| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:18 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 511/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.6.0 (landing page) Pau Badia-i-Mompel
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
| kjohnson2 | macOS 12.6.1 Monterey / 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: 2.6.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings decoupleR_2.6.0.tar.gz |
| StartedAt: 2023-10-15 20:39:48 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 21:07:16 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 1648.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: decoupleR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings decoupleR_2.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/decoupleR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.6.0’
* 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 for sufficient/correct file permissions ... 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 R 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
[2023-10-15 20:40:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:40:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:40:17] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 20:40:17] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-10-15 20:40:17] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 20:40:17] [TRACE] [OmnipathR] Contains 6 files.
[2023-10-15 20:40:17] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-10-15 20:40:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:40:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:40:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 20:40:17] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2023-10-15 20:40:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-15 20:40:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:40:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-15 20:40:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:40:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-15 20:40:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:40:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-15 20:40:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:40:18] [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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_dorothea 320.726 4.816 330.393
get_collectri 79.381 1.888 84.140
run_fgsea 19.567 0.895 20.462
get_progeny 7.082 0.891 15.325
run_aucell 5.422 0.727 6.150
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘decoupleR.Rmd’ using ‘UTF-8’... OK
‘pw_bk.Rmd’ using ‘UTF-8’... OK
‘pw_sc.Rmd’ using ‘UTF-8’... OK
‘tf_bk.Rmd’ using ‘UTF-8’... OK
‘tf_sc.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/decoupleR.Rcheck/00check.log’
for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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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[2023-10-15 20:49:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:49:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:32] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 20:49:32] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-10-15 20:49:32] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 20:49:32] [TRACE] [OmnipathR] Contains 5 files.
[2023-10-15 20:49:32] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-10-15 20:49:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:49:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 20:49:32] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2023-10-15 20:49:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-15 20:49:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-15 20:49:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-15 20:49:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-15 20:49:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:33] [TRACE] [OmnipathR] Cache locked: FALSE
[2023-10-15 20:49:33] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-10-15 20:49:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:34] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-10-15 20:49:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:35] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-10-15 20:49:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:35] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-10-15 20:49:35] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-10-15 20:49:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-10-15 20:49:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:49:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:49:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:36] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2023-10-15 20:49:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2023-10-15 20:49:36] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2023-10-15 20:49:36] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2023-10-15 20:49:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:49:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:36] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2023-10-15 20:49:36] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2023-10-15 20:49:37] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-10-15 20:49:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-10-15 20:49:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:38] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-10-15 20:49:38] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-10-15 20:49:38] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-10-15 20:49:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:49:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:49:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:46] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2023-10-15 20:49:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-10-15 20:49:48] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-10-15 20:49:48] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2023-10-15 20:49:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:49:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:48] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2023-10-15 20:49:48] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2023-10-15 20:49:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-10-15 20:49:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-10-15 20:49:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:49:56] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-10-15 20:49:56] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-10-15 20:49:56] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2023-10-15 20:49:59] [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`
[2023-10-15 20:49:59] [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`
[2023-10-15 20:49:59] [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`
[2023-10-15 20:50:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:50:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:50:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:50:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:50:09] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`.
[2023-10-15 20:50:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2023-10-15 20:50:11] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2023-10-15 20:50:11] [INFO] [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1]
[2023-10-15 20:50:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:50:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:50:11] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`.
[2023-10-15 20:50:11] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2023-10-15 20:50:32] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2023-10-15 20:50:50] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any
[2023-10-15 20:55:18] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2023-10-15 20:55:27] [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`
[2023-10-15 20:55:27] [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`
[2023-10-15 20:55:27] [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`
[2023-10-15 20:55:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:55:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:55:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:55:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:55:33] [INFO] [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `unknown` to `started`.
[2023-10-15 20:55:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`.
[2023-10-15 20:55:34] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`.
[2023-10-15 20:55:34] [INFO] [OmnipathR] Download ready [key=73101f94a89eabbc8c12583d15dce08671d9e187, version=1]
[2023-10-15 20:55:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:55:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:55:34] [INFO] [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `started` to `ready`.
