[ Started: 2023-04-20 01:29:28 CEST ]
[ OmnipathR v3.6.6 for BioC-3.16 from https://github.com/saezlab/OmnipathR@RELEASE_3_16 ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.16/2023-04-20_0117/OmnipathR/OmnipathR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.6.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2023-04-20 01:29:50] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:29:50] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-20 01:29:50] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:29:50] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-20 01:29:50] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-20 01:29:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:29:50] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-04-20 01:29:50] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> ### Name: nichenet_lr_network_omnipath
> ### Title: Builds ligand-receptor network for NicheNet using OmniPath
> ### Aliases: nichenet_lr_network_omnipath
> 
> ### ** Examples
> 
> # use only ligand-receptor interactions (not for example ECM-adhesion):
> op_lr_network <- nichenet_lr_network_omnipath(ligand_receptor = TRUE)
[2023-04-20 01:50:41] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2023-04-20 01:50:41] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-04-20 01:50:44] [SUCCESS] [OmnipathR] Loaded 134592 interactions from cache.
[2023-04-20 01:50:44] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&parent=ligand&causality=trans&license=academic`
[2023-04-20 01:50:44] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&parent=ligand&causality=trans&license=academic`
[2023-04-20 01:50:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&parent=ligand&causality=trans&license=academic`
[2023-04-20 01:50:45] [INFO]    [OmnipathR] Cache item `2a15aeb93fb3cf6bac1547f2ba66c2fc7b13dbb7` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:50:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2a15aeb93fb3cf6bac1547f2ba66c2fc7b13dbb7-1.rds`.
[2023-04-20 01:50:45] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2a15aeb93fb3cf6bac1547f2ba66c2fc7b13dbb7-1.rds`.
[2023-04-20 01:50:45] [INFO]    [OmnipathR] Download ready [key=2a15aeb93fb3cf6bac1547f2ba66c2fc7b13dbb7, version=1]
[2023-04-20 01:50:45] [INFO]    [OmnipathR] Cache item `2a15aeb93fb3cf6bac1547f2ba66c2fc7b13dbb7` version 1: status changed from `started` to `ready`.
[2023-04-20 01:50:45] [SUCCESS] [OmnipathR] Downloaded 14473 intercellular communication role records.
[2023-04-20 01:50:45] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&parent=receptor&causality=rec&license=academic`
[2023-04-20 01:50:45] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&parent=receptor&causality=rec&license=academic`
[2023-04-20 01:50:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&parent=receptor&causality=rec&license=academic`
[2023-04-20 01:50:46] [INFO]    [OmnipathR] Cache item `25fe0675450687d111d5db59b62172077f839cdb` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:50:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/25fe0675450687d111d5db59b62172077f839cdb-1.rds`.
[2023-04-20 01:50:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/25fe0675450687d111d5db59b62172077f839cdb-1.rds`.
[2023-04-20 01:50:46] [INFO]    [OmnipathR] Download ready [key=25fe0675450687d111d5db59b62172077f839cdb, version=1]
[2023-04-20 01:50:46] [INFO]    [OmnipathR] Cache item `25fe0675450687d111d5db59b62172077f839cdb` version 1: status changed from `started` to `ready`.
[2023-04-20 01:50:46] [SUCCESS] [OmnipathR] Downloaded 32950 intercellular communication role records.
[2023-04-20 01:51:05] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-04-20 01:51:05] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?license=academic`
[2023-04-20 01:51:06] [SUCCESS] [OmnipathR] Loaded 332447 intercellular communication role records from cache.
[2023-04-20 01:51:06] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-04-20 01:51:06] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-04-20 01:51:06] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
> 
> # use only CellPhoneDB and Guide to Pharmacology:
> op_lr_network <- nichenet_lr_network_omnipath(
+     resources = c('CellPhoneDB', 'Guide2Pharma')
+ )
[2023-04-20 01:51:07] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB,Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-04-20 01:51:07] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB,Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-04-20 01:51:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB,Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-04-20 01:51:07] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB,Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic` (attempt 1/3); error: HTTP error 500.
[2023-04-20 01:51:12] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB,Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-04-20 01:51:12] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB,Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic` (attempt 2/3); error: HTTP error 500.
[2023-04-20 01:51:17] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB,Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-04-20 01:51:17] [ERROR]   [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB,Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic` (attempt 3/3); error: HTTP error 500.
Error in open.connection(5L, "rb") : HTTP error 500.
