Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-20 11:36:22 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4666 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4401 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4428 |
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 511/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
decoupleR 2.11.0 (landing page) Pau Badia-i-Mompel
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
kjohnson1 | macOS 13.6.6 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: 2.11.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:decoupleR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings decoupleR_2.11.0.tar.gz |
StartedAt: 2024-05-17 23:58:05 -0400 (Fri, 17 May 2024) |
EndedAt: 2024-05-18 00:34:17 -0400 (Sat, 18 May 2024) |
EllapsedTime: 2172.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: decoupleR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:decoupleR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings decoupleR_2.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/decoupleR.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 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 '2.11.0' * 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 [2024-05-17 23:58:40] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-17 23:58:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 23:58:40] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-05-17 23:58:40] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-17 23:58:40] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-05-17 23:58:40] [TRACE] [OmnipathR] Contains 8 files. [2024-05-17 23:58:40] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-17 23:58:40] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-17 23:58:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 23:58:41] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-05-17 23:58:41] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-05-17 23:58:41] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-17 23:58:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 23:58:41] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-17 23:58:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 23:58:41] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-17 23:58:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 23:58:41] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-17 23:58:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 23:58:41] [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 551.18 9.08 561.22 get_collectri 135.58 2.22 140.87 run_fgsea 21.93 0.06 22.16 run_aucell 8.52 0.71 9.28 get_progeny 6.02 0.38 7.79 * 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-3.20-bioc/meat/decoupleR.Rcheck/00check.log' for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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 RC (2024-04-16 r86468 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") | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% [2024-05-18 00:14:23] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:23] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-05-18 00:14:23] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-18 00:14:23] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-05-18 00:14:23] [TRACE] [OmnipathR] Contains 8 files. [2024-05-18 00:14:23] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-18 00:14:23] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:23] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-05-18 00:14:23] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-05-18 00:14:23] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-18 00:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:23] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-18 00:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:23] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-18 00:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:23] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-18 00:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:23] [TRACE] [OmnipathR] Cache locked: FALSE [2024-05-18 00:14:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-18 00:14:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-18 00:14:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:24] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-05-18 00:14:24] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:14:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:24] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-05-18 00:14:24] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:14:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:24] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-05-18 00:14:24] [TRACE] [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-05-18 00:14:24] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-05-18 00:14:25] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-05-18 00:14:25] [TRACE] [OmnipathR] HTTP 200 [2024-05-18 00:14:25] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-05-18 00:14:25] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:14:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:25] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-05-18 00:14:26] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-05-18 00:14:26] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-05-18 00:14:26] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-05-18 00:14:26] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:14:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:26] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:14:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:26] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-05-18 00:14:26] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-05-18 00:14:26] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-05-18 00:14:26] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-05-18 00:14:27] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-05-18 00:14:27] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-05-18 00:14:27] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:14:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:27] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-05-18 00:14:27] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-05-18 00:14:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-18 00:14:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-18 00:14:27] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-18 00:14:27] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-18 00:14:27] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-18 00:14:27] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-18 00:14:27] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-18 00:14:27] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-18 00:14:28] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-18 00:14:28] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:14:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:28] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:14:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:28] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`. [2024-05-18 00:14:28] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`. [2024-05-18 00:14:28] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`. [2024-05-18 00:14:28] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1] [2024-05-18 00:14:28] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:14:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:28] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`. [2024-05-18 00:14:28] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records. [2024-05-18 00:14:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-18 00:14:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-18 00:14:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-18 00:14:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-18 00:14:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-18 00:14:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-18 00:14:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-18 00:14:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-18 00:14:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-18 00:14:32] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-18 00:14:32] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:14:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:32] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:14:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:32] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`. [2024-05-18 00:14:32] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-05-18 00:14:34] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-05-18 00:14:34] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1] [2024-05-18 00:14:34] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:14:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:34] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`. [2024-05-18 00:14:34] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records. [2024-05-18 00:14:37] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-18 00:14:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:37] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-18 00:14:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:14:37] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-18 00:14:39] [TRACE] [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-05-18 