Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:12 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 tokay2


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? here 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 2.0.0  (landing page)
Jesús Vélez
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/decoupleR
git_branch: RELEASE_3_14
git_last_commit: b00f6bf
git_last_commit_date: 2021-10-26 13:10:14 -0500 (Tue, 26 Oct 2021)
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    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: decoupleR
Version: 2.0.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:decoupleR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings decoupleR_2.0.0.tar.gz
StartedAt: 2022-01-20 18:32:18 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 18:44:37 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 739.4 seconds
RetCode: 0
Status:   OK  
CheckDir: decoupleR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:decoupleR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings decoupleR_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/decoupleR.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'decoupleR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'decoupleR' version '2.0.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
run_consensus: no visible binding for global variable 'condition'
Undefined global functions or variables:
  condition
* 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/decoupleR.Rcheck/00check.log'
for details.



Installation output

decoupleR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/decoupleR_2.0.0.tar.gz && rm -rf decoupleR.buildbin-libdir && mkdir decoupleR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=decoupleR.buildbin-libdir decoupleR_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL decoupleR_2.0.0.zip && rm decoupleR_2.0.0.tar.gz decoupleR_2.0.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  372k  100  372k    0     0  1419k      0 --:--:-- --:--:-- --:--:-- 1422k

install for i386

* installing *source* package 'decoupleR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'decoupleR'
    finding HTML links ... done
    convert_f_defaults                      html  
    convert_to_                             html  
    decouple                                html  
    decoupleR-package                       html  
    dot-decoupler_mat_format                html  
    dot-decoupler_network_format            html  
    filter_regulons                         html  
    get_profile_of                          html  
    intersect_regulons                      html  
    pipe                                    html  
    pivot_wider_profile                     html  
    randomize_matrix                        html  
    run_aucell                              html  
    run_consensus                           html  
    run_fgsea                               html  
    run_gsva                                html  
    run_mdt                                 html  
    run_mlm                                 html  
    run_ora                                 html  
    run_udt                                 html  
    run_ulm                                 html  
    run_viper                               html  
    run_wmean                               html  
    run_wsum                                html  
    tidyeval                                html  
** 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

install for x64

* installing *source* package 'decoupleR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'decoupleR' as decoupleR_2.0.0.zip
* DONE (decoupleR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'decoupleR' successfully unpacked and MD5 sums checked

Tests output

decoupleR.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")
== Skipped tests ===============================================================
* On CRAN (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
  32.59    2.23  249.26 

decoupleR.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
== Skipped tests ===============================================================
* On CRAN (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
  36.56    0.96  279.57 

Example timings

decoupleR.Rcheck/examples_i386/decoupleR-Ex.timings

nameusersystemelapsed
convert_f_defaults0.120.020.14
convert_to_0.220.020.24
decouple000
filter_regulons0.030.000.04
get_profile_of000
intersect_regulons0.090.000.12
pipe000
pivot_wider_profile0.020.000.02
randomize_matrix000
run_aucell2.690.252.95
run_fgsea1.370.031.41
run_gsva1.190.091.31
run_mdt0.140.000.14
run_mlm0.170.000.17
run_ora0.310.000.31
run_udt0.280.000.28
run_ulm0.140.020.16
run_viper0.740.110.84
run_wmean1.860.091.95
run_wsum1.120.001.13
tidyeval000

decoupleR.Rcheck/examples_x64/decoupleR-Ex.timings

nameusersystemelapsed
convert_f_defaults0.130.000.13
convert_to_0.750.000.75
decouple000
filter_regulons0.030.000.03
get_profile_of000
intersect_regulons0.050.000.05
pipe000
pivot_wider_profile000
randomize_matrix000
run_aucell2.800.042.84
run_fgsea1.010.001.02
run_gsva2.070.052.12
run_mdt0.120.000.13
run_mlm0.170.000.17
run_ora0.330.000.33
run_udt0.20.00.2
run_ulm0.220.000.22
run_viper0.640.080.72
run_wmean1.350.001.34
run_wsum1.120.001.13
tidyeval000