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This page was generated on 2025-08-30 12:09 -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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: sesame
Version: 1.27.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sesame_1.27.1.tar.gz
StartedAt: 2025-08-29 11:32:56 -0000 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 11:46:37 -0000 (Fri, 29 Aug 2025)
EllapsedTime: 820.9 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sesame_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/sesame.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 43.364  0.538  44.039
inferSex                      26.350  0.271  26.700
imputeBetas                   24.821  0.338  25.359
sesameQC_calcStats            23.103  0.127  23.338
sesameQC_plotHeatSNPs         21.852  0.183  22.106
inferSpecies                  18.864  0.599  19.513
ELBAR                         17.876  0.163  18.085
compareMouseStrainReference   17.447  0.088  17.588
matchDesign                   16.021  0.099  16.164
diffRefSet                    15.892  0.227  16.166
compareReference              14.590  0.183  14.813
sesameQC_plotBar              13.369  0.251  13.677
getRefSet                     13.267  0.088  13.388
sesameQC_plotBetaByDesign     12.837  0.071  12.958
DMR                           10.143  0.244  10.410
visualizeGene                  9.632  0.151   9.818
inferStrain                    9.032  0.395   9.451
DML                            8.550  0.359   8.936
deIdentify                     8.706  0.131   8.870
sdf_read_table                 8.360  0.140   8.521
inferTissue                    8.135  0.099   8.261
estimateLeukocyte              7.686  0.140   7.857
dyeBiasCorrMostBalanced        7.339  0.072   7.431
getMask                        7.174  0.140   7.342
dyeBiasNL                      7.114  0.079   7.217
createUCSCtrack                6.220  0.116   6.355
openSesame                     6.106  0.107   6.261
reIdentify                     6.009  0.112   6.137
probeSuccessRate               5.771  0.079   5.867
bisConversionControl           5.185  0.068   5.270
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

sesame.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
 21.514   0.963  22.512 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML8.5500.3598.936
DMLpredict1.4410.0401.484
DMR10.143 0.24410.410
ELBAR17.876 0.16318.085
MValueToBetaValue0.0000.0000.001
SigDF0.3400.0200.361
addMask0.0860.0000.085
betasCollapseToPfx0.0170.0000.016
bisConversionControl5.1850.0685.270
calcEffectSize1.3