[ Started: 2024-03-20 13:20:30 CET ] [ OmnipathR v3.8.2 for BioC-3.17 from https://github.com/saezlab/OmnipathR@RELEASE_3_17 ] * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘OmnipathR’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘bioc_workshop.Rmd’ using rmarkdown [2024-03-20 13:20:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:39] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-20 13:20:39] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-20 13:20:39] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-20 13:20:39] [TRACE] [OmnipathR] Contains 1 files. [2024-03-20 13:20:39] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-20 13:20:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-20 13:20:39] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-20 13:20:39] [TRACE] [OmnipathR] Reading JSON from `/tmp/Rtmpb7fRJg/Rinst5954a77c337e8/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-20 13:20:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:39] [TRACE] [OmnipathR] Reading JSON from `/tmp/Rtmpb7fRJg/Rinst5954a77c337e8/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-20 13:20:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:39] [TRACE] [OmnipathR] Reading JSON from `/tmp/Rtmpb7fRJg/Rinst5954a77c337e8/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-20 13:20:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:39] [TRACE] [OmnipathR] Reading JSON from `/tmp/Rtmpb7fRJg/Rinst5954a77c337e8/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-20 13:20:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:39] [TRACE] [OmnipathR] Cache locked: FALSE [2024-03-20 13:20:39] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-20 13:20:39] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-20 13:20:39] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-20 13:20:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:39] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`. [2024-03-20 13:20:39] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2024-03-20 13:20:40] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2024-03-20 13:20:40] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1] [2024-03-20 13:20:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:40] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`. [2024-03-20 13:20:43] [SUCCESS] [OmnipathR] Downloaded 128218 interactions. [2024-03-20 13:20:45] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-20 13:20:45] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-20 13:20:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-20 13:20:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:46] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2024-03-20 13:20:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2024-03-20 13:20:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2024-03-20 13:20:46] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2024-03-20 13:20:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:46] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2024-03-20 13:20:47] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships. [2024-03-20 13:20:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-20 13:20:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-20 13:20:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-20 13:20:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:48] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2024-03-20 13:20:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-03-20 13:20:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-03-20 13:20:49] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2024-03-20 13:20:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:49] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2024-03-20 13:20:51] [SUCCESS] [OmnipathR] Downloaded 81529 interactions. [2024-03-20 13:20:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic` [2024-03-20 13:20:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic` [2024-03-20 13:20:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic` [2024-03-20 13:20:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:51] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`. [2024-03-20 13:20:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2024-03-20 13:20:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2024-03-20 13:20:52] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1] [2024-03-20 13:20:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:52] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`. [2024-03-20 13:20:52] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes. [2024-03-20 13:20:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-20 13:20:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-20 13:20:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-20 13:20:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-20 13:20:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:52] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2024-03-20 13:20:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2024-03-20 13:20:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2024-03-20 13:20:53] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2024-03-20 13:20:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:53] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2024-03-20 13:20:53] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records. [2024-03-20 13:20:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-20 13:20:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-03-20 13:20:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-03-20 13:20:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-03-20 13:20:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:53] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`. [2024-03-20 13:20:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2024-03-20 13:20:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2024-03-20 13:20:53] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1] [2024-03-20 13:20:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:53] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`. [2024-03-20 13:20:53] [SUCCESS] [OmnipathR] Downloaded 0 annotation records. [2024-03-20 13:20:53] [FATAL] [OmnipathR] Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest. [2024-03-20 13:20:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-20 13:20:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:54] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2024-03-20 13:20:54] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-20 13:20:54] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache. [2024-03-20 13:20:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-20 13:20:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2024-03-20 13:20:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2024-03-20 13:20:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2024-03-20 13:20:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:54] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`. [2024-03-20 13:20:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2024-03-20 13:20:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2024-03-20 13:20:54] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1] [2024-03-20 13:20:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:54] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`. [2024-03-20 13:20:54] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records. [2024-03-20 13:20:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-20 13:20:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:55] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-20 13:20:55] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-20 13:20:55] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-20 13:20:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:55] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2024-03-20 13:20:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2024-03-20 13:20:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2024-03-20 13:20:55] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2024-03-20 