| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:23 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 506/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.5.0 (landing page) Pau Badia-i-Mompel
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | 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/site-library --timings decoupleR_2.5.0.tar.gz |
| StartedAt: 2023-04-11 19:45:00 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 19:53:48 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 528.6 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/site-library --timings decoupleR_2.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/decoupleR.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-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 22.04.2 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
[2023-04-11 19:45:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 19:45:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:45:30] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 19:45:30] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-04-11 19:45:30] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 19:45:30] [TRACE] [OmnipathR] Contains 6 files.
[2023-04-11 19:45:30] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-04-11 19:45:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 19:45:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:45:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 19:45:30] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-11 19:45:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-11 19:45:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:45:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-11 19:45:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:45:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-11 19:45:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:45:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-11 19:45:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:45:30] [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 ... WARNING
Found the following significant warnings:
Warning: 'OmnipathR::import_dorothea_interactions' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
run_fgsea 21.321 0.226 21.547
get_dorothea 20.485 0.573 23.667
run_aucell 7.060 0.199 7.260
get_progeny 5.917 0.338 13.869
* 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:
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
[ FAIL 1 | WARN 342 | SKIP 0 | PASS 34 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-utils-dataset-converters.R:84:5'): missing quos ──────────────
`convert_to_foo()` did not throw the expected error.
[ FAIL 1 | WARN 342 | 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 WARNING, 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.fail
R version 4.3.0 alpha (2023-04-03 r84154)
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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[2023-04-11 19:48:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 19:48:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:20] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 19:48:20] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-04-11 19:48:20] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 19:48:20] [TRACE] [OmnipathR] Contains 4 files.
[2023-04-11 19:48:20] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-04-11 19:48:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 19:48:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 19:48:20] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-11 19:48:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-11 19:48:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-11 19:48:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-11 19:48:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-11 19:48:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:20] [TRACE] [OmnipathR] Cache locked: FALSE
[2023-04-11 19:48:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-11 19:48:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-11 19:48:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-11 19:48:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:23] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-04-11 19:48:23] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-04-11 19:48:23] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-04-11 19:48:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 19:48:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 19:48:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:24] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2023-04-11 19:48:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2023-04-11 19:48:24] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2023-04-11 19:48:24] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2023-04-11 19:48:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 19:48:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:24] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2023-04-11 19:48:24] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2023-04-11 19:48:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-11 19:48:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:26] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-11 19:48:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:26] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-04-11 19:48:26] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-04-11 19:48:26] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-04-11 19:48:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 19:48:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 19:48:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:33] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2023-04-11 19:48:34] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-04-11 19:48:36] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-04-11 19:48:36] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2023-04-11 19:48:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 19:48:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:36] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2023-04-11 19:48:36] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2023-04-11 19:48:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-11 19:48:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:40] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-11 19:48:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:43] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-04-11 19:48:43] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-04-11 19:48:43] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2023-04-11 19:48:45] [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`
[2023-04-11 19:48:45] [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`
[2023-04-11 19:48:45] [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`
[2023-04-11 19:48:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 19:48:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 19:48:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:49] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2023-04-11 19:48:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2023-04-11 19:48:50] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2023-04-11 19:48:50] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2023-04-11 19:48:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 19:48:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:48:50] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2023-04-11 19:48:59] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2023-04-11 19:49:08] [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`
[2023-04-11 19:49:08] [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`
[2023-04-11 19:49:08] [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`
[2023-04-11 19:49:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 19:49:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:49:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 19:49:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:49:11] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2023-04-11 19:49:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2023-04-11 19:49:12] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2023-04-11 19:49:12] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2023-04-11 19:49:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 19:49:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:49:12] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2023-04-11 19:49:20] [SUCCESS] [OmnipathR] Downloaded 234298 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 342 | SKIP 0 | PASS 34 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-utils-dataset-converters.R:84:5'): missing quos ──────────────
`convert_to_foo()` did not throw the expected error.
[ FAIL 1 | WARN 342 | SKIP 0 | PASS 34 ]
Error: Test failures
Execution halted
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.094 | 0.020 | 0.115 | |
| convert_f_defaults | 0.071 | 0.028 | 0.099 | |
| decouple | 0.001 | 0.000 | 0.001 | |
| dot-fit_preprocessing | 0.023 | 0.003 | 0.026 | |
| extract_sets | 0.025 | 0.001 | 0.024 | |
| filt_minsize | 0.038 | 0.004 | 0.042 | |
| get_dorothea | 20.485 | 0.573 | 23.667 | |
| get_profile_of | 0.001 | 0.000 | 0.000 | |
| get_progeny | 5.917 | 0.338 | 13.869 | |
| get_resource | 0.599 | 0.020 | 2.788 | |
| get_toy_data | 0.003 | 0.000 | 0.003 | |
| intersect_regulons | 0.024 | 0.000 | 0.024 | |
| pipe | 0 | 0 | 0 | |
| pivot_wider_profile | 0.000 | 0.000 | 0.001 | |
| randomize_matrix | 0.000 | 0.000 | 0.001 | |
| rename_net | 0.039 | 0.000 | 0.039 | |
| run_aucell | 7.060 | 0.199 | 7.260 | |
| run_consensus | 2.328 | 0.084 | 2.412 | |
| run_fgsea | 21.321 | 0.226 | 21.547 | |
| run_gsva | 0.988 | 0.056 | 1.044 | |
| run_mdt | 0.233 | 0.023 | 0.254 | |
| run_mlm | 0.177 | 0.000 | 0.177 | |
| run_ora | 0.557 | 0.000 | 0.557 | |
| run_udt | 0.263 | 0.000 | 0.263 | |
| run_ulm | 0.271 | 0.000 | 0.271 | |
| run_viper | 0.716 | 0.004 | 0.720 | |
| run_wmean | 2.279 | 0.013 | 2.291 | |
| run_wsum | 0.925 | 0.087 | 1.013 | |
| show_methods | 0.043 | 0.008 | 0.052 | |
| show_resources | 0.164 | 0.012 | 0.857 | |
| tidyeval | 0 | 0 | 0 | |