##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r OmnipathR -R && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe 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
[2022-04-12 12:34:01] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2022-04-12 12:34:01] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2022-04-12 12:34:01] [TRACE]   [OmnipathR] Cache locked: FALSE
[2022-04-12 12:34:02] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f4de1f63d60f35d18bb262dd6de84d1cccd9cc97-1.rds`.
[2022-04-12 12:34:02] [INFO]    [OmnipathR] Loaded from cache: `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`
[2022-04-12 12:34:03] [SUCCESS] [OmnipathR] Loaded 73802 interactions from cache.
[2022-04-12 12:34:12] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2022-04-12 12:34:12] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 12:34:13] [SUCCESS] [OmnipathR] Loaded 39042 enzyme-substrate relationships from cache.
[2022-04-12 12:34:15] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2022-04-12 12:34:15] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 12:34:16] [SUCCESS] [OmnipathR] Loaded 43729 interactions from cache.
[2022-04-12 12:34:17] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2022-04-12 12:34:17] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/complexes?license=academic`
[2022-04-12 12:34:17] [SUCCESS] [OmnipathR] Loaded 21953 protein complexes from cache.
[2022-04-12 12:34:18] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2022-04-12 12:34:18] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2022-04-12 12:34:19] [SUCCESS] [OmnipathR] Loaded 63410 annotation records from cache.
[2022-04-12 12:34:20] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2022-04-12 12:34:20] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2022-04-12 12:34:20] [SUCCESS] [OmnipathR] Loaded 0 annotation records from cache.
[2022-04-12 12:34:21] [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.
[2022-04-12 12:34:22] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2022-04-12 12:34:22] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2022-04-12 12:34:22] [SUCCESS] [OmnipathR] Loaded 63410 annotation records from cache.
[2022-04-12 12:34:24] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2022-04-12 12:34:24] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2022-04-12 12:34:24] [SUCCESS] [OmnipathR] Loaded 3590 annotation records from cache.
[2022-04-12 12:34:25] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2022-04-12 12:34:25] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2022-04-12 12:34:25] [SUCCESS] [OmnipathR] Loaded 2333 annotation records from cache.
[2022-04-12 12:34:26] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2022-04-12 12:34:26] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 12:34:27] [SUCCESS] [OmnipathR] Loaded 43729 interactions from cache.
[2022-04-12 12:34:27] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2022-04-12 12:34:27] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2022-04-12 12:34:27] [SUCCESS] [OmnipathR] Loaded 2333 annotation records from cache.
[2022-04-12 12:34:30] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2022-04-12 12:34:30] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?license=academic`
[2022-04-12 12:34:31] [SUCCESS] [OmnipathR] Loaded 288967 intercellular communication role records from cache.
[2022-04-12 12:34:33] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/498f91238951df23d4d71705063f40254eddbfbf-1.rds`.
[2022-04-12 12:34:33] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2022-04-12 12:34:34] [SUCCESS] [OmnipathR] Loaded 43797 interactions from cache.
[2022-04-12 12:34:34] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2022-04-12 12:34:34] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2022-04-12 12:34:35] [SUCCESS] [OmnipathR] Loaded 23598 intercellular communication role records from cache.
[2022-04-12 12:34:35] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2022-04-12 12:34:35] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2022-04-12 12:34:35] [SUCCESS] [OmnipathR] Loaded 19993 intercellular communication role records from cache.
[2022-04-12 12:34:36] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2022-04-12 12:34:36] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2022-04-12 12:34:36] [SUCCESS] [OmnipathR] Loaded 29369 intercellular communication role records from cache.
[2022-04-12 12:34:43] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2022-04-12 12:34:43] [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`
[2022-04-12 12:34:44] [SUCCESS] [OmnipathR] Loaded 77498 interactions from cache.
[2022-04-12 12:34:45] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2022-04-12 12:34:45] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2022-04-12 12:34:45] [SUCCESS] [OmnipathR] Loaded 23598 intercellular communication role records from cache.
[2022-04-12 12:34:45] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2022-04-12 12:34:45] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2022-04-12 12:34:45] [SUCCESS] [OmnipathR] Loaded 29369 intercellular communication role records from cache.
[2022-04-12 12:35:20] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2022-04-12 12:35:20] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?license=academic`
[2022-04-12 12:35:20] [SUCCESS] [OmnipathR] Loaded 288967 intercellular communication role records from cache.
[2022-04-12 12:35:21] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2022-04-12 12:35:21] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2022-04-12 12:35:21] [SUCCESS] [OmnipathR] Loaded 19993 intercellular communication role records from cache.
[2022-04-12 12:35:23] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2022-04-12 12:35:24] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell_summary`
[2022-04-12 12:35:24] [SUCCESS] [OmnipathR] Loaded 1125 records from cache.
[2022-04-12 12:35:24] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2022-04-12 12:35:24] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `genes(PREFERRED)`, for organism 9606 (only reviewed: TRUE)
[2022-04-12 12:35:24] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,genes(PREFERRED)
[2022-04-12 12:35:24] [TRACE]   [OmnipathR] Looking up in cache: `https://www.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`.
[2022-04-12 12:35:24] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/11eb810ae342ef823eec8d744d4ff3085012e1f4-1.rds`.
[2022-04-12 12:35:24] [SUCCESS] [OmnipathR] UniProt (www.uniprot.org): loaded 20386 records from cache
[2022-04-12 12:35:26] [INFO]    [OmnipathR] Looking up in cache `http://purl.obolibrary.org/obo/go/go-basic.obo`: key=663f8a0321e09c16870d151bd7559c9385d22288, latest version=1.
[2022-04-12 12:35:26] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo
[2022-04-12 12:35:26] [TRACE]   [OmnipathR] Processing OBO file `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo`.
[2022-04-12 12:35:36] [TRACE]   [OmnipathR] Finished processing OBO file `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo`.
[2022-04-12 12:35:37] [TRACE]   [OmnipathR] Converting ontology relations from table to graph.
[2022-04-12 12:35:38] [INFO]    [OmnipathR] Loading database `Gene Ontology (basic)`.
[2022-04-12 12:35:38] [INFO]    [OmnipathR] Looking up in cache `http://purl.obolibrary.org/obo/go/go-basic.obo`: key=663f8a0321e09c16870d151bd7559c9385d22288, latest version=1.
[2022-04-12 12:35:38] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo
[2022-04-12 12:35:38] [TRACE]   [OmnipathR] Processing OBO file `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo`.
[2022-04-12 12:35:43] [TRACE]   [OmnipathR] Finished processing OBO file `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo`.
[2022-04-12 12:35:44] [INFO]    [OmnipathR] Loaded database `Gene Ontology (basic)`.
--- finished re-building 'bioc_workshop.Rmd'

