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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.13.25.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.13.25’
* 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 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 ... OK
* 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 code 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 whether startup messages can be suppressed ... NOTE
[2024-09-23 22:32:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:32:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:32:23] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-09-23 22:32:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-09-23 22:32:23] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-09-23 22:32:23] [TRACE]   [OmnipathR] Contains 1 files.
[2024-09-23 22:32:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-09-23 22:32:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:32:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:32:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-09-23 22:32:24] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-09-23 22:32:24] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-09-23 22:32:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:32:24] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-09-23 22:32:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:32:24] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-09-23 22:32:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:32:24] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-09-23 22:32:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:32:24] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* 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
[2024-09-23 22:32:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:32:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:32:42] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-09-23 22:32:42] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-09-23 22:32:42] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-09-23 22:32:42] [TRACE]   [OmnipathR] Contains 1 files.
[2024-09-23 22:32:42] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-09-23 22:32:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:32:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:32:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-09-23 22:32:42] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-09-23 22:32:42] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-09-23 22:32:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:32:42] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-09-23 22:32:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:32:42] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-09-23 22:32:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:32:42] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-09-23 22:32:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:32:42] [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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: omnipath-interactions
> ### Title: Molecular interactions from OmniPath
> ### Aliases: omnipath-interactions omnipath_interactions
> ###   import_omnipath_interactions omnipath pathwayextra
> ###   import_pathwayextra_interactions kinaseextra
> ###   import_kinaseextra_interactions ligrecextra
> ###   import_ligrecextra_interactions post_translational
> ###   import_post_translational_interactions dorothea
> ###   import_dorothea_interactions tf_target import_tf_target_interactions
> ###   transcriptional import_transcriptional_interactions collectri
> ###   mirna_target import_mirnatarget_interactions tf_mirna
> ###   import_tf_mirna_interactions lncrna_mrna
> ###   import_lncrna_mrna_interactions small_molecule
> ###   import_small_molecule_protein_interactions all_interactions
> ###   import_all_interactions
> 
> ### ** Examples
> 
> op <- omnipath(resources = c("CA1", "SIGNOR", "SignaLink3"))
[2024-09-23 22:41:06] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[CA1,SIGNOR,SignaLink3],datasets=omnipath]
[2024-09-23 22:41:06] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[CA1,SIGNOR,SignaLink3],datasets=omnipath,query_type=interactions]
[2024-09-23 22:41:07] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-09-23 22:41:07] [TRACE]   [OmnipathR] Orthology targets: 
[2024-09-23 22:41:07] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-23 22:41:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:07] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:07] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:07] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:07] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:07] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:09] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:10] [INFO]    [OmnipathR] Cache item `029da7bc67579749c5723c06c82d60c331a10ad3` version 1: status changed from `unknown` to `started`.
[2024-09-23 22:41:10] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/029da7bc67579749c5723c06c82d60c331a10ad3-1.rds`.
[2024-09-23 22:41:10] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/029da7bc67579749c5723c06c82d60c331a10ad3-1.rds`.
[2024-09-23 22:41:10] [INFO]    [OmnipathR] Download ready [key=029da7bc67579749c5723c06c82d60c331a10ad3, version=1]
[2024-09-23 22:41:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:10] [INFO]    [OmnipathR] Cache item `029da7bc67579749c5723c06c82d60c331a10ad3` version 1: status changed from `started` to `ready`.
[2024-09-23 22:41:13] [SUCCESS] [OmnipathR] Downloaded 63078 interactions.
> op
# A tibble: 63,078 × 15
   source target source_genesymbol target_genesymbol is_directed is_stimulation
   <chr>  <chr>  <chr>             <chr>                   <dbl>          <dbl>
 1 Q13976 Q13507 PRKG1             TRPC3                       1              0
 2 Q13976 Q9HCX4 PRKG1             TRPC7                       1              1
 3 Q13438 Q9HBA0 OS9               TRPV4                       1              1
 4 P18031 Q9H1D0 PTPN1             TRPV6                       1              0
 5 P63244 Q9BX84 RACK1             TRPM6                       1              0
 6 P17612 Q9GZU1 PRKACA            MCOLN1                      1              0
 7 Q16539 P49137 MAPK14            MAPKAPK2                    1              1
 8 P49137 Q13151 MAPKAPK2          HNRNPA0                     1              1
 9 P49137 O95453 MAPKAPK2          PARN                        1              0
10 O60674 P19235 JAK2              EPOR                        1              1
# ℹ 63,068 more rows
# ℹ 9 more variables: is_inhibition <dbl>, consensus_direction <dbl>,
#   consensus_stimulation <dbl>, consensus_inhibition <dbl>, sources <chr>,
#   references <chr>, curation_effort <dbl>, n_references <int>,
#   n_resources <int>
> 
> interactions = omnipath_interactions(
+     resources = "SignaLink3",
+     organism = 9606
+ )
[2024-09-23 22:41:13] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,organisms=9606,query_type=interactions]
[2024-09-23 22:41:13] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-09-23 22:41:13] [TRACE]   [OmnipathR] Orthology targets: 
[2024-09-23 22:41:14] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-23 22:41:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:14] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:14] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2024-09-23 22:41:14] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:14] [SUCCESS] [OmnipathR] Loaded 1796 interactions from cache.
