2024-03-15 13:19:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:07] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`. [2024-03-15 13:19:07] [SUCCESS] [OmnipathR] Downloaded 6869 interactions. [2024-03-15 13:19:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:19:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:07] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:07] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:07] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:07] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:07] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:08] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:08] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`. [2024-03-15 13:19:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2024-03-15 13:19:08] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2024-03-15 13:19:08] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1] [2024-03-15 13:19:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:08] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`. [2024-03-15 13:19:08] [SUCCESS] [OmnipathR] Downloaded 2834 interactions. [2024-03-15 13:19:08] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:19:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-03-15 13:19:08] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-03-15 13:19:08] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-03-15 13:19:08] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-03-15 13:19:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-03-15 13:19:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-03-15 13:19:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-03-15 13:19:09] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-03-15 13:19:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:09] [INFO] [OmnipathR] Cache item `6188267638afb6533911b8411bda12cf39f3b567` version 1: status changed from `unknown` to `started`. [2024-03-15 13:19:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6188267638afb6533911b8411bda12cf39f3b567-1.rds`. [2024-03-15 13:19:09] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6188267638afb6533911b8411bda12cf39f3b567-1.rds`. [2024-03-15 13:19:09] [INFO] [OmnipathR] Download ready [key=6188267638afb6533911b8411bda12cf39f3b567, version=1] [2024-03-15 13:19:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:09] [INFO] [OmnipathR] Cache item `6188267638afb6533911b8411bda12cf39f3b567` version 1: status changed from `started` to `ready`. [2024-03-15 13:19:09] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-03-15 13:19:09] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: DoRothEA [2024-03-15 13:19:10] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: DoRothEA [2024-03-15 13:19:16] [SUCCESS] [OmnipathR] Downloaded 6127 interactions. [2024-03-15 13:19:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:19:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-15 13:19:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-15 13:19:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-15 13:19:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-15 13:19:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-15 13:19:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-15 13:19:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-15 13:19:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-15 13:19:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:16] [INFO] [OmnipathR] Cache item `c379f6c4e64c654ffb321b3134d065934007cc0e` version 1: status changed from `unknown` to `started`. [2024-03-15 13:19:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c379f6c4e64c654ffb321b3134d065934007cc0e-1.rds`. [2024-03-15 13:19:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c379f6c4e64c654ffb321b3134d065934007cc0e-1.rds`. [2024-03-15 13:19:16] [INFO] [OmnipathR] Download ready [key=c379f6c4e64c654ffb321b3134d065934007cc0e, version=1] [2024-03-15 13:19:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:16] [INFO] [OmnipathR] Cache item `c379f6c4e64c654ffb321b3134d065934007cc0e` version 1: status changed from `started` to `ready`. [2024-03-15 13:19:18] [SUCCESS] [OmnipathR] Downloaded 31896 interactions. [2024-03-15 13:19:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:19:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:18] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:18] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:18] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:18] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:18] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`. [2024-03-15 13:19:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2024-03-15 13:19:18] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2024-03-15 13:19:18] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1] [2024-03-15 13:19:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:18] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`. [2024-03-15 13:19:18] [SUCCESS] [OmnipathR] Downloaded 716 interactions. [2024-03-15 13:19:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2024-03-15 13:19:18] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2024-03-15 13:19:18] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2024-03-15 13:19:18] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2024-03-15 13:19:18] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2024-03-15 13:19:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2024-03-15 13:19:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2024-03-15 13:19:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2024-03-15 13:19:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:18] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`. [2024-03-15 13:19:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2024-03-15 13:19:18] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2024-03-15 13:19:18] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1] [2024-03-15 13:19:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:18] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`. [2024-03-15 13:19:18] [SUCCESS] [OmnipathR] Downloaded 32 interactions. [2024-03-15 13:19:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:19:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:19] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:19] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:19] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:49] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2024-03-15 13:19:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2024-03-15 13:19:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2024-03-15 13:19:49] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2024-03-15 13:19:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:49] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2024-03-15 13:19:50] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships. [2024-03-15 13:19:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:50] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:50] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:50] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:50] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:50] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:50] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:50] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2024-03-15 13:19:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-03-15 13:19:51] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-03-15 13:19:51] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2024-03-15 13:19:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:51] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2024-03-15 13:19:53] [SUCCESS] [OmnipathR] Downloaded 81529 interactions. [2024-03-15 13:19:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:19:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:54] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:54] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:54] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:54] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-15 