--- re-building 'drug_targets.Rmd' using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'igraph'

The following objects are masked from 'package:dplyr':

    as_data_frame, groups, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

[2022-04-12 12:35:50] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2022-04-12 12:35:50] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 12:35:51] [SUCCESS] [OmnipathR] Loaded 43729 interactions from cache.
--- finished re-building 'drug_targets.Rmd'

--- re-building 'nichenet.Rmd' using rmarkdown
--- finished re-building 'nichenet.Rmd'

--- re-building 'omnipath_intro.Rmd' using rmarkdown

Attaching package: 'tidyr'

The following object is masked from 'package:igraph':

    crossing

Loading required package: supraHex
Loading required package: hexbin
[2022-04-12 12:37:46] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2022-04-12 12:37:46] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 12:37:46] [SUCCESS] [OmnipathR] Loaded 14001 interactions from cache.
[2022-04-12 12:37:56] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`.
[2022-04-12 12:37:56] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2022-04-12 12:37:56] [SUCCESS] [OmnipathR] Loaded 994 interactions from cache.
[2022-04-12 12:37:59] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2022-04-12 12:37:59] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2022-04-12 12:37:59] [SUCCESS] [OmnipathR] Loaded 3727 interactions from cache.
[2022-04-12 12:38:04] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2022-04-12 12:38:04] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 12:38:04] [SUCCESS] [OmnipathR] Loaded 2852 interactions from cache.
[2022-04-12 12:38:12] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cde98994cdbb4dd0e43d69b43a01b3491332287d-1.rds`.
[2022-04-12 12:38:12] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2022-04-12 12:38:12] [SUCCESS] [OmnipathR] Loaded 6245 interactions from cache.
[2022-04-12 12:38:13] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/8281969bb1ab7f3f99e3f1632559158df24b9a40-1.rds`.
[2022-04-12 12:38:13] [INFO]    [OmnipathR] Loaded from cache: `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`
[2022-04-12 12:38:14] [SUCCESS] [OmnipathR] Loaded 15821 interactions from cache.
[2022-04-12 12:38:15] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2022-04-12 12:38:15] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 12:38:15] [SUCCESS] [OmnipathR] Loaded 728 interactions from cache.
[2022-04-12 12:38:17] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2022-04-12 12:38:17] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 12:38:18] [SUCCESS] [OmnipathR] Loaded 39042 enzyme-substrate relationships from cache.
[2022-04-12 12:38:19] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2022-04-12 12:38:19] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 12:38:20] [SUCCESS] [OmnipathR] Loaded 43729 interactions from cache.
Quitting from lines 418-452 (omnipath_intro.Rmd) 
Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics:
schannel: next InitializeSecurityContext failed: SEC_E_MESSAGE_ALTERED (0x8009030F) - The message or signature supplied for verification has been altered
--- failed re-building 'omnipath_intro.Rmd'

