[ Started: 2023-06-15 23:04:52 CEST ]
[ OmnipathR v3.9.6 for BioC-3.17 from https://github.com/saezlab/OmnipathR@master ]
* 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
Warning in png(..., res = dpi, units = "in") :
unable to open connection to X11 display ''
[2023-06-15 23:05:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:02] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-06-15 23:05:02] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-06-15 23:05:02] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-06-15 23:05:02] [TRACE] [OmnipathR] Contains 1 files.
[2023-06-15 23:05:02] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-06-15 23:05:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-06-15 23:05:02] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-06-15 23:05:02] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpcyogVS/Rinst14d2b37e434fee/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-06-15 23:05:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:02] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpcyogVS/Rinst14d2b37e434fee/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-06-15 23:05:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:02] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpcyogVS/Rinst14d2b37e434fee/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-06-15 23:05:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:02] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpcyogVS/Rinst14d2b37e434fee/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-06-15 23:05:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:02] [TRACE] [OmnipathR] Cache locked: FALSE
[2023-06-15 23:05:02] [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`
[2023-06-15 23:05:02] [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`
[2023-06-15 23:05:02] [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`
[2023-06-15 23:05:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:03] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2023-06-15 23:05:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2023-06-15 23:05:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2023-06-15 23:05:03] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2023-06-15 23:05:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:03] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2023-06-15 23:05:06] [SUCCESS] [OmnipathR] Downloaded 121661 interactions.
[2023-06-15 23:05:09] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-06-15 23:05:09] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-06-15 23:05:09] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-06-15 23:05:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:10] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2023-06-15 23:05:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2023-06-15 23:05:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2023-06-15 23:05:10] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2023-06-15 23:05:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:10] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2023-06-15 23:05:11] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships.
[2023-06-15 23:05:12] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-06-15 23:05:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-06-15 23:05:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-06-15 23:05:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:13] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2023-06-15 23:05:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-06-15 23:05:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-06-15 23:05:13] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2023-06-15 23:05:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:13] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2023-06-15 23:05:16] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2023-06-15 23:05:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2023-06-15 23:05:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2023-06-15 23:05:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2023-06-15 23:05:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:17] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2023-06-15 23:05:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2023-06-15 23:05:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2023-06-15 23:05:17] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2023-06-15 23:05:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:17] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2023-06-15 23:05:17] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes.
[2023-06-15 23:05:17] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-06-15 23:05:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-06-15 23:05:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-06-15 23:05:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-06-15 23:05:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:19] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2023-06-15 23:05:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-06-15 23:05:19] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-06-15 23:05:19] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2023-06-15 23:05:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:19] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2023-06-15 23:05:19] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2023-06-15 23:05:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-06-15 23:05:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2023-06-15 23:05:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2023-06-15 23:05:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2023-06-15 23:05:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:20] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2023-06-15 23:05:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2023-06-15 23:05:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2023-06-15 23:05:20] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2023-06-15 23:05:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:20] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2023-06-15 23:05:20] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2023-06-15 23:05:20] [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.
[2023-06-15 23:05:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-06-15 23:05:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:20] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-06-15 23:05:20] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-06-15 23:05:20] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2023-06-15 23:05:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-06-15 23:05:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:20] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2023-06-15 23:05:20] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2023-06-15 23:05:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2023-06-15 23:05:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:24] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2023-06-15 23:05:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2023-06-15 23:05:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2023-06-15 23:05:24] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2023-06-15 23:05:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:24] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2023-06-15 23:05:24] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records.
[2023-06-15 23:05:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-06-15 23:05:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:24] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-06-15 23:05:24] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-06-15 23:05:24] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-06-15 23:05:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:25] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2023-06-15 23:05:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2023-06-15 23:05:25] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2023-06-15 23:05:25] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2023-06-15 23:05:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:25] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2023-06-15 23:05:25] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records.
[2023-06-15 23:05:25] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-06-15 23:05:25] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-06-15 23:05:27] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2023-06-15 23:05:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-06-15 23:05:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:28] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2023-06-15 23:05:28] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-06-15 23:05:28] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2023-06-15 23:05:28] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2023-06-15 23:05:28] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2023-06-15 23:05:28] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2023-06-15 23:05:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:29] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2023-06-15 23:05:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-06-15 23:05:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-06-15 23:05:31] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2023-06-15 23:05:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:31] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2023-06-15 23:05:31] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records.
