| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:14:59 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 | ||||
|
To the developers/maintainers of the decoupleR package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 485/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.5.0 (landing page) Pau Badia-i-Mompel
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: decoupleR |
| Version: 2.5.0 |
| 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/library --timings decoupleR_2.5.0.tar.gz |
| StartedAt: 2023-02-06 23:08:35 -0000 (Mon, 06 Feb 2023) |
| EndedAt: 2023-02-06 23:21:21 -0000 (Mon, 06 Feb 2023) |
| EllapsedTime: 765.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: decoupleR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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/library --timings decoupleR_2.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/decoupleR.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.5.0’
* 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 dependencies in R code ... NOTE
[2023-02-06 23:09:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 23:09:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:09:05] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-02-06 23:09:05] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-02-06 23:09:05] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-02-06 23:09:05] [TRACE] [OmnipathR] Contains 2 files.
[2023-02-06 23:09:05] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-02-06 23:09:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 23:09:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:09:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-02-06 23:09:05] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-02-06 23:09:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-02-06 23:09:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:09:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-02-06 23:09:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:09:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-02-06 23:09:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:09:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-02-06 23:09:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:09:05] [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 31.570 0.269 33.341
run_fgsea 22.956 0.017 22.993
run_consensus 10.518 1.222 18.808
run_aucell 8.880 0.177 9.172
get_progeny 8.048 0.216 16.388
* 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:
[120] 0.112 | 0.112 [120]
[121] 0.991 - 1.000 [121]
[122] 0.991 - 1.000 [122]
[123] 0.123 - 0.126 [123]
[124] 0.123 - 0.126 [124]
[125] 0.156 | 0.156 [125]
[126] 0.156 | 0.156 [126]
[127] 0.592 | 0.592 [127]
`actual$p_value[132:139]`: 0.125 0.592 0.592 0.175 0.175 0.198 0.198 0.592
`expected$p_value[132:139]`: 0.125 0.592 0.592 0.184 0.184 0.198 0.198 0.592
[ FAIL 1 | WARN 340 | SKIP 0 | PASS 34 ]
Error: Test failures
Execution halted
* 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 ERROR, 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/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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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[2023-02-06 23:13:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 23:13:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:24] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-02-06 23:13:24] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-02-06 23:13:24] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-02-06 23:13:24] [TRACE] [OmnipathR] Contains 4 files.
[2023-02-06 23:13:24] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-02-06 23:13:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 23:13:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-02-06 23:13:24] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-02-06 23:13:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-02-06 23:13:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-02-06 23:13:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-02-06 23:13:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-02-06 23:13:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:24] [TRACE] [OmnipathR] Cache locked: FALSE
[2023-02-06 23:13:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-02-06 23:13:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-02-06 23:13:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-02-06 23:13:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:28] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-02-06 23:13:28] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-02-06 23:13:28] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-02-06 23:13:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 23:13:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 23:13:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:29] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2023-02-06 23:13:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2023-02-06 23:13:29] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2023-02-06 23:13:29] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2023-02-06 23:13:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 23:13:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:29] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2023-02-06 23:13:29] [SUCCESS] [OmnipathR] Downloaded 3516 annotation records.
[2023-02-06 23:13:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-02-06 23:13:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:31] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-02-06 23:13:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-06 23:13:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-06 23:13:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-06 23:13:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 23:13:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 23:13:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:40] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2023-02-06 23:13:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-02-06 23:13:43] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-02-06 23:13:43] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2023-02-06 23:13:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 23:13:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:43] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2023-02-06 23:13:43] [SUCCESS] [OmnipathR] Downloaded 700257 annotation records.
[2023-02-06 23:13:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-02-06 23:13:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-02-06 23:13:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:52] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-02-06 23:13:52] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-06 23:13:52] [SUCCESS] [OmnipathR] Loaded 700257 annotation records from cache.
[2023-02-06 23:13:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-02-06 23:13:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-02-06 23:13:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-02-06 23:13:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 23:13:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 23:13:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:57] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2023-02-06 23:13:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2023-02-06 23:13:58] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2023-02-06 23:13:58] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2023-02-06 23:13:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 23:13:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:13:58] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2023-02-06 23:14:12] [SUCCESS] [OmnipathR] Downloaded 278482 interactions.
