Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-03-18 11:07:23 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 riesling1


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 511/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffcyt 1.15.0  (landing page)
Lukas M. Weber
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/diffcyt
git_branch: master
git_last_commit: 4d4f49e
git_last_commit_date: 2021-10-26 12:43:31 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'FlowSOM' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: diffcyt
Version: 1.15.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:diffcyt.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings diffcyt_1.15.0.tar.gz
StartedAt: 2022-03-17 18:56:05 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 19:00:22 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 257.5 seconds
RetCode: 0
Status:   OK  
CheckDir: diffcyt.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:diffcyt.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings diffcyt_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/diffcyt.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'diffcyt/DESCRIPTION' ... OK
* this is package 'diffcyt' version '1.15.0'
* 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 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     9.98   0.14   10.14
testDA_GLMM 9.88   0.03    9.91
plotHeatmap 6.14   0.05    6.19
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/diffcyt.Rcheck/00check.log'
for details.



Installation output

diffcyt.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL diffcyt
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'diffcyt' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'diffcyt'
    finding HTML links ... done
    calcCounts                              html  
    finding level-2 HTML links ... done

    calcMedians                             html  
    calcMediansByClusterMarker              html  
    calcMediansBySampleMarker               html  
    createContrast                          html  
    createDesignMatrix                      html  
    createFormula                           html  
    diffcyt                                 html  
    generateClusters                        html  
    plotHeatmap                             html  
    prepareData                             html  
    testDA_GLMM                             html  
    testDA_edgeR                            html  
    testDA_voom                             html  
    testDS_LMM                              html  
    testDS_limma                            html  
    topClusters                             html  
    topTable                                html  
    transformData                           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
* DONE (diffcyt)
Making 'packages.html' ... done

Tests output

diffcyt.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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(diffcyt)
> 
> test_check("diffcyt")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
   8.32    0.93    9.25 

Example timings

diffcyt.Rcheck/diffcyt-Ex.timings

nameusersystemelapsed
calcCounts1.610.051.65
calcMedians1.440.061.53
calcMediansByClusterMarker1.280.091.37
calcMediansBySampleMarker1.310.031.38
createContrast000
createDesignMatrix000
createFormula000
diffcyt 9.98 0.1410.14
generateClusters1.360.031.39
plotHeatmap6.140.056.19
prepareData0.020.000.01
testDA_GLMM9.880.039.91
testDA_edgeR1.360.021.37
testDA_voom1.770.001.77
testDS_LMM3.480.013.50
testDS_limma2.880.032.92
topTable4.600.004.61
transformData0.050.000.05