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This page was generated on 2023-03-27 05:50:39 -0000 (Mon, 27 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" 6083
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BUILD results for OmnipathR on kunpeng1


To the developers/maintainers of the OmnipathR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1407/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.7.8  (landing page)
Denes Turei
Snapshot Date: 2023-03-24 01:40:07 -0000 (Fri, 24 Mar 2023)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: 3877294
git_last_commit_date: 2023-03-22 13:52:55 -0000 (Wed, 22 Mar 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    ERROR  skipped

Summary

Package: OmnipathR
Version: 3.7.8
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR
StartedAt: 2023-03-24 14:01:54 -0000 (Fri, 24 Mar 2023)
EndedAt: 2023-03-24 14:17:43 -0000 (Fri, 24 Mar 2023)
EllapsedTime: 948.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR
###
##############################################################################
##############################################################################


* checking for file ‘OmnipathR/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
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:11] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] Contains 1 files.
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpCG8LKA/Rinst29a46b2427cbd4/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpCG8LKA/Rinst29a46b2427cbd4/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpCG8LKA/Rinst29a46b2427cbd4/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpCG8LKA/Rinst29a46b2427cbd4/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-03-24 14:02:11] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-03-24 14:02:11] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-03-24 14:02:11] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-03-24 14:02:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:14] [INFO]    [OmnipathR] Cache item `f4de1f63d60f35d18bb262dd6de84d1cccd9cc97` version 1: status changed from `unknown` to `started`.
[2023-03-24 14:02:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f4de1f63d60f35d18bb262dd6de84d1cccd9cc97-1.rds`.
[2023-03-24 14:02:14] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f4de1f63d60f35d18bb262dd6de84d1cccd9cc97-1.rds`.
[2023-03-24 14:02:14] [INFO]    [OmnipathR] Download ready [key=f4de1f63d60f35d18bb262dd6de84d1cccd9cc97, version=1]
[2023-03-24 14:02:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:14] [INFO]    [OmnipathR] Cache item `f4de1f63d60f35d18bb262dd6de84d1cccd9cc97` version 1: status changed from `started` to `ready`.
[2023-03-24 14:02:17] [SUCCESS] [OmnipathR] Downloaded 74513 interactions.
[2023-03-24 14:02:21] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-03-24 14:02:21] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-03-24 14:02:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-03-24 14:02:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:23] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2023-03-24 14:02:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2023-03-24 14:02:24] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2023-03-24 14:02:24] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2023-03-24 14:02:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:24] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2023-03-24 14:02:26] [SUCCESS] [OmnipathR] Downloaded 42248 enzyme-substrate relationships.
[2023-03-24 14:02:27] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-03-24 14:02:27] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-03-24 14:02:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-03-24 14:02:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:29] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2023-03-24 14:02:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-03-24 14:02:30] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-03-24 14:02:30] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2023-03-24 14:02:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:30] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2023-03-24 14:02:32] [SUCCESS] [OmnipathR] Downloaded 40014 interactions.
[2023-03-24 14:02:33] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2023-03-24 14:02:33] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2023-03-24 14:02:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2023-03-24 14:02:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:37] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2023-03-24 14:02:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2023-03-24 14:02:37] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2023-03-24 14:02:37] [INFO]    [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2023-03-24 14:02:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:37] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2023-03-24 14:02:37] [SUCCESS] [OmnipathR] Downloaded 32761 protein complexes.
[2023-03-24 14:02:38] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-24 14:02:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-03-24 14:02:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-03-24 14:02:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-03-24 14:02:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:41] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2023-03-24 14:02:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-03-24 14:02:42] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-03-24 14:02:42] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2023-03-24 14:02:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:42] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2023-03-24 14:02:42] [SUCCESS] [OmnipathR] Downloaded 73481 annotation records.
[2023-03-24 14:02:43] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-24 14:02:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:44] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2023-03-24 14:02:44] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2023-03-24 14:02:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2023-03-24 14:02:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:44] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2023-03-24 14:02:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2023-03-24 14:02:44] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2023-03-24 14:02:44] [INFO]    [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2023-03-24 14:02:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:44] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2023-03-24 14:02:44] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2023-03-24 14:02:45] [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.
[2023-03-24 14:02:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-24 14:02:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:46] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-03-24 14:02:46] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-03-24 14:02:46] [SUCCESS] [OmnipathR] Loaded 73481 annotation records from cache.