> 
> pathways <- omnipath()
[2024-09-23 22:41:14] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2024-09-23 22:41:14] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2024-09-23 22:41:14] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-09-23 22:41:14] [TRACE]   [OmnipathR] Orthology targets: 
[2024-09-23 22:41:14] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:14] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-09-23 22:41:14] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:18] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
> pathways
# A tibble: 81,529 × 15
   source target source_genesymbol target_genesymbol is_directed is_stimulation
   <chr>  <chr>  <chr>             <chr>                   <dbl>          <dbl>
 1 P0DP23 P48995 CALM1             TRPC1                       1              0
 2 P0DP25 P48995 CALM3             TRPC1                       1              0
 3 P0DP24 P48995 CALM2             TRPC1                       1              0
 4 Q03135 P48995 CAV1              TRPC1                       1              1
 5 P14416 P48995 DRD2              TRPC1                       1              1
 6 Q99750 P48995 MDFI              TRPC1                       1              0
 7 Q14571 P48995 ITPR2             TRPC1                       1              1
 8 P29966 P48995 MARCKS            TRPC1                       1              0
 9 Q13255 P48995 GRM1              TRPC1                       1              1
10 Q13586 P48995 STIM1             TRPC1                       1              1
# ℹ 81,519 more rows
# ℹ 9 more variables: is_inhibition <dbl>, consensus_direction <dbl>,
#   consensus_stimulation <dbl>, consensus_inhibition <dbl>, sources <chr>,
#   references <chr>, curation_effort <dbl>, n_references <int>,
#   n_resources <int>
> 
> interactions <-
+     pathwayextra(
+         resources = c("BioGRID", "IntAct"),
+         organism = 9606
+     )
[2024-09-23 22:41:18] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[BioGRID,IntAct],organisms=9606,datasets=pathwayextra]
[2024-09-23 22:41:18] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[BioGRID,IntAct],organisms=9606,datasets=pathwayextra,query_type=interactions]
[2024-09-23 22:41:18] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-09-23 22:41:18] [TRACE]   [OmnipathR] Orthology targets: 
[2024-09-23 22:41:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-23 22:41:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:19] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:19] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:19] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:19] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:19] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:19] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:19] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:20] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:20] [INFO]    [OmnipathR] Cache item `aa665c2ecdd9e913e13934eeb12c1fa7b0d21884` version 1: status changed from `unknown` to `started`.
[2024-09-23 22:41:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/aa665c2ecdd9e913e13934eeb12c1fa7b0d21884-1.rds`.
[2024-09-23 22:41:21] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/aa665c2ecdd9e913e13934eeb12c1fa7b0d21884-1.rds`.
[2024-09-23 22:41:21] [INFO]    [OmnipathR] Download ready [key=aa665c2ecdd9e913e13934eeb12c1fa7b0d21884, version=1]
[2024-09-23 22:41:21] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:21] [INFO]    [OmnipathR] Cache item `aa665c2ecdd9e913e13934eeb12c1fa7b0d21884` version 1: status changed from `started` to `ready`.
[2024-09-23 22:41:21] [SUCCESS] [OmnipathR] Downloaded 2439 interactions.
> 
> kinase_substrate <-
+    kinaseextra(
+        resources = c('PhosphoPoint', 'PhosphoSite'),
+        organism = 9606
+    )
[2024-09-23 22:41:21] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=9606,datasets=kinaseextra]
[2024-09-23 22:41:21] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=9606,datasets=kinaseextra,query_type=interactions]
[2024-09-23 22:41:21] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-09-23 22:41:21] [TRACE]   [OmnipathR] Orthology targets: 
[2024-09-23 22:41:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-23 22:41:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:22] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:22] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:22] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:22] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:22] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:23] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:23] [INFO]    [OmnipathR] Cache item `7db24bdf2093c17feeea2eea249fad461c5a1d09` version 1: status changed from `unknown` to `started`.
