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This page was generated on 2025-09-19 12:03 -0400 (Fri, 19 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4808
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4541
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 1967/2330HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.27.1  (landing page)
Wanding Zhou
Snapshot Date: 2025-09-18 13:45 -0400 (Thu, 18 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: 2025-09-19 05:03:38 -0400 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 05:22:03 -0400 (Fri, 19 Sep 2025)
EllapsedTime: 1105.2 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 40.435  1.449  41.896
imputeBetas                   24.815  0.646  25.477
inferSex                      21.036  1.543  22.581
sesameQC_calcStats            19.111  0.300  19.419
ELBAR                         18.498  0.298  18.874
sesameQC_plotHeatSNPs         17.757  0.454  18.212
diffRefSet                    17.402  0.321  17.783
inferSpecies                  15.382  1.311  16.694
getRefSet                     14.786  0.250  15.050
compareReference              12.203  0.227  12.470
compareMouseStrainReference   12.177  0.199  12.478
sesameQC_plotBar              11.257  0.173  11.431
matchDesign                   11.108  0.307  11.420
DMR                           10.602  0.338  10.942
estimateLeukocyte             10.121  0.183  10.305
getMask                        9.978  0.173  10.216
sesameQC_plotBetaByDesign      9.891  0.086   9.980
DML                            8.794  0.364   9.328
dyeBiasNL                      8.382  0.077   8.460
visualizeGene                  8.239  0.137   8.377
dyeBiasCorrMostBalanced        7.572  0.095   7.668
sdf_read_table                 7.303  0.125   7.428
inferStrain                    6.667  0.485   7.160
createUCSCtrack                7.021  0.065   7.087
inferTissue                    6.714  0.338   7.056
deIdentify                     5.968  0.076   6.047
probeSuccessRate               5.052  0.120   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 
 18.257   0.967  19.215 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0010.0000.001
DML8.7940.3649.328
DMLpredict1.4120.0341.446
DMR10.602 0.33810.942
ELBAR18.498 0.29818.874
MValueToBetaValue000
SigDF0.2970.0160.313
addMask0.1650.0070.172
betasCollapseToPfx0.0130.0000.013
bisConversionControl4.8590.1044.976
calcEffectSize1.4480.0581.506
checkLevels3.5020.1443.646
cnSegmentation0.3370.0110.348
compareMouseStrainReference12.177 0.19912.478
compareMouseTissueReference000
compareReference12.203 0.22712.470
controls2.3060.0562.363
createUCSCtrack7.0210.0657.087
deIdentify5.9680.0766.047
detectionPnegEcdf1.1530.0141.205
diffRefSet17.402 0.32117.783
dmContrasts2.4260.0412.469
dyeBiasCorr3.2810.0833.365
dyeBiasCorrMostBalanced7.5720.0957.668
dyeBiasL2.8690.0892.966
dyeBiasNL8.3820.0778.460
estimateLeukocyte10.121 0.18310.305
formatVCF3.6010.0723.685
getAFTypeIbySumAlleles2.7680.0682.837
getAFs2.0060.0812.088
getBetas1.4440.0461.490
getMask 9.978 0.17310.216
getRefSet14.786 0.25015.050
imputeBetas24.815 0.64625.477
imputeBetasByGenomicNeighbors40.435 1.44941.896
imputeBetasMatrixByMean0.0010.0010.001
inferEthnicity0.0010.0000.001
inferInfiniumIChannel0.2300.1030.333
inferSex21.036 1.54322.581
inferSpecies15.382 1.31116.694
inferStrain6.6670.4857.160
inferTissue6.7140.3387.056
initFileSet1.1740.0331.207
listAvailableMasks1.2490.0381.288
mLiftOver000
mapFileSet0.0330.0010.033
mapToMammal402.5010.1202.621
matchDesign11.108 0.30711.420
meanIntensity2.4960.1282.625
medianTotalIntensity0.7650.0970.863
noMasked3.4890.0853.575
noob1.8040.1151.920
openSesame4.8240.1094.941
openSesameToFile1.3490.0341.384
pOOBAH1.2490.0041.253
palgen0.0330.0070.040
parseGEOsignalMU2.8490.0712.920
predictAge2.4290.0762.505
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.4070.0020.410
prefixMaskButC0.1140.0000.115
prefixMaskButCG0.0460.0000.046
prepSesame3.4170.1383.556
prepSesameList0.0010.0010.001
print.DMLSummary2.9240.2043.127
print.fileSet1.2280.0311.261
probeID_designType0.0010.0000.001
probeSuccessRate5.0520.1205.176
qualityMask1.7270.0541.781
reIdentify4.2180.0424.261
readFileSet0.0510.0010.052
readIDATpair0.1140.0010.114
recommendedMaskNames0.0010.0000.000
resetMask0.3730.0170.390
scrub2.1870.2012.388
scrubSoft3.0870.0553.143
sdfPlatform0.2840.0170.301
sdf_read_table7.3030.1257.428
sdf_write_table1.6680.0701.866
searchIDATprefixes0.0030.0010.005
sesame-package2.2280.1092.338
sesameAnno_attachManifest000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV0.0000.0010.000
sesameQC_calcStats19.111 0.30019.419
sesameQC_getStats1.7810.0191.801
sesameQC_plotBar11.257 0.17311.431
sesameQC_plotBetaByDesign9.8910.0869.980
sesameQC_plotHeatSNPs17.757 0.45418.212
sesameQC_plotIntensVsBetas1.7770.0291.805
sesameQC_plotRedGrnQQ1.5830.0421.625
sesameQC_rankStats2.9440.0883.032
sesameQCtoDF1.5710.0221.592
sesame_checkVersion0.0020.0010.003
sesamize000
setMask0.0880.0020.090
signalMU0.8950.0170.912
sliceFileSet0.0350.0000.034
summaryExtractTest2.5490.0512.599
totalIntensities2.4050.0612.465
updateSigDF3.0750.0913.166
visualizeGene8.2390.1378.377
visualizeProbes1.0770.0031.081
visualizeRegion0.3270.0000.328
visualizeSegments1.6660.0131.679