[2023-06-15 23:05:32] [TRACE] [OmnipathR] Bypassing call: `import_intercell_network(high_confidence = TRUE)`.
[2023-06-15 23:05:32] [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.
[2023-06-15 23:05:32] [TRACE] [OmnipathR] Bypassing call: `import_intercell_network()`.
[2023-06-15 23:05:32] [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.
[2023-06-15 23:05:32] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2023-06-15 23:05:32] [TRACE] [OmnipathR] Bypassing call: ` loc_consensus_percentile = 50, simplify = TRUE)`.
[2023-06-15 23:05:32] [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.
[2023-06-15 23:05:32] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-06-15 23:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:32] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2023-06-15 23:05:32] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2023-06-15 23:05:32] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2023-06-15 23:05:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:32] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2023-06-15 23:05:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2023-06-15 23:05:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2023-06-15 23:05:32] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2023-06-15 23:05:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-15 23:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-06-15 23:05:32] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2023-06-15 23:05:32] [SUCCESS] [OmnipathR] Downloaded 1098 records.
[2023-06-15 23:05:32] [TRACE] [OmnipathR] Bypassing call: `translate_ids(d, uniprot_id = uniprot, genesymbol)`.
[2023-06-15 23:05:32] [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.
[2023-06-15 23:05:32] [TRACE] [OmnipathR] Bypassing call: `go_ontology_download()`.
[2023-06-15 23:05:32] [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.
[2023-06-15 23:05:32] [TRACE] [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`.
[2023-06-15 23:05:32] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2023-06-15 23:05:32] [TRACE] [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`.
[2023-06-15 23:05:32] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
--- finished re-building ‘bioc_workshop.Rmd’
--- re-building ‘db_manager.Rmd’ using rmarkdown
[2023-06-15 23:05:33] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: `(function (to, from = "accession", reviewed = TRUE, organism = 9606) `.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: `{`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` .slow_doctest()`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` From <- To <- NULL`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` strip_semicol <- function(v) {`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` sub(";$", "", v)`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` }`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` ids <- c(.nse_ensure_str(!!enquo(to)), .nse_ensure_str(!!enquo(from)))`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` reviewed <- if ("trembl" %in% ids) `.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` FALSE`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` else if ("swissprot" %in% ids) `.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` TRUE`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` else reviewed`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` to <- .nse_ensure_str(!!enquo(to)) %>% uniprot_id_type`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` from <- .nse_ensure_str(!!enquo(from)) %>% uniprot_id_type`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` reens <- "ENS[A-Z]+\\d+"`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` to_ens <- to == "xref_ensembl"`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` from_ens <- from == "xref_ensembl"`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` log_trace(paste0("Creating ID mapping table from `%s` to `%s`, ", `.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` "for organism %d (only reviewed: %s)"), from, to, organism, `.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` reviewed)`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` c(from, to) %>% all_uniprots(reviewed = reviewed, organism = organism) %>% `.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` rename(From = 1, To = 2) %>% mutate(From = strip_semicol(From), `.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` To = strip_semicol(To)) %>% separate_rows(From, sep = ";") %>% `.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` separate_rows(To, sep = ";") %>% filter(!is.na(From) & `.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` !is.na(To)) %>% {`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` if (from_ens) `.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` mutate(., From = str_extract(From, reens))`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` else .`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` } %>% {`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` if (to_ens) `.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` mutate(., To = str_extract(To, reens))`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` else .`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: ` } %>% trim_and_distinct`.
[2023-06-15 23:05:33] [TRACE] [OmnipathR] Bypassing call: `})(to = "genesymbol", organism = 9606L)`.
[2023-06-15 23:05:33] [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.
[2023-06-15 23:05:33] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building ‘db_manager.Rmd’
--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2023-06-15 23:05:44] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-06-15 23:05:44] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-06-15 23:05:46] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
Warning: ImageMagick was built without librsvg which causes poor qualty of SVG rendering.
