| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-09-23 11:48 -0400 (Mon, 23 Sep 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4440 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4451 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4484 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4431 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4429 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1439/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.13.25 (landing page) Denes Turei
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: OmnipathR |
| Version: 3.13.25 |
| 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 |
| StartedAt: 2024-09-22 23:05:22 -0400 (Sun, 22 Sep 2024) |
| EndedAt: 2024-09-22 23:13:46 -0400 (Sun, 22 Sep 2024) |
| EllapsedTime: 504.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
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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: aarch64-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 Ventura 13.6.7
* 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
[2024-09-22 23:05:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:05:32] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-09-22 23:05:32] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-09-22 23:05:32] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-09-22 23:05:32] [TRACE] [OmnipathR] Contains 1 files.
[2024-09-22 23:05:32] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-09-22 23:05:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:05:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-09-22 23:05:32] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-09-22 23:05:32] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-09-22 23:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:05:32] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-09-22 23:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:05:32] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-09-22 23:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:05:32] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-09-22 23:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:05:32] [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
[2024-09-22 23:05:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:05:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:05:37] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-09-22 23:05:37] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-09-22 23:05:37] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-09-22 23:05:37] [TRACE] [OmnipathR] Contains 1 files.
[2024-09-22 23:05:37] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-09-22 23:05:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:05:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:05:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-09-22 23:05:37] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-09-22 23:05:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-09-22 23:05:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:05:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-09-22 23:05:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:05:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-09-22 23:05:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:05:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-09-22 23:05:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:05:37] [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"))
[2024-09-22 23:12:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CA1,SIGNOR,SignaLink3],datasets=omnipath]
[2024-09-22 23:12:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CA1,SIGNOR,SignaLink3],datasets=omnipath,query_type=interactions]
[2024-09-22 23:12:37] [TRACE] [OmnipathR] Organism(s): 9606
[2024-09-22 23:12:37] [TRACE] [OmnipathR] Orthology targets:
[2024-09-22 23:12:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-22 23:12:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:38] [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`
[2024-09-22 23:12:38] [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`
[2024-09-22 23:12:38] [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`
[2024-09-22 23:12:38] [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`
[2024-09-22 23:12:38] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:12:38] [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`
[2024-09-22 23:12:38] [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`
[2024-09-22 23:12:40] [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`
[2024-09-22 23:12:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:40] [INFO] [OmnipathR] Cache item `029da7bc67579749c5723c06c82d60c331a10ad3` version 1: status changed from `unknown` to `started`.
[2024-09-22 23:12:40] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/029da7bc67579749c5723c06c82d60c331a10ad3-1.rds`.
[2024-09-22 23:12:40] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/029da7bc67579749c5723c06c82d60c331a10ad3-1.rds`.
[2024-09-22 23:12:40] [INFO] [OmnipathR] Download ready [key=029da7bc67579749c5723c06c82d60c331a10ad3, version=1]
[2024-09-22 23:12:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:40] [INFO] [OmnipathR] Cache item `029da7bc67579749c5723c06c82d60c331a10ad3` version 1: status changed from `started` to `ready`.
[2024-09-22 23:12:41] [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
+ )
[2024-09-22 23:12:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,organisms=9606,query_type=interactions]
[2024-09-22 23:12:41] [TRACE] [OmnipathR] Organism(s): 9606
[2024-09-22 23:12:41] [TRACE] [OmnipathR] Orthology targets:
[2024-09-22 23:12:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-22 23:12:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:42] [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`
[2024-09-22 23:12:42] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2024-09-22 23:12:42] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:12:42] [SUCCESS] [OmnipathR] Loaded 1796 interactions from cache.