13:19:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:54] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`. [2024-03-15 13:19:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2024-03-15 13:19:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2024-03-15 13:19:54] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1] [2024-03-15 13:19:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:54] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`. [2024-03-15 13:19:55] [SUCCESS] [OmnipathR] Downloaded 17826 enzyme-substrate relationships. [2024-03-15 13:19:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:19:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:19:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:55] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2024-03-15 13:19:55] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2024-03-15 13:19:55] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2024-03-15 13:19:55] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2024-03-15 13:19:55] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2024-03-15 13:19:55] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2024-03-15 13:19:55] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2024-03-15 13:19:56] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2024-03-15 13:19:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:56] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`. [2024-03-15 13:19:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2024-03-15 13:19:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2024-03-15 13:19:56] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1] [2024-03-15 13:19:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:56] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`. [2024-03-15 13:19:56] [SUCCESS] [OmnipathR] Downloaded 7194 protein complexes. [2024-03-15 13:19:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:19:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic` [2024-03-15 13:19:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic` [2024-03-15 13:19:56] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic` [2024-03-15 13:19:56] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic` [2024-03-15 13:19:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic` [2024-03-15 13:19:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic` [2024-03-15 13:19:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic` [2024-03-15 13:19:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic` [2024-03-15 13:19:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:57] [INFO] [OmnipathR] Cache item `929c2072937af212fa00922d04d210172bd315c8` version 1: status changed from `unknown` to `started`. [2024-03-15 13:19:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/929c2072937af212fa00922d04d210172bd315c8-1.rds`. [2024-03-15 13:19:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/929c2072937af212fa00922d04d210172bd315c8-1.rds`. [2024-03-15 13:19:57] [INFO] [OmnipathR] Download ready [key=929c2072937af212fa00922d04d210172bd315c8, version=1] [2024-03-15 13:19:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:57] [INFO] [OmnipathR] Cache item `929c2072937af212fa00922d04d210172bd315c8` version 1: status changed from `started` to `ready`. [2024-03-15 13:19:57] [SUCCESS] [OmnipathR] Downloaded 95 annotation records. [2024-03-15 13:19:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:19:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic` [2024-03-15 13:19:57] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic` [2024-03-15 13:19:57] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic` [2024-03-15 13:19:57] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic` [2024-03-15 13:19:57] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic` [2024-03-15 13:19:57] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic` [2024-03-15 13:19:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic` [2024-03-15 13:19:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic` [2024-03-15 13:19:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:57] [INFO] [OmnipathR] Cache item `20cd5eb55475c83ea15e2d2ddb162dcdd528116f` version 1: status changed from `unknown` to `started`. [2024-03-15 13:19:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20cd5eb55475c83ea15e2d2ddb162dcdd528116f-1.rds`. [2024-03-15 13:19:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20cd5eb55475c83ea15e2d2ddb162dcdd528116f-1.rds`. [2024-03-15 13:19:57] [INFO] [OmnipathR] Download ready [key=20cd5eb55475c83ea15e2d2ddb162dcdd528116f, version=1] [2024-03-15 13:19:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:57] [INFO] [OmnipathR] Cache item `20cd5eb55475c83ea15e2d2ddb162dcdd528116f` version 1: status changed from `started` to `ready`. [2024-03-15 13:19:57] [SUCCESS] [OmnipathR] Downloaded 7 annotation records. [2024-03-15 13:19:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:19:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic` [2024-03-15 13:19:57] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic` [2024-03-15 13:19:57] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic` [2024-03-15 13:19:57] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic` [2024-03-15 13:19:57] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic` [2024-03-15 13:19:57] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic` [2024-03-15 13:19:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic` [2024-03-15 13:19:58] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic` [2024-03-15 13:19:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:58] [INFO] [OmnipathR] Cache item `acaa653138834ed8b6d7d52ce1b3529953f720a2` version 1: status changed from `unknown` to `started`. [2024-03-15 13:19:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/acaa653138834ed8b6d7d52ce1b3529953f720a2-1.rds`. [2024-03-15 13:19:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/acaa653138834ed8b6d7d52ce1b3529953f720a2-1.rds`. [2024-03-15 13:19:58] [INFO] [OmnipathR] Download ready [key=acaa653138834ed8b6d7d52ce1b3529953f720a2, version=1] [2024-03-15 13:19:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:58] [INFO] [OmnipathR] Cache item `acaa653138834ed8b6d7d52ce1b3529953f720a2` version 1: status changed from `started` to `ready`. [2024-03-15 13:19:58] [SUCCESS] [OmnipathR] Downloaded 28 annotation records. [2024-03-15 13:19:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:19:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-15 13:19:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-15 13:19:58] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-15 13:19:58] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-15 13:19:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-15 13:19:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-15 13:19:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-15 13:19:58] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-15 13:19:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:58] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2024-03-15 13:19:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2024-03-15 13:19:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2024-03-15 13:19:58] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2024-03-15 13:19:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:58] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2024-03-15 13:19:58] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records. [2024-03-15 13:19:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2024-03-15 13:19:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2024-03-15 13:19:58] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2024-03-15 13:19:58] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2024-03-15 13:19:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2024-03-15 