[2024-09-23 22:41:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/7db24bdf2093c17feeea2eea249fad461c5a1d09-1.rds`.
[2024-09-23 22:41:24] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/7db24bdf2093c17feeea2eea249fad461c5a1d09-1.rds`.
[2024-09-23 22:41:24] [INFO]    [OmnipathR] Download ready [key=7db24bdf2093c17feeea2eea249fad461c5a1d09, version=1]
[2024-09-23 22:41:24] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:24] [INFO]    [OmnipathR] Cache item `7db24bdf2093c17feeea2eea249fad461c5a1d09` version 1: status changed from `started` to `ready`.
[2024-09-23 22:41:25] [SUCCESS] [OmnipathR] Downloaded 11432 interactions.
> 
> ligand_receptor <- ligrecextra(
+     resources = c('HPRD', 'Guide2Pharma'),
+     organism = 9606
+ )
[2024-09-23 22:41:25] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[HPRD,Guide2Pharma],organisms=9606,datasets=ligrecextra]
[2024-09-23 22:41:25] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[HPRD,Guide2Pharma],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2024-09-23 22:41:25] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-09-23 22:41:25] [TRACE]   [OmnipathR] Orthology targets: 
[2024-09-23 22:41:25] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-23 22:41:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:25] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:25] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:25] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:25] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:25] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:25] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:25] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:26] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:26] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:26] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:27] [INFO]    [OmnipathR] Cache item `393dd95dc380ac2e0800d32dc3f2fbbc88166e57` version 1: status changed from `unknown` to `started`.
[2024-09-23 22:41:27] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/393dd95dc380ac2e0800d32dc3f2fbbc88166e57-1.rds`.
[2024-09-23 22:41:27] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/393dd95dc380ac2e0800d32dc3f2fbbc88166e57-1.rds`.
[2024-09-23 22:41:27] [INFO]    [OmnipathR] Download ready [key=393dd95dc380ac2e0800d32dc3f2fbbc88166e57, version=1]
[2024-09-23 22:41:27] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:27] [INFO]    [OmnipathR] Cache item `393dd95dc380ac2e0800d32dc3f2fbbc88166e57` version 1: status changed from `started` to `ready`.
[2024-09-23 22:41:27] [SUCCESS] [OmnipathR] Downloaded 1881 interactions.
> 
> interactions <- post_translational(resources = "BioGRID")
[2024-09-23 22:41:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=BioGRID,query_type=interactions]
[2024-09-23 22:41:27] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-09-23 22:41:27] [TRACE]   [OmnipathR] Orthology targets: 
[2024-09-23 22:41:28] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-23 22:41:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:28] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:28] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:28] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:28] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:28] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:29] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:29] [INFO]    [OmnipathR] Cache item `108f2cda262af403a026484add1c5a2c3d9c94fe` version 1: status changed from `unknown` to `started`.
[2024-09-23 22:41:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/108f2cda262af403a026484add1c5a2c3d9c94fe-1.rds`.
[2024-09-23 22:41:29] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/108f2cda262af403a026484add1c5a2c3d9c94fe-1.rds`.
[2024-09-23 22:41:29] [INFO]    [OmnipathR] Download ready [key=108f2cda262af403a026484add1c5a2c3d9c94fe, version=1]
[2024-09-23 22:41:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:29] [INFO]    [OmnipathR] Cache item `108f2cda262af403a026484add1c5a2c3d9c94fe` version 1: status changed from `started` to `ready`.
[2024-09-23 22:41:30] [SUCCESS] [OmnipathR] Downloaded 2526 interactions.
