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This page was generated on 2025-09-25 12:04 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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 1969/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.27.1  (landing page)
Wanding Zhou
Snapshot Date: 2025-09-24 13:45 -0400 (Wed, 24 Sep 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
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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings sesame_1.27.1.tar.gz
StartedAt: 2025-09-25 04:14:54 -0400 (Thu, 25 Sep 2025)
EndedAt: 2025-09-25 04:33:33 -0400 (Thu, 25 Sep 2025)
EllapsedTime: 1119.2 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings sesame_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/sesame.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘1.27.1’
* 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 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 32.757  0.531  33.291
sesameQC_calcStats            19.715  1.603  21.319
inferSex                      21.001  0.230  21.233
ELBAR                         19.726  0.453  20.239
diffRefSet                    17.998  0.236  18.235
inferSpecies                  17.330  0.745  18.075
sesameQC_plotHeatSNPs         17.011  0.569  17.584
imputeBetas                   17.105  0.424  17.531
compareMouseStrainReference   13.985  0.224  14.219
DMR                           12.719  0.291  13.019
sesameQC_plotBar              11.793  0.549  12.343
compareReference              11.890  0.276  12.170
matchDesign                   11.777  0.082  11.863
getRefSet                     11.343  0.068  11.411
DML                           10.139  0.474  10.633
sesameQC_plotBetaByDesign      9.694  0.472  10.169
estimateLeukocyte              8.488  0.129   8.629
visualizeGene                  8.146  0.189   8.336
dyeBiasCorrMostBalanced        8.203  0.104   8.315
dyeBiasNL                      7.916  0.082   8.000
inferStrain                    7.283  0.417   7.706
sdf_read_table                 7.398  0.093   7.492
createUCSCtrack                6.754  0.114   6.868
inferTissue                    6.561  0.197   6.759
deIdentify                     6.090  0.095   6.187
getMask                        5.932  0.121   6.054
bisConversionControl           5.237  0.078   5.385
probeSuccessRate               5.154  0.118   5.272
* 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-3.22-bioc/R/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 Patched (2025-08-23 r88802) -- "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 
 19.573   1.002  20.563 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0010.0010.001
DML10.139 0.47410.633
DMLpredict2.0360.0352.072
DMR12.719 0.29113.019
ELBAR19.726 0.45320.239
MValueToBetaValue000
SigDF0.4970.0350.532
addMask0.2720.0080.280
betasCollapseToPfx0.0230.0000.023
bisConversionControl5.2370.0785.385
calcEffectSize1.4640.0291.525
checkLevels3.1730.0653.243
cnSegmentation0.3500.0120.362
compareMouseStrainReference13.985 0.22414.219
compareMouseTissueReference0.0010.0000.000
compareReference11.890 0.27612.170
controls3.3290.0663.396
createUCSCtrack6.7540.1146.868
deIdentify6.0900.0956.187
detectionPnegEcdf1.4190.0211.440
diffRefSet17.998 0.23618.235
dmContrasts2.9840.0433.027
dyeBiasCorr3.2550.0873.343
dyeBiasCorrMostBalanced8.2030.1048.315
dyeBiasL3.2330.0723.305
dyeBiasNL7.9160.0828.000
estimateLeukocyte8.4880.1298.629
formatVCF2.2390.0542.293
getAFTypeIbySumAlleles1.6150.0401.656
getAFs1.0360.0651.101
getBetas0.7940.0270.821
getMask5.9320.1216.054
getRefSet11.343 0.06811.411
imputeBetas17.105 0.42417.531
imputeBetasByGenomicNeighbors32.757 0.53133.291
imputeBetasMatrixByMean0.0010.0000.001
inferEthnicity0.0000.0000.001
inferInfiniumIChannel0.2390.0620.301
inferSex21.001 0.23021.233
inferSpecies17.330 0.74518.075
inferStrain7.2830.4177.706
inferTissue6.5610.1976.759
initFileSet1.1510.0291.180
listAvailableMasks1.2190.0281.247
mLiftOver0.0010.0000.000
mapFileSet0.0330.0000.033
mapToMammal402.3780.0622.441
matchDesign11.777 0.08211.863
meanIntensity2.5010.0552.556
medianTotalIntensity0.8280.0160.844
noMasked3.4920.0623.554
noob1.9500.0031.952
openSesame4.8300.1264.965
openSesameToFile1.2900.0211.312
pOOBAH1.2510.0041.255
palgen0.0380.0030.041
parseGEOsignalMU3.0160.0633.080
predictAge2.3470.0442.392
predictAgeHorvath3530.0000.0000.001
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.4590.0020.460
prefixMaskButC0.1470.0000.146
prefixMaskButCG0.0640.0000.064
prepSesame3.4230.0723.496
prepSesameList0.0010.0000.002
print.DMLSummary2.9280.1493.077
print.fileSet1.2150.0321.247
probeID_designType0.0010.0000.000
probeSuccessRate5.1540.1185.272
qualityMask1.7360.0431.779
reIdentify4.4230.0484.471
readFileSet0.0510.0020.052
readIDATpair0.1230.0020.126
recommendedMaskNames000
resetMask0.3830.0130.396
scrub2.1830.1522.334
scrubSoft3.1070.0053.112
sdfPlatform0.2840.0120.297
sdf_read_table7.3980.0937.492
sdf_write_table1.7280.0631.927
searchIDATprefixes0.0050.0000.006
sesame-package2.2820.1122.394
sesameAnno_attachManifest000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV000
sesameQC_calcStats19.715 1.60321.319
sesameQC_getStats1.7990.0541.854
sesameQC_plotBar11.793 0.54912.343
sesameQC_plotBetaByDesign 9.694 0.47210.169
sesameQC_plotHeatSNPs17.011 0.56917.584
sesameQC_plotIntensVsBetas2.2380.0792.317
sesameQC_plotRedGrnQQ1.6210.0501.671
sesameQC_rankStats3.3270.1223.450
sesameQCtoDF1.8280.0211.849
sesame_checkVersion0.0050.0000.005
sesamize000
setMask0.1050.0100.115
signalMU0.7830.0490.832
sliceFileSet0.0330.0010.034
summaryExtractTest2.8950.2033.098
totalIntensities2.3360.0702.405
updateSigDF3.0140.1193.133
visualizeGene8.1460.1898.336
visualizeProbes1.0650.0181.083
visualizeRegion0.3110.0010.313
visualizeSegments1.8490.1491.998