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This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 1.26.0  (landing page)
Wanding Zhou
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: RELEASE_3_21
git_last_commit: bc933e0
git_last_commit_date: 2025-04-15 11:34:53 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for sesame on kjohnson1

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: 1.26.0
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_1.26.0.tar.gz
StartedAt: 2025-10-15 12:20:05 -0400 (Wed, 15 Oct 2025)
EndedAt: 2025-10-15 12:34:44 -0400 (Wed, 15 Oct 2025)
EllapsedTime: 879.2 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/sesame.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* 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 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.26.0’
* 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 45.469  1.723  47.679
inferSex                      29.137  1.577  31.186
sesameQC_calcStats            24.571  3.000  28.096
imputeBetas                   23.317  2.089  25.722
sesameQC_plotHeatSNPs         21.977  1.975  24.295
inferSpecies                  19.934  1.020  21.179
diffRefSet                    20.173  0.707  21.570
sesameQC_plotBar              19.844  0.410  20.435
ELBAR                         15.476  3.325  19.073
getRefSet                     17.632  0.476  18.326
sesameQC_plotBetaByDesign     13.273  1.705  15.155
matchDesign                   13.317  0.782  14.475
visualizeGene                 12.630  0.665  13.465
compareReference              12.646  0.464  13.319
compareMouseStrainReference   12.243  0.405  12.743
sdf_read_table                11.097  0.474  11.808
dyeBiasCorrMostBalanced       10.878  0.373  11.747
estimateLeukocyte             10.297  0.462  10.848
DML                            9.540  0.920  10.547
DMR                            9.887  0.255  10.157
inferStrain                    8.971  0.771   9.896
inferTissue                    7.665  0.950   8.734
getMask                        7.777  0.511   8.414
createUCSCtrack                7.838  0.401   8.319
probeSuccessRate               7.244  0.784   8.129
bisConversionControl           7.368  0.213   7.704
dyeBiasNL                      6.291  0.530   6.897
openSesame                     5.730  0.713   6.536
deidentify                     6.116  0.239   6.428
prepSesame                     5.514  0.776   6.365
* 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 ‘1.26.0’
** 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 (2025-06-14 r88325) -- "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 
 25.434   1.752  27.661 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0000.0010.000
DML 9.540 0.92010.547
DMLpredict1.4290.1131.548
DMR 9.887 0.25510.157
ELBAR15.476 3.32519.073
MValueToBetaValue000
SigDF0.2490.0440.306
addMask0.0760.0050.084
betasCollapseToPfx0.0130.0000.013
bisConversionControl7.3680.2137.704
calcEffectSize1.4430.1161.569
checkLevels4.0630.1984.294
cnSegmentation0.2860.0630.350
compareMouseStrainReference12.243 0.40512.743
compareMouseTissueReference000
compareReference12.646 0.46413.319
controls2.5920.2232.881
createUCSCtrack7.8380.4018.319
deidentify6.1160.2396.428
detectionPnegEcdf1.6610.0801.759
diffRefSet20.173 0.70721.570
dmContrasts2.3070.1442.475
dyeBiasCorr3.2610.3643.736
dyeBiasCorrMostBalanced10.878 0.37311.747
dyeBiasL2.6250.2612.942
dyeBiasNL6.2910.5306.897
estimateLeukocyte10.297 0.46210.848
formatVCF2.6050.2362.888
getAFTypeIbySumAlleles1.9810.2532.260
getAFs1.0050.1861.202
getBetas0.8990.1881.099
getMask7.7770.5118.414
getRefSet17.632 0.47618.326
imputeBetas23.317 2.08925.722
imputeBetasByGenomicNeighbors45.469 1.72347.679
imputeBetasMatrixByMean0.0010.0000.002
inferEthnicity0.0000.0000.001
inferInfiniumIChannel0.3990.3790.817
inferSex29.137 1.57731.186
inferSpecies19.934 1.02021.179
inferStrain8.9710.7719.896
inferTissue7.6650.9508.734
initFileSet1.3560.2361.614
listAvailableMasks1.5790.2051.804
mLiftOver0.0000.0020.001
mapFileSet0.0480.0050.054
mapToMammal404.1940.5614.826
matchDesign13.317 0.78214.475
meanIntensity2.9760.3063.427
medianTotalIntensity0.9140.1191.057
noMasked4.5830.2374.855
noob2.7180.3913.132
openSesame5.7300.7136.536
openSesameToFile1.7930.3592.189
pOOBAH1.5830.1151.714
palgen0.0510.0080.063
parseGEOsignalMU4.1630.4434.668
predictAge3.3040.1223.448
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.6340.0100.654
prefixMaskButC0.1720.0040.179
prefixMaskButCG0.0680.0020.070
prepSesame5.5140.7766.365
prepSesameList0.0020.0000.003
print.DMLSummary3.4050.3953.861
print.fileSet1.3510.2061.602
probeID_designType000
probeSuccessRate7.2440.7848.129
qualityMask2.6220.2732.930
reIdentify4.7480.1374.924
readFileSet0.0820.0050.087
readIDATpair0.1440.0060.152
recommendedMaskNames0.0000.0000.001
resetMask0.3700.0580.431
scrub2.8140.2743.105
scrubSoft4.1170.7824.937
sdfPlatform0.3040.0460.351
sdf_read_table11.097 0.47411.808
sdf_write_table2.9550.1353.135
searchIDATprefixes0.0030.0020.006
sesame-package3.3340.3423.720
sesameAnno_attachManifest0.0000.0000.001
sesameAnno_buildAddressFile0.0000.0000.001
sesameAnno_buildManifestGRanges000
sesameAnno_download0.0010.0000.000
sesameAnno_readManifestTSV000
sesameQC_calcStats24.571 3.00028.096
sesameQC_getStats2.4600.0622.539
sesameQC_plotBar19.844 0.41020.435
sesameQC_plotBetaByDesign13.273 1.70515.155
sesameQC_plotHeatSNPs21.977 1.97524.295
sesameQC_plotIntensVsBetas1.9750.2002.191
sesameQC_plotRedGrnQQ1.6570.1311.798
sesameQC_rankStats3.8280.2834.151
sesameQCtoDF2.7080.0382.777
sesame_checkVersion0.0050.0020.007
sesamize0.0010.0010.000
setMask0.0740.0020.076
signalMU1.0470.0651.121
sliceFileSet0.0500.0030.053
summaryExtractTest3.9130.5044.475
totalIntensities2.9880.2993.311
updateSigDF4.2010.4574.789
visualizeGene12.630 0.66513.465
visualizeProbes1.2530.0581.333
visualizeRegion0.3780.0230.408
visualizeSegments2.4130.2502.704