>
> pathways <- omnipath()
[2024-09-22 23:12:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2024-09-22 23:12:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2024-09-22 23:12:42] [TRACE] [OmnipathR] Organism(s): 9606
[2024-09-22 23:12:42] [TRACE] [OmnipathR] Orthology targets:
[2024-09-22 23:12:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:12:42] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-09-22 23:12:42] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:12:43] [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
+ )
[2024-09-22 23:12:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[BioGRID,IntAct],organisms=9606,datasets=pathwayextra]
[2024-09-22 23:12:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[BioGRID,IntAct],organisms=9606,datasets=pathwayextra,query_type=interactions]
[2024-09-22 23:12:43] [TRACE] [OmnipathR] Organism(s): 9606
[2024-09-22 23:12:43] [TRACE] [OmnipathR] Orthology targets:
[2024-09-22 23:12:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-22 23:12:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:44] [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`
[2024-09-22 23:12:44] [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`
[2024-09-22 23:12:44] [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`
[2024-09-22 23:12:44] [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`
[2024-09-22 23:12:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:12:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:12:44] [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`
[2024-09-22 23:12:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:12:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:45] [INFO] [OmnipathR] Cache item `aa665c2ecdd9e913e13934eeb12c1fa7b0d21884` version 1: status changed from `unknown` to `started`.
[2024-09-22 23:12:45] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/aa665c2ecdd9e913e13934eeb12c1fa7b0d21884-1.rds`.
[2024-09-22 23:12:45] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/aa665c2ecdd9e913e13934eeb12c1fa7b0d21884-1.rds`.
[2024-09-22 23:12:45] [INFO] [OmnipathR] Download ready [key=aa665c2ecdd9e913e13934eeb12c1fa7b0d21884, version=1]
[2024-09-22 23:12:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:45] [INFO] [OmnipathR] Cache item `aa665c2ecdd9e913e13934eeb12c1fa7b0d21884` version 1: status changed from `started` to `ready`.
[2024-09-22 23:12:45] [SUCCESS] [OmnipathR] Downloaded 2439 interactions.
>
> kinase_substrate <-
+ kinaseextra(
+ resources = c('PhosphoPoint', 'PhosphoSite'),
+ organism = 9606
+ )
[2024-09-22 23:12:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=9606,datasets=kinaseextra]
[2024-09-22 23:12:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=9606,datasets=kinaseextra,query_type=interactions]
[2024-09-22 23:12:45] [TRACE] [OmnipathR] Organism(s): 9606
[2024-09-22 23:12:45] [TRACE] [OmnipathR] Orthology targets:
[2024-09-22 23:12:46] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-22 23:12:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:46] [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`
[2024-09-22 23:12:46] [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`
[2024-09-22 23:12:46] [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`
[2024-09-22 23:12:46] [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`
[2024-09-22 23:12:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:12:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:12:46] [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`
[2024-09-22 23:12:47] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:12:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:48] [INFO] [OmnipathR] Cache item `7db24bdf2093c17feeea2eea249fad461c5a1d09` version 1: status changed from `unknown` to `started`.
[2024-09-22 23:12:48] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/7db24bdf2093c17feeea2eea249fad461c5a1d09-1.rds`.
[2024-09-22 23:12:48] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/7db24bdf2093c17feeea2eea249fad461c5a1d09-1.rds`.
[2024-09-22 23:12:48] [INFO] [OmnipathR] Download ready [key=7db24bdf2093c17feeea2eea249fad461c5a1d09, version=1]
[2024-09-22 23:12:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:48] [INFO] [OmnipathR] Cache item `7db24bdf2093c17feeea2eea249fad461c5a1d09` version 1: status changed from `started` to `ready`.
[2024-09-22 23:12:48] [SUCCESS] [OmnipathR] Downloaded 11432 interactions.
>
> ligand_receptor <- ligrecextra(
+ resources = c('HPRD', 'Guide2Pharma'),
+ organism = 9606
+ )
[2024-09-22 23:12:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[HPRD,Guide2Pharma],organisms=9606,datasets=ligrecextra]
[2024-09-22 23:12:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[HPRD,Guide2Pharma],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2024-09-22 23:12:48] [TRACE] [OmnipathR] Organism(s): 9606
[2024-09-22 23:12:48] [TRACE] [OmnipathR] Orthology targets:
[2024-09-22 23:12:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-22 23:12:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:49] [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`
[2024-09-22 23:12:49] [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`
[2024-09-22 23:12:49] [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`
[2024-09-22 23:12:49] [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`
[2024-09-22 23:12:49] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:12:49] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:12:49] [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`
[2024-09-22 23:12:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:12:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:50] [INFO] [OmnipathR] Cache item `393dd95dc380ac2e0800d32dc3f2fbbc88166e57` version 1: status changed from `unknown` to `started`.