[2023-02-06 23:14:26] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-02-06 23:14:26] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-02-06 23:14:26] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-02-06 23:14:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 23:14:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:14:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 23:14:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:14:40] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2023-02-06 23:14:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2023-02-06 23:14:41] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2023-02-06 23:14:41] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2023-02-06 23:14:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 23:14:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-06 23:14:41] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2023-02-06 23:14:54] [SUCCESS] [OmnipathR] Downloaded 256977 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 340 | SKIP 0 | PASS 34 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-statistic-fgsea.R:26'): test run_fgsea ───────────────────────
`res_1` (`actual`) not equal to `exp_1` (`expected`).
actual vs expected
p_value
actual[1, ] 0.075479709
actual[2, ] 0.075479709
- actual[3, ] 0.511687342
+ expected[3, ] 0.548454870
- actual[4, ] 0.511687342
+ expected[4, ] 0.548454870
actual[5, ] 0.010000000
actual[6, ] 0.010000000
actual[7, ] 0.076411558
actual vs expected
p_value
actual[12, ] 0.010000000
actual[13, ] 0.114238030
actual[14, ] 0.114238030
- actual[15, ] 0.510665738
+ expected[15, ] 0.522337972
- actual[16, ] 0.510665738
+ expected[16, ] 0.522337972
actual[17, ] 0.010000000
actual[18, ] 0.010000000
actual[19, ] 0.004682543
actual[20, ] 0.004682543
- actual[21, ] 0.219233595
+ expected[21, ] 0.294730294
and 10 more ...
actual vs expected
p_value
actual[34, ] 1.000000000
actual[35, ] 0.010000000
actual[36, ] 0.010000000
- actual[37, ] 0.091542106
+ expected[37, ] 0.103646587
- actual[38, ] 0.091542106
+ expected[38, ] 0.103646587
actual[39, ] 0.592371428
actual[40, ] 0.592371428
actual[41, ] 0.010000000
actual vs expected
p_value
actual[52, ] 0.976649086
actual[53, ] 0.010000000
actual[54, ] 0.010000000
- actual[55, ] 0.066624941
+ expected[55, ] 0.076411558
- actual[56, ] 0.066624941
+ expected[56, ] 0.076411558
actual[57, ] 0.592371428
actual[58, ] 0.592371428
actual[59, ] 0.010000000
actual[60, ] 0.010000000
- actual[61, ] 0.111211902
+ expected[61, ] 0.108185775
and 4 more ...
actual vs expected
p_value
actual[70, ] 1.000000000
actual[71, ] 0.010000000
actual[72, ] 0.010000000
- actual[73, ] 0.256981914
+ expected[73, ] 0.469812943
- actual[74, ] 0.256981914
+ expected[74, ] 0.469812943
- actual[75, ] 0.133907888
+ expected[75, ] 0.132394821
- actual[76, ] 0.133907888
+ expected[76, ] 0.132394821
actual[77, ] 0.123204721
actual[78, ] 0.123204721
- actual[79, ] 0.146641013
+ expected[79, ] 0.207618744
and 4 more ...
actual vs expected
p_value
actual[88, ] 0.177906190
actual[89, ] 0.154281338
actual[90, ] 0.154281338
- actual[91, ] 0.434796297
+ expected[91, ] 0.487321278
- actual[92, ] 0.434796297
+ expected[92, ] 0.487321278
actual[93, ] 0.009411332
actual[94, ] 0.009411332
actual[95, ] 0.005020222
actual[96, ] 0.005020222
- actual[97, ] 0.294730294
+ expected[97, ] 0.493157392
and 4 more ...
actual vs expected
p_value
actual[106, ] 0.199193619
actual[107, ] 0.213918294
actual[108, ] 0.213918294
- actual[109, ] 0.873886766
+ expected[109, ] 0.944265891
- actual[110, ] 0.873886766
+ expected[110, ] 0.944265891
actual[111, ] 0.187029368
actual[112, ] 0.187029368
actual[113, ] 0.180210408
actual vs expected
p_value
actual[118, ] 0.126342554
actual[119, ] 0.111593916
actual[120, ] 0.111593916
- actual[121, ] 0.991185346
+ expected[121, ] 1.000000000
- actual[122, ] 0.991185346
+ expected[122, ] 1.000000000
- actual[123, ] 0.123316421
+ expected[123, ] 0.126342554
- actual[124, ] 0.123316421
+ expected[124, ] 0.126342554
actual[125, ] 0.155922629
actual[126, ] 0.155922629
actual[127, ] 0.592371428
actual vs expected
p_value
actual[132, ] 0.124515409
actual[133, ] 0.592371428
actual[134, ] 0.592371428
- actual[135, ] 0.174865133
+ expected[135, ] 0.183988307
- actual[136, ] 0.174865133
+ expected[136, ] 0.183988307
actual[137, ] 0.198360798
actual[138, ] 0.198360798
actual[139, ] 0.592371428
`actual$p_value[1:7]`: 0.075 0.075 0.512 0.512 0.010 0.010 0.076
`expected$p_value[1:7]`: 0.075 0.075 0.548 0.548 0.010 0.010 0.076
actual$p_value | expected$p_value
[12] 0.010 | 0.010 [12]
[13] 0.114 | 0.114 [13]
[14] 0.114 | 0.114 [14]
[15] 0.511 - 0.522 [15]
[16] 0.511 - 0.522 [16]
[17] 0.010 | 0.010 [17]
[18] 0.010 | 0.010 [18]
[19] 0.005 | 0.005 [19]
[20] 0.005 | 0.005 [20]
[21] 0.219 - 0.295 [21]
... ... ... and 10 more ...
