Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:33 -0400 (Fri, 15 Oct 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 497/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffcyt 1.12.0  (landing page)
Lukas M. Weber
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/diffcyt
git_branch: RELEASE_3_13
git_last_commit: 7e8f4d3
git_last_commit_date: 2021-05-19 12:34:44 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:diffcyt.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings diffcyt_1.12.0.tar.gz
StartedAt: 2021-10-14 18:23:07 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 18:28:58 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 351.4 seconds
RetCode: 0
Status:   OK  
CheckDir: diffcyt.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:diffcyt.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings diffcyt_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/diffcyt.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.12.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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     13.891  0.119  14.019
testDA_GLMM 13.579  0.053  13.646
plotHeatmap  7.910  0.058   7.978
testDS_LMM   6.749  0.043   6.796
topTable     6.447  0.041   6.498
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/diffcyt.Rcheck/00check.log’
for details.



Installation output

diffcyt.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/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 4.1.1 (2021-08-10) -- "Kick Things"
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 
 14.667   0.725  15.387 

Example timings

diffcyt.Rcheck/diffcyt-Ex.timings

nameusersystemelapsed
calcCounts2.1180.0502.169
calcMedians2.5380.0502.592
calcMediansByClusterMarker1.8250.0471.872
calcMediansBySampleMarker1.4740.0291.505
createContrast000
createDesignMatrix0.0140.0020.016
createFormula0.0050.0010.007
diffcyt13.891 0.11914.019
generateClusters1.5630.0281.592
plotHeatmap7.9100.0587.978
prepareData0.0450.0010.046
testDA_GLMM13.579 0.05313.646
testDA_edgeR2.0230.0342.059
testDA_voom2.3190.0182.339
testDS_LMM6.7490.0436.796
testDS_limma2.9520.0192.973
topTable6.4470.0416.498
transformData0.0990.0010.100