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This page was generated on 2025-08-08 12:09 -0400 (Fri, 08 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4815
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 1954/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.27.1  (landing page)
Wanding Zhou
Snapshot Date: 2025-08-07 13:45 -0400 (Thu, 07 Aug 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for sesame on lconway

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: 2025-08-08 00:04:32 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 00:17:33 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 780.7 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 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 37.692  1.455  39.352
inferSex                      23.888  1.318  25.330
sesameQC_calcStats            22.685  1.786  24.626
sesameQC_plotHeatSNPs         19.381  1.942  21.495
imputeBetas                   19.272  1.583  20.985
ELBAR                         16.661  2.952  19.832
diffRefSet                    16.735  0.634  17.493
inferSpecies                  15.350  0.675  16.133
sesameQC_plotBar              13.910  0.453  14.484
compareMouseStrainReference   13.495  0.438  14.065
sesameQC_plotBetaByDesign     11.724  1.422  13.278
getRefSet                     12.555  0.461  13.102
compareReference              12.141  0.528  12.760
matchDesign                   11.335  0.823  12.261
DML                            9.036  1.279  10.402
visualizeGene                  9.634  0.655  10.379
DMR                            9.388  0.301   9.786
sdf_read_table                 9.179  0.428   9.670
inferTissue                    7.222  1.499   8.816
dyeBiasCorrMostBalanced        8.141  0.338   8.539
inferStrain                    7.700  0.608   8.357
estimateLeukocyte              7.425  0.578   8.060
getMask                        6.629  0.607   7.298
dyeBiasNL                      6.588  0.561   7.208
deIdentify                     6.624  0.346   7.015
createUCSCtrack                6.257  0.339   6.648
openSesame                     5.679  0.681   6.426
probeSuccessRate               5.617  0.483   6.150
bisConversionControl           4.991  0.258   5.292
reIdentify                     4.885  0.291   5.203
* 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-x86_64/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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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 
 22.919   1.931  24.992 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML 9.036 1.27910.402
DMLpredict1.3950.1111.518
DMR9.3880.3019.786
ELBAR16.661 2.95219.832
MValueToBetaValue000
SigDF0.320.080.41
addMask0.0830.0000.084
betasCollapseToPfx0.0110.0000.012
bisConversionControl4.9910.2585.292
calcEffectSize1.1950.1181.322
checkLevels3.9070.2394.188
cnSegmentation0.3100.0850.406
compareMouseStrainReference13.495 0.43814.065
compareMouseTissueReference0.0000.0000.001
compareReference12.141 0.52812.760
controls2.1710.2142.402
createUCSCtrack6.2570.3396.648
deIdentify6.6240.3467.015
detectionPnegEcdf1.4090.0141.430
diffRefSet16.735 0.63417.493
dmContrasts2.0690.2172.297
dyeBiasCorr2.9880.2503.255
dyeBiasCorrMostBalanced8.1410.3388.539
dyeBiasL1.4560.1471.612
dyeBiasNL6.5880.5617.208
estimateLeukocyte7.4250.5788.060
formatVCF2.2960.2722.580
getAFTypeIbySumAlleles1.8060.1962.019
getAFs1.0600.1101.175
getBetas1.8480.1261.985
getMask6.6290.6077.298
getRefSet12.555 0.46113.102
imputeBetas19.272 1.58320.985
imputeBetasByGenomicNeighbors37.692 1.45539.352
imputeBetasMatrixByMean0.0010.0010.001
inferEthnicity0.0010.0000.001
inferInfiniumIChannel0.3850.4450.833
inferSex23.888 1.31825.330
inferSpecies15.350 0.67516.133
inferStrain7.7000.6088.357
inferTissue7.2221.4998.816
initFileSet1.3440.3131.673
listAvailableMasks1.4490.1741.635
mLiftOver0.0010.0020.002
mapFileSet0.0410.0030.045
mapToMammal403.2360.3903.662
matchDesign11.335 0.82312.261
meanIntensity2.9090.2223.159
medianTotalIntensity0.8810.0580.949
noMasked4.1360.2254.394
noob2.5240.6153.177
openSesame5.6790.6816.426
openSesameToFile1.7650.2101.986
pOOBAH1.5150.0071.529
palgen0.0440.0080.052
parseGEOsignalMU3.1590.1753.353
predictAge2.6720.1232.817
predictAgeHorvath3530.0010.0000.000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.6310.0020.637
prefixMaskButC0.1580.0010.160
prefixMaskButCG0.0680.0000.069
prepSesame4.1200.4024.554
prepSesameList0.0010.0010.002
print.DMLSummary2.9400.7473.733
print.fileSet1.2360.2581.504
probeID_designType0.0010.0000.001
probeSuccessRate5.6170.4836.150
qualityMask2.1760.3962.586
reIdentify4.8850.2915.203
readFileSet0.0530.0040.058
readIDATpair0.1410.0020.144
recommendedMaskNames000
resetMask0.4020.0720.476
scrub2.4100.0182.439
scrubSoft3.3651.1544.564
sdfPlatform0.2980.0880.389
sdf_read_table9.1790.4289.670
sdf_write_table2.7320.1612.927
searchIDATprefixes0.0030.0030.006
sesame-package2.5850.4623.075
sesameAnno_attachManifest000
sesameAnno_buildAddressFile0.0000.0000.001
sesameAnno_buildManifestGRanges0.0010.0000.000
sesameAnno_download0.0000.0010.000
sesameAnno_readManifestTSV0.0000.0000.001
sesameQC_calcStats22.685 1.78624.626
sesameQC_getStats2.3420.0152.374
sesameQC_plotBar13.910 0.45314.484
sesameQC_plotBetaByDesign11.724 1.42213.278
sesameQC_plotHeatSNPs19.381 1.94221.495
sesameQC_plotIntensVsBetas2.2780.4582.778
sesameQC_plotRedGrnQQ1.1560.1221.294
sesameQC_rankStats3.4770.2773.783
sesameQCtoDF2.2830.1662.486
sesame_checkVersion0.0030.0010.004
sesamize0.0000.0010.001
setMask0.1220.0010.123
signalMU0.8690.0670.947
sliceFileSet0.0350.0040.039
summaryExtractTest3.1020.8964.070
totalIntensities2.6600.4053.100
updateSigDF3.3990.4613.923
visualizeGene 9.634 0.65510.379
visualizeProbes1.3410.0321.381
visualizeRegion0.3670.0100.377
visualizeSegments1.8680.5792.474