[2024-09-22 23:12:50] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/393dd95dc380ac2e0800d32dc3f2fbbc88166e57-1.rds`.
[2024-09-22 23:12:50] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/393dd95dc380ac2e0800d32dc3f2fbbc88166e57-1.rds`.
[2024-09-22 23:12:50] [INFO] [OmnipathR] Download ready [key=393dd95dc380ac2e0800d32dc3f2fbbc88166e57, version=1]
[2024-09-22 23:12:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:50] [INFO] [OmnipathR] Cache item `393dd95dc380ac2e0800d32dc3f2fbbc88166e57` version 1: status changed from `started` to `ready`.
[2024-09-22 23:12:50] [SUCCESS] [OmnipathR] Downloaded 1881 interactions.
>
> interactions <- post_translational(resources = "BioGRID")
[2024-09-22 23:12:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=BioGRID,query_type=interactions]
[2024-09-22 23:12:50] [TRACE] [OmnipathR] Organism(s): 9606
[2024-09-22 23:12:50] [TRACE] [OmnipathR] Orthology targets:
[2024-09-22 23:12:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-22 23:12:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:50] [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`
[2024-09-22 23:12:50] [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`
[2024-09-22 23:12:50] [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`
[2024-09-22 23:12:50] [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`
[2024-09-22 23:12:50] [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`
[2024-09-22 23:12:50] [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`
[2024-09-22 23:12:50] [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`
[2024-09-22 23:12:51] [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`
[2024-09-22 23:12:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:51] [INFO] [OmnipathR] Cache item `108f2cda262af403a026484add1c5a2c3d9c94fe` version 1: status changed from `unknown` to `started`.
[2024-09-22 23:12:52] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/108f2cda262af403a026484add1c5a2c3d9c94fe-1.rds`.
[2024-09-22 23:12:52] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/108f2cda262af403a026484add1c5a2c3d9c94fe-1.rds`.
[2024-09-22 23:12:52] [INFO] [OmnipathR] Download ready [key=108f2cda262af403a026484add1c5a2c3d9c94fe, version=1]
[2024-09-22 23:12:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:52] [INFO] [OmnipathR] Cache item `108f2cda262af403a026484add1c5a2c3d9c94fe` version 1: status changed from `started` to `ready`.
[2024-09-22 23:12:52] [SUCCESS] [OmnipathR] Downloaded 2526 interactions.
>
> dorothea_grn <- dorothea(
+ resources = c('DoRothEA', 'ARACNe-GTEx_DoRothEA'),
+ organism = 9606,
+ dorothea_levels = c('A', 'B', 'C')
+ )
[2024-09-22 23:12:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],resources=[DoRothEA,ARACNe-GTEx_DoRothEA],organisms=9606,query_type=interactions,datasets=dorothea]
[2024-09-22 23:12:52] [TRACE] [OmnipathR] Organism(s): 9606
[2024-09-22 23:12:52] [TRACE] [OmnipathR] Orthology targets:
[2024-09-22 23:12:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-22 23:12:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:52] [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`
[2024-09-22 23:12:52] [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`
[2024-09-22 23:12:52] [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`
[2024-09-22 23:12:52] [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`
[2024-09-22 23:12:52] [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`
[2024-09-22 23:12:52] [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`
[2024-09-22 23:12:52] [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`
[2024-09-22 23:12:54] [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`
[2024-09-22 23:12:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:54] [INFO] [OmnipathR] Cache item `ce66cb9846294c226acee9ccf50a608c089386dd` version 1: status changed from `unknown` to `started`.
[2024-09-22 23:12:54] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ce66cb9846294c226acee9ccf50a608c089386dd-1.rds`.
[2024-09-22 23:12:54] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ce66cb9846294c226acee9ccf50a608c089386dd-1.rds`.
[2024-09-22 23:12:54] [INFO] [OmnipathR] Download ready [key=ce66cb9846294c226acee9ccf50a608c089386dd, version=1]
[2024-09-22 23:12:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:54] [INFO] [OmnipathR] Cache item `ce66cb9846294c226acee9ccf50a608c089386dd` version 1: status changed from `started` to `ready`.
