| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-22 11:35:34 -0400 (Wed, 22 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 3444 |
| 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 527/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.10.0 (landing page) Pau Badia-i-Mompel
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the decoupleR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decoupleR.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: decoupleR |
| Version: 2.10.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:decoupleR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings decoupleR_2.10.0.tar.gz |
| StartedAt: 2024-05-22 01:00:44 -0400 (Wed, 22 May 2024) |
| EndedAt: 2024-05-22 01:37:42 -0400 (Wed, 22 May 2024) |
| EllapsedTime: 2218.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: decoupleR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:decoupleR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings decoupleR_2.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/decoupleR.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'decoupleR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'decoupleR' version '2.10.0'
* 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 whether package 'decoupleR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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 dependencies in R code ... NOTE
[2024-05-22 01:01:21] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:01:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:01:21] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-22 01:01:21] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-05-22 01:01:21] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-22 01:01:21] [TRACE] [OmnipathR] Contains 8 files.
[2024-05-22 01:01:21] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-05-22 01:01:21] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:01:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:01:21] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-22 01:01:22] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-22 01:01:22] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-22 01:01:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:01:22] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-22 01:01:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:01:22] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-22 01:01:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:01:22] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-22 01:01:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:01:22] [TRACE] [OmnipathR] Cache locked: FALSE
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'run_gsva.Rd':
'GSVA::gsva' 'GeneSetCollection'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_dorothea 545.75 9.29 555.58
get_collectri 131.96 2.27 138.38
run_fgsea 23.36 0.10 23.61
run_aucell 8.72 0.70 9.47
get_progeny 6.56 0.39 8.79
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
35. │ │ ├─enquo(arg) %>% ...
36. │ │ └─rlang::enquo(arg)
37. │ └─rlang::enquo(organism)
38. ├─OmnipathR::ncbi_taxid(.)
39. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
40. ├─purrr::map_int(., taxon_name, "ncbi")
41. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
42. │ └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
43. └─rlang::sym(organism_b)
44. └─rlang:::abort_coercion(x, "a symbol")
45. └─rlang::abort(msg, call = call)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 34 ]
Error: Test failures
Execution halted
* 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, 1 WARNING, 1 NOTE
See
'F:/biocbuild/bbs-3.19-bioc/meat/decoupleR.Rcheck/00check.log'
for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'decoupleR' ... ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (decoupleR)
decoupleR.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(decoupleR)
>
> test_check("decoupleR")
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[2024-05-22 01:17:09] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:17:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:09] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-22 01:17:09] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-05-22 01:17:09] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-22 01:17:09] [TRACE] [OmnipathR] Contains 8 files.
[2024-05-22 01:17:09] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-05-22 01:17:10] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:17:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:10] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-22 01:17:10] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-22 01:17:10] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-22 01:17:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:10] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-22 01:17:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:10] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-22 01:17:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:10] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-22 01:17:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:10] [TRACE] [OmnipathR] Cache locked: FALSE
[2024-05-22 01:17:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-22 01:17:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-22 01:17:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:11] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-22 01:17:11] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:17:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:11] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-22 01:17:11] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:17:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:11] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-05-22 01:17:11] [TRACE] [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-05-22 01:17:11] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-22 01:17:11] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-22 01:17:12] [TRACE] [OmnipathR] HTTP 200
[2024-05-22 01:17:12] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-05-22 01:17:12] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:17:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:12] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-05-22 01:17:12] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-05-22 01:17:12] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-05-22 01:17:12] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-05-22 01:17:12] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:17:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:12] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:17:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:12] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-05-22 01:17:12] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-05-22 01:17:12] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-05-22 01:17:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-05-22 01:17:13] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-05-22 01:17:13] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-05-22 01:17:13] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:17:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:13] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-05-22 01:17:13] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-05-22 01:17:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-22 01:17:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:14] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-22 01:17:14] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-22 01:17:14] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-22 01:17:14] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-22 01:17:14] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-22 01:17:14] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-22 01:17:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-22 01:17:14] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-22 01:17:14] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:17:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:14] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:17:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:14] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2024-05-22 01:17:14] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-05-22 01:17:14] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-05-22 01:17:14] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2024-05-22 01:17:14] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:17:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:14] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2024-05-22 01:17:14] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2024-05-22 01:17:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-22 01:17:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-22 01:17:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-22 01:17:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-22 01:17:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-22 01:17:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-22 01:17:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-22 01:17:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-22 01:17:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-22 01:17:19] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-22 01:17:19] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:17:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:19] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:17:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:19] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2024-05-22 01:17:19] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-05-22 01:17:21] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-05-22 01:17:21] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2024-05-22 01:17:21] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:17:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:21] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2024-05-22 01:17:21] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2024-05-22 01:17:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-22 01:17:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-22 01:17:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-22 01:17:26] [TRACE] [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-05-22 01:17:26] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-22 01:17:26] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2024-05-22 01:17:28] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2024-05-22 01:17:28] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-05-22 01:17:28] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-05-22 01:17:28] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-05-22 01:17:28] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-05-22 01:17:28] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-05-22 01:17:28] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-05-22 01:17:28] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-05-22 01:17:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-05-22 01:17:49] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:17:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:49] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:17:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:49] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`.