13:19:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2024-03-15 13:19:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2024-03-15 13:19:59] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2024-03-15 13:19:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:59] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2024-03-15 13:19:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2024-03-15 13:19:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2024-03-15 13:19:59] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2024-03-15 13:19:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:19:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:19:59] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2024-03-15 13:19:59] [SUCCESS] [OmnipathR] Downloaded 1098 records. [2024-03-15 13:19:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2024-03-15 13:19:59] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2024-03-15 13:19:59] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2024-03-15 13:19:59] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2024-03-15 13:19:59] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2024-03-15 13:19:59] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2024-03-15 13:19:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2024-03-15 13:20:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2024-03-15 13:20:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:00] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`. [2024-03-15 13:20:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2024-03-15 13:20:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2024-03-15 13:20:01] [INFO] [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1] [2024-03-15 13:20:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:01] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`. [2024-03-15 13:20:02] [SUCCESS] [OmnipathR] Downloaded 236086 intercellular communication role records. [2024-03-15 13:20:02] [TRACE] [OmnipathR] Bypassing call: `import_intercell_network(high_confidence = TRUE)`. [2024-03-15 13:20:02] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2024-03-15 13:20:02] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`. [2024-03-15 13:20:02] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. --- finished re-building ‘omnipath_intro.Rmd’ --- re-building ‘paths.Rmd’ using rmarkdown [2024-03-15 13:20:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:05] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:20:05] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-15 13:20:05] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:20:05] [TRACE] [OmnipathR] Contains 21 files. [2024-03-15 13:20:05] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-15 13:20:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-15 13:20:05] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-15 13:20:05] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-15 13:20:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:05] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-15 13:20:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:05] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-15 13:20:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:05] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-15 13:20:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:05] [TRACE] [OmnipathR] Cache locked: FALSE [2024-03-15 13:20:05] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-03-15 13:20:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:05] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-03-15 13:20:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:05] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-03-15 13:20:05] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-03-15 13:20:05] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-03-15 13:20:05] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-03-15 13:20:05] [TRACE] [OmnipathR] HTTP 200 [2024-03-15 13:20:05] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-03-15 13:20:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:05] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-03-15 13:20:06] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-03-15 13:20:06] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-03-15 13:20:06] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-03-15 13:20:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:06] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-03-15 13:20:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-15 13:20:06] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-03-15 13:20:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-03-15 13:20:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-15 13:20:06] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-03-15 13:20:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:06] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-03-15 13:20:06] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-03-15 13:20:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:20:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:06] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-15 13:20:06] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-15 13:20:06] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-15 13:20:06] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-15 13:20:06] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-15 13:20:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-15 13:20:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-15 13:20:06] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-15 13:20:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:06] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`. [2024-03-15 13:20:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2024-03-15 13:20:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2024-03-15 13:20:06] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1] [2024-03-15 13:20:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:06] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`. [2024-03-15 13:20:06] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records. [2024-03-15 13:20:06] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2024-03-15 13:20:06] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2024-03-15 13:20:06] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2024-03-15 13:20:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:06] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`. [2024-03-15 13:20:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2024-03-15 13:20:06] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2024-03-15 13:20:06] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2024-03-15 13:20:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2024-03-15 13:20:07] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1] [2024-03-15 13:20:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:07] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`. [2024-03-15 13:20:07] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records [2024-03-15 13:20:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2024-03-15 13:20:07] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2024-03-15 13:20:07] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2024-03-15 13:20:07] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2024-03-15 13:20:07] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2024-03-15 13:20:07] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2024-03-15 13:20:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2024-03-15 13:20:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2024-03-15 13:20:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:07] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`. [2024-03-15 13:20:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2024-03-15 13:20:08] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2024-03-15 13:20:08] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1] [2024-03-15 