[2023-03-24 14:02:48] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-24 14:02:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:48] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2023-03-24 14:02:48] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2023-03-24 14:02:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2023-03-24 14:02:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:49] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2023-03-24 14:02:49] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2023-03-24 14:02:49] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2023-03-24 14:02:49] [INFO]    [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2023-03-24 14:02:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:49] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2023-03-24 14:02:49] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records.
[2023-03-24 14:02:51] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-24 14:02:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:51] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-03-24 14:02:51] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-03-24 14:02:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-03-24 14:02:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:52] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2023-03-24 14:02:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2023-03-24 14:02:52] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2023-03-24 14:02:52] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2023-03-24 14:02:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:02:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:52] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2023-03-24 14:02:52] [SUCCESS] [OmnipathR] Downloaded 2451 annotation records.
[2023-03-24 14:02:53] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-03-24 14:02:53] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-03-24 14:02:55] [SUCCESS] [OmnipathR] Loaded 40014 interactions from cache.
[2023-03-24 14:02:56] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-24 14:02:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:02:56] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2023-03-24 14:02:56] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-03-24 14:02:56] [SUCCESS] [OmnipathR] Loaded 2451 annotation records from cache.
[2023-03-24 14:02:57] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2023-03-24 14:02:57] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2023-03-24 14:02:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2023-03-24 14:03:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:03:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:03:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:03:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:03:22] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2023-03-24 14:03:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-03-24 14:03:24] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-03-24 14:03:24] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2023-03-24 14:03:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:03:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:03:24] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2023-03-24 14:03:24] [SUCCESS] [OmnipathR] Downloaded 323572 intercellular communication role records.
[2023-03-24 14:03:25] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-03-24 14:03:25] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-03-24 14:03:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-03-24 14:03:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:03:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:03:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:03:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:03:28] [INFO]    [OmnipathR] Cache item `498f91238951df23d4d71705063f40254eddbfbf` version 1: status changed from `unknown` to `started`.
[2023-03-24 14:03:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/498f91238951df23d4d71705063f40254eddbfbf-1.rds`.
[2023-03-24 14:03:28] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/498f91238951df23d4d71705063f40254eddbfbf-1.rds`.
[2023-03-24 14:03:28] [INFO]    [OmnipathR] Download ready [key=498f91238951df23d4d71705063f40254eddbfbf, version=1]
[2023-03-24 14:03:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:03:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:03:28] [INFO]    [OmnipathR] Cache item `498f91238951df23d4d71705063f40254eddbfbf` version 1: status changed from `started` to `ready`.
[2023-03-24 14:03:31] [SUCCESS] [OmnipathR] Downloaded 40681 interactions.
[2023-03-24 14:03:31] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-03-24 14:03:31] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-03-24 14:03:31] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-03-24 14:03:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:03:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:03:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:03:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:03:33] [INFO]    [OmnipathR] Cache item `1ac430724a20c137fc374a8499adabb468a12835` version 1: status changed from `unknown` to `started`.
[2023-03-24 14:03:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2023-03-24 14:03:33] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2023-03-24 14:03:33] [INFO]    [OmnipathR] Download ready [key=1ac430724a20c137fc374a8499adabb468a12835, version=1]
[2023-03-24 14:03:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:03:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:03:33] [INFO]    [OmnipathR] Cache item `1ac430724a20c137fc374a8499adabb468a12835` version 1: status changed from `started` to `ready`.
[2023-03-24 14:03:33] [SUCCESS] [OmnipathR] Downloaded 27928 intercellular communication role records.
[2023-03-24 14:03:33] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-03-24 14:03:33] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-03-24 14:03:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-03-24 14:03:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:03:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:03:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:03:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:03:37] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2023-03-24 14:03:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-03-24 14:03:37] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-03-24 14:03:37] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2023-03-24 14:03:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:03:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:03:37] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2023-03-24 14:03:37] [SUCCESS] [OmnipathR] Downloaded 21325 intercellular communication role records.
[2023-03-24 14:03:37] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-03-24 14:03:37] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-03-24 14:03:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-03-24 14:03:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:03:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:03:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:03:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:03:39] [INFO]    [OmnipathR] Cache item `552757063f9934c7b745a9c4247c3b5282a66c88` version 1: status changed from `unknown` to `started`.
