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This page was generated on 2024-03-04 11:37:17 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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

Package 560/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffcyt 1.22.0  (landing page)
Lukas M. Weber
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/diffcyt
git_branch: RELEASE_3_18
git_last_commit: 6ec9e43
git_last_commit_date: 2023-10-24 11:04:15 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for diffcyt on lconway


To the developers/maintainers of the diffcyt package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: diffcyt
Version: 1.22.0
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_1.22.0.tar.gz
StartedAt: 2024-03-03 20:11:57 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 20:16:51 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 293.7 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_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/diffcyt.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘diffcyt/DESCRIPTION’ ... OK
* this is package ‘diffcyt’ version ‘1.22.0’
* 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     10.393  0.164  10.648
testDA_GLMM  9.069  0.090   9.212
plotHeatmap  6.712  0.090   6.851
topTable     5.202  0.076   5.336
testDS_LMM   4.984  0.052   5.069
* 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-3.18-bioc/meat/diffcyt.Rcheck/00check.log’
for details.



Installation output

diffcyt.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 
 11.491   0.743  12.319 

Example timings

diffcyt.Rcheck/diffcyt-Ex.timings

nameusersystemelapsed
calcCounts2.1750.0552.252
calcMedians2.0420.0722.134
calcMediansByClusterMarker1.4640.0351.510
calcMediansBySampleMarker1.3480.0311.393
createContrast0.0000.0000.001
createDesignMatrix0.0090.0020.011
createFormula0.0030.0010.004
diffcyt10.393 0.16410.648
generateClusters1.4230.0281.466
plotHeatmap6.7120.0906.851
prepareData0.0210.0010.023
testDA_GLMM9.0690.0909.212
testDA_edgeR2.0980.0352.160
testDA_voom2.0340.0472.104
testDS_LMM4.9840.0525.069
testDS_limma2.6520.0382.712
topTable5.2020.0765.336
transformData0.0570.0000.058