[2024-09-22 23:12:55] [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"))
[2024-09-22 23:12:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[DoRothEA,SIGNOR],query_type=interactions,datasets=tf_target]
[2024-09-22 23:12:55] [TRACE] [OmnipathR] Organism(s): 9606
[2024-09-22 23:12:55] [TRACE] [OmnipathR] Orthology targets:
[2024-09-22 23:12:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-22 23:12:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:56] [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`
[2024-09-22 23:12:56] [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`
[2024-09-22 23:12:56] [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`
[2024-09-22 23:12:56] [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`
[2024-09-22 23:12:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:12:56] [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`
[2024-09-22 23:12:56] [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`
[2024-09-22 23:12:57] [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`
[2024-09-22 23:12:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:57] [INFO] [OmnipathR] Cache item `8276e09e9336e7886c5a256f51a7e3d7d28f62ca` version 1: status changed from `unknown` to `started`.
[2024-09-22 23:12:57] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8276e09e9336e7886c5a256f51a7e3d7d28f62ca-1.rds`.
[2024-09-22 23:12:57] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8276e09e9336e7886c5a256f51a7e3d7d28f62ca-1.rds`.
[2024-09-22 23:12:57] [INFO] [OmnipathR] Download ready [key=8276e09e9336e7886c5a256f51a7e3d7d28f62ca, version=1]
[2024-09-22 23:12:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:12:57] [INFO] [OmnipathR] Cache item `8276e09e9336e7886c5a256f51a7e3d7d28f62ca` version 1: status changed from `started` to `ready`.
[2024-09-22 23:12:57] [SUCCESS] [OmnipathR] Downloaded 13904 interactions.
>
> grn <- transcriptional(resources = c("PAZAR", "ORegAnno", "DoRothEA"))
[2024-09-22 23:12:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],resources=[PAZAR,ORegAnno,DoRothEA],query_type=interactions]
[2024-09-22 23:12:57] [TRACE] [OmnipathR] Organism(s): 9606
[2024-09-22 23:12:57] [TRACE] [OmnipathR] Orthology targets:
[2024-09-22 23:12:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-22 23:12:58] [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.
[2024-09-22 23:12:58] [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`
[2024-09-22 23:12:58] [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`
[2024-09-22 23:12:58] [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`
[2024-09-22 23:12:58] [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`
[2024-09-22 23:12:58] [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`
[2024-09-22 23:12:58] [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`
[2024-09-22 23:12:58] [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`
[2024-09-22 23:12:59] [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`
[2024-09-22 23:12:59] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:12:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:00] [INFO] [OmnipathR] Cache item `fed61c7ea10ed87b5184e4f70ee57689f412965a` version 1: status changed from `unknown` to `started`.
[2024-09-22 23:13:00] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/fed61c7ea10ed87b5184e4f70ee57689f412965a-1.rds`.
[2024-09-22 23:13:00] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/fed61c7ea10ed87b5184e4f70ee57689f412965a-1.rds`.
[2024-09-22 23:13:00] [INFO] [OmnipathR] Download ready [key=fed61c7ea10ed87b5184e4f70ee57689f412965a, version=1]
[2024-09-22 23:13:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:00] [INFO] [OmnipathR] Cache item `fed61c7ea10ed87b5184e4f70ee57689f412965a` version 1: status changed from `started` to `ready`.
[2024-09-22 23:13:00] [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()
[2024-09-22 23:13:00] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions,datasets=collectri]
[2024-09-22 23:13:00] [TRACE] [OmnipathR] Organism(s): 9606
[2024-09-22 23:13:00] [TRACE] [OmnipathR] Orthology targets:
[2024-09-22 23:13:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:13:00] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:13:00] [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`
[2024-09-22 23:13:00] [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`
[2024-09-22 23:13:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:13:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:13:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:13:03] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:13:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:03] [INFO] [OmnipathR] Cache item `e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02` version 1: status changed from `unknown` to `started`.
[2024-09-22 23:13:03] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02-1.rds`.
[2024-09-22 23:13:03] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02-1.rds`.
[2024-09-22 23:13:03] [INFO] [OmnipathR] Download ready [key=e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02, version=1]
[2024-09-22 23:13:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:03] [INFO] [OmnipathR] Cache item `e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02` version 1: status changed from `started` to `ready`.
