Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:15 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for decoupleR on nebbiolo2


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.

raw results

Package 468/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decoupleR 2.0.1  (landing page)
Pau Badia-i-Mompel
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/decoupleR
git_branch: RELEASE_3_14
git_last_commit: 4b4c2e8
git_last_commit_date: 2022-04-01 10:15:12 -0400 (Fri, 01 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: decoupleR
Version: 2.0.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings decoupleR_2.0.1.tar.gz
StartedAt: 2022-04-12 07:05:06 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 07:07:40 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 154.0 seconds
RetCode: 0
Status:   OK  
CheckDir: decoupleR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings decoupleR_2.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/decoupleR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.0.1’
* 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
[2022-04-12 07:05:31] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2022-04-12 07:05:31] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2022-04-12 07:05:31] [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 8.570  0.208   8.778
run_aucell   6.828  0.472   7.260
get_progeny  4.129  0.197   5.709
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/decoupleR.Rcheck/00check.log’
for details.



Installation output

decoupleR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL decoupleR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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)

Tests output

decoupleR.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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")
[2022-04-12 07:06:55] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2022-04-12 07:06:55] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2022-04-12 07:06:55] [TRACE]   [OmnipathR] Cache locked: FALSE
[2022-04-12 07:06:57] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2022-04-12 07:06:57] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2022-04-12 07:06:57] [SUCCESS] [OmnipathR] Loaded 3516 annotation records from cache.
[2022-04-12 07:07:02] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2022-04-12 07:07:02] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2022-04-12 07:07:02] [SUCCESS] [OmnipathR] Loaded 700257 annotation records from cache.
[2022-04-12 07:07:08] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2022-04-12 07:07:08] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2022-04-12 07:07:08] [SUCCESS] [OmnipathR] Loaded 700257 annotation records from cache.
[2022-04-12 07:07:10] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2022-04-12 07:07:10] [INFO]    [OmnipathR] Loaded from cache: `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`
[2022-04-12 07:07:12] [SUCCESS] [OmnipathR] Loaded 278482 interactions from cache.
[2022-04-12 07:07:18] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2022-04-12 07:07:18] [INFO]    [OmnipathR] Loaded from cache: `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`
[2022-04-12 07:07:22] [SUCCESS] [OmnipathR] Loaded 256977 interactions from cache.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 36 ]
> 
> proc.time()
   user  system elapsed 
 82.481   4.235  66.105 

Example timings

decoupleR.Rcheck/decoupleR-Ex.timings

nameusersystemelapsed
check_corr0.1040.0000.105
convert_f_defaults0.0430.0040.047
decouple000
dot-fit_preprocessing0.3020.2400.542
extract_sets0.0500.0040.054
filt_minsize0.0940.0040.098
get_dorothea8.5700.2088.778
get_profile_of000
get_progeny4.1290.1975.709
get_resource0.1440.0001.286
get_toy_data0.0030.0030.006
intersect_regulons0.0490.0010.050
pipe000
pivot_wider_profile0.0010.0000.000
randomize_matrix000
rename_net0.060.000.06
run_aucell6.8280.4727.260
run_consensus2.1040.0842.189
run_fgsea0.9370.0641.001
run_gsva1.2090.0801.289
run_mdt0.4620.0150.342
run_mlm0.1970.0000.196
run_ora0.4810.0000.480
run_udt0.4520.0240.475
run_ulm0.3210.0000.321
run_viper0.6610.0120.673
run_wmean1.1870.0321.219
run_wsum1.1830.0121.195
show_methods0.0460.0000.047
show_resources0.0680.0070.676
tidyeval000