`actual$p_value[34:41]`: 1.000 0.010 0.010 0.092 0.092 0.592 0.592 0.010
`expected$p_value[34:41]`: 1.000 0.010 0.010 0.104 0.104 0.592 0.592 0.010
actual$p_value | expected$p_value
[52] 0.977 | 0.977 [52]
[53] 0.010 | 0.010 [53]
[54] 0.010 | 0.010 [54]
[55] 0.067 - 0.076 [55]
[56] 0.067 - 0.076 [56]
[57] 0.592 | 0.592 [57]
[58] 0.592 | 0.592 [58]
[59] 0.010 | 0.010 [59]
[60] 0.010 | 0.010 [60]
[61] 0.111 - 0.108 [61]
... ... ... and 4 more ...
actual$p_value | expected$p_value
[70] 1.000 | 1.000 [70]
[71] 0.010 | 0.010 [71]
[72] 0.010 | 0.010 [72]
[73] 0.257 - 0.470 [73]
[74] 0.257 - 0.470 [74]
[75] 0.134 - 0.132 [75]
[76] 0.134 - 0.132 [76]
[77] 0.123 | 0.123 [77]
[78] 0.123 | 0.123 [78]
[79] 0.147 - 0.208 [79]
... ... ... and 4 more ...
actual$p_value | expected$p_value
[88] 0.178 | 0.178 [88]
[89] 0.154 | 0.154 [89]
[90] 0.154 | 0.154 [90]
[91] 0.435 - 0.487 [91]
[92] 0.435 - 0.487 [92]
[93] 0.009 | 0.009 [93]
[94] 0.009 | 0.009 [94]
[95] 0.005 | 0.005 [95]
[96] 0.005 | 0.005 [96]
[97] 0.295 - 0.493 [97]
... ... ... and 4 more ...
`actual$p_value[106:113]`: 0.199 0.214 0.214 0.874 0.874 0.187 0.187 0.180
`expected$p_value[106:113]`: 0.199 0.214 0.214 0.944 0.944 0.187 0.187 0.180
actual$p_value | expected$p_value
[118] 0.126 | 0.126 [118]
[119] 0.112 | 0.112 [119]
[120] 0.112 | 0.112 [120]
[121] 0.991 - 1.000 [121]
[122] 0.991 - 1.000 [122]
[123] 0.123 - 0.126 [123]
[124] 0.123 - 0.126 [124]
[125] 0.156 | 0.156 [125]
[126] 0.156 | 0.156 [126]
[127] 0.592 | 0.592 [127]
`actual$p_value[132:139]`: 0.125 0.592 0.592 0.175 0.175 0.198 0.198 0.592
`expected$p_value[132:139]`: 0.125 0.592 0.592 0.184 0.184 0.198 0.198 0.592
[ FAIL 1 | WARN 340 | SKIP 0 | PASS 34 ]
Error: Test failures
Execution halted
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.189 | 0.009 | 0.201 | |
| convert_f_defaults | 0.066 | 0.008 | 0.075 | |
| decouple | 0 | 0 | 0 | |
| dot-fit_preprocessing | 0.038 | 0.003 | 0.043 | |
| extract_sets | 0.045 | 0.000 | 0.046 | |
| filt_minsize | 0.094 | 0.003 | 0.098 | |
| get_dorothea | 31.570 | 0.269 | 33.341 | |
| get_profile_of | 0.001 | 0.000 | 0.001 | |
| get_progeny | 8.048 | 0.216 | 16.388 | |
| get_resource | 0.581 | 0.024 | 3.431 | |
| get_toy_data | 0.002 | 0.000 | 0.003 | |
| intersect_regulons | 0.042 | 0.000 | 0.043 | |
| pipe | 0.001 | 0.000 | 0.000 | |
| pivot_wider_profile | 0.000 | 0.000 | 0.001 | |
| randomize_matrix | 0 | 0 | 0 | |
| rename_net | 0.056 | 0.000 | 0.056 | |
| run_aucell | 8.880 | 0.177 | 9.172 | |
| run_consensus | 10.518 | 1.222 | 18.808 | |
| run_fgsea | 22.956 | 0.017 | 22.993 | |
| run_gsva | 1.399 | 0.047 | 1.570 | |
| run_mdt | 0.365 | 0.020 | 0.393 | |
| run_mlm | 0.228 | 0.000 | 0.229 | |
| run_ora | 0.942 | 0.000 | 0.949 | |
| run_udt | 0.404 | 0.000 | 0.408 | |
| run_ulm | 0.353 | 0.000 | 0.353 | |
| run_viper | 0.979 | 0.024 | 1.056 | |
| run_wmean | 1.469 | 0.012 | 1.483 | |
| run_wsum | 1.481 | 0.004 | 1.485 | |
| show_methods | 0.063 | 0.000 | 0.065 | |
| show_resources | 0.195 | 0.008 | 1.140 | |
| tidyeval | 0 | 0 | 0 | |