[2024-09-22 23:13:04] [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"))
[2024-09-22 23:13:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miRTarBase,miRecords],query_type=interactions,datasets=mirnatarget]
[2024-09-22 23:13:04] [TRACE] [OmnipathR] Organism(s): 9606
[2024-09-22 23:13:04] [TRACE] [OmnipathR] Orthology targets:
[2024-09-22 23:13:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-22 23:13:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:04] [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`
[2024-09-22 23:13:04] [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`
[2024-09-22 23:13:04] [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`
[2024-09-22 23:13:04] [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`
[2024-09-22 23:13:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:13:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:13:04] [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`
[2024-09-22 23:13:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:13:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:05] [INFO] [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `unknown` to `started`.
[2024-09-22 23:13:05] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`.
[2024-09-22 23:13:05] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`.
[2024-09-22 23:13:05] [INFO] [OmnipathR] Download ready [key=fc18df7465bfc9f5b72d079bc3dc9408636597cc, version=1]
[2024-09-22 23:13:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:05] [INFO] [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `started` to `ready`.
[2024-09-22 23:13:06] [SUCCESS] [OmnipathR] Downloaded 8906 interactions.
>
> interactions <- tf_mirna(resources = "TransmiR")
[2024-09-22 23:13:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,query_type=interactions,datasets=tf_mirna]
[2024-09-22 23:13:06] [TRACE] [OmnipathR] Organism(s): 9606
[2024-09-22 23:13:06] [TRACE] [OmnipathR] Orthology targets:
[2024-09-22 23:13:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-22 23:13:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:06] [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`
[2024-09-22 23:13:06] [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`
[2024-09-22 23:13:06] [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`
[2024-09-22 23:13:06] [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`
[2024-09-22 23:13:06] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:13:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:13:06] [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`
[2024-09-22 23:13:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:13:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:07] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`.
[2024-09-22 23:13:07] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2024-09-22 23:13:07] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2024-09-22 23:13:07] [INFO] [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1]
[2024-09-22 23:13:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:07] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`.
[2024-09-22 23:13:07] [SUCCESS] [OmnipathR] Downloaded 3868 interactions.
>
> interactions <- lncrna_mrna(resources = c("ncRDeathDB"))
[2024-09-22 23:13:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=ncRDeathDB,query_type=interactions,datasets=lncrna_mrna]
[2024-09-22 23:13:07] [TRACE] [OmnipathR] Organism(s): 9606
[2024-09-22 23:13:07] [TRACE] [OmnipathR] Orthology targets:
[2024-09-22 23:13:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-22 23:13:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:07] [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`
[2024-09-22 23:13:07] [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`
[2024-09-22 23:13:07] [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`
[2024-09-22 23:13:07] [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`
[2024-09-22 23:13:07] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:13:07] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:13:07] [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`
[2024-09-22 23:13:08] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:08] [INFO] [OmnipathR] Cache item `f327904e6e8d62e0cafeae1a4c3b8cc1af68503f` version 1: status changed from `unknown` to `started`.
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f327904e6e8d62e0cafeae1a4c3b8cc1af68503f-1.rds`.
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f327904e6e8d62e0cafeae1a4c3b8cc1af68503f-1.rds`.
[2024-09-22 23:13:08] [INFO] [OmnipathR] Download ready [key=f327904e6e8d62e0cafeae1a4c3b8cc1af68503f, version=1]
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:08] [INFO] [OmnipathR] Cache item `f327904e6e8d62e0cafeae1a4c3b8cc1af68503f` version 1: status changed from `started` to `ready`.
[2024-09-22 23:13:08] [SUCCESS] [OmnipathR] Downloaded 129 interactions.
>
> # What are the targets of aspirin?
> interactions <- small_molecule(sources = "ASPIRIN")
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=ASPIRIN,query_type=interactions,datasets=small_molecule]
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Organism(s): 9606
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Orthology targets:
[2024-09-22 23:13:08] [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`
[2024-09-22 23:13:08] [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`
[2024-09-22 23:13:08] [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`
[2024-09-22 23:13:08] [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`
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2024-09-22 23:13:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2024-09-22 23:13:08] [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`
[2024-09-22 23:13:08] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:08] [INFO] [OmnipathR] Cache item `f9f812113b53ae5b9c2613603e0c3316aa921419` version 1: status changed from `unknown` to `started`.