> 
> dorothea_grn <- dorothea(
+     resources = c('DoRothEA', 'ARACNe-GTEx_DoRothEA'),
+     organism = 9606,
+     dorothea_levels = c('A', 'B', 'C')
+ )
[2024-09-23 22:41:30] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],resources=[DoRothEA,ARACNe-GTEx_DoRothEA],organisms=9606,query_type=interactions,datasets=dorothea]
[2024-09-23 22:41:30] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-09-23 22:41:30] [TRACE]   [OmnipathR] Orthology targets: 
[2024-09-23 22:41:30] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-23 22:41:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:30] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-09-23 22:41:30] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-09-23 22:41:30] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-09-23 22:41:30] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-09-23 22:41:30] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-09-23 22:41:30] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-09-23 22:41:30] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-09-23 22:41:32] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-09-23 22:41:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:32] [INFO]    [OmnipathR] Cache item `ce66cb9846294c226acee9ccf50a608c089386dd` version 1: status changed from `unknown` to `started`.
[2024-09-23 22:41:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ce66cb9846294c226acee9ccf50a608c089386dd-1.rds`.
[2024-09-23 22:41:32] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ce66cb9846294c226acee9ccf50a608c089386dd-1.rds`.
[2024-09-23 22:41:32] [INFO]    [OmnipathR] Download ready [key=ce66cb9846294c226acee9ccf50a608c089386dd, version=1]
[2024-09-23 22:41:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:32] [INFO]    [OmnipathR] Cache item `ce66cb9846294c226acee9ccf50a608c089386dd` version 1: status changed from `started` to `ready`.
[2024-09-23 22:41:34] [SUCCESS] [OmnipathR] Downloaded 32617 interactions.
> dorothea_grn
# A tibble: 32,617 × 16
   source target source_genesymbol target_genesymbol is_directed is_stimulation
   <chr>  <chr>  <chr>             <chr>                   <dbl>          <dbl>
 1 P01106 O14746 MYC               TERT                        1              1
 2 P84022 P05412 SMAD3             JUN                         1              1
 3 Q13485 P05412 SMAD4             JUN                         1              1
 4 P08047 P04075 SP1               ALDOA                       1              1
 5 P04637 P08069 TP53              IGF1R                       1              0
 6 Q05516 P20248 ZBTB16            CCNA2                       1              0
 7 Q01196 P08700 RUNX1             IL3                         1              0
 8 P42224 P38936 STAT1             CDKN1A                      1              1
 9 P40763 P38936 STAT3             CDKN1A                      1              1
10 Q04206 P08183 RELA              ABCB1                       1              1
# ℹ 32,607 more rows
# ℹ 10 more variables: is_inhibition <dbl>, consensus_direction <dbl>,
#   consensus_stimulation <dbl>, consensus_inhibition <dbl>, sources <chr>,
#   references <chr>, curation_effort <dbl>, dorothea_level <chr>,
#   n_references <dbl>, n_resources <int>
> 
> interactions <- tf_target(resources = c("DoRothEA", "SIGNOR"))
[2024-09-23 22:41:34] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[DoRothEA,SIGNOR],query_type=interactions,datasets=tf_target]
[2024-09-23 22:41:34] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-09-23 22:41:34] [TRACE]   [OmnipathR] Orthology targets: 
[2024-09-23 22:41:35] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-23 22:41:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:35] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:35] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:35] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:35] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:35] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:35] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:37] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:37] [INFO]    [OmnipathR] Cache item `8276e09e9336e7886c5a256f51a7e3d7d28f62ca` version 1: status changed from `unknown` to `started`.
[2024-09-23 22:41:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8276e09e9336e7886c5a256f51a7e3d7d28f62ca-1.rds`.
[2024-09-23 22:41:37] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8276e09e9336e7886c5a256f51a7e3d7d28f62ca-1.rds`.
[2024-09-23 22:41:37] [INFO]    [OmnipathR] Download ready [key=8276e09e9336e7886c5a256f51a7e3d7d28f62ca, version=1]
[2024-09-23 22:41:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:37] [INFO]    [OmnipathR] Cache item `8276e09e9336e7886c5a256f51a7e3d7d28f62ca` version 1: status changed from `started` to `ready`.
[2024-09-23 22:41:38] [SUCCESS] [OmnipathR] Downloaded 13904 interactions.
> 
> grn <- transcriptional(resources = c("PAZAR", "ORegAnno", "DoRothEA"))
[2024-09-23 22:41:38] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],resources=[PAZAR,ORegAnno,DoRothEA],query_type=interactions]
[2024-09-23 22:41:38] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-09-23 22:41:38] [TRACE]   [OmnipathR] Orthology targets: 
[2024-09-23 22:41:38] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-23 22:41:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
Warning in omnipath_check_param(.) :
  The following resources are not available: PAZAR. Check the resource names for spelling mistakes.