For better results use image_read_svg() which uses the rsvg package.
*** caught segfault ***
address (nil), cause 'memory not mapped'
Traceback:
1: magick_image_write(image, format, quality, depth, density, comment, compression)
2: magick::image_write(magick::image_trim(img), x)
3: plot_crop(f)
4: in_dir(d, expr)
5: in_base_dir(for (f in get_plot_files()) plot_crop(f))
6: (function (before, options, envir) { if (before) return() in_base_dir(for (f in get_plot_files()) plot_crop(f))})(before = FALSE, options = list(eval = TRUE, echo = TRUE, results = "markup", tidy = FALSE, tidy.opts = NULL, collapse = FALSE, prompt = FALSE, comment = "##", highlight = TRUE, size = "normalsize", background = "#F7F7F7", strip.white = TRUE, cache = 0, cache.path = "drug_targets_cache/html/", cache.vars = NULL, cache.lazy = TRUE, dependson = NULL, autodep = FALSE, cache.rebuild = FALSE, fig.keep = "high", fig.show = "asis", fig.align = "default", fig.path = "/tmp/RtmpcyogVS/Rbuild14d2b34de0667e/OmnipathR/vignettes/drug_targets_files/figure-html/", dev = "svg", dev.args = NULL, dpi = 192, fig.ext = "svg", fig.width = 8, fig.height = 5, fig.env = "figure", fig.cap = NULL, fig.scap = NA, fig.lp = "fig:", fig.subcap = NULL, fig.pos = "", out.width = "100%", out.height = NULL, out.extra = NULL, fig.retina = 2, external = TRUE, sanitize = FALSE, interval = 1, aniopts = "controls,loop", warning = TRUE, error = FALSE, message = TRUE, render = NULL, ref.label = NULL, child = NULL, engine = "R", split = FALSE, include = TRUE, purl = TRUE, crop = TRUE, label = "unnamed-chunk-12", code = c("V(cisplatin_network)$node_type <-", " ifelse(", " V(cisplatin_network)$name %in% source_nodes,", " \"direct drug target\",", " ifelse(", " V(cisplatin_network)$name %in% target_nodes,", " \"POI\",", " \"intermediate node\"", " )", " )", "", "ggraph(", " cisplatin_network,", " layout = \"lgl\",", " area = vcount(cisplatin_network)^2.3,", " repulserad = vcount(cisplatin_network)^1.2,", " coolexp = 1.1", ") +", "geom_edge_link(", " aes(", " start_cap = label_rect(node1.name),", " end_cap = label_rect(node2.name)),", " arrow = arrow(length = unit(4, \"mm\")", " ),", " edge_width = .5,", " edge_alpha = .2", ") +", "geom_node_point() +", "geom_node_label(aes(label = name, color = node_type)) +", "scale_color_discrete(", " guide = guide_legend(title = \"Node type\")", ") +", "theme_bw() +", "xlab(\"\") +", "ylab(\"\") +", "ggtitle(\"Cisplatin induced network\")" ), out.width.px = "100%", out.height.px = 480, params.src = "", fig.alt = NULL, fig.num = 1), envir = <environment>)
7: do.call(hook, args, envir = envir)
8: run_hooks(before = FALSE, options, env)
9: eng_r(options)
10: block_exec(params)
11: call_block(x)
12: process_group.block(group)
13: process_group(group)
14: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0") && !xfun::check_old_package("learnr", "0.11.3")) rlang::entrace(e))
15: withCallingHandlers(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0") && !xfun::check_old_package("learnr", "0.11.3")) rlang::entrace(e)), error = function(e) { setwd(wd) write_utf8(res, output %n% stdout()) message("\nQuitting from lines ", paste(current_lines(i), collapse = "-"), if (labels[i] != "") sprintf(" [%s]", labels[i]), sprintf(" (%s)", knit_concord$get("infile"))) })
16: process_file(text, output)
17: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
18: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
19: vweave_rmarkdown(...)
20: engine$weave(file, quiet = quiet, encoding = enc)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
25: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
[ Finished: 2023-06-15 23:05:50 CEST ]