[2024-05-22 01:17:49] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2024-05-22 01:17:52] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2024-05-22 01:17:52] [INFO] [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1]
[2024-05-22 01:17:52] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:17:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:17:52] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`.
[2024-05-22 01:17:52] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-05-22 01:18:15] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2024-05-22 01:18:36] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any; excluding resources: none
[2024-05-22 01:26:19] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2024-05-22 01:26:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-05-22 01:26:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-05-22 01:26:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-05-22 01:26:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-05-22 01:26:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-05-22 01:26:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-05-22 01:26:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-05-22 01:26:33] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-05-22 01:26:33] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:26:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:26:33] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:26:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:26:33] [INFO] [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `unknown` to `started`.
[2024-05-22 01:26:33] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`.
[2024-05-22 01:26:35] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`.
[2024-05-22 01:26:35] [INFO] [OmnipathR] Download ready [key=73101f94a89eabbc8c12583d15dce08671d9e187, version=1]
[2024-05-22 01:26:35] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:26:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:26:35] [INFO] [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `started` to `ready`.
[2024-05-22 01:26:35] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-05-22 01:26:47] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2024-05-22 01:26:58] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any; excluding resources: none
[2024-05-22 01:32:22] [SUCCESS] [OmnipathR] Downloaded 5294 interactions.
[2024-05-22 01:32:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-05-22 01:32:22] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-05-22 01:32:22] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-05-22 01:32:22] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-05-22 01:32:22] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-05-22 01:32:22] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-05-22 01:32:22] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-05-22 01:32:26] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-05-22 01:32:26] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:32:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:32:26] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:32:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:32:26] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `unknown` to `started`.
[2024-05-22 01:32:26] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-05-22 01:32:27] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-05-22 01:32:27] [INFO] [OmnipathR] Download ready [key=82abc02990e13a4b0186ba97e7e04cb7c5c780b2, version=1]
[2024-05-22 01:32:27] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:32:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:32:27] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `started` to `ready`.
[2024-05-22 01:32:27] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-05-22 01:32:32] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any
[2024-05-22 01:32:37] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any; excluding resources: none
[2024-05-22 01:34:33] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2024-05-22 01:34:33] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-22 01:34:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:34:33] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-22 01:34:33] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-22 01:34:33] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-22 01:34:33] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-22 01:34:33] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-22 01:34:33] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-22 01:34:33] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-22 01:34:34] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-22 01:34:34] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:34:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:34:34] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:34:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:34:34] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2024-05-22 01:34:34] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-05-22 01:34:34] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-05-22 01:34:34] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2024-05-22 01:34:34] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 01:34:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:34:34] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2024-05-22 01:34:34] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-05-22 01:34:34] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2024-05-22 01:34:34] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2024-05-22 01:34:35] [SUCCESS] [OmnipathR] Downloaded 232 interactions.
[2024-05-22 01:34:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-05-22 01:34:35] [TRACE] [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-05-22 01:34:35] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-05-22 01:34:35] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-05-22 01:34:40] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any
[2024-05-22 01:34:46] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any; excluding resources: none
[2024-05-22 01:36:52] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2024-05-22 01:36:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-22 01:36:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-22 01:36:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-22 01:36:52] [TRACE] [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-05-22 01:36:52] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-22 01:36:52] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-05-22 01:36:52] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2024-05-22 01:36:52] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2024-05-22 01:36:53] [SUCCESS] [OmnipathR] Downloaded 232 interactions.
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Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 34 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-omnipath.R:19:3'): test get_progeny mouse ──────────────────────
Error in `sym(organism_b)`: Can't convert an integer vector to a symbol.
Backtrace:
▆
1. ├─decoupleR::get_progeny(organism = "mouse") at test-omnipath.R:19:3
2. │ ├─... %>% ...