[2023-10-15 20:55:34] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2023-10-15 20:55:47] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2023-10-15 20:55:58] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any
[2023-10-15 20:58:55] [SUCCESS] [OmnipathR] Downloaded 234298 interactions.
[2023-10-15 20:59:02] [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&license=academic`
[2023-10-15 20:59:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-10-15 20:59:02] [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&license=academic`
[2023-10-15 20:59:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:59:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:59:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:59:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:59:07] [INFO] [OmnipathR] Cache item `099e7af92f71a88d7560d65cea14c1970f66c0b6` version 1: status changed from `unknown` to `started`.
[2023-10-15 20:59:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/099e7af92f71a88d7560d65cea14c1970f66c0b6-1.rds`.
[2023-10-15 20:59:07] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/099e7af92f71a88d7560d65cea14c1970f66c0b6-1.rds`.
[2023-10-15 20:59:07] [INFO] [OmnipathR] Download ready [key=099e7af92f71a88d7560d65cea14c1970f66c0b6, version=1]
[2023-10-15 20:59:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 20:59:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-15 20:59:08] [INFO] [OmnipathR] Cache item `099e7af92f71a88d7560d65cea14c1970f66c0b6` version 1: status changed from `started` to `ready`.
[2023-10-15 20:59:08] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2023-10-15 20:59:12] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any
[2023-10-15 20:59:16] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any
[2023-10-15 21:00:26] [SUCCESS] [OmnipathR] Downloaded 64495 interactions.
[2023-10-15 21:00:27] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/099e7af92f71a88d7560d65cea14c1970f66c0b6-1.rds`.
[2023-10-15 21:00:27] [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&license=academic`
[2023-10-15 21:00:27] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2023-10-15 21:00:31] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any
[2023-10-15 21:00:35] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any
[2023-10-15 21:01:43] [SUCCESS] [OmnipathR] Downloaded 64495 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 0 | WARN 357 | SKIP 0 | PASS 35 ]
[ FAIL 0 | WARN 357 | SKIP 0 | PASS 35 ]
>
> proc.time()
user system elapsed
779.590 32.475 829.674
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.101 | 0.000 | 0.101 | |
| convert_f_defaults | 0.082 | 0.015 | 0.098 | |
| decouple | 0.001 | 0.000 | 0.001 | |
| dot-fit_preprocessing | 0.027 | 0.000 | 0.027 | |
| extract_sets | 0.029 | 0.000 | 0.029 | |
| filt_minsize | 0.059 | 0.000 | 0.059 | |
| get_collectri | 79.381 | 1.888 | 84.140 | |
| get_dorothea | 320.726 | 4.816 | 330.393 | |
| get_profile_of | 0 | 0 | 0 | |
| get_progeny | 7.082 | 0.891 | 15.325 | |
| get_resource | 0.604 | 0.077 | 2.723 | |
| get_toy_data | 0.003 | 0.000 | 0.003 | |
| intersect_regulons | 0.016 | 0.012 | 0.027 | |
| pipe | 0 | 0 | 0 | |
| pivot_wider_profile | 0.000 | 0.000 | 0.001 | |
| randomize_matrix | 0 | 0 | 0 | |
| rename_net | 0.039 | 0.000 | 0.038 | |
| run_aucell | 5.422 | 0.727 | 6.150 | |
| run_consensus | 2.969 | 0.392 | 3.360 | |
| run_fgsea | 19.567 | 0.895 | 20.462 | |
| run_gsva | 0.912 | 0.088 | 1.000 | |
| run_mdt | 0.231 | 0.024 | 0.252 | |
| run_mlm | 0.106 | 0.000 | 0.106 | |
| run_ora | 0.578 | 0.024 | 0.602 | |
| run_udt | 0.262 | 0.004 | 0.266 | |
| run_ulm | 0.208 | 0.004 | 0.212 | |
| run_viper | 0.647 | 0.028 | 0.675 | |
| run_wmean | 1.007 | 0.028 | 1.035 | |
| run_wsum | 1.011 | 0.040 | 1.051 | |
| show_methods | 0.046 | 0.004 | 0.050 | |
| show_resources | 0.176 | 0.008 | 0.940 | |
| tidyeval | 0 | 0 | 0 | |