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This page was generated on 2025-08-30 12:05 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 1959/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.27.1  (landing page)
Wanding Zhou
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 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: 2025-08-30 03:02:19 -0400 (Sat, 30 Aug 2025)
EndedAt: 2025-08-30 03:18:12 -0400 (Sat, 30 Aug 2025)
EllapsedTime: 952.9 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 (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 ‘1.27.1’
* 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 31.622  0.691  32.315
inferSex                      18.768  0.245  19.015
sesameQC_calcStats            17.522  0.080  17.605
imputeBetas                   15.835  0.347  16.189
sesameQC_plotHeatSNPs         15.843  0.213  16.057
inferSpecies                  12.928  0.653  13.582
diffRefSet                    13.082  0.357  13.440
ELBAR                         12.986  0.241  13.228
compareMouseStrainReference   11.728  0.097  11.825
sesameQC_plotBar              11.413  0.241  11.655
matchDesign                   10.700  0.131  10.834
getRefSet                     10.759  0.062  10.821
compareReference              10.198  0.160  10.359
sesameQC_plotBetaByDesign     10.135  0.153  10.291
visualizeGene                  8.778  0.243   9.022
DMR                            7.942  0.294   8.236
sdf_read_table                 7.349  0.128   7.477
inferStrain                    6.418  0.409   6.830
DML                            6.322  0.239   6.562
estimateLeukocyte              6.417  0.115   6.532
dyeBiasCorrMostBalanced        6.106  0.099   6.205
inferTissue                    5.845  0.116   5.962
getMask                        5.539  0.121   5.663
deIdentify                     5.271  0.116   5.389
dyeBiasNL                      5.205  0.086   5.293
createUCSCtrack                4.971  0.183   5.155
* 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 (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 
 18.830   0.906  19.727 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML6.3220.2396.562
DMLpredict1.3040.0561.362
DMR7.9420.2948.236
ELBAR12.986 0.24113.228
MValueToBetaValue000
SigDF0.2860.0160.301
addMask0.0970.0000.097
betasCollapseToPfx0.0120.0000.012
bisConversionControl4.3940.0614.455
calcEffectSize1.1350.0381.173
checkLevels3.4170.0543.472
cnSegmentation0.2770.0110.289
compareMouseStrainReference11.728 0.09711.825
compareMouseTissueReference000
compareReference10.198 0.16010.359
controls1.9150.0591.975
createUCSCtrack4.9710.1835.155
deIdentify5.2710.1165.389
detectionPnegEcdf0.9040.0120.916
diffRefSet13.082 0.35713.440
dmContrasts1.8330.0291.862
dyeBiasCorr2.6430.1092.752
dyeBiasCorrMostBalanced6.1060.0996.205
dyeBiasL3.1290.0693.198
dyeBiasNL5.2050.0865.293
estimateLeukocyte6.4170.1156.532
formatVCF2.0170.0472.063
getAFTypeIbySumAlleles1.5370.0471.584
getAFs0.8970.0160.913
getBetas0.7260.0220.748
getMask5.5390.1215.663
getRefSet10.759 0.06210.821
imputeBetas15.835 0.34716.189
imputeBetasByGenomicNeighbors31.622 0.69132.315
imputeBetasMatrixByMean0.0010.0000.001
inferEthnicity0.0000.0000.001
inferInfiniumIChannel0.2280.0660.294
inferSex18.768 0.24519.015
inferSpecies12.928 0.65313.582
inferStrain6.4180.4096.830
inferTissue5.8450.1165.962
initFileSet1.1030.0341.137
listAvailableMasks1.2190.0341.252
mLiftOver000
mapFileSet0.0300.0020.032
mapToMammal402.4860.0752.561
matchDesign10.700 0.13110.834
meanIntensity2.4600.0512.512
medianTotalIntensity0.7520.0510.803
noMasked3.4610.0463.506
noob2.0710.0062.077
openSesame4.8190.0664.894
openSesameToFile1.3720.0021.377
pOOBAH1.1750.0001.175
palgen0.0340.0000.034
parseGEOsignalMU2.7560.0512.807
predictAge2.3560.0402.395
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.440.000.44
prefixMaskButC0.1340.0000.134
prefixMaskButCG0.0520.0000.053
prepSesame3.3100.0233.335
prepSesameList0.0010.0000.001
print.DMLSummary2.6150.0492.664
print.fileSet1.1320.0201.152
probeID_designType000
probeSuccessRate4.7670.0914.858
qualityMask2.0820.0472.129
reIdentify4.5030.0334.537
readFileSet0.0510.0020.053
readIDATpair0.1020.0000.102
recommendedMaskNames000
resetMask0.3760.0110.388
scrub2.0260.0002.026
scrubSoft3.110.003.11
sdfPlatform0.2940.0080.302
sdf_read_table7.3490.1287.477
sdf_write_table1.7280.0651.953
searchIDATprefixes0.0050.0030.009
sesame-package2.3980.0362.435
sesameAnno_attachManifest0.0010.0000.000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV0.0000.0000.001
sesameQC_calcStats17.522 0.08017.605
sesameQC_getStats1.5640.0021.567
sesameQC_plotBar11.413 0.24111.655
sesameQC_plotBetaByDesign10.135 0.15310.291
sesameQC_plotHeatSNPs15.843 0.21316.057
sesameQC_plotIntensVsBetas1.6710.0261.697
sesameQC_plotRedGrnQQ1.7820.0421.824
sesameQC_rankStats3.2060.0463.252
sesameQCtoDF1.8040.0011.805
sesame_checkVersion0.0030.0000.003
sesamize000
setMask0.0910.0000.091
signalMU0.7510.0160.767
sliceFileSet0.0330.0000.033
summaryExtractTest2.9220.1353.057
totalIntensities2.4880.0592.547
updateSigDF3.3310.1043.436
visualizeGene8.7780.2439.022
visualizeProbes1.0740.0051.079
visualizeRegion0.3060.0010.306
visualizeSegments1.6970.0791.777