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This page was generated on 2025-10-13 11:41 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.6.6 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: 2025-10-09 13:40 -0400 (Thu, 09 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 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 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: 2025-10-11 13:45:38 -0400 (Sat, 11 Oct 2025)
EndedAt: 2025-10-11 14:00:47 -0400 (Sat, 11 Oct 2025)
EllapsedTime: 908.6 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 46.159  1.646  48.941
inferSex                      29.768  1.569  32.929
sesameQC_calcStats            24.460  2.363  27.982
imputeBetas                   23.226  2.236  26.225
sesameQC_plotHeatSNPs         22.837  1.768  25.183
inferSpecies                  20.293  1.090  22.033
diffRefSet                    20.269  0.639  22.055
sesameQC_plotBar              18.741  0.505  19.667
ELBAR                         15.826  2.857  18.974
getRefSet                     17.830  0.505  19.074
sesameQC_plotBetaByDesign     13.421  1.468  15.318
matchDesign                   13.420  1.001  14.861
compareMouseStrainReference   12.875  0.483  14.100
compareReference              12.911  0.418  13.865
visualizeGene                 12.382  0.615  13.559
sdf_read_table                11.219  0.494  12.146
dyeBiasCorrMostBalanced       10.835  0.307  11.808
estimateLeukocyte             10.363  0.544  11.432
DML                            9.790  0.925  10.894
DMR                           10.259  0.264  10.599
inferStrain                    9.056  0.745  10.173
inferTissue                    7.934  0.848   8.983
getMask                        8.027  0.553   8.959
createUCSCtrack                7.886  0.340   8.676
probeSuccessRate               7.339  0.632   8.181
bisConversionControl           7.331  0.210   7.765
dyeBiasNL                      6.350  0.666   7.321
deidentify                     6.201  0.253   6.696
openSesame                     5.917  0.505   6.827
prepSesame                     5.731  0.557   6.420
scrubSoft                      4.077  0.961   5.130
reIdentify                     4.794  0.236   5.202
noMasked                       4.707  0.265   5.268
* 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 
 26.013   1.802  28.925 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0010.0000.001
DML 9.790 0.92510.894
DMLpredict1.4580.1031.578
DMR10.259 0.26410.599
ELBAR15.826 2.85718.974
MValueToBetaValue0.0010.0010.000
SigDF0.3110.0530.368
addMask0.0620.0020.065
betasCollapseToPfx0.0140.0010.015
bisConversionControl7.3310.2107.765
calcEffectSize1.4420.1341.699
checkLevels4.2000.2204.718
cnSegmentation0.3050.0570.382
compareMouseStrainReference12.875 0.48314.100
compareMouseTissueReference000
compareReference12.911 0.41813.865
controls2.5400.1752.746
createUCSCtrack7.8860.3408.676
deidentify6.2010.2536.696
detectionPnegEcdf1.6840.0531.799
diffRefSet20.269 0.63922.055
dmContrasts2.1960.1412.586
dyeBiasCorr3.4080.2593.917
dyeBiasCorrMostBalanced10.835 0.30711.808
dyeBiasL2.5950.2333.076
dyeBiasNL6.3500.6667.321
estimateLeukocyte10.363 0.54411.432
formatVCF2.7010.2113.033
getAFTypeIbySumAlleles2.0820.2312.445
getAFs1.0070.0941.149
getBetas0.9590.1491.153
getMask8.0270.5538.959
getRefSet17.830 0.50519.074
imputeBetas23.226 2.23626.225
imputeBetasByGenomicNeighbors46.159 1.64648.941
imputeBetasMatrixByMean0.0010.0010.002
inferEthnicity0.0010.0000.001
inferInfiniumIChannel0.4290.4880.954
inferSex29.768 1.56932.929
inferSpecies20.293 1.09022.033
inferStrain 9.056 0.74510.173
inferTissue7.9340.8488.983
initFileSet1.4180.2081.664
listAvailableMasks1.5900.1971.828
mLiftOver0.0000.0010.002
mapFileSet0.0480.0040.055
mapToMammal404.3770.4684.959
matchDesign13.420 1.00114.861
meanIntensity3.0660.4443.803
medianTotalIntensity0.9360.1701.183
noMasked4.7070.2655.268
noob2.7170.3973.319
openSesame5.9170.5056.827
openSesameToFile1.8200.3042.215
pOOBAH1.5960.1191.824
palgen0.0500.0070.061
parseGEOsignalMU4.1180.3994.712
predictAge3.4850.1483.701
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.5950.0110.620
prefixMaskButC0.1530.0050.160
prefixMaskButCG0.0540.0030.059
prepSesame5.7310.5576.420
prepSesameList0.0010.0010.002
print.DMLSummary3.4530.5614.101
print.fileSet1.3660.1871.584
probeID_designType000
probeSuccessRate7.3390.6328.181
qualityMask2.6920.3063.066
reIdentify4.7940.2365.202
readFileSet0.0830.0050.090
readIDATpair0.1450.0170.164
recommendedMaskNames0.0000.0010.000
resetMask0.3650.0690.438
scrub2.8080.6373.506
scrubSoft4.0770.9615.130
sdfPlatform0.2960.0480.350
sdf_read_table11.219 0.49412.146
sdf_write_table3.0200.1683.314
searchIDATprefixes0.0040.0030.009
sesame-package3.4370.3913.914
sesameAnno_attachManifest000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV000
sesameQC_calcStats24.460 2.36327.982
sesameQC_getStats2.4210.1352.707
sesameQC_plotBar18.741 0.50519.667
sesameQC_plotBetaByDesign13.421 1.46815.318
sesameQC_plotHeatSNPs22.837 1.76825.183
sesameQC_plotIntensVsBetas1.9800.3402.406
sesameQC_plotRedGrnQQ1.6630.1831.904
sesameQC_rankStats4.0300.2834.389
sesameQCtoDF2.7290.0382.850
sesame_checkVersion0.0050.0010.006
sesamize000
setMask0.0750.0030.079
signalMU1.1220.0881.229
sliceFileSet0.0500.0030.053
summaryExtractTest3.9480.5124.620
totalIntensities3.0190.3013.435
updateSigDF4.3060.4404.891
visualizeGene12.382 0.61513.559
visualizeProbes1.2960.0451.379
visualizeRegion0.3820.0210.417
visualizeSegments2.4720.3122.845