[2023-03-24 14:03:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2023-03-24 14:03:40] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2023-03-24 14:03:40] [INFO]    [OmnipathR] Download ready [key=552757063f9934c7b745a9c4247c3b5282a66c88, version=1]
[2023-03-24 14:03:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:03:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:03:40] [INFO]    [OmnipathR] Cache item `552757063f9934c7b745a9c4247c3b5282a66c88` version 1: status changed from `started` to `ready`.
[2023-03-24 14:03:40] [SUCCESS] [OmnipathR] Downloaded 43967 intercellular communication role records.
[2023-03-24 14:04:22] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-03-24 14:04:22] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-03-24 14:04:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-03-24 14:05:31] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic` (attempt 1/3); error: OpenSSL SSL_read: Connection reset by peer, errno 104
[2023-03-24 14:05:36] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-03-24 14:05:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:05:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:05:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:05:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:05:39] [INFO]    [OmnipathR] Cache item `3098404926bc0cf155d043ff0c6efe64e3424b74` version 1: status changed from `unknown` to `started`.
[2023-03-24 14:05:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2023-03-24 14:05:40] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2023-03-24 14:05:40] [INFO]    [OmnipathR] Download ready [key=3098404926bc0cf155d043ff0c6efe64e3424b74, version=1]
[2023-03-24 14:05:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:05:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:05:40] [INFO]    [OmnipathR] Cache item `3098404926bc0cf155d043ff0c6efe64e3424b74` version 1: status changed from `started` to `ready`.
Warning: closing unused connection 4 (https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic)
[2023-03-24 14:05:45] [SUCCESS] [OmnipathR] Downloaded 80237 interactions.
[2023-03-24 14:05:45] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2023-03-24 14:05:45] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-03-24 14:05:45] [SUCCESS] [OmnipathR] Loaded 27928 intercellular communication role records from cache.
[2023-03-24 14:05:45] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2023-03-24 14:05:45] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-03-24 14:05:45] [SUCCESS] [OmnipathR] Loaded 43967 intercellular communication role records from cache.
[2023-03-24 14:09:43] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-03-24 14:09:43] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?license=academic`
[2023-03-24 14:09:43] [SUCCESS] [OmnipathR] Loaded 323572 intercellular communication role records from cache.
[2023-03-24 14:09:44] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-03-24 14:09:44] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-03-24 14:09:44] [SUCCESS] [OmnipathR] Loaded 21325 intercellular communication role records from cache.
[2023-03-24 14:09:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-24 14:09:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:09:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2023-03-24 14:09:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2023-03-24 14:09:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2023-03-24 14:09:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:09:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:09:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:09:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:09:47] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2023-03-24 14:09:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2023-03-24 14:09:47] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2023-03-24 14:09:47] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2023-03-24 14:09:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:09:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:09:47] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2023-03-24 14:09:47] [SUCCESS] [OmnipathR] Downloaded 1097 records.
[2023-03-24 14:09:47] [INFO]    [OmnipathR] Loading database `Ensembl organism names`.
[2023-03-24 14:09:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:09:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:09:47] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2023-03-24 14:09:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:09:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:09:47] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2023-03-24 14:09:47] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2023-03-24 14:09:47] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2023-03-24 14:09:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2023-03-24 14:09:50] [TRACE]   [OmnipathR] HTTP 200
[2023-03-24 14:09:50] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2023-03-24 14:09:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:09:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:09:50] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2023-03-24 14:09:50] [INFO]    [OmnipathR] Loaded database `Ensembl organism names`.
[2023-03-24 14:09:50] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2023-03-24 14:09:50] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `genes(PREFERRED)`, for organism 9606 (only reviewed: TRUE)
[2023-03-24 14:09:50] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,genes(PREFERRED)
[2023-03-24 14:09:50] [TRACE]   [OmnipathR] Looking up in cache: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`.
[2023-03-24 14:09:50] [INFO]    [OmnipathR] Cache record does not exist: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2023-03-24 14:09:50] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`.
[2023-03-24 14:09:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:09:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:09:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:09:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:09:50] [INFO]    [OmnipathR] Cache item `1ada9cda5e2120624b9e561db9e74f4ddcc5185b` version 1: status changed from `unknown` to `started`.
[2023-03-24 14:09:50] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/1ada9cda5e2120624b9e561db9e74f4ddcc5185b-1.rds`.
[2023-03-24 14:09:50] [INFO]    [OmnipathR] Retrieving URL: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2023-03-24 14:09:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2023-03-24 14:09:57] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/1ada9cda5e2120624b9e561db9e74f4ddcc5185b-1.rds`.