13:20:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:55] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2024-03-20 13:20:55] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records. [2024-03-20 13:20:55] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-03-20 13:20:55] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-20 13:20:57] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache. [2024-03-20 13:20:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-20 13:20:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:58] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2024-03-20 13:20:58] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-20 13:20:58] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache. [2024-03-20 13:20:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic` [2024-03-20 13:20:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic` [2024-03-20 13:20:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic` [2024-03-20 13:20:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:20:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:20:59] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`. [2024-03-20 13:20:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2024-03-20 13:21:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2024-03-20 13:21:01] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1] [2024-03-20 13:21:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:21:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:21:01] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`. [2024-03-20 13:21:01] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records. [2024-03-20 13:21:02] [TRACE] [OmnipathR] Bypassing call: `import_intercell_network(high_confidence = TRUE)`. [2024-03-20 13:21:02] [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. [2024-03-20 13:21:02] [TRACE] [OmnipathR] Bypassing call: `import_intercell_network()`. [2024-03-20 13:21:02] [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. [2024-03-20 13:21:02] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `. [2024-03-20 13:21:02] [TRACE] [OmnipathR] Bypassing call: ` loc_consensus_percentile = 50, simplify = TRUE)`. [2024-03-20 13:21:02] [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. [2024-03-20 13:21:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-20 13:21:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:21:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2024-03-20 13:21:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2024-03-20 13:21:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2024-03-20 13:21:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:21:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:21:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:21:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:21:02] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2024-03-20 13:21:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2024-03-20 13:21:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2024-03-20 13:21:02] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2024-03-20 13:21:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:21:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:21:02] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2024-03-20 13:21:02] [SUCCESS] [OmnipathR] Downloaded 1098 records. [2024-03-20 13:21:02] [TRACE] [OmnipathR] Bypassing call: `translate_ids(d, uniprot_id = uniprot, genesymbol)`. [2024-03-20 13:21:02] [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. [2024-03-20 13:21:02] [TRACE] [OmnipathR] Bypassing call: `go_ontology_download()`. [2024-03-20 13:21:02] [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. [2024-03-20 13:21:02] [TRACE] [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`. [2024-03-20 13:21:02] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2024-03-20 13:21:02] [TRACE] [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`. [2024-03-20 13:21:02] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. --- finished re-building ‘bioc_workshop.Rmd’ --- re-building ‘db_manager.Rmd’ using rmarkdown [2024-03-20 13:21:03] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: `(function (to, from = "accession", reviewed = TRUE, organism = 9606) `. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: `{`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` .slow_doctest()`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` From <- To <- NULL`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` strip_semicol <- function(v) {`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` sub(";$", "", v)`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` }`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` ids <- c(.nse_ensure_str(!!enquo(to)), .nse_ensure_str(!!enquo(from)))`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` reviewed <- if ("trembl" %in% ids) `. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` FALSE`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` else if ("swissprot" %in% ids) `. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` TRUE`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` else reviewed`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` to <- .nse_ensure_str(!!enquo(to)) %>% uniprot_id_type`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` from <- .nse_ensure_str(!!enquo(from)) %>% uniprot_id_type`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` reens <- "ENS[A-Z]+\\d+"`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` to_ens <- to == "xref_ensembl"`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` from_ens <- from == "xref_ensembl"`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` log_trace(paste0("Creating ID mapping table from `%s` to `%s`, ", `. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` "for organism %d (only reviewed: %s)"), from, to, organism, `. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` reviewed)`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` c(from, to) %>% all_uniprots(reviewed = reviewed, organism = organism) %>% `. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` rename(From = 1, To = 2) %>% mutate(From = strip_semicol(From), `. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` To = strip_semicol(To)) %>% separate_rows(From, sep = ";") %>% `. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` separate_rows(To, sep = ";") %>% filter(!is.na(From) & `. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` !is.na(To)) %>% {`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` if (from_ens) `. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` mutate(., From = str_extract(From, reens))`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` else .`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` } %>% {`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` if (to_ens) `. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` mutate(., To = str_extract(To, reens))`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` else .