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This page was generated on 2025-10-13 11:38 -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 nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings sesame_1.26.0.tar.gz
StartedAt: 2025-10-13 03:39:23 -0400 (Mon, 13 Oct 2025)
EndedAt: 2025-10-13 03:56:12 -0400 (Mon, 13 Oct 2025)
EllapsedTime: 1009.3 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings sesame_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/sesame.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 33.086  0.944  34.037
inferSex                      21.286  0.412  21.702
sesameQC_calcStats            17.960  0.676  18.637
sesameQC_plotHeatSNPs         17.370  0.360  17.776
imputeBetas                   16.813  0.828  17.645
inferSpecies                  15.309  0.959  16.270
diffRefSet                    13.988  1.003  14.994
ELBAR                         13.098  0.299  13.399
compareReference              11.594  0.423  12.020
matchDesign                   10.925  0.809  11.740
getRefSet                     11.181  0.355  11.536
sesameQC_plotBar              11.166  0.354  11.522
compareMouseStrainReference   11.034  0.219  11.259
sesameQC_plotBetaByDesign     10.434  0.329  10.766
visualizeGene                  8.795  0.364   9.164
DMR                            7.998  0.361   8.360
estimateLeukocyte              7.908  0.426   8.335
sdf_read_table                 7.470  0.303   7.773
inferStrain                    6.745  0.577   7.324
DML                            6.748  0.482   7.234
dyeBiasCorrMostBalanced        6.266  0.266   6.534
inferTissue                    6.197  0.173   6.370
getMask                        5.821  0.402   6.228
deidentify                     5.387  0.503   5.894
probeSuccessRate               5.101  0.315   5.416
openSesame                     4.871  0.534   5.412
dyeBiasNL                      5.248  0.125   5.377
createUCSCtrack                4.990  0.269   5.260
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

sesame.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 19.049   1.093  20.146 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML6.7480.4827.234
DMLpredict1.3140.1071.422
DMR7.9980.3618.360
ELBAR13.098 0.29913.399
MValueToBetaValue0.0010.0000.001
SigDF0.3060.0430.349
addMask0.0820.0000.082
betasCollapseToPfx0.0110.0000.012
bisConversionControl4.2870.2264.515
calcEffectSize1.3060.1011.409
checkLevels2.9510.1253.092
cnSegmentation0.2810.0450.325
compareMouseStrainReference11.034 0.21911.259
compareMouseTissueReference000
compareReference11.594 0.42312.020
controls1.9600.1512.111
createUCSCtrack4.9900.2695.260
deidentify5.3870.5035.894
detectionPnegEcdf0.8590.0270.886
diffRefSet13.988 1.00314.994
dmContrasts1.9400.0962.036
dyeBiasCorr2.6370.2132.850
dyeBiasCorrMostBalanced6.2660.2666.534
dyeBiasL2.1840.2612.445
dyeBiasNL5.2480.1255.377
estimateLeukocyte7.9080.4268.335
formatVCF2.0940.1302.225
getAFTypeIbySumAlleles1.7210.1121.835
getAFs0.7660.0950.861
getBetas0.8540.0620.916
getMask5.8210.4026.228
getRefSet11.181 0.35511.536
imputeBetas16.813 0.82817.645
imputeBetasByGenomicNeighbors33.086 0.94434.037
imputeBetasMatrixByMean0.0020.0000.002
inferEthnicity0.0000.0000.001
inferInfiniumIChannel0.2530.6130.866
inferSex21.286 0.41221.702
inferSpecies15.309 0.95916.270
inferStrain6.7450.5777.324
inferTissue6.1970.1736.370
initFileSet1.2140.0761.290
listAvailableMasks1.2490.0851.333
mLiftOver0.0000.0010.001
mapFileSet0.0330.0010.033
mapToMammal402.7820.1622.947
matchDesign10.925 0.80911.740
meanIntensity2.8630.4693.333
medianTotalIntensity0.8290.1690.998
noMasked3.5390.3573.895
noob2.0810.3172.398
openSesame4.8710.5345.412
openSesameToFile1.3710.1371.510
pOOBAH1.2480.0501.299
palgen0.0330.0060.038
parseGEOsignalMU2.9120.2043.117
predictAge2.3830.2122.594
predictAgeHorvath3530.0010.0000.000
predictAgeSkinBlood000
predictMouseAgeInMonth0.0000.0000.001
prefixMask0.3810.0140.394
prefixMaskButC0.0970.0010.099
prefixMaskButCG0.0350.0020.036
prepSesame4.0030.3514.356
prepSesameList0.0000.0020.001
print.DMLSummary2.7980.3903.189
print.fileSet1.1740.0871.262
probeID_designType0.0010.0000.000
probeSuccessRate5.1010.3155.416
qualityMask2.0050.2082.215
reIdentify4.2520.1704.422
readFileSet0.0530.0020.055
readIDATpair0.1120.0020.113
recommendedMaskNames0.0010.0000.001
resetMask0.4020.0540.455
scrub2.2170.2842.501
scrubSoft3.2570.1203.377
sdfPlatform0.2940.0720.367
sdf_read_table7.4700.3037.773
sdf_write_table1.6970.1241.889
searchIDATprefixes0.0030.0020.006
sesame-package2.4550.1702.627
sesameAnno_attachManifest000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download0.0000.0000.001
sesameAnno_readManifestTSV000
sesameQC_calcStats17.960 0.67618.637
sesameQC_getStats1.6450.0071.653
sesameQC_plotBar11.166 0.35411.522
sesameQC_plotBetaByDesign10.434 0.32910.766
sesameQC_plotHeatSNPs17.370 0.36017.776
sesameQC_plotIntensVsBetas1.9710.0982.070
sesameQC_plotRedGrnQQ1.6610.0641.726
sesameQC_rankStats4.0020.1914.194
sesameQCtoDF1.9710.0261.997
sesame_checkVersion0.0040.0000.004
sesamize000
setMask0.0860.0000.086
signalMU1.0470.1081.155
sliceFileSet0.0320.0010.034
summaryExtractTest2.7340.2242.959
totalIntensities2.5490.1482.699
updateSigDF3.2190.2163.438
visualizeGene8.7950.3649.164
visualizeProbes1.0570.0061.062
visualizeRegion0.3130.0240.337
visualizeSegments1.7140.1481.862