Build/check report for BioC 3.22 - CHECK results for markeR on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4637
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 markeR on kjohnson3

To the developers/maintainers of the markeR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/markeR.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: markeR

Version: 0.99.6

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:markeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings markeR_0.99.6.tar.gz

StartedAt: 2025-10-26 20:22:46 -0400 (Sun, 26 Oct 2025)

EndedAt: 2025-10-26 20:24:38 -0400 (Sun, 26 Oct 2025)

EllapsedTime: 111.3 seconds

RetCode: 0

Status: OK

CheckDir: markeR.Rcheck

Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:markeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings markeR_0.99.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/markeR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘markeR/DESCRIPTION’ ... OK
* this is package ‘markeR’ version ‘0.99.6’
* package encoding: UTF-8
* 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 ‘markeR’ 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 code 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 whether startup messages can be suppressed ... 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
geneset_similarity 16.903  0.124  17.032
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

markeR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘markeR’ ...
** this is package ‘markeR’ version ‘0.99.6’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (markeR)

Tests output

markeR.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(markeR)
Warning: markeR has been tested with ggplot2 <= 3.5.2. Using newer versions may cause incompatibilities.
> 
> test_check("markeR")
Loading required package: usethis

Attaching package: 'devtools'

The following object is masked from 'package:testthat':

    test_file

Considering unidirectional gene signature mode for signature Signature1
No id variables; using all as measure variables
Considering unidirectional gene signature mode for signature Signature2
No id variables; using all as measure variables
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature2
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature2
Considering unidirectional gene signature mode for signature Signature1
No id variables; using all as measure variables
Considering unidirectional gene signature mode for signature Signature2
No id variables; using all as measure variables
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature2
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature2
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature1
No id variables; using all as measure variables
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature1
Considering bidirectional gene signature mode for signature BiSig
Considering bidirectional gene signature mode for signature BiSig
No id variables; using all as measure variables
No id variables; using all as measure variables
Considering bidirectional gene signature mode for signature BiSig
Running simulations for signature Sig1
Running simulations for signature SigA
Running simulations for signature Sig1
Running simulations for signature Sig2
Running simulations for signature SigX
Using gene as id variables
Using gene as id variables
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature2
Ignoring unknown labels:
* colour : ""
Ignoring unknown labels:
* colour : ""
Ignoring unknown labels:
* colour : ""
Ignoring unknown labels:
* colour : ""
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature2
Ignoring unknown labels:
* colour : ""
`geom_smooth()` using formula = 'y ~ x'
Ignoring unknown labels:
* colour : ""
`geom_smooth()` using formula = 'y ~ x'
Ignoring unknown labels:
* colour : ""
`geom_smooth()` using formula = 'y ~ x'
Ignoring unknown labels:
* colour : ""
`geom_smooth()` using formula = 'y ~ x'
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature2
Ignoring unknown labels:
* colour : ""
Ignoring unknown labels:
* colour : ""
Ignoring unknown labels:
* colour : ""
Ignoring unknown labels:
* colour : ""
Considering unidirectional gene signature mode for signature Signature1
No id variables; using all as measure variables
Considering unidirectional gene signature mode for signature Signature2
No id variables; using all as measure variables
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature2
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature2
Considering unidirectional gene signature mode for signature Signature1
No id variables; using all as measure variables
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature1
No id variables; using all as measure variables
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature2
Ignoring unknown labels:
* colour : ""
Ignoring unknown labels:
* colour : ""
Ignoring unknown labels:
* colour : ""
Ignoring unknown labels:
* colour : ""
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature2
Ignoring unknown labels:
* colour : ""
`geom_smooth()` using formula = 'y ~ x'
Ignoring unknown labels:
* colour : ""
`geom_smooth()` using formula = 'y ~ x'
Ignoring unknown labels:
* colour : ""
`geom_smooth()` using formula = 'y ~ x'
Ignoring unknown labels:
* colour : ""
`geom_smooth()` using formula = 'y ~ x'
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Signature1
Considering unidirectional gene signature mode for signature Sig1
`geom_smooth()` using formula = 'y ~ x'
Using metadata column 'sampleID' to match samples (data column names).
Considering unidirectional gene signature mode for signature Sig1
No id variables; using all as measure variables
`geom_smooth()` using formula = 'y ~ x'
Using metadata column 'sampleID' to match samples (data column names).
Using metadata column 'sample' to match samples (data column names).
Using metadata column 'sample' to match samples (data column names).
Using metadata column 'sample' to match samples (data column names).
Using metadata column 'sample' to match samples (data column names).
Using metadata column 'sample' to match samples (data column names).
Using metadata column 'sample' to match samples (data column names).
Using metadata column 'sample' to match samples (data column names).
Using metadata column 'sample' to match samples (data column names).
[ FAIL 0 | WARN 106 | SKIP 0 | PASS 212 ]

[ FAIL 0 | WARN 106 | SKIP 0 | PASS 212 ]
> 
> proc.time()
   user  system elapsed 
 33.416   0.681  34.275

Example timings

markeR.Rcheck/markeR-Ex.timings

name	user	system	elapsed
AUC_Scores	0.949	0.016	0.965
CalculateScores	0.010	0.001	0.010
CalculateScores_Ranking	0	0	0
CalculateScores_logmedian	0	0	0
CalculateScores_ssGSEA_bidirectional	0	0	0
CalculateScores_ssGSEA_unidirectional	0	0	0
CohenD_IndividualGenes	0.241	0.005	0.247
CohenD_allConditions	0	0	0
CorrelationHeatmap	0.921	0.007	0.927
ExpressionHeatmap	0.147	0.001	0.148
FPR_Simulation	1.597	0.006	1.604
IndividualGenes_Violins	0.405	0.007	0.411
PlotScores	1.599	0.011	1.611
ROC_Scores	0.113	0.001	0.114
ROCandAUCplot	0.203	0.001	0.203
VariableAssociation	0.734	0.004	0.738
VisualiseIndividualGenes	1.096	0.008	1.112
calculateDE	0.008	0.000	0.008
compute_stat_tests	0	0	0
generate_all_contrasts	0	0	0
geneset_similarity	16.903	0.124	17.032
getRanking	0	0	0
identify_variable_type	0	0	0
plotCombinedGSEA	0.144	0.005	0.148
plotGSEAenrichment	0.141	0.001	0.142
plotNESlollipop	0.659	0.002	0.661
plotPCA	0.182	0.001	0.182
plotVolcano	0.297	0.001	0.298
runGSEA	2.841	0.008	2.850
ssGSEA_alternative	0	0	0