`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: ` } %>% trim_and_distinct`. [2024-03-20 13:21:03] [TRACE] [OmnipathR] Bypassing call: `})(to = "genesymbol", organism = 9606L)`. [2024-03-20 13:21:03] [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. [2024-03-20 13:21:03] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2024-03-20 13:21:14] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-03-20 13:21:14] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-20 13:21:16] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache. The magick package is required to crop "/tmp/Rtmpb7fRJg/Rbuild5954a61c613c2/OmnipathR/vignettes/drug_targets_files/figure-html/unnamed-chunk-12-1.png" but not available. --- finished re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2024-03-20 13:21:19] [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` [2024-03-20 13:21:19] [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` [2024-03-20 13:21:19] [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` [2024-03-20 13:21:23] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` (attempt 1/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2024-03-20 13:21:28] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-03-20 13:21:33] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` (attempt 2/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2024-03-20 13:21:38] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-03-20 13:21:41] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` (attempt 3/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Quitting from lines 56-58 [load-interactions] (extra_attrs.Rmd) Error: processing vignette 'extra_attrs.Rmd' failed with diagnostics: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 --- failed re-building ‘extra_attrs.Rmd’ --- re-building ‘nichenet.Rmd’ using rmarkdown Warning in for (i in 1:n) { : closing unused connection 5 (https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic) Warning in for (i in 1:n) { : closing unused connection 4 (https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic) --- finished re-building ‘nichenet.Rmd’ --- re-building ‘omnipath_intro.Rmd’ using rmarkdown [2024-03-20 13:21:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-20 13:21:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:21:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-20 13:21:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:21:44] [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` [2024-03-20 13:21:44] [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` [2024-03-20 13:21:44] [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` [2024-03-20 13:21:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:21:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:21:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:21:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:21:47] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`. [2024-03-20 13:21:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2024-03-20 13:21:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2024-03-20 13:21:47] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1] [2024-03-20 13:21:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:21:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:21:47] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`. [2024-03-20 13:21:48] [SUCCESS] [OmnipathR] Downloaded 64485 interactions. [2024-03-20 13:21:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-20 13:21:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:21:53] [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` [2024-03-20 13:21:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-20 13:21:53] [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` [2024-03-20 13:21:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:21:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:21:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:21:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:21:53] [INFO] [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `unknown` to `started`. [2024-03-20 13:21:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`. [2024-03-20 13:21:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`. [2024-03-20 13:21:53] [INFO] [OmnipathR] Download ready [key=5ef52c90ffa996b5425a92df0ae5e7d825269078, version=1] [2024-03-20 13:21:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:21:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:21:53] [INFO] [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `started` to `ready`. [2024-03-20 13:21:53] [SUCCESS] [OmnipathR] Downloaded 1532 interactions. [2024-03-20 13:21:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-20 13:21:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:21:54] [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` [2024-03-20 13:21:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-20 13:21:54] [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` [2024-03-20 13:21:54] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` (attempt 1/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2024-03-20 13:21:59] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-20 13:22:00] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` (attempt 2/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2024-03-20 13:22:05] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-20 13:22:06] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` (attempt 3/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Quitting from lines 283-294 [kinaseextra] (omnipath_intro.Rmd) Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 --- failed re-building ‘omnipath_intro.Rmd’ --- re-building ‘paths.Rmd’ using rmarkdown [2024-03-20 13:22:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-20 13:22:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:22:06] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-20 13:22:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-20 13:22:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-20 13:22:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:22:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:22:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:22:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:22:06] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`. [2024-03-20 13:22:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2024-03-20 13:22:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2024-03-20 13:22:06] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1] [2024-03-20 13:22:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:22:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:22:06] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`. [2024-03-20 13:22:06] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records. [2024-03-20 13:22:06] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2024-03-20 13:22:06] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2024-03-20 13:22:06] [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`. [2024-03-20 13:22:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:22:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:22:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:22:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:22:06] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`. [2024-03-20 13:22:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2024-03-20 13:22:06] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2024-03-20 13:22:06] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2024-03-20 13:22:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2024-03-20 13:22:07] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1] [2024-03-20 13:22:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 13:22:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 13:22:07] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`. [2024-03-20 13:22:07] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records [2024-03-20 13:22:07] [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` [2024-03-20 13:22:07] [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` [2024-03-20 13:22:07] [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` [2024-03-20 13:22:11] [WARN] [OmnipathR] Failed to download `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` (attempt 1/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2024-03-20 13:22:16] [TRACE] [OmnipathR] Attempt 2/3: `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` [2024-03-20 13:22:20] [WARN] [OmnipathR] Failed to download `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` (attempt 2/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2024-03-20 13:22:25] [TRACE] [OmnipathR] Attempt 3/3: `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` [2024-03-20 13:22:29] [ERROR] [OmnipathR] Failed to download `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` (attempt 3/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Quitting from lines 88-97 [tfs-from-network] (paths.Rmd) Error: processing vignette 'paths.Rmd' failed with diagnostics: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 --- failed re-building ‘paths.Rmd’ SUMMARY: processing the following files failed: ‘extra_attrs.Rmd’ ‘omnipath_intro.Rmd’ ‘paths.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2024-03-20 13:22:29 CET ]