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This page was generated on 2023-10-20 09:38:01 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 511/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decoupleR 2.6.0  (landing page)
Pau Badia-i-Mompel
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/decoupleR
git_branch: RELEASE_3_17
git_last_commit: 55eb7fb
git_last_commit_date: 2023-04-25 11:30:09 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    TIMEOUT    OK  

CHECK results for decoupleR on kjohnson2


To the developers/maintainers of the decoupleR package:
- 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.

raw results

Summary

Package: decoupleR
Version: 2.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.6.0.tar.gz
StartedAt: 2023-10-17 14:19:19 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 14:59:19 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 2400.4 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: decoupleR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/decoupleR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.6.0’
* 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 dependencies in R code ... NOTE
[2023-10-17 14:20:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-17 14:20:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:20:13] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-17 14:20:13] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-10-17 14:20:13] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-17 14:20:13] [TRACE]   [OmnipathR] Contains 6 files.
[2023-10-17 14:20:13] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-10-17 14:20:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-17 14:20:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:20:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-17 14:20:13] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2023-10-17 14:20:13] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-17 14:20:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:20:13] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-17 14:20:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:20:14] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-17 14:20:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:20:14] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-17 14:20:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:20:14] [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  587.152  7.217 909.946
get_collectri 133.865  1.789 213.424
run_fgsea      19.284  0.316  30.033
get_progeny     7.699  0.474  23.116
run_aucell      7.103  0.229  11.176
run_consensus   3.596  0.075   5.625
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

Installation output

decoupleR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL decoupleR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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)

Tests output

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: aarch64-apple-darwin20 (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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[2023-10-17 14:43:05] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-17 14:43:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:05] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-17 14:43:05] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-10-17 14:43:05] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-17 14:43:05] [TRACE]   [OmnipathR] Contains 5 files.
[2023-10-17 14:43:05] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-10-17 14:43:05] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-17 14:43:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-17 14:43:06] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2023-10-17 14:43:06] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-17 14:43:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:06] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-17 14:43:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:06] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-17 14:43:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:06] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-17 14:43:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:06] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-10-17 14:43:07] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-10-17 14:43:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:08] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-10-17 14:43:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:09] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-10-17 14:43:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:09] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-10-17 14:43:09] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-10-17 14:43:09] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-10-17 14:43:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-17 14:43:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-17 14:43:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:10] [INFO]    [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2023-10-17 14:43:10] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2023-10-17 14:43:10] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2023-10-17 14:43:10] [INFO]    [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2023-10-17 14:43:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-17 14:43:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:10] [INFO]    [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2023-10-17 14:43:10] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2023-10-17 14:43:11] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-10-17 14:43:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:12] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-10-17 14:43:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-10-17 14:43:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-10-17 14:43:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-10-17 14:43:19] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-17 14:43:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:19] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-17 14:43:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:19] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2023-10-17 14:43:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-10-17 14:43:24] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-10-17 14:43:24] [INFO]    [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2023-10-17 14:43:24] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-17 14:43:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:24] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2023-10-17 14:43:24] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2023-10-17 14:43:29] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-10-17 14:43:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:30] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-10-17 14:43:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:33] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-10-17 14:43:33] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-10-17 14:43:33] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2023-10-17 14:43:39] [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`
[2023-10-17 14:43:39] [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`
[2023-10-17 14:43:39] [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`
[2023-10-17 14:43:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-17 14:43:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-17 14:43:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:43:56] [INFO]    [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`.
[2023-10-17 14:43:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2023-10-17 14:44:01] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2023-10-17 14:44:01] [INFO]    [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1]
[2023-10-17 14:44:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-17 14:44:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-17 14:44:01] [INFO]    [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`.
[2023-10-17 14:44:01] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2023-10-17 14:44:43] [TRACE]   [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2023-10-17 14:45:19] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any
[2023-10-17 14:59:10] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.

Example timings

decoupleR.Rcheck/decoupleR-Ex.timings

nameusersystemelapsed
check_corr0.1240.0150.215
convert_f_defaults0.0900.0120.158
decouple0.0010.0000.001
dot-fit_preprocessing0.0280.0040.051
extract_sets0.0320.0020.055
filt_minsize0.0540.0020.083
get_collectri133.865 1.789213.424
get_dorothea587.152 7.217909.946
get_profile_of000
get_progeny 7.699 0.47423.116
get_resource0.3660.0772.371
get_toy_data0.0040.0010.006
intersect_regulons0.0290.0020.046
pipe000
pivot_wider_profile0.0000.0010.001
randomize_matrix0.0000.0010.001
rename_net0.0480.0020.074
run_aucell 7.103 0.22911.176
run_consensus3.5960.0755.625
run_fgsea19.284 0.31630.033
run_gsva1.2840.1562.268
run_mdt0.3520.0300.635
run_mlm0.1520.0070.241
run_ora0.7840.0321.232
run_udt0.4880.0140.765
run_ulm0.2990.0090.475
run_viper0.8770.1271.491
run_wmean1.4780.0422.331
run_wsum1.3570.0392.142
show_methods0.0620.0080.104
show_resources0.0680.0060.889
tidyeval0.0010.0000.001