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This page was generated on 2025-09-23 12:04 -0400 (Tue, 23 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4816
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4605
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4549
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: 2025-09-22 13:45 -0400 (Mon, 22 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: 2025-09-23 04:11:23 -0400 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 04:29:39 -0400 (Tue, 23 Sep 2025)
EllapsedTime: 1096.2 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 32.918  0.598  33.519
diffRefSet                    19.780  0.341  20.195
inferSex                      19.904  0.110  20.016
sesameQC_calcStats            18.576  1.180  19.758
ELBAR                         19.265  0.446  19.734
sesameQC_plotHeatSNPs         17.564  0.518  18.085
imputeBetas                   16.707  0.376  17.086
inferSpecies                  15.485  0.774  16.260
compareReference              13.340  0.369  13.740
compareMouseStrainReference   12.607  0.243  12.892
sesameQC_plotBar              11.910  0.500  12.412
getRefSet                     12.142  0.185  12.327
DMR                           11.328  0.506  11.897
matchDesign                   11.705  0.049  11.759
sesameQC_plotBetaByDesign     10.803  0.471  11.275
dyeBiasCorrMostBalanced        9.360  0.133   9.494
DML                            8.468  0.469   8.971
visualizeGene                  8.496  0.291   8.791
estimateLeukocyte              8.610  0.134   8.748
sdf_read_table                 7.531  0.428   7.960
dyeBiasNL                      7.781  0.127   7.909
createUCSCtrack                7.106  0.136   7.245
inferStrain                    6.696  0.428   7.128
inferTissue                    6.811  0.165   6.979
deIdentify                     6.686  0.110   6.799
getMask                        6.231  0.159   6.392
bisConversionControl           5.247  0.104   5.353
probeSuccessRate               5.240  0.111   5.352
openSesame                     4.937  0.072   5.016
* 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 
 19.327   1.498  20.815 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML8.4680.4698.971
DMLpredict1.5420.0401.582
DMR11.328 0.50611.897
ELBAR19.265 0.44619.734
MValueToBetaValue0.0000.0000.001
SigDF0.4210.0200.480
addMask0.2490.0050.258
betasCollapseToPfx0.0150.0000.015
bisConversionControl5.2470.1045.353
calcEffectSize2.0040.0852.090
checkLevels3.4690.1233.592
cnSegmentation0.3250.0140.339
compareMouseStrainReference12.607 0.24312.892
compareMouseTissueReference000
compareReference13.340 0.36913.740
controls2.4940.0562.570
createUCSCtrack7.1060.1367.245
deIdentify6.6860.1106.799
detectionPnegEcdf1.3400.0211.377
diffRefSet19.780 0.34120.195
dmContrasts3.0300.1313.162
dyeBiasCorr3.2360.1033.339
dyeBiasCorrMostBalanced9.3600.1339.494
dyeBiasL3.1150.0863.200
dyeBiasNL7.7810.1277.909
estimateLeukocyte8.6100.1348.748
formatVCF3.5160.0623.579
getAFTypeIbySumAlleles2.6430.0612.704
getAFs1.3630.0151.378
getBetas0.9270.0130.940
getMask6.2310.1596.392
getRefSet12.142 0.18512.327
imputeBetas16.707 0.37617.086
imputeBetasByGenomicNeighbors32.918 0.59833.519
imputeBetasMatrixByMean0.0010.0000.001
inferEthnicity0.0000.0010.001
inferInfiniumIChannel0.2370.0550.292
inferSex19.904 0.11020.016
inferSpecies15.485 0.77416.260
inferStrain6.6960.4287.128
inferTissue6.8110.1656.979
initFileSet1.1550.0351.190
listAvailableMasks1.2240.0251.250
mLiftOver000
mapFileSet0.0330.0000.033
mapToMammal402.3020.0482.351
matchDesign11.705 0.04911.759
meanIntensity2.4140.0482.462
medianTotalIntensity0.7590.0080.767
noMasked3.4540.0533.507
noob1.9700.0121.983
openSesame4.9370.0725.016
openSesameToFile1.4390.0031.446
pOOBAH1.3080.0131.321
palgen0.0420.0060.047
parseGEOsignalMU2.9900.0623.058
predictAge2.3030.0732.377
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.4600.0020.463
prefixMaskButC0.1410.0010.142
prefixMaskButCG0.0580.0010.059
prepSesame3.5340.1083.644
prepSesameList0.0010.0000.002
print.DMLSummary2.8880.1803.069
print.fileSet1.2650.0411.306
probeID_designType0.0000.0000.001
probeSuccessRate5.2400.1115.352
qualityMask1.7500.0491.799
reIdentify4.3790.0454.424
readFileSet0.0520.0010.053
readIDATpair0.1000.0040.104
recommendedMaskNames000
resetMask0.3940.0220.416
scrub2.2160.1522.367
scrubSoft3.1900.0523.242
sdfPlatform0.2730.0100.283
sdf_read_table7.5310.4287.960
sdf_write_table1.7210.0941.950
searchIDATprefixes0.0040.0010.006
sesame-package2.1420.2542.397
sesameAnno_attachManifest000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges0.0000.0000.001
sesameAnno_download000
sesameAnno_readManifestTSV000
sesameQC_calcStats18.576 1.18019.758
sesameQC_getStats1.7940.0351.828
sesameQC_plotBar11.910 0.50012.412
sesameQC_plotBetaByDesign10.803 0.47111.275
sesameQC_plotHeatSNPs17.564 0.51818.085
sesameQC_plotIntensVsBetas2.2250.0752.300
sesameQC_plotRedGrnQQ1.6580.0541.712
sesameQC_rankStats3.3630.1953.558
sesameQCtoDF1.7570.0421.799
sesame_checkVersion0.0030.0000.003
sesamize000
setMask0.0990.0020.101
signalMU0.7710.0260.797
sliceFileSet0.0330.0010.034
summaryExtractTest2.9290.1403.069
totalIntensities2.3840.0692.454
updateSigDF3.0750.1163.191
visualizeGene8.4960.2918.791
visualizeProbes1.1380.0411.180
visualizeRegion0.3180.0020.319
visualizeSegments1.8800.1272.007