Calls: nichenet_lr_network_omnipath ... <Anonymous> -> do.call -> <Anonymous> -> download_base
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘bioc_workshop.Rmd’ using ‘UTF-8’... OK
  ‘db_manager.Rmd’ using ‘UTF-8’... OK
  ‘drug_targets.Rmd’ using ‘UTF-8’... OK
  ‘extra_attrs.Rmd’ using ‘UTF-8’... OK
  ‘nichenet.Rmd’ using ‘UTF-8’... OK
  ‘omnipath_intro.Rmd’ using ‘UTF-8’... OK
  ‘paths.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘bioc_workshop.Rmd’ using rmarkdown
[2023-04-20 01:51:22] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:51:22] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-20 01:51:22] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:51:22] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-20 01:51:22] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-20 01:51:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:51:22] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-04-20 01:51:22] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-04-20 01:51:22] [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`
[2023-04-20 01:51:22] [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`
[2023-04-20 01:51:22] [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`
[2023-04-20 01:51:22] [WARN]    [OmnipathR] Failed to download `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` (attempt 1/3); error: HTTP error 500.
[2023-04-20 01:51:27] [TRACE]   [OmnipathR] Attempt 2/3: `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`
[2023-04-20 01:51:27] [WARN]    [OmnipathR] Failed to download `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` (attempt 2/3); error: HTTP error 500.
[2023-04-20 01:51:32] [TRACE]   [OmnipathR] Attempt 3/3: `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`
[2023-04-20 01:51:33] [ERROR]   [OmnipathR] Failed to download `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` (attempt 3/3); error: HTTP error 500.
Quitting from lines 225-227 (bioc_workshop.Rmd) 
Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics:
HTTP error 500.
--- failed re-building ‘bioc_workshop.Rmd’

--- re-building ‘db_manager.Rmd’ using rmarkdown
[2023-04-20 01:51:34] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:51:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-20 01:51:34] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:51:34] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-20 01:51:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-20 01:51:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:51:34] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-04-20 01:51:34] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-04-20 01:51:34] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2023-04-20 01:51:34] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `genes(PREFERRED)`, for organism 9606 (only reviewed: TRUE)
[2023-04-20 01:51:34] [INFO]    [OmnipathR] Loading database `Ensembl organism names`.
[2023-04-20 01:51:34] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2023-04-20 01:51:34] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2023-04-20 01:51:34] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2023-04-20 01:51:34] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2023-04-20 01:51:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2023-04-20 01:51:34] [TRACE]   [OmnipathR] HTTP 200
[2023-04-20 01:51:34] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2023-04-20 01:51:34] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2023-04-20 01:51:35] [INFO]    [OmnipathR] Loaded database `Ensembl organism names`.
[2023-04-20 01:51:35] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,genes(PREFERRED)
[2023-04-20 01:51:35] [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`.
[2023-04-20 01:51:35] [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`
[2023-04-20 01:51:35] [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`.
[2023-04-20 01:51:35] [INFO]    [OmnipathR] Cache item `1ada9cda5e2120624b9e561db9e74f4ddcc5185b` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:51:35] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1ada9cda5e2120624b9e561db9e74f4ddcc5185b-1.rds`.
[2023-04-20 01:51:35] [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`
[2023-04-20 01:51:35] [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`
[2023-04-20 01:51:41] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/1ada9cda5e2120624b9e561db9e74f4ddcc5185b-1.rds`.
[2023-04-20 01:51:41] [INFO]    [OmnipathR] Download ready [key=1ada9cda5e2120624b9e561db9e74f4ddcc5185b, version=1]
[2023-04-20 01:51:41] [INFO]    [OmnipathR] Cache item `1ada9cda5e2120624b9e561db9e74f4ddcc5185b` version 1: status changed from `started` to `ready`.
[2023-04-20 01:51:41] [SUCCESS] [OmnipathR] UniProt (legacy.uniprot.org): downloaded 20404 records
[2023-04-20 01:51:41] [INFO]    [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2023-04-20 01:51:53] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:51:53] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-20 01:51:53] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:51:53] [TRACE]   [OmnipathR] Contains 3 files.
[2023-04-20 01:51:53] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-20 01:51:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:51:53] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-04-20 01:51:53] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-04-20 01:51:53] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-20 01:51:53] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-20 01:51:53] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-20 01:51:53] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:51:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-04-20 01:51:54] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-04-20 01:51:54] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2023-04-20 01:51:54] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2023-04-20 01:51:56] [SUCCESS] [OmnipathR] Downloaded 92262 interactions.
--- finished re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2023-04-20 01:52:01] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:52:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-20 01:52:01] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:52:01] [TRACE]   [OmnipathR] Contains 2 files.
