Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:07:32 -0500 (Mon, 24 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" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 diffcyt on machv2


To the developers/maintainers of the diffcyt package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/diffcyt.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 505/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffcyt 1.14.0  (landing page)
Lukas M. Weber
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/diffcyt
git_branch: RELEASE_3_14
git_last_commit: 18cad99
git_last_commit_date: 2021-10-26 12:43:31 -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    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: diffcyt
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:diffcyt.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings diffcyt_1.14.0.tar.gz
StartedAt: 2022-01-23 12:21:10 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 12:27:46 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 395.6 seconds
RetCode: 0
Status:   OK  
CheckDir: diffcyt.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:diffcyt.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings diffcyt_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/diffcyt.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘diffcyt/DESCRIPTION’ ... OK
* this is package ‘diffcyt’ version ‘1.14.0’
* 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 ‘diffcyt’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calcCounts: no visible binding for global variable ‘cluster_id’
calcCounts: no visible binding for global variable ‘sample_id’
calcMedians: no visible binding for global variable ‘cluster_id’
calcMedians: no visible binding for global variable ‘sample_id’
calcMedians: no visible binding for global variable ‘value’
calcMediansByClusterMarker: no visible binding for global variable
  ‘cluster_id’
calcMediansByClusterMarker: no visible binding for global variable
  ‘marker_id’
calcMediansByClusterMarker: no visible binding for global variable
  ‘value’
calcMediansBySampleMarker: no visible binding for global variable
  ‘sample_id’
calcMediansBySampleMarker: no visible binding for global variable
  ‘marker_id’
calcMediansBySampleMarker: no visible binding for global variable
  ‘value’
Undefined global functions or variables:
  cluster_id marker_id sample_id value
* 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
diffcyt     17.030  0.149  17.200
testDA_GLMM 15.242  0.043  15.313
plotHeatmap  9.532  0.087   9.626
testDS_LMM   6.941  0.027   6.976
topTable     6.363  0.038   6.405
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/diffcyt.Rcheck/00check.log’
for details.



Installation output

diffcyt.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘diffcyt’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (diffcyt)

Tests output

diffcyt.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(diffcyt)
> 
> test_check("diffcyt")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
 16.084   0.794  16.863 

Example timings

diffcyt.Rcheck/diffcyt-Ex.timings

nameusersystemelapsed
calcCounts2.8710.0722.954
calcMedians3.1550.0583.217
calcMediansByClusterMarker2.1730.0592.239
calcMediansBySampleMarker1.8900.0381.931
createContrast0.0010.0000.000
createDesignMatrix0.0130.0020.015
createFormula0.0040.0010.006
diffcyt17.030 0.14917.200
generateClusters1.9100.0301.942
plotHeatmap9.5320.0879.626
prepareData0.0510.0010.052
testDA_GLMM15.242 0.04315.313
testDA_edgeR2.2890.0252.317
testDA_voom2.1900.0142.205
testDS_LMM6.9410.0276.976
testDS_limma3.3910.0263.424
topTable6.3630.0386.405
transformData0.1050.0020.107