Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-01 17:18:16 -0500 (Wed, 01 Dec 2021).

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: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
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 20.04.3 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: 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: 2021-11-30 15:51:11 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 15:57:28 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 377.0 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     16.750  0.153  16.919
testDA_GLMM 14.196  0.064  14.319
plotHeatmap  8.722  0.067   8.797
testDS_LMM   7.408  0.031   7.445
topTable     5.760  0.046   5.811
* 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
###
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* 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 
 14.554   0.702  15.249 

Example timings

diffcyt.Rcheck/diffcyt-Ex.timings

nameusersystemelapsed
calcCounts2.3620.0532.416
calcMedians3.0630.0513.117
calcMediansByClusterMarker2.0820.0512.135
calcMediansBySampleMarker1.8440.0431.889
createContrast0.0000.0000.001
createDesignMatrix0.0160.0020.018
createFormula0.0060.0010.006
diffcyt16.750 0.15316.919
generateClusters1.8850.0401.927
plotHeatmap8.7220.0678.797
prepareData0.0380.0010.040
testDA_GLMM14.196 0.06414.319
testDA_edgeR1.9940.0232.020
testDA_voom1.9860.0152.002
testDS_LMM7.4080.0317.445
testDS_limma3.6010.0183.621
topTable5.7600.0465.811
transformData0.0650.0000.066