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This page was generated on 2025-10-07 12:04 -0400 (Tue, 07 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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 1.27.1  (landing page)
Wanding Zhou
Snapshot Date: 2025-10-06 13:45 -0400 (Mon, 06 Oct 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: 2025-10-07 04:18:10 -0400 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 04:36:20 -0400 (Tue, 07 Oct 2025)
EllapsedTime: 1090.1 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 34.560  0.689  35.251
inferSex                      21.724  0.181  21.907
sesameQC_plotHeatSNPs         20.119  0.349  20.469
ELBAR                         19.299  0.274  19.575
imputeBetas                   18.809  0.425  19.236
sesameQC_calcStats            18.493  0.159  18.654
inferSpecies                  16.148  0.712  16.861
compareMouseStrainReference   15.680  0.263  15.974
diffRefSet                    14.038  0.202  14.241
DMR                           12.852  0.466  13.323
compareReference              12.878  0.243  13.186
getRefSet                     12.051  0.134  12.185
sesameQC_plotBar              11.769  0.227  11.997
matchDesign                   11.183  0.079  11.268
sesameQC_plotBetaByDesign     10.230  0.156  10.389
DML                            9.164  0.408   9.575
visualizeGene                  8.482  0.208   8.691
inferStrain                    7.394  0.412   7.808
sdf_read_table                 7.532  0.113   7.645
inferTissue                    6.868  0.148   7.017
dyeBiasNL                      6.293  0.062   6.358
dyeBiasCorrMostBalanced        6.234  0.106   6.341
getMask                        6.146  0.120   6.271
bisConversionControl           6.160  0.076   6.273
estimateLeukocyte              6.016  0.089   6.105
checkLevels                    5.703  0.144   5.847
probeSuccessRate               5.350  0.095   5.445
deIdentify                     5.248  0.066   5.315
createUCSCtrack                5.164  0.080   5.245
openSesame                     5.019  0.150   5.176
* 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 
 18.362   0.957  19.306 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML9.1640.4089.575
DMLpredict1.5590.0621.621
DMR12.852 0.46613.323
ELBAR19.299 0.27419.575
MValueToBetaValue000
SigDF0.3620.0170.379
addMask0.1010.0000.101
betasCollapseToPfx0.0130.0000.013
bisConversionControl6.1600.0766.273
calcEffectSize2.0730.0612.153
checkLevels5.7030.1445.847
cnSegmentation0.3130.0200.333
compareMouseStrainReference15.680 0.26315.974
compareMouseTissueReference000
compareReference12.878 0.24313.186
controls1.9890.0402.029
createUCSCtrack5.1640.0805.245
deIdentify5.2480.0665.315
detectionPnegEcdf0.9260.0040.930
diffRefSet14.038 0.20214.241
dmContrasts1.8200.0281.849
dyeBiasCorr2.5980.1002.698
dyeBiasCorrMostBalanced6.2340.1066.341
dyeBiasL2.1920.0612.254
dyeBiasNL6.2930.0626.358
estimateLeukocyte6.0160.0896.105
formatVCF1.9950.0542.048
getAFTypeIbySumAlleles1.5130.0391.551
getAFs1.0180.0141.032
getBetas0.710.020.73
getMask6.1460.1206.271
getRefSet12.051 0.13412.185
imputeBetas18.809 0.42519.236
imputeBetasByGenomicNeighbors34.560 0.68935.251
imputeBetasMatrixByMean0.0010.0000.001
inferEthnicity0.0010.0000.000
inferInfiniumIChannel0.2460.0630.309
inferSex21.724 0.18121.907
inferSpecies16.148 0.71216.861
inferStrain7.3940.4127.808
inferTissue6.8680.1487.017
initFileSet1.1710.0331.205
listAvailableMasks1.2520.0331.285
mLiftOver000
mapFileSet0.0330.0000.033
mapToMammal402.4820.0562.539
matchDesign11.183 0.07911.268
meanIntensity2.6520.0472.699
medianTotalIntensity0.8270.0270.855
noMasked3.4370.0483.485
noob1.8240.0091.832
openSesame5.0190.1505.176
openSesameToFile1.3840.0041.391
pOOBAH1.2840.0171.302
palgen0.0350.0050.041
parseGEOsignalMU2.9890.0583.048
predictAge2.5120.0562.568
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth0.0000.0000.001
prefixMask0.5000.0010.500
prefixMaskButC0.1330.0000.133
prefixMaskButCG0.0530.0000.053
prepSesame3.5680.0763.645
prepSesameList0.0010.0000.001
print.DMLSummary3.0820.1553.238
print.fileSet1.2560.0461.302
probeID_designType0.0010.0000.000
probeSuccessRate5.3500.0955.445
qualityMask1.8670.0451.912
reIdentify4.5340.0474.581
readFileSet0.0560.0000.056
readIDATpair0.1120.0000.111
recommendedMaskNames000
resetMask0.4220.0050.427
scrub2.3880.1342.522
scrubSoft3.1030.0533.156
sdfPlatform0.3120.0110.323
sdf_read_table7.5320.1137.645
sdf_write_table1.7240.0491.774
searchIDATprefixes0.0040.0010.005
sesame-package2.3030.0502.353
sesameAnno_attachManifest000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV000
sesameQC_calcStats18.493 0.15918.654
sesameQC_getStats1.7190.0101.729
sesameQC_plotBar11.769 0.22711.997
sesameQC_plotBetaByDesign10.230 0.15610.389
sesameQC_plotHeatSNPs20.119 0.34920.469
sesameQC_plotIntensVsBetas1.9600.0271.987
sesameQC_plotRedGrnQQ1.7890.0221.811
sesameQC_rankStats3.5510.0643.615
sesameQCtoDF1.9280.0081.936
sesame_checkVersion0.0030.0010.004
sesamize000
setMask0.0900.0000.091
signalMU0.8020.0170.820
sliceFileSet0.0330.0010.035
summaryExtractTest2.7190.0992.818
totalIntensities2.4540.0872.541
updateSigDF3.2770.1013.662
visualizeGene8.4820.2088.691
visualizeProbes1.0810.0141.095
visualizeRegion0.3310.0000.331
visualizeSegments1.8610.0431.904