[2024-09-23 22:41:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-09-23 22:41:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-09-23 22:41:39] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-09-23 22:41:39] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-09-23 22:41:39] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-09-23 22:41:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-09-23 22:41:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-09-23 22:41:40] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-09-23 22:41:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:41] [INFO]    [OmnipathR] Cache item `fed61c7ea10ed87b5184e4f70ee57689f412965a` version 1: status changed from `unknown` to `started`.
[2024-09-23 22:41:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/fed61c7ea10ed87b5184e4f70ee57689f412965a-1.rds`.
[2024-09-23 22:41:41] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/fed61c7ea10ed87b5184e4f70ee57689f412965a-1.rds`.
[2024-09-23 22:41:41] [INFO]    [OmnipathR] Download ready [key=fed61c7ea10ed87b5184e4f70ee57689f412965a, version=1]
[2024-09-23 22:41:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:41] [INFO]    [OmnipathR] Cache item `fed61c7ea10ed87b5184e4f70ee57689f412965a` version 1: status changed from `started` to `ready`.
[2024-09-23 22:41:42] [SUCCESS] [OmnipathR] Downloaded 31896 interactions.
> grn
# A tibble: 31,896 × 16
   source target source_genesymbol target_genesymbol is_directed is_stimulation
   <chr>  <chr>  <chr>             <chr>                   <dbl>          <dbl>
 1 P01106 O14746 MYC               TERT                        1              1
 2 P84022 P05412 SMAD3             JUN                         1              1
 3 Q13485 P05412 SMAD4             JUN                         1              1
 4 Q04206 P25445 RELA              FAS                         1              1
 5 P08047 P04075 SP1               ALDOA                       1              1
 6 P04637 P08069 TP53              IGF1R                       1              0
 7 Q05516 P20248 ZBTB16            CCNA2                       1              0
 8 Q01196 P08700 RUNX1             IL3                         1              0
 9 P42224 P38936 STAT1             CDKN1A                      1              1
10 P40763 P38936 STAT3             CDKN1A                      1              1
# ℹ 31,886 more rows
# ℹ 10 more variables: is_inhibition <dbl>, consensus_direction <dbl>,
#   consensus_stimulation <dbl>, consensus_inhibition <dbl>, sources <chr>,
#   references <chr>, curation_effort <dbl>, dorothea_level <chr>,
#   n_references <dbl>, n_resources <int>
> 
> collectri_grn <- collectri()
[2024-09-23 22:41:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=interactions,datasets=collectri]
[2024-09-23 22:41:43] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-09-23 22:41:43] [TRACE]   [OmnipathR] Orthology targets: 
[2024-09-23 22:41:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:43] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:43] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:43] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:43] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:45] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:45] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:45] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:45] [INFO]    [OmnipathR] Cache item `e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02` version 1: status changed from `unknown` to `started`.
[2024-09-23 22:41:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02-1.rds`.
[2024-09-23 22:41:46] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02-1.rds`.
[2024-09-23 22:41:46] [INFO]    [OmnipathR] Download ready [key=e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02, version=1]
[2024-09-23 22:41:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:46] [INFO]    [OmnipathR] Cache item `e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02` version 1: status changed from `started` to `ready`.
[2024-09-23 22:41:49] [SUCCESS] [OmnipathR] Downloaded 64495 interactions.
> collectri_grn
# A tibble: 64,495 × 15
   source  target source_genesymbol target_genesymbol is_directed is_stimulation
   <chr>   <chr>  <chr>             <chr>                   <dbl>          <dbl>
 1 P01106  O14746 MYC               TERT                        1              1
 2 P17947  P02818 SPI1              BGLAP                       1              1
 3 COMPLE… P05412 FOSL1_JUNB        JUN                         1              1
 4 COMPLE… P05412 FOS_JUN           JUN                         1              1
 5 COMPLE… P05412 FOS_JUNB          JUN                         1              1
 6 COMPLE… P05412 FOSL2_JUND        JUN                         1              1
 7 COMPLE… P05412 FOSL2_JUN         JUN                         1              1
 8 COMPLE… P05412 JUN               JUN                         1              1
 9 COMPLE… P05412 FOSB_JUNB         JUN                         1              1
10 COMPLE… P05412 JUNB              JUN                         1              1
# ℹ 64,485 more rows
# ℹ 9 more variables: is_inhibition <dbl>, consensus_direction <dbl>,
#   consensus_stimulation <dbl>, consensus_inhibition <dbl>, sources <chr>,
#   references <chr>, curation_effort <dbl>, n_references <dbl>,
#   n_resources <int>
> 
> interactions <- mirna_target( resources = c("miRTarBase", "miRecords"))
[2024-09-23 22:41:49] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[miRTarBase,miRecords],query_type=interactions,datasets=mirnatarget]
[2024-09-23 22:41:49] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-09-23 22:41:49] [TRACE]   [OmnipathR] Orthology targets: 
[2024-09-23 22:41:49] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-23 22:41:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:49] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:49] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:49] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:49] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:49] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:49] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:49] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:50] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:50] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:51] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:51] [INFO]    [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `unknown` to `started`.