[2023-04-20 01:52:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-20 01:52:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:52:01] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-04-20 01:52:01] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-04-20 01:52:02] [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`
[2023-04-20 01:52:02] [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`
[2023-04-20 01:52:02] [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`
[2023-04-20 01:52:02] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:52:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2023-04-20 01:52:03] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2023-04-20 01:52:03] [INFO]    [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2023-04-20 01:52:03] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2023-04-20 01:52:12] [SUCCESS] [OmnipathR] Downloaded 134592 interactions.
[2023-04-20 01:55:37] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2023-04-20 01:55:37] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2023-04-20 01:55:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2023-04-20 01:55:37] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:55:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2023-04-20 01:55:38] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2023-04-20 01:55:38] [INFO]    [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2023-04-20 01:55:38] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2023-04-20 01:55:38] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records.
[2023-04-20 01:55:38] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2023-04-20 01:55:38] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2023-04-20 01:55:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2023-04-20 01:55:38] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` (attempt 1/3); error: HTTP error 500.
[2023-04-20 01:55:43] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2023-04-20 01:55:43] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` (attempt 2/3); error: HTTP error 500.
[2023-04-20 01:55:48] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2023-04-20 01:55:49] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:55:49] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2023-04-20 01:55:49] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2023-04-20 01:55:49] [INFO]    [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2023-04-20 01:55:49] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2023-04-20 01:55:49] [SUCCESS] [OmnipathR] Downloaded 70 enzyme-substrate relationships.
Warning in .Internal(lapply(X, FUN)) :
  closing unused connection 5 (https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination)
Warning in .Internal(lapply(X, FUN)) :
  closing unused connection 4 (https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination)
--- finished re-building ‘extra_attrs.Rmd’

--- re-building ‘nichenet.Rmd’ using rmarkdown
--- finished re-building ‘nichenet.Rmd’

--- re-building ‘omnipath_intro.Rmd’ using rmarkdown
[2023-04-20 01:55:51] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:55:51] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-20 01:55:51] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:55:51] [TRACE]   [OmnipathR] Contains 4 files.
[2023-04-20 01:55:51] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-20 01:55:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:55:51] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-04-20 01:55:51] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-04-20 01:55:53] [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`
[2023-04-20 01:55:53] [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`
[2023-04-20 01:55:53] [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`
[2023-04-20 01:55:54] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:55:54] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2023-04-20 01:55:54] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2023-04-20 01:55:54] [INFO]    [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2023-04-20 01:55:54] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2023-04-20 01:55:56] [SUCCESS] [OmnipathR] Downloaded 64574 interactions.
[2023-04-20 01:56:01] [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`
[2023-04-20 01:56:01] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2023-04-20 01:56:01] [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`
[2023-04-20 01:56:02] [INFO]    [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:56:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`.
[2023-04-20 01:56:02] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`.
[2023-04-20 01:56:02] [INFO]    [OmnipathR] Download ready [key=5ef52c90ffa996b5425a92df0ae5e7d825269078, version=1]
[2023-04-20 01:56:02] [INFO]    [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `started` to `ready`.
[2023-04-20 01:56:02] [SUCCESS] [OmnipathR] Downloaded 1526 interactions.
[2023-04-20 01:56:02] [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`
[2023-04-20 01:56:02] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2023-04-20 01:56:02] [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`
[2023-04-20 01:56:02] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:56:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2023-04-20 01:56:02] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2023-04-20 01:56:02] [INFO]    [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2023-04-20 01:56:02] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2023-04-20 01:56:03] [SUCCESS] [OmnipathR] Downloaded 6880 interactions.
[2023-04-20 01:56:03] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-20 01:56:03] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-20 01:56:03] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-20 01:56:03] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:56:03] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2023-04-20 01:56:03] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2023-04-20 01:56:03] [INFO]    [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2023-04-20 01:56:03] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2023-04-20 01:56:03] [SUCCESS] [OmnipathR] Downloaded 3008 interactions.
[2023-04-20 01:56:04] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-04-20 01:56:04] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-04-20 01:56:04] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-04-20 01:56:04] [INFO]    [OmnipathR] Cache item `cde98994cdbb4dd0e43d69b43a01b3491332287d` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:56:04] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cde98994cdbb4dd0e43d69b43a01b3491332287d-1.rds`.
[2023-04-20 01:56:04] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cde98994cdbb4dd0e43d69b43a01b3491332287d-1.rds`.
[2023-04-20 01:56:04] [INFO]    [OmnipathR] Download ready [key=cde98994cdbb4dd0e43d69b43a01b3491332287d, version=1]
[2023-04-20 01:56:04] [INFO]    [OmnipathR] Cache item `cde98994cdbb4dd0e43d69b43a01b3491332287d` version 1: status changed from `started` to `ready`.