[2023-03-24 14:09:57] [INFO]    [OmnipathR] Download ready [key=1ada9cda5e2120624b9e561db9e74f4ddcc5185b, version=1]
[2023-03-24 14:09:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:09:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:09:57] [INFO]    [OmnipathR] Cache item `1ada9cda5e2120624b9e561db9e74f4ddcc5185b` version 1: status changed from `started` to `ready`.
[2023-03-24 14:09:57] [SUCCESS] [OmnipathR] UniProt (legacy.uniprot.org): downloaded 20404 records
[2023-03-24 14:09:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:09:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:09:58] [INFO]    [OmnipathR] Looking up in cache `http://purl.obolibrary.org/obo/go/go-basic.obo`: key=663f8a0321e09c16870d151bd7559c9385d22288, no version available.
[2023-03-24 14:09:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:09:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:09:58] [INFO]    [OmnipathR] Created new version for cache record 663f8a0321e09c16870d151bd7559c9385d22288: version 1.
[2023-03-24 14:09:58] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo
[2023-03-24 14:09:58] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/go/go-basic.obo`
[2023-03-24 14:09:58] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/go/go-basic.obo`
[2023-03-24 14:10:23] [TRACE]   [OmnipathR] HTTP 200
[2023-03-24 14:10:23] [INFO]    [OmnipathR] Download ready [key=663f8a0321e09c16870d151bd7559c9385d22288, version=1]
[2023-03-24 14:10:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:10:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:10:23] [INFO]    [OmnipathR] Cache item `663f8a0321e09c16870d151bd7559c9385d22288` version 1: status changed from `unknown` to `ready`.
[2023-03-24 14:10:23] [TRACE]   [OmnipathR] Processing OBO file `/home/biocbuild/.cache/OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo`.
[2023-03-24 14:10:33] [TRACE]   [OmnipathR] Finished processing OBO file `/home/biocbuild/.cache/OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo`.
[2023-03-24 14:10:33] [TRACE]   [OmnipathR] Converting ontology relations from table to graph.
[2023-03-24 14:10:34] [INFO]    [OmnipathR] Loading database `Gene Ontology (basic)`.
[2023-03-24 14:10:34] [INFO]    [OmnipathR] Looking up in cache `http://purl.obolibrary.org/obo/go/go-basic.obo`: key=663f8a0321e09c16870d151bd7559c9385d22288, latest version=1.
[2023-03-24 14:10:34] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo
[2023-03-24 14:10:34] [TRACE]   [OmnipathR] Processing OBO file `/home/biocbuild/.cache/OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo`.
[2023-03-24 14:10:46] [TRACE]   [OmnipathR] Finished processing OBO file `/home/biocbuild/.cache/OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo`.
[2023-03-24 14:10:46] [INFO]    [OmnipathR] Loaded database `Gene Ontology (basic)`.
--- finished re-building ‘bioc_workshop.Rmd’

--- re-building ‘db_manager.Rmd’ using rmarkdown
[2023-03-24 14:14:19] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2023-03-24 14:14:19] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `genes(PREFERRED)`, for organism 9606 (only reviewed: TRUE)
[2023-03-24 14:14:19] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,genes(PREFERRED)
[2023-03-24 14:14:19] [TRACE]   [OmnipathR] Looking up in cache: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`.
[2023-03-24 14:14:19] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/1ada9cda5e2120624b9e561db9e74f4ddcc5185b-1.rds`.
[2023-03-24 14:14:19] [SUCCESS] [OmnipathR] UniProt (legacy.uniprot.org): loaded 20404 records from cache
[2023-03-24 14:14:19] [INFO]    [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2023-03-24 14:14:32] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-03-24 14:14:32] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-03-24 14:14:34] [SUCCESS] [OmnipathR] Loaded 40014 interactions from cache.
--- finished re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2023-03-24 14:14:40] [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`
[2023-03-24 14:14:40] [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`
[2023-03-24 14:14:40] [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`
[2023-03-24 14:14:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:14:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:14:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:14:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:14:47] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2023-03-24 14:14:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2023-03-24 14:14:48] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2023-03-24 14:14:48] [INFO]    [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2023-03-24 14:14:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-24 14:14:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-24 14:14:48] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2023-03-24 14:14:58] [SUCCESS] [OmnipathR] Downloaded 80237 interactions.
Killed