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f9f812113b53ae5b9c2613603e0c3316aa921419-1.rds`.
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f9f812113b53ae5b9c2613603e0c3316aa921419-1.rds`.
[2024-09-22 23:13:08] [INFO] [OmnipathR] Download ready [key=f9f812113b53ae5b9c2613603e0c3316aa921419, version=1]
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:08] [INFO] [OmnipathR] Cache item `f9f812113b53ae5b9c2613603e0c3316aa921419` version 1: status changed from `started` to `ready`.
[2024-09-22 23:13:08] [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
+ )
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Organism(s): 9606
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Orthology targets:
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/d4a3f6fd0083bc974e7269e2ff6b02df9633e303-1.rds`.
[2024-09-22 23:13:08] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2024-09-22 23:13:08] [SUCCESS] [OmnipathR] Loaded 26 records from cache.
[2024-09-22 23:13:08] [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]
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Organism(s): 9606
[2024-09-22 23:13:08] [TRACE] [OmnipathR] Orthology targets:
[2024-09-22 23:13:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-22 23:13:09] [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.
[2024-09-22 23:13:09] [WARN] [OmnipathR] Unknown parameter: `q_info`.
[2024-09-22 23:13:09] [WARN] [OmnipathR] Unknown parameter: `q_info`.
[2024-09-22 23:13:09] [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`
[2024-09-22 23:13:09] [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`
[2024-09-22 23:13:09] [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`
[2024-09-22 23:13:09] [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`
[2024-09-22 23:13:09] [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`
[2024-09-22 23:13:09] [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`
[2024-09-22 23:13:09] [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
[2024-09-22 23:13:09] [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`
[2024-09-22 23:13:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:09] [INFO] [OmnipathR] Cache item `2e3b7153d123252b67dd2076e3434c75fe26903b` version 1: status changed from `unknown` to `started`.
[2024-09-22 23:13:09] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2e3b7153d123252b67dd2076e3434c75fe26903b-1.rds`.
[2024-09-22 23:13:09] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2e3b7153d123252b67dd2076e3434c75fe26903b-1.rds`.
[2024-09-22 23:13:09] [INFO] [OmnipathR] Download ready [key=2e3b7153d123252b67dd2076e3434c75fe26903b, version=1]
[2024-09-22 23:13:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:09] [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.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘OmnipathR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2024-09-22 15:23:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 15:23:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 15:23:41] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-09-22 15:23:41] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-09-22 15:23:41] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-09-22 15:23:41] [TRACE] [OmnipathR] Contains 1 files. [2024-09-22 15:23:41] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-09-22 15:23:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 15:23:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 15:23:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-09-22 15:23:41] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-09-22 15:23:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-09-22 15:23:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 15:23:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-09-22 15:23:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 15:23:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-09-22 15:23:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 15:23:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-09-22 15:23:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 15:23:41] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-09-22 15:23:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 15:23:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 15:23:42] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-09-22 15:23:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-09-22 15:23:42] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-09-22 15:23:42] [TRACE] [OmnipathR] Contains 1 files. [2024-09-22 15:23:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-09-22 15:23:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 15:23:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 15:23:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-09-22 15:23:42] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-09-22 15:23:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-09-22 15:23:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 15:23:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-09-22 15:23:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 15:23:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-09-22 15:23:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 15:23:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-09-22 15:23:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 15:23:42] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.
> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2024-09-22 23:13:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:10] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-09-22 23:13:10] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-09-22 23:13:10] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-09-22 23:13:10] [TRACE] [OmnipathR] Contains 65 files.
