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This page was generated on 2025-10-04 12:06 -0400 (Sat, 04 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 1974/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.27.1  (landing page)
Wanding Zhou
Snapshot Date: 2025-10-03 13:45 -0400 (Fri, 03 Oct 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: 2025-10-03 21:42:04 -0400 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 21:46:45 -0400 (Fri, 03 Oct 2025)
EllapsedTime: 281.5 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 13.531  0.503  14.094
inferSex                       9.242  0.495   9.758
sesameQC_calcStats             8.557  0.835   9.511
imputeBetas                    7.804  0.636   8.494
sesameQC_plotHeatSNPs          7.532  0.697   8.267
sesameQC_plotBar               7.139  0.256   7.407
inferSpecies                   6.963  0.327   7.327
ELBAR                          5.675  1.076   6.776
diffRefSet                     6.213  0.214   6.452
getRefSet                      5.472  0.182   5.657
* 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 
  8.027   0.434   8.464 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML2.9290.2963.244
DMLpredict0.4330.0360.469
DMR3.0290.0783.117
ELBAR5.6751.0766.776
MValueToBetaValue0.0000.0000.001
SigDF0.0900.0160.105
addMask0.0250.0010.026
betasCollapseToPfx0.0050.0000.004
bisConversionControl2.1540.0692.255
calcEffectSize0.3790.0290.409
checkLevels1.6210.0611.685
cnSegmentation0.0850.0140.099
compareMouseStrainReference3.5950.1333.759
compareMouseTissueReference0.0000.0010.000
compareReference3.8680.1854.063
controls0.7340.0610.796
createUCSCtrack2.3380.1412.492
deIdentify2.0090.0852.118
detectionPnegEcdf0.3920.0070.399
diffRefSet6.2130.2146.452
dmContrasts0.7460.0580.805
dyeBiasCorr0.9940.1251.139
dyeBiasCorrMostBalanced3.3060.0933.430
dyeBiasL0.9400.0550.996
dyeBiasNL2.1090.1642.281
estimateLeukocyte3.0200.1433.167
formatVCF0.7460.0600.808
getAFTypeIbySumAlleles0.5660.0690.636
getAFs0.3980.0570.457
getBetas0.2820.0330.315
getMask2.2020.2472.468
getRefSet5.4720.1825.657
imputeBetas7.8040.6368.494
imputeBetasByGenomicNeighbors13.531 0.50314.094
imputeBetasMatrixByMean0.0000.0000.001
inferEthnicity0.0010.0000.001
inferInfiniumIChannel0.1390.1640.311
inferSex9.2420.4959.758
inferSpecies6.9630.3277.327
inferStrain2.8690.2853.174
inferTissue2.4630.2682.738
initFileSet0.3710.0810.460
listAvailableMasks0.4090.0860.502
mLiftOver0.0000.0000.001
mapFileSet0.0160.0030.018
mapToMammal400.8060.1330.951
matchDesign4.4730.3054.794
meanIntensity0.9420.1161.061
medianTotalIntensity0.2650.0300.295
noMasked1.3520.1361.504
noob0.8070.0880.897
openSesame1.8070.2282.057
openSesameToFile0.5850.0680.653
pOOBAH0.5220.0280.557
palgen0.0160.0020.019
parseGEOsignalMU1.2590.1041.370
predictAge1.0380.0631.105
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.1990.0010.200
prefixMaskButC0.0530.0010.054
prefixMaskButCG0.0220.0010.022
prepSesame1.3870.1641.645
prepSesameList0.0010.0010.000
print.DMLSummary1.1480.1191.271
print.fileSet0.3870.1040.493
probeID_designType000
probeSuccessRate2.0190.1982.222
qualityMask0.5910.1020.694
reIdentify1.5760.0441.622
readFileSet0.0270.0030.031
readIDATpair0.0440.0040.048
recommendedMaskNames0.0000.0010.000
resetMask0.1080.0210.129
scrub1.1020.1771.279
scrubSoft1.3570.2461.607
sdfPlatform0.0870.0110.097
sdf_read_table3.4080.1613.579
sdf_write_table0.9290.0431.008
searchIDATprefixes0.0010.0010.003
sesame-package0.9100.1271.042
sesameAnno_attachManifest000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV0.0000.0010.000
sesameQC_calcStats8.5570.8359.511
sesameQC_getStats0.8170.0430.865
sesameQC_plotBar7.1390.2567.407
sesameQC_plotBetaByDesign3.8680.5844.453
sesameQC_plotHeatSNPs7.5320.6978.267
sesameQC_plotIntensVsBetas0.7110.1050.816
sesameQC_plotRedGrnQQ0.4390.0630.503
sesameQC_rankStats1.2950.2061.506
sesameQCtoDF0.8900.0390.930
sesame_checkVersion0.0020.0000.002
sesamize000
setMask0.0280.0020.030
signalMU0.3310.0530.384
sliceFileSet0.0160.0010.017
summaryExtractTest1.0760.1201.196
totalIntensities0.8880.1031.012
updateSigDF1.0830.1251.221
visualizeGene3.5540.2173.788
visualizeProbes0.3780.0120.390
visualizeRegion0.1160.0070.124
visualizeSegments0.7770.0380.819