3. │ └─decoupleR::get_resource("PROGENy", organism = organism)
4. │ └─... %>% ...
5. ├─rlang::set_names(., c("source", "target", "weight", "p_value"))
6. ├─dplyr::select(., pathway, genesymbol, weight, p_value)
7. ├─dplyr::bind_rows(.)
8. │ └─rlang::list2(...)
9. ├─purrr::map(...)
10. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
11. │ └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
12. ├─dplyr::group_split(.)
13. ├─dplyr::group_by(., pathway)
14. ├─dplyr::select(., genesymbol, p_value, pathway, weight)
15. ├─dplyr::mutate(., weight = as.double(weight), p_value = as.double(p_value))
16. ├─dplyr::distinct(., pathway, genesymbol, .keep_all = TRUE)
17. ├─... %>% ...
18. ├─OmnipathR::translate_ids(., uniprot, genesymbol, organism = organism)
19. ├─OmnipathR::orthology_translate_column(...)
20. │ ├─... %>% ...
21. │ └─OmnipathR::get_db(db_name, param = orthology_param)
22. │ └─OmnipathR::load_db(key, param = param)
23. │ ├─rlang::exec(loader, !!!param)
24. │ └─OmnipathR (local) `<fn>`(organism_a = 9606L, organism_b = 10090L)
25. │ └─environment() %>% as.list %>% ...
26. ├─rlang::set_names(., c(ORTHO_SOURCE_COL, ORTHO_TARGET_COL))
27. ├─dplyr::select(., -any_of("hgroup"))
28. ├─rlang::exec(oma_pairwise_translated, !!!.)
29. ├─OmnipathR (local) `<fn>`(...)
30. │ └─... %>% ...
31. ├─dplyr::filter(., !is.na(id_organism_a) & !is.na(id_organism_b))
32. ├─OmnipathR::translate_ids(...)
33. │ ├─... %>% ncbi_taxid
34. │ ├─OmnipathR:::.nse_ensure_str(!!enquo(organism))
35. │ │ ├─enquo(arg) %>% ...
36. │ │ └─rlang::enquo(arg)
37. │ └─rlang::enquo(organism)
38. ├─OmnipathR::ncbi_taxid(.)
39. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
40. ├─purrr::map_int(., taxon_name, "ncbi")
41. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
42. │ └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
43. └─rlang::sym(organism_b)
44. └─rlang:::abort_coercion(x, "a symbol")
45. └─rlang::abort(msg, call = call)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 34 ]
Error: Test failures
Execution halted
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.11 | 0.01 | 0.13 | |
| convert_f_defaults | 0.08 | 0.00 | 0.07 | |
| decouple | 0 | 0 | 0 | |
| dot-fit_preprocessing | 0.01 | 0.00 | 0.01 | |
| extract_sets | 0.02 | 0.02 | 0.04 | |
| filt_minsize | 0.04 | 0.00 | 0.04 | |
| get_collectri | 131.96 | 2.27 | 138.38 | |
| get_dorothea | 545.75 | 9.29 | 555.58 | |
| get_profile_of | 0 | 0 | 0 | |
| get_progeny | 6.56 | 0.39 | 8.79 | |
| get_resource | 0.50 | 0.07 | 1.66 | |
| get_toy_data | 0 | 0 | 0 | |
| intersect_regulons | 0.02 | 0.00 | 0.05 | |
| pipe | 0 | 0 | 0 | |
| pivot_wider_profile | 0 | 0 | 0 | |
| randomize_matrix | 0 | 0 | 0 | |
| rename_net | 0.04 | 0.00 | 0.04 | |
| run_aucell | 8.72 | 0.70 | 9.47 | |
| run_consensus | 1.94 | 0.05 | 1.97 | |
| run_fgsea | 23.36 | 0.10 | 23.61 | |
| run_gsva | 1.61 | 0.69 | 2.56 | |
| run_mdt | 0.29 | 0.17 | 0.22 | |
| run_mlm | 0.16 | 0.08 | 0.13 | |
| run_ora | 0.61 | 0.13 | 0.57 | |
| run_udt | 0.42 | 0.00 | 0.43 | |
| run_ulm | 0.06 | 0.00 | 0.06 | |
| run_viper | 0.61 | 0.19 | 0.97 | |
| run_wmean | 0.93 | 0.02 | 0.94 | |
| run_wsum | 1.01 | 0.00 | 1.02 | |
| show_methods | 0.08 | 0.00 | 0.09 | |
| show_resources | 0.08 | 0.00 | 0.47 | |
| tidyeval | 0 | 0 | 0 | |