[2024-09-23 22:41:51] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`.
[2024-09-23 22:41:51] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`.
[2024-09-23 22:41:51] [INFO]    [OmnipathR] Download ready [key=fc18df7465bfc9f5b72d079bc3dc9408636597cc, version=1]
[2024-09-23 22:41:51] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:51] [INFO]    [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `started` to `ready`.
[2024-09-23 22:41:51] [SUCCESS] [OmnipathR] Downloaded 8906 interactions.
> 
> interactions <- tf_mirna(resources = "TransmiR")
[2024-09-23 22:41:51] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,query_type=interactions,datasets=tf_mirna]
[2024-09-23 22:41:51] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-09-23 22:41:51] [TRACE]   [OmnipathR] Orthology targets: 
[2024-09-23 22:41:52] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-23 22:41:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:52] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:52] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:52] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:52] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:52] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:52] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:52] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:53] [INFO]    [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`.
[2024-09-23 22:41:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2024-09-23 22:41:53] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2024-09-23 22:41:53] [INFO]    [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1]
[2024-09-23 22:41:53] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:53] [INFO]    [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`.
[2024-09-23 22:41:53] [SUCCESS] [OmnipathR] Downloaded 3868 interactions.
> 
> interactions <- lncrna_mrna(resources = c("ncRDeathDB"))
[2024-09-23 22:41:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=ncRDeathDB,query_type=interactions,datasets=lncrna_mrna]
[2024-09-23 22:41:53] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-09-23 22:41:53] [TRACE]   [OmnipathR] Orthology targets: 
[2024-09-23 22:41:53] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-23 22:41:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:53] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:53] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:53] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:54] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:54] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:54] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:54] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:54] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-23 22:41:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:54] [INFO]    [OmnipathR] Cache item `f327904e6e8d62e0cafeae1a4c3b8cc1af68503f` version 1: status changed from `unknown` to `started`.
[2024-09-23 22:41:54] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f327904e6e8d62e0cafeae1a4c3b8cc1af68503f-1.rds`.
[2024-09-23 22:41:54] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f327904e6e8d62e0cafeae1a4c3b8cc1af68503f-1.rds`.
[2024-09-23 22:41:54] [INFO]    [OmnipathR] Download ready [key=f327904e6e8d62e0cafeae1a4c3b8cc1af68503f, version=1]
[2024-09-23 22:41:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:54] [INFO]    [OmnipathR] Cache item `f327904e6e8d62e0cafeae1a4c3b8cc1af68503f` version 1: status changed from `started` to `ready`.
[2024-09-23 22:41:54] [SUCCESS] [OmnipathR] Downloaded 129 interactions.
> 
> # What are the targets of aspirin?
> interactions <- small_molecule(sources = "ASPIRIN")
[2024-09-23 22:41:54] [TRACE]   [OmnipathR] Arguments for OmniPath query: [sources=ASPIRIN,query_type=interactions,datasets=small_molecule]
[2024-09-23 22:41:54] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-09-23 22:41:54] [TRACE]   [OmnipathR] Orthology targets: 
[2024-09-23 22:41:54] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2024-09-23 22:41:54] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2024-09-23 22:41:54] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2024-09-23 22:41:54] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2024-09-23 22:41:54] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2024-09-23 22:41:54] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2024-09-23 22:41:54] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2024-09-23 22:41:55] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2024-09-23 22:41:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:55] [INFO]    [OmnipathR] Cache item `f9f812113b53ae5b9c2613603e0c3316aa921419` version 1: status changed from `unknown` to `started`.
[2024-09-23 22:41:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f9f812113b53ae5b9c2613603e0c3316aa921419-1.rds`.