13:20:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:08] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`. [2024-03-15 13:20:11] [SUCCESS] [OmnipathR] Downloaded 121170 interactions. [2024-03-15 13:20:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:20:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2024-03-15 13:20:11] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2024-03-15 13:20:11] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2024-03-15 13:20:11] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2024-03-15 13:20:11] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2024-03-15 13:20:11] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2024-03-15 13:20:11] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2024-03-15 13:20:12] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2024-03-15 13:20:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:12] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`. [2024-03-15 13:20:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2024-03-15 13:20:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2024-03-15 13:20:13] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1] [2024-03-15 13:20:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:13] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`. [2024-03-15 13:20:13] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records. [2024-03-15 13:20:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2024-03-15 13:20:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2024-03-15 13:20:13] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2024-03-15 13:20:13] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2024-03-15 13:20:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2024-03-15 13:20:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2024-03-15 13:20:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2024-03-15 13:20:14] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2024-03-15 13:20:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:14] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`. [2024-03-15 13:20:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2024-03-15 13:20:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2024-03-15 13:20:14] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1] [2024-03-15 13:20:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:14] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`. [2024-03-15 13:20:14] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records. [2024-03-15 13:20:14] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-15 13:20:14] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-15 13:20:14] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-15 13:20:14] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-15 13:20:14] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-15 13:20:14] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-15 13:20:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-15 13:20:14] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-15 13:20:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:14] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`. [2024-03-15 13:20:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2024-03-15 13:20:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2024-03-15 13:20:14] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1] [2024-03-15 13:20:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:14] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`. [2024-03-15 13:20:14] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records. [2024-03-15 13:20:14] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2024-03-15 13:20:14] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2024-03-15 13:20:14] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2024-03-15 13:20:14] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2024-03-15 13:20:14] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2024-03-15 13:20:14] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2024-03-15 13:20:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2024-03-15 13:20:15] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2024-03-15 13:20:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:15] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`. [2024-03-15 13:20:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2024-03-15 13:20:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2024-03-15 13:20:15] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1] [2024-03-15 13:20:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:15] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`. [2024-03-15 13:20:15] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records. [2024-03-15 13:20:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-15 13:20:15] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2024-03-15 13:20:15] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-15 13:20:15] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache. [2024-03-15 13:20:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2024-03-15 13:20:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2024-03-15 13:20:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2024-03-15 13:20:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2024-03-15 13:20:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2024-03-15 13:20:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2024-03-15 13:20:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2024-03-15 13:20:15] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2024-03-15 13:20:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:15] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`. [2024-03-15 13:20:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2024-03-15 13:20:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2024-03-15 13:20:15] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1] [2024-03-15 13:20:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:15] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`. [2024-03-15 13:20:15] [SUCCESS] [OmnipathR] Downloaded 14602 intercellular communication role records. [2024-03-15 13:20:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-15 13:20:15] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2024-03-15 13:20:15] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-15 13:20:15] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache. [2024-03-15 13:20:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2024-03-15 13:20:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2024-03-15 13:20:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2024-03-15 13:20:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2024-03-15 13:20:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2024-03-15 13:20:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2024-03-15 13:20:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2024-03-15 13:20:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2024-03-15 13:20:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:16] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`. [2024-03-15 13:20:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2024-03-15 13:20:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2024-03-15 13:20:16] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1] [2024-03-15 13:20:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:16] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`. [2024-03-15 13:20:16] [SUCCESS] [OmnipathR] Downloaded 26412 intercellular communication role records. [2024-03-15 13:20:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-15 13:20:16] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2024-03-15 13:20:16] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-15 13:20:16] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache. [2024-03-15 13:20:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-15 13:20:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-15 