00:14:39] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-18 00:14:39] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache. [2024-05-18 00:14:41] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`. [2024-05-18 00:14:41] [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` [2024-05-18 00:14:41] [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` [2024-05-18 00:14:41] [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` [2024-05-18 00:14:41] [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` [2024-05-18 00:14:41] [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` [2024-05-18 00:14:41] [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` [2024-05-18 00:14:41] [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` [2024-05-18 00:15:01] [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` [2024-05-18 00:15:01] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:15:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:15:01] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:15:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:15:01] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`. [2024-05-18 00:15:01] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`. [2024-05-18 00:15:03] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`. [2024-05-18 00:15:03] [INFO] [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1] [2024-05-18 00:15:03] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:15:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:15:03] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`. [2024-05-18 00:15:03] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-05-18 00:15:26] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any [2024-05-18 00:15:47] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any; excluding resources: none [2024-05-18 00:23:13] [SUCCESS] [OmnipathR] Downloaded 278830 interactions. [2024-05-18 00:23:25] [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` [2024-05-18 00:23:25] [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` [2024-05-18 00:23:25] [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` [2024-05-18 00:23:25] [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` [2024-05-18 00:23:25] [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` [2024-05-18 00:23:25] [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` [2024-05-18 00:23:25] [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` [2024-05-18 00:23:29] [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` [2024-05-18 00:23:29] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:23:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:23:29] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:23:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:23:29] [INFO] [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `unknown` to `started`. [2024-05-18 00:23:29] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`. [2024-05-18 00:23:31] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`. [2024-05-18 00:23:31] [INFO] [OmnipathR] Download ready [key=73101f94a89eabbc8c12583d15dce08671d9e187, version=1] [2024-05-18 00:23:31] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:23:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:23:31] [INFO] [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `started` to `ready`. [2024-05-18 00:23:31] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-05-18 00:23:42] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any [2024-05-18 00:23:54] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any; excluding resources: none [2024-05-18 00:29:06] [SUCCESS] [OmnipathR] Downloaded 5294 interactions. [2024-05-18 00:29:06] [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` [2024-05-18 00:29:06] [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` [2024-05-18 00:29:06] [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` [2024-05-18 00:29:06] [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` [2024-05-18 00:29:06] [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` [2024-05-18 00:29:06] [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` [2024-05-18 00:29:06] [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` [2024-05-18 00:29:10] [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` [2024-05-18 00:29:10] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:29:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:29:11] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:29:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:29:11] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `unknown` to `started`. [2024-05-18 00:29:11] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2024-05-18 00:29:11] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2024-05-18 00:29:11] [INFO] [OmnipathR] Download ready [key=82abc02990e13a4b0186ba97e7e04cb7c5c780b2, version=1] [2024-05-18 00:29:11] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:29:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:29:12] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `started` to `ready`. [2024-05-18 00:29:12] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-05-18 00:29:16] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any [2024-05-18 00:29:21] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any; excluding resources: none [2024-05-18 00:31:21] [SUCCESS] [OmnipathR] Downloaded 64958 interactions. [2024-05-18 00:31:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-18 00:31:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:31:21] [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` [2024-05-18 00:31:21] [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` [2024-05-18 00:31:21] [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` [2024-05-18 00:31:21] [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` [2024-05-18 00:31:21] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2024-05-18 00:31:21] [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` [2024-05-18 00:31:21] [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` [2024-05-18 00:31:22] [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` [2024-05-18 00:31:22] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:31:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:31:22] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:31:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:31:22] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`. [2024-05-18 00:31:22] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2024-05-18 00:31:22] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2024-05-18 00:31:22] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1] [2024-05-18 00:31:22] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-18 00:31:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:31:22] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`. [2024-05-18 00:31:22] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-05-18 00:31:22] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2024-05-18 00:31:22] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none [2024-05-18 00:31:23] [SUCCESS] [OmnipathR] Downloaded 232 interactions. [2024-05-18 00:31:23] [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` [2024-05-18 00:31:23] [TRACE] [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2024-05-18 00:31:23] [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` [2024-05-18 00:31:23] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-05-18 00:31:29] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any [2024-05-18 00:31:33] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any; excluding resources: none [2024-05-18 00:33:29] [SUCCESS] [OmnipathR] Downloaded 64958 interactions. [2024-05-18 00:33:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-18 00:33:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-18 00:33:30] [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` [2024-05-18 00:33:30] [TRACE] [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2024-05-18 00:33:30] [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` [2024-05-18 00:33:30] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-05-18 00:33:30] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2024-05-18 00:33:30] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none [2024-05-18 00:33:31] [SUCCESS] [OmnipathR] Downloaded 232 interactions. | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% 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 | 0.08 | 0.01 | 0.09 | |
convert_f_defaults | 0.04 | 0.00 | 0.05 | |
decouple | 0 | 0 | 0 | |
dot-fit_preprocessing | 0.02 | 0.00 | 0.02 | |
extract_sets | 0.01 | 0.02 | 0.03 | |
filt_minsize | 0.05 | 0.00 | 0.05 | |
get_collectri | 135.58 | 2.22 | 140.87 | |
get_dorothea | 551.18 | 9.08 | 561.22 | |
get_profile_of | 0 | 0 | 0 | |
get_progeny | 6.02 | 0.38 | 7.79 | |
get_resource | 0.35 | 0.04 | 1.55 | |
get_toy_data | 0 | 0 | 0 | |
intersect_regulons | 0.04 | 0.00 | 0.04 | |
pipe | 0 | 0 | 0 | |
pivot_wider_profile | 0 | 0 | 0 | |
randomize_matrix | 0 | 0 | 0 | |
rename_net | 0.03 | 0.00 | 0.03 | |
run_aucell | 8.52 | 0.71 | 9.28 | |
run_consensus | 2.05 | 0.01 | 2.06 | |
run_fgsea | 21.93 | 0.06 | 22.16 | |
run_gsva | 1.55 | 0.46 | 1.61 | |
run_mdt | 0.17 | 0.17 | 0.17 | |
run_mlm | 0.11 | 0.08 | 0.09 | |
run_ora | 0.57 | 0.23 | 0.44 | |
run_udt | 0.36 | 0.05 | 0.33 | |
run_ulm | 0.07 | 0.00 | 0.06 | |
run_viper | 0.86 | 0.11 | 1.27 | |
run_wmean | 0.81 | 0.01 | 0.83 | |
run_wsum | 0.70 | 0.05 | 0.75 | |
show_methods | 0.06 | 0.02 | 0.10 | |
show_resources | 0.09 | 0.00 | 0.65 | |
tidyeval | 0 | 0 | 0 | |