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This page was generated on 2025-09-30 12:06 -0400 (Tue, 30 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4843
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4575
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 1971/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.27.1  (landing page)
Wanding Zhou
Snapshot Date: 2025-09-29 13:45 -0400 (Mon, 29 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: 2025-09-29 21:38:35 -0400 (Mon, 29 Sep 2025)
EndedAt: 2025-09-29 21:43:15 -0400 (Mon, 29 Sep 2025)
EllapsedTime: 280.5 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 13.741  0.567  14.336
inferSex                       8.912  0.477   9.414
sesameQC_calcStats             8.262  0.806   9.175
sesameQC_plotHeatSNPs          8.194  0.719   8.978
imputeBetas                    7.491  0.615   8.141
sesameQC_plotBar               6.665  0.223   6.935
ELBAR                          5.639  1.078   6.763
inferSpecies                   6.154  0.314   6.479
diffRefSet                     6.114  0.204   6.322
getRefSet                      5.383  0.146   5.532
sesameQC_plotBetaByDesign      4.438  0.707   5.159
* 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 
  8.705   0.453   9.167 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML2.9570.3183.339
DMLpredict0.4090.0360.445
DMR2.9980.0783.079
ELBAR5.6391.0786.763
MValueToBetaValue000
SigDF0.0910.0160.118
addMask0.0170.0010.018
betasCollapseToPfx0.0040.0000.004
bisConversionControl2.1520.0712.253
calcEffectSize0.3730.0490.433
checkLevels1.6510.1071.774
cnSegmentation0.0830.0240.107
compareMouseStrainReference3.5710.1713.761
compareMouseTissueReference000
compareReference3.8420.1834.033
controls0.7270.0830.810
createUCSCtrack2.3260.1292.457
deIdentify1.9830.0912.101
detectionPnegEcdf0.3970.0070.405
diffRefSet6.1140.2046.322
dmContrasts0.7170.0630.782
dyeBiasCorr0.9700.1131.086
dyeBiasCorrMostBalanced3.2310.1153.351
dyeBiasL0.9110.0560.968
dyeBiasNL2.5910.1622.762
estimateLeukocyte3.0830.1433.241
formatVCF0.7510.0970.848
getAFTypeIbySumAlleles0.5170.0710.589
getAFs0.3750.0440.420
getBetas0.2580.0340.292
getMask2.2320.2252.460
getRefSet5.3830.1465.532
imputeBetas7.4910.6158.141
imputeBetasByGenomicNeighbors13.741 0.56714.336
imputeBetasMatrixByMean0.0000.0000.001
inferEthnicity0.0010.0000.000
inferInfiniumIChannel0.1380.1460.296
inferSex8.9120.4779.414
inferSpecies6.1540.3146.479
inferStrain2.7450.2693.025
inferTissue2.2860.2822.598
initFileSet0.3650.0530.420
listAvailableMasks0.3990.0530.455
mLiftOver0.0000.0010.000
mapFileSet0.0160.0010.016
mapToMammal400.7880.1230.915
matchDesign4.3710.2824.661
meanIntensity0.9100.0981.009
medianTotalIntensity0.2660.0450.311
noMasked1.3540.1031.463
noob0.8040.1020.908
openSesame1.8020.2592.079
openSesameToFile0.5720.0680.647
pOOBAH0.5240.0360.561
palgen0.0140.0030.017
parseGEOsignalMU1.2530.0981.353
predictAge1.0220.0641.088
predictAgeHorvath3530.0000.0000.001
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.1960.0030.199
prefixMaskButC0.0500.0010.051
prefixMaskButCG0.0190.0010.020
prepSesame1.3200.1451.476
prepSesameList0.0010.0010.001
print.DMLSummary1.1070.1281.357
print.fileSet0.3700.0560.433
probeID_designType0.0010.0000.000
probeSuccessRate2.0070.1792.219
qualityMask0.5570.0460.604
reIdentify1.7080.0701.786
readFileSet0.0270.0030.029
readIDATpair0.0410.0040.045
recommendedMaskNames000
resetMask0.1100.0250.136
scrub0.9240.1101.033
scrubSoft1.4020.3051.716
sdfPlatform0.0870.0120.098
sdf_read_table3.3400.1673.517
sdf_write_table0.9290.0460.986
searchIDATprefixes0.0020.0010.003
sesame-package0.8690.0770.946
sesameAnno_attachManifest000
sesameAnno_buildAddressFile0.0000.0010.000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV000
sesameQC_calcStats8.2620.8069.175
sesameQC_getStats0.8450.0390.887
sesameQC_plotBar6.6650.2236.935
sesameQC_plotBetaByDesign4.4380.7075.159
sesameQC_plotHeatSNPs8.1940.7198.978
sesameQC_plotIntensVsBetas0.7210.1260.847
sesameQC_plotRedGrnQQ0.4460.0580.511
sesameQC_rankStats1.2500.1401.391
sesameQCtoDF0.8810.0300.910
sesame_checkVersion0.0010.0000.001
sesamize000
setMask0.0260.0030.028
signalMU0.3190.0280.348
sliceFileSet0.0150.0010.017
summaryExtractTest0.9280.1141.042
totalIntensities0.8510.1100.962
updateSigDF1.0990.1761.297
visualizeGene3.5340.1963.740
visualizeProbes0.3730.0130.387
visualizeRegion0.1130.0080.122
visualizeSegments0.8700.0840.956