13:20:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-15 13:20:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-15 13:20:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-15 13:20:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-15 13:20:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-15 13:20:17] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-15 13:20:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:17] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`. [2024-03-15 13:20:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2024-03-15 13:20:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2024-03-15 13:20:17] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1] [2024-03-15 13:20:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:17] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`. [2024-03-15 13:20:18] [SUCCESS] [OmnipathR] Downloaded 30053 interactions. [2024-03-15 13:20:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:20:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2024-03-15 13:20:18] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2024-03-15 13:20:18] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2024-03-15 13:20:18] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2024-03-15 13:20:18] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2024-03-15 13:20:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2024-03-15 13:20:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2024-03-15 13:20:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2024-03-15 13:20:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:18] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`. [2024-03-15 13:20:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2024-03-15 13:20:18] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2024-03-15 13:20:18] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1] [2024-03-15 13:20:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:18] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`. [2024-03-15 13:20:18] [SUCCESS] [OmnipathR] Downloaded 1144 annotation records. [2024-03-15 13:20:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:20:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2024-03-15 13:20:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2024-03-15 13:20:19] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2024-03-15 13:20:19] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2024-03-15 13:20:19] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2024-03-15 13:20:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2024-03-15 13:20:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2024-03-15 13:20:19] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2024-03-15 13:20:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:19] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`. [2024-03-15 13:20:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2024-03-15 13:20:19] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2024-03-15 13:20:19] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1] [2024-03-15 13:20:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:19] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`. [2024-03-15 13:20:19] [SUCCESS] [OmnipathR] Downloaded 1080 annotation records. [2024-03-15 13:20:20] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`. [2024-03-15 13:20:20] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2024-03-15 13:20:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:20:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-15 13:20:20] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-15 13:20:20] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-15 13:20:20] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-15 13:20:20] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-15 13:20:20] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-15 13:20:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-15 13:20:20] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-15 13:20:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:20] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`. [2024-03-15 13:20:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2024-03-15 13:20:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2024-03-15 13:20:20] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1] [2024-03-15 13:20:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:20] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`. [2024-03-15 13:20:20] [SUCCESS] [OmnipathR] Downloaded 322 interactions. [2024-03-15 13:20:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:20:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-15 13:20:20] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-15 13:20:20] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-15 13:20:20] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-15 13:20:20] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-15 13:20:20] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-15 13:20:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-15 13:20:22] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-15 13:20:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:22] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2024-03-15 13:20:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2024-03-15 13:20:22] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2024-03-15 13:20:22] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2024-03-15 13:20:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:22] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2024-03-15 13:20:22] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records. [2024-03-15 13:20:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:20:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:23] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-15 13:20:23] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-15 13:20:23] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-15 13:20:23] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-15 13:20:23] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-15 13:20:23] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-15 13:20:23] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-15 13:20:23] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-15 13:20:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:23] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`. [2024-03-15 13:20:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2024-03-15 13:20:23] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2024-03-15 13:20:23] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1] [2024-03-15 13:20:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-15 13:20:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:23] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`. [2024-03-15 13:20:23] [SUCCESS] [OmnipathR] Downloaded 2029 annotation records. [2024-03-15 13:20:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:20:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-15 13:20:25] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2024-03-15 13:20:25] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-15 13:20:25] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache. [2024-03-15 13:20:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-15 13:20:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-15 13:20:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-15 13:20:25] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2024-03-15 13:20:25] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-15 13:20:25] [SUCCESS] [OmnipathR] Loaded 2029 annotation records from cache. --- finished re-building ‘paths.Rmd’ SUMMARY: processing the following file failed: ‘bioc_workshop.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 3 ERRORs, 2 WARNINGs, 3 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-15_1307/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2024-03-15 13:20:34 CET ]