[2023-04-20 01:56:04] [SUCCESS] [OmnipathR] Downloaded 6127 interactions.
[2023-04-20 01:56:05] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-04-20 01:56:05] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-04-20 01:56:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-04-20 01:56:05] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 1/3); error: HTTP error 500.
[2023-04-20 01:56:10] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-04-20 01:56:10] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 2/3); error: HTTP error 500.
[2023-04-20 01:56:15] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-04-20 01:56:15] [ERROR]   [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 3/3); error: HTTP error 500.
Quitting from lines 339-359 (omnipath_intro.Rmd) 
Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics:
HTTP error 500.
--- failed re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
[2023-04-20 01:56:16] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:56:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-20 01:56:16] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:56:16] [TRACE]   [OmnipathR] Contains 6 files.
[2023-04-20 01:56:16] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-20 01:56:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-04-20 01:56:16] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-04-20 01:56:16] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-04-20 01:56:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2023-04-20 01:56:17] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2023-04-20 01:56:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2023-04-20 01:56:17] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:56:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2023-04-20 01:56:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2023-04-20 01:56:17] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2023-04-20 01:56:17] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2023-04-20 01:56:17] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2023-04-20 01:56:17] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2023-04-20 01:56:17] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2023-04-20 01:56:17] [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`.
[2023-04-20 01:56:17] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:56:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2023-04-20 01:56:17] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2023-04-20 01:56:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2023-04-20 01:56:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2023-04-20 01:56:17] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2023-04-20 01:56:17] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2023-04-20 01:56:17] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2023-04-20 01:56:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2023-04-20 01:56:17] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2023-04-20 01:56:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2023-04-20 01:56:18] [INFO]    [OmnipathR] Cache item `ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:56:18] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41-1.rds`.
[2023-04-20 01:56:18] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41-1.rds`.
[2023-04-20 01:56:18] [INFO]    [OmnipathR] Download ready [key=ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41, version=1]
[2023-04-20 01:56:18] [INFO]    [OmnipathR] Cache item `ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41` version 1: status changed from `started` to `ready`.
[2023-04-20 01:56:20] [SUCCESS] [OmnipathR] Downloaded 87651 interactions.
[2023-04-20 01:56:21] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2023-04-20 01:56:21] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2023-04-20 01:56:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2023-04-20 01:56:21] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:56:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2023-04-20 01:56:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2023-04-20 01:56:22] [INFO]    [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2023-04-20 01:56:22] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2023-04-20 01:56:22] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records.
[2023-04-20 01:56:22] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2023-04-20 01:56:22] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2023-04-20 01:56:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2023-04-20 01:56:23] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:56:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2023-04-20 01:56:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2023-04-20 01:56:23] [INFO]    [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2023-04-20 01:56:23] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2023-04-20 01:56:23] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records.
[2023-04-20 01:56:23] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-04-20 01:56:23] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-04-20 01:56:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-04-20 01:56:23] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:56:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-04-20 01:56:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-04-20 01:56:23] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2023-04-20 01:56:23] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2023-04-20 01:56:23] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records.
[2023-04-20 01:56:23] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2023-04-20 01:56:23] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2023-04-20 01:56:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2023-04-20 01:56:24] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2023-04-20 01:56:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2023-04-20 01:56:24] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2023-04-20 01:56:24] [INFO]    [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2023-04-20 01:56:24] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2023-04-20 01:56:24] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records.
[2023-04-20 01:56:24] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-04-20 01:56:24] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-04-20 01:56:24] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2023-04-20 01:56:24] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2023-04-20 01:56:24] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2023-04-20 01:56:24] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2023-04-20 01:56:24] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` (attempt 1/3); error: HTTP error 500.
[2023-04-20 01:56:29] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2023-04-20 01:56:29] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` (attempt 2/3); error: HTTP error 500.
[2023-04-20 01:56:34] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2023-04-20 01:56:35] [ERROR]   [OmnipathR] Failed to download `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` (attempt 3/3); error: HTTP error 500.
Quitting from lines 141-188 (paths.Rmd) 
Error: processing vignette 'paths.Rmd' failed with diagnostics:
HTTP error 500.
--- failed re-building ‘paths.Rmd’

SUMMARY: processing the following files failed:
  ‘bioc_workshop.Rmd’ ‘omnipath_intro.Rmd’ ‘paths.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.16/2023-04-20_0117/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2023-04-20 01:56:41 CEST ]