Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-09-29 12:06 -0400 (Mon, 29 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4833
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4621
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4566
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 1969/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.27.1  (landing page)
Wanding Zhou
Snapshot Date: 2025-09-28 13:45 -0400 (Sun, 28 Sep 2025)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: devel
git_last_commit: e90f911
git_last_commit_date: 2025-06-21 02:29:58 -0400 (Sat, 21 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  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
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for sesame on kjohnson3

To the developers/maintainers of the sesame package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sesame.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: sesame
Version: 1.27.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sesame.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sesame_1.27.1.tar.gz
StartedAt: 2025-09-28 21:39:02 -0400 (Sun, 28 Sep 2025)
EndedAt: 2025-09-28 21:43:42 -0400 (Sun, 28 Sep 2025)
EllapsedTime: 280.3 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sesame.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sesame_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/sesame.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 ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.27.1’
* 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 ‘sesame’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
imputeBetasByGenomicNeighbors 13.651  0.475  14.150
inferSex                       8.972  0.481   9.482
sesameQC_calcStats             8.458  0.794   9.361
sesameQC_plotHeatSNPs          7.834  0.830   8.683
imputeBetas                    7.589  0.514   8.106
ELBAR                          5.702  1.074   6.781
inferSpecies                   6.271  0.328   6.631
sesameQC_plotBar               6.383  0.150   6.537
diffRefSet                     6.114  0.222   6.357
getRefSet                      5.257  0.190   5.458
* 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

sesame.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘sesame’ ...
** this is package ‘sesame’ version ‘1.27.1’
** 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 (sesame)

Tests output

sesame.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.

> library(testthat)
> library(sesame)
Loading required package: sesameData
Loading required package: ExperimentHub
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading sesameData.

----------------------------------------------------------
| SEnsible Step-wise Analysis of DNA MEthylation (SeSAMe)
| --------------------------------------------------------
| Please cache auxiliary data by "sesameDataCache()".
| This needs to be done only once per SeSAMe installation.
----------------------------------------------------------

> 
> test_check("sesame")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
  8.487   0.466   8.969 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML2.9470.3113.320
DMLpredict0.4050.0360.443
DMR2.9580.0743.044
ELBAR5.7021.0746.781
MValueToBetaValue000
SigDF0.0890.0120.101
addMask0.0150.0010.016
betasCollapseToPfx0.0040.0000.004
bisConversionControl2.1760.0672.247
calcEffectSize0.3680.0310.402
checkLevels1.6290.0571.690
cnSegmentation0.0790.0130.092
compareMouseStrainReference3.5760.1163.697
compareMouseTissueReference000
compareReference3.8910.1824.107
controls0.7460.0450.791
createUCSCtrack2.2570.1782.442
deIdentify1.9570.0722.040
detectionPnegEcdf0.3830.0060.390
diffRefSet6.1140.2226.357
dmContrasts0.7350.0800.815
dyeBiasCorr0.9570.0911.052
dyeBiasCorrMostBalanced3.2340.0883.326
dyeBiasL0.9050.0480.955
dyeBiasNL2.5290.1682.708
estimateLeukocyte3.0010.1303.134
formatVCF0.7340.0520.789
getAFTypeIbySumAlleles0.5660.0760.641
getAFs0.4060.0540.468
getBetas0.2700.0360.306
getMask2.2030.1592.373
getRefSet5.2570.1905.458
imputeBetas7.5890.5148.106
imputeBetasByGenomicNeighbors13.651 0.47514.150
imputeBetasMatrixByMean0.0000.0000.001
inferEthnicity0.0010.0000.000
inferInfiniumIChannel0.1380.1560.298
inferSex8.9720.4819.482
inferSpecies6.2710.3286.631
inferStrain2.7730.2413.057
inferTissue2.3070.2912.614
initFileSet0.3650.0560.423
listAvailableMasks0.3970.0580.457
mLiftOver0.0000.0010.000
mapFileSet0.0160.0010.018
mapToMammal400.7890.1040.898
matchDesign4.3770.2994.695
meanIntensity0.9240.1071.031
medianTotalIntensity0.2760.0440.323
noMasked1.4060.1481.579
noob0.8230.1090.934
openSesame1.7630.2342.008
openSesameToFile0.5810.0640.646
pOOBAH0.5300.0270.557
palgen0.0150.0020.019
parseGEOsignalMU1.3060.1011.457
predictAge1.0790.0701.156
predictAgeHorvath353000
predictAgeSkinBlood0.0010.0000.000
predictMouseAgeInMonth000
prefixMask0.1960.0010.198
prefixMaskButC0.0510.0010.053
prefixMaskButCG0.0190.0010.020
prepSesame1.3460.1501.496
prepSesameList0.0000.0010.000
print.DMLSummary1.1250.1171.261
print.fileSet0.3710.0390.410
probeID_designType000
probeSuccessRate2.0090.1432.157
qualityMask0.5610.0590.654
reIdentify1.6970.0751.776
readFileSet0.0270.0030.030
readIDATpair0.0370.0020.040
recommendedMaskNames0.0000.0000.001
resetMask0.1130.0180.131
scrub0.9280.1191.049
scrubSoft1.4000.3021.704
sdfPlatform0.0850.0130.098
sdf_read_table3.3480.1593.531
sdf_write_table0.9400.0410.987
searchIDATprefixes0.0010.0010.003
sesame-package0.9450.1021.089
sesameAnno_attachManifest000
sesameAnno_buildAddressFile0.0000.0000.001
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV000
sesameQC_calcStats8.4580.7949.361
sesameQC_getStats0.8360.0450.880
sesameQC_plotBar6.3830.1506.537
sesameQC_plotBetaByDesign4.3160.5694.889
sesameQC_plotHeatSNPs7.8340.8308.683
sesameQC_plotIntensVsBetas0.7180.1070.835
sesameQC_plotRedGrnQQ0.4420.0700.518
sesameQC_rankStats1.2840.1521.446
sesameQCtoDF0.8720.0360.912
sesame_checkVersion0.0020.0000.001
sesamize000
setMask0.0220.0020.023
signalMU0.3280.0340.362
sliceFileSet0.0150.0010.016
summaryExtractTest0.9610.1381.104
totalIntensities0.8570.1320.990
updateSigDF1.0780.2081.291
visualizeGene3.6090.2003.817
visualizeProbes0.4040.0130.418
visualizeRegion0.1210.0050.126
visualizeSegments0.8390.0860.925