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This page was generated on 2025-08-15 12:09 -0400 (Fri, 15 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4554
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 1956/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.27.1  (landing page)
Wanding Zhou
Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 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 24.04.3 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 13.7.7 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 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: 2025-08-14 23:39:34 -0400 (Thu, 14 Aug 2025)
EndedAt: 2025-08-14 23:52:23 -0400 (Thu, 14 Aug 2025)
EllapsedTime: 769.9 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_1.27.1.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 37.780  1.439  39.446
inferSex                      24.087  1.127  25.314
sesameQC_calcStats            22.847  1.353  24.340
sesameQC_plotHeatSNPs         20.474  1.625  22.234
imputeBetas                   18.773  1.412  20.304
ELBAR                         16.228  2.900  19.308
diffRefSet                    16.684  0.613  17.407
sesameQC_plotBar              14.952  0.741  15.799
inferSpecies                  13.770  0.688  14.545
getRefSet                     12.978  0.411  13.464
compareMouseStrainReference   12.905  0.396  13.403
compareReference              11.860  0.494  12.441
sesameQC_plotBetaByDesign     10.587  1.497  12.163
matchDesign                   10.669  0.826  11.570
DML                            9.027  1.291  10.431
sdf_read_table                 9.367  0.469  10.192
visualizeGene                  9.226  0.536   9.817
DMR                            9.362  0.280   9.704
estimateLeukocyte              8.330  0.537   8.938
inferTissue                    7.065  1.346   8.471
inferStrain                    7.500  0.576   8.113
getMask                        6.805  0.606   7.456
dyeBiasCorrMostBalanced        6.770  0.299   7.117
dyeBiasNL                      6.363  0.478   6.877
createUCSCtrack                6.227  0.339   6.625
deIdentify                     6.084  0.315   6.441
reIdentify                     6.125  0.244   6.424
probeSuccessRate               5.768  0.559   6.384
openSesame                     5.348  0.574   5.981
sesameQC_rankStats             5.011  0.597   5.640
bisConversionControl           5.033  0.272   5.360
* 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 
 22.226   1.904  24.373 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0010.0000.001
DML 9.027 1.29110.431
DMLpredict1.3510.1121.472
DMR9.3620.2809.704
ELBAR16.228 2.90019.308
MValueToBetaValue000
SigDF0.3300.0720.406
addMask0.1000.0010.102
betasCollapseToPfx0.0150.0000.015
bisConversionControl5.0330.2725.360
calcEffectSize1.2460.1411.403
checkLevels4.0550.2484.341
cnSegmentation0.2870.0500.338
compareMouseStrainReference12.905 0.39613.403
compareMouseTissueReference000
compareReference11.860 0.49412.441
controls2.1350.2262.383
createUCSCtrack6.2270.3396.625
deIdentify6.0840.3156.441
detectionPnegEcdf1.3380.0191.365
diffRefSet16.684 0.61317.407
dmContrasts1.9520.1962.164
dyeBiasCorr2.9180.2183.156
dyeBiasCorrMostBalanced6.7700.2997.117
dyeBiasL2.4600.1432.616
dyeBiasNL6.3630.4786.877
estimateLeukocyte8.3300.5378.938
formatVCF2.2300.2572.502
getAFTypeIbySumAlleles1.8560.2052.079
getAFs1.0340.0491.089
getBetas0.9810.1351.131
getMask6.8050.6067.456
getRefSet12.978 0.41113.464
imputeBetas18.773 1.41220.304
imputeBetasByGenomicNeighbors37.780 1.43939.446
imputeBetasMatrixByMean0.0010.0010.002
inferEthnicity0.0000.0000.001
inferInfiniumIChannel0.3530.4110.772
inferSex24.087 1.12725.314
inferSpecies13.770 0.68814.545
inferStrain7.5000.5768.113
inferTissue7.0651.3468.471
initFileSet1.2140.2451.477
listAvailableMasks1.3040.1851.502
mLiftOver0.0000.0020.003
mapFileSet0.0340.0060.040
mapToMammal403.1640.3973.592
matchDesign10.669 0.82611.570
meanIntensity2.7540.2263.007
medianTotalIntensity0.8680.0600.936
noMasked3.9130.1864.130
noob2.4100.4942.928
openSesame5.3480.5745.981
openSesameToFile1.7380.2121.968
pOOBAH1.4770.0101.497
palgen0.0460.0100.057
parseGEOsignalMU3.0720.1623.256
predictAge2.5040.1172.640
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.5690.0030.575
prefixMaskButC0.1480.0010.150
prefixMaskButCG0.0550.0000.057
prepSesame3.8840.4184.328
prepSesameList0.0010.0000.002
print.DMLSummary2.9700.8533.847
print.fileSet1.2270.2571.494
probeID_designType0.0000.0010.000
probeSuccessRate5.7680.5596.384
qualityMask2.2590.3942.679
reIdentify6.1250.2446.424
readFileSet0.0530.0040.057
readIDATpair0.1520.0020.154
recommendedMaskNames0.0000.0010.001
resetMask0.3940.0520.452
scrub2.4560.3352.814
scrubSoft3.4640.6904.177
sdfPlatform0.3090.1050.417
sdf_read_table 9.367 0.46910.192
sdf_write_table2.7010.1592.890
searchIDATprefixes0.0030.0020.005
sesame-package2.4390.3242.782
sesameAnno_attachManifest000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges0.0000.0010.001
sesameAnno_download000
sesameAnno_readManifestTSV0.0000.0000.001
sesameQC_calcStats22.847 1.35324.340
sesameQC_getStats2.4430.1142.577
sesameQC_plotBar14.952 0.74115.799
sesameQC_plotBetaByDesign10.587 1.49712.163
sesameQC_plotHeatSNPs20.474 1.62522.234
sesameQC_plotIntensVsBetas2.2050.4392.665
sesameQC_plotRedGrnQQ1.1330.1401.286
sesameQC_rankStats5.0110.5975.640
sesameQCtoDF2.1960.0122.216
sesame_checkVersion0.0030.0010.004
sesamize000
setMask0.1060.0010.107
signalMU1.0630.2751.348
sliceFileSet0.0370.0020.040
summaryExtractTest2.7140.6503.395
totalIntensities2.6500.3082.978
updateSigDF3.3580.4133.802
visualizeGene9.2260.5369.817
visualizeProbes1.5080.0281.547
visualizeRegion0.4040.0020.407
visualizeSegments1.7910.4152.221