[2024-09-23 22:41:55] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f9f812113b53ae5b9c2613603e0c3316aa921419-1.rds`.
[2024-09-23 22:41:55] [INFO]    [OmnipathR] Download ready [key=f9f812113b53ae5b9c2613603e0c3316aa921419, version=1]
[2024-09-23 22:41:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:55] [INFO]    [OmnipathR] Cache item `f9f812113b53ae5b9c2613603e0c3316aa921419` version 1: status changed from `started` to `ready`.
[2024-09-23 22:41:55] [SUCCESS] [OmnipathR] Downloaded 0 interactions.
> # The prostaglandin synthases:
> interactions
# A tibble: 0 × 14
# ℹ 14 variables: source <chr>, target <chr>, source_genesymbol <chr>,
#   target_genesymbol <chr>, is_directed <chr>, is_stimulation <chr>,
#   is_inhibition <chr>, consensus_direction <chr>,
#   consensus_stimulation <chr>, consensus_inhibition <chr>, sources <chr>,
#   references <chr>, curation_effort <chr>, n_references <lgl>
> 
> interactions <- all_interactions(
+     resources = c("HPRD", "BioGRID"),
+     organism = 9606
+ )
[2024-09-23 22:41:55] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-09-23 22:41:55] [TRACE]   [OmnipathR] Orthology targets: 
[2024-09-23 22:41:55] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2024-09-23 22:41:55] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/d4a3f6fd0083bc974e7269e2ff6b02df9633e303-1.rds`.
[2024-09-23 22:41:55] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2024-09-23 22:41:55] [SUCCESS] [OmnipathR] Loaded 26 records from cache.
[2024-09-23 22:41:55] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],types=[lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional],fields=[type,dorothea_level],datasets=[collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,...],q_info=[header=<NULL>,format=[json,tab,table,text,tsv],license=[academic,commercial,for_profit,forprofit,ignore,non_profit,nonprofit],password=<NULL>,limit=<NULL>,datasets=[collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,...],types=[lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional],sources=<NULL>,resources=<NULL>,databases=[ABS,ACSN,ACSN_SignaLink3,ARACNe-GTEx_DoRothEA,ARN,Adhesome,AlzPathway,BEL-Large-Corpus_ProtMapper,Baccin2019,BioGRID,...],...],resources=[HPRD,BioGRID],organisms=9606,query_type=ineractions]
[2024-09-23 22:41:55] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-09-23 22:41:55] [TRACE]   [OmnipathR] Orthology targets: 
[2024-09-23 22:41:55] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-23 22:41:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
Warning in omnipath_check_param(.) :
  The following resources are not available: HPRD, BioGRID. Check the resource names for spelling mistakes.
[2024-09-23 22:41:56] [WARN]    [OmnipathR] Unknown parameter: `q_info`.
[2024-09-23 22:41:56] [WARN]    [OmnipathR] Unknown parameter: `q_info`.
[2024-09-23 22:41:56] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional`
[2024-09-23 22:41:56] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional`
[2024-09-23 22:41:56] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional`
[2024-09-23 22:41:56] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional`
[2024-09-23 22:41:56] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional`
[2024-09-23 22:41:56] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional`
[2024-09-23 22:41:56] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional`
Warning: The following named parsers don't match the column names: dorothea_level
[2024-09-23 22:41:56] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional`
[2024-09-23 22:41:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:56] [INFO]    [OmnipathR] Cache item `2e3b7153d123252b67dd2076e3434c75fe26903b` version 1: status changed from `unknown` to `started`.
[2024-09-23 22:41:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2e3b7153d123252b67dd2076e3434c75fe26903b-1.rds`.
[2024-09-23 22:41:56] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2e3b7153d123252b67dd2076e3434c75fe26903b-1.rds`.
[2024-09-23 22:41:56] [INFO]    [OmnipathR] Download ready [key=2e3b7153d123252b67dd2076e3434c75fe26903b, version=1]
[2024-09-23 22:41:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 22:41:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 22:41:56] [INFO]    [OmnipathR] Cache item `2e3b7153d123252b67dd2076e3434c75fe26903b` version 1: status changed from `started` to `ready`.
Error in omnipath_check_result(result, url) : 
  Failed to download data from OmniPath:
URL: https://omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional

Failed to download data from OmniPath:
URL: http://no-tls.omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional

Calls: all_interactions ... %>% -> omnipath_post_download -> omnipath_check_result
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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.