--- re-building 'paths.Rmd' using rmarkdown
[2022-04-12 12:38:26] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2022-04-12 12:38:26] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2022-04-12 12:38:26] [SUCCESS] [OmnipathR] Loaded 3476 annotation records from cache.
[2022-04-12 12:38:26] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2022-04-12 12:38:28] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2022-04-12 12:38:28] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): loaded 1987 records from cache
[2022-04-12 12:38:37] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41-1.rds`.
[2022-04-12 12:38:37] [INFO]    [OmnipathR] Loaded from cache: `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`
[2022-04-12 12:38:39] [SUCCESS] [OmnipathR] Loaded 90024 interactions from cache.
[2022-04-12 12:38:50] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2022-04-12 12:38:50] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2022-04-12 12:38:50] [SUCCESS] [OmnipathR] Loaded 348289 annotation records from cache.
[2022-04-12 12:39:04] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/bff4a3e667dd430d687de100bd8432e1fadd5d3d-1.rds`.
[2022-04-12 12:39:04] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=sec&license=academic`
[2022-04-12 12:39:04] [SUCCESS] [OmnipathR] Loaded 9707 intercellular communication role records from cache.
[2022-04-12 12:39:05] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2022-04-12 12:39:05] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2022-04-12 12:39:05] [SUCCESS] [OmnipathR] Loaded 19993 intercellular communication role records from cache.
[2022-04-12 12:39:14] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/37a6749854419bf778be37a7053bcaba8173aa40-1.rds`.
[2022-04-12 12:39:14] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=pmtm&license=academic`
[2022-04-12 12:39:14] [SUCCESS] [OmnipathR] Loaded 19856 intercellular communication role records from cache.
[2022-04-12 12:39:14] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2022-04-12 12:39:15] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2022-04-12 12:39:15] [SUCCESS] [OmnipathR] Loaded 19993 intercellular communication role records from cache.
[2022-04-12 12:39:16] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/1a787c9aceb59267b238ebd678a711c3fedf0d33-1.rds`.
[2022-04-12 12:39:16] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=sec&causality=trans&license=academic`
[2022-04-12 12:39:16] [SUCCESS] [OmnipathR] Loaded 13593 intercellular communication role records from cache.
[2022-04-12 12:39:16] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2022-04-12 12:39:16] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2022-04-12 12:39:16] [SUCCESS] [OmnipathR] Loaded 19993 intercellular communication role records from cache.
[2022-04-12 12:39:19] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/77083b97fe6cc7634b5082dc5f5aa90120f867f0-1.rds`.
[2022-04-12 12:39:19] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=pmtm&causality=rec&license=academic`
[2022-04-12 12:39:19] [SUCCESS] [OmnipathR] Loaded 23105 intercellular communication role records from cache.
[2022-04-12 12:39:19] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2022-04-12 12:39:19] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2022-04-12 12:39:19] [SUCCESS] [OmnipathR] Loaded 19993 intercellular communication role records from cache.
[2022-04-12 12:39:24] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2022-04-12 12:39:24] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2022-04-12 12:39:25] [SUCCESS] [OmnipathR] Loaded 42541 interactions from cache.
[2022-04-12 12:39:28] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2022-04-12 12:39:28] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2022-04-12 12:39:28] [SUCCESS] [OmnipathR] Loaded 1145 annotation records from cache.
[2022-04-12 12:39:36] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2022-04-12 12:39:36] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2022-04-12 12:39:36] [SUCCESS] [OmnipathR] Loaded 1082 annotation records from cache.
[2022-04-12 12:39:45] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/fcb9b617e2cd1880fcda07c1509f5e941632e47b-1.rds`.
[2022-04-12 12:39:45] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&entity_types=protein&license=academic`
[2022-04-12 12:39:46] [SUCCESS] [OmnipathR] Loaded 37468 interactions from cache.
[2022-04-12 12:39:46] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/b66455a04c1c3908ec8bb3b116a5ad645607e9bd-1.rds`.
[2022-04-12 12:39:46] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=ligand&causality=trans&license=academic`
[2022-04-12 12:39:46] [SUCCESS] [OmnipathR] Loaded 8434 intercellular communication role records from cache.
[2022-04-12 12:39:47] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2022-04-12 12:39:47] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2022-04-12 12:39:47] [SUCCESS] [OmnipathR] Loaded 19993 intercellular communication role records from cache.
[2022-04-12 12:39:51] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3-1.rds`.
[2022-04-12 12:39:51] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=receptor&causality=rec&license=academic`
[2022-04-12 12:39:51] [SUCCESS] [OmnipathR] Loaded 14800 intercellular communication role records from cache.
[2022-04-12 12:39:58] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2022-04-12 12:39:58] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2022-04-12 12:39:58] [SUCCESS] [OmnipathR] Loaded 4618 interactions from cache.
[2022-04-12 12:40:00] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2022-04-12 12:40:00] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2022-04-12 12:40:00] [SUCCESS] [OmnipathR] Loaded 63410 annotation records from cache.
[2022-04-12 12:40:04] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2022-04-12 12:40:04] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2022-04-12 12:40:04] [SUCCESS] [OmnipathR] Loaded 1952 annotation records from cache.
[2022-04-12 12:40:11] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2022-04-12 12:40:11] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2022-04-12 12:40:11] [SUCCESS] [OmnipathR] Loaded 63410 annotation records from cache.
[2022-04-12 12:40:12] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2022-04-12 12:40:12] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2022-04-12 12:40:12] [SUCCESS] [OmnipathR] Loaded 1952 annotation records from cache.
--- finished re-building 'paths.Rmd'

SUMMARY: processing the following file failed:
  'omnipath_intro.Rmd'

Error: Vignette re-building failed.
Execution halted