[2024-09-22 23:13:10] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-09-22 23:13:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-22 23:13:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-09-22 23:13:10] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-09-22 23:13:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-09-22 23:13:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-09-22 23:13:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-09-22 23:13:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-09-22 23:13:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-09-22 23:13:10] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
3.538 0.364 30.117
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.000 | 0.001 | 0.000 | |
| all_uniprot_acs | 0.006 | 0.001 | 0.007 | |
| all_uniprots | 0.278 | 0.040 | 179.831 | |
| ancestors | 0.003 | 0.000 | 0.004 | |
| annotated_network | 0.236 | 0.027 | 3.154 | |
| annotation_categories | 35.119 | 0.023 | 36.533 | |
| annotation_resources | 0.019 | 0.002 | 0.701 | |
| annotations | 0.087 | 0.009 | 0.826 | |
| biomart_query | 0.437 | 0.027 | 2.833 | |
| bioplex1 | 0.003 | 0.001 | 0.004 | |
| bioplex2 | 0.003 | 0.000 | 0.003 | |
| bioplex3 | 0.003 | 0.001 | 0.004 | |
| bioplex_all | 0.003 | 0.000 | 0.003 | |
| bioplex_hct116_1 | 0.003 | 0.000 | 0.004 | |
| bma_motif_es | 0.112 | 0.012 | 0.841 | |
| bma_motif_vs | 0.049 | 0.003 | 0.588 | |
| chalmers_gem | 0.003 | 0.001 | 0.004 | |
| chalmers_gem_id_mapping_table | 0.002 | 0.000 | 0.003 | |
| chalmers_gem_id_type | 0.009 | 0.000 | 0.009 | |
| chalmers_gem_metabolites | 0.003 | 0.001 | 0.004 | |
| chalmers_gem_network | 0.003 | 0.000 | 0.003 | |
| chalmers_gem_raw | 0.003 | 0.000 | 0.003 | |
| chalmers_gem_reactions | 0.003 | 0.000 | 0.003 | |
| common_name | 0.01 | 0.00 | 0.01 | |
| complex_genes | 0.145 | 0.011 | 1.938 | |
| complex_resources | 0.031 | 0.001 | 0.548 | |
| complexes | 0.049 | 0.003 | 0.564 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.012 | 0.000 | 0.013 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 1.496 | 0.099 | 10.845 | |
| curated_ligrec_stats | 9.291 | 0.521 | 69.940 | |
| database_summary | 0.473 | 0.033 | 3.173 | |
| descendants | 0.004 | 0.000 | 0.004 | |
| ensembl_dataset | 0.004 | 0.000 | 0.005 | |
| ensembl_id_mapping_table | 0.742 | 0.029 | 20.730 | |
| ensembl_id_type | 0 | 0 | 0 | |
| ensembl_name | 0.017 | 0.001 | 0.017 | |
| ensembl_organisms | 0.046 | 0.001 | 0.046 | |
| ensembl_organisms_raw | 0.044 | 0.001 | 0.045 | |
| ensembl_orthology | 0 | 0 | 0 | |
| enzsub_graph | 0.786 | 0.024 | 2.747 | |
| enzsub_resources | 0.018 | 0.002 | 0.602 | |
| enzyme_substrate | 0.288 | 0.007 | 0.806 | |
| evex_download | 0.003 | 0.001 | 0.003 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 3.581 | 0.061 | 6.569 | |
| extra_attrs | 1.899 | 0.015 | 1.913 | |
| extra_attrs_to_cols | 3.005 | 0.014 | 3.018 | |
| filter_by_resource | 1.814 | 0.050 | 4.361 | |
| filter_extra_attrs | 5.626 | 0.047 | 7.194 | |
| filter_intercell | 2.838 | 0.210 | 7.862 | |
| filter_intercell_network | 0.007 | 0.001 | 0.008 | |
| find_all_paths | 2.104 | 0.068 | 2.845 | |
| from_evidences | 0.000 | 0.001 | 0.000 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.004 | 0.001 | 0.013 | |
| giant_component | 3.585 | 0.139 | 7.061 | |
| go_annot_download | 4.129 | 0.205 | 4.224 | |
| go_annot_slim | 0.001 | 0.000 | 0.000 | |
| go_ontology_download | 0.003 | 0.001 | 0.003 | |
| guide2pharma_download | 0.003 | 0.000 | 0.003 | |
| harmonizome_download | 0.003 | 0.001 | 0.003 | |
| has_extra_attrs | 1.963 | 0.025 | 1.989 | |
| hmdb_id_mapping_table | 0.003 | 0.000 | 0.004 | |
| hmdb_id_type | 0.001 | 0.000 | 0.001 | |
| hmdb_metabolite_fields | 0 | 0 | 0 | |
| hmdb_protein_fields | 0 | 0 | 0 | |
| hmdb_table | 0.004 | 0.000 | 0.004 | |
| homologene_download | 0.003 | 0.000 | 0.003 | |
| homologene_raw | 0.007 | 0.000 | 0.007 | |
| homologene_uniprot_orthology | 0.004 | 0.001 | 0.004 | |
| hpo_download | 0.831 | 0.077 | 2.312 | |
| htridb_download | 0.003 | 0.000 | 0.004 | |
| id_translation_resources | 0.000 | 0.000 | 0.001 | |
| id_types | 0.012 | 0.001 | 0.012 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.107 | 0.012 | 0.357 | |
| interaction_graph | 0.184 | 0.006 | 0.807 | |
| interaction_resources | 0.020 | 0.002 | 0.610 | |
| interaction_types | 0.016 | 0.001 | 0.017 | |
| intercell | 0.135 | 0.018 | 0.666 | |
| intercell_categories | 0.104 | 0.012 | 0.357 | |
| intercell_consensus_filter | 0.421 | 0.038 | 2.085 | |
| intercell_generic_categories | 0.014 | 0.001 | 0.015 | |
| intercell_network | 0.003 | 0.000 | 0.003 | |
| intercell_resources | 0.033 | 0.006 | 0.555 | |
| intercell_summary | 0.017 | 0.004 | 0.022 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.009 | 0.000 | 0.011 | |
| is_trembl | 0.009 | 0.001 | 0.010 | |
| is_uniprot | 0.004 | 0.000 | 0.004 | |
| kegg_info | 0.003 | 0.001 | 0.004 | |
| kegg_open | 0.004 | 0.000 | 0.003 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.003 | 0.001 | 0.004 | |
| kegg_pathway_list | 0.004 | 0.000 | 0.004 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.026 | 0.005 | 4.313 | |
| kegg_process | 0.006 | 0.000 | 0.006 | |
| latin_name | 0.017 | 0.001 | 0.017 | |
| load_db | 0.019 | 0.001 | 0.020 | |
| ncbi_taxid | 0.017 | 0.000 | 0.017 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.003 | 0.000 | 0.004 | |
| nichenet_gr_network | 0.017 | 0.001 | 0.018 | |
| nichenet_gr_network_evex | 0.003 | 0.000 | 0.003 | |
| nichenet_gr_network_harmonizome | 0.003 | 0.000 | 0.003 | |
| nichenet_gr_network_htridb | 0.002 | 0.001 | 0.003 | |
| nichenet_gr_network_omnipath | 3.875 | 0.306 | 6.561 | |
| nichenet_gr_network_pathwaycommons | 0.003 | 0.000 | 0.003 | |
| nichenet_gr_network_regnetwork | 0.003 | 0.000 | 0.003 | |
| nichenet_gr_network_remap | 0.002 | 0.001 | 0.003 | |
| nichenet_gr_network_trrust | 0.002 | 0.000 | 0.003 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.007 | 0.000 | 0.008 | |
| nichenet_lr_network_guide2pharma | 0.003 | 0.001 | 0.003 | |
| nichenet_lr_network_omnipath | 0.008 | 0.000 | 0.008 | |
| nichenet_lr_network_ramilowski | 0.003 | 0.001 | 0.003 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.012 | 0.001 | 0.014 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.019 | 0.001 | 0.020 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.008 | 0.001 | 0.009 | |
| nichenet_signaling_network_cpdb | 0.003 | 0.000 | 0.003 | |
| nichenet_signaling_network_evex | 0.003 | 0.000 | 0.003 | |
| nichenet_signaling_network_harmonizome | 0.002 | 0.000 | 0.003 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 2.698 | 0.188 | 5.354 | |
| nichenet_signaling_network_pathwaycommons | 0.003 | 0.000 | 0.003 | |
| nichenet_signaling_network_vinayagam | 0.003 | 0.000 | 0.004 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0.000 | 0.000 | 0.001 | |
| obo_parser | 0.027 | 0.003 | 0.182 | |
| oma_code | 0.009 | 0.000 | 0.009 | |
| oma_organisms | 0.038 | 0.001 | 0.038 | |
| oma_pairwise | 0.005 | 0.000 | 0.005 | |
| oma_pairwise_genesymbols | 0.003 | 0.000 | 0.004 | |
| oma_pairwise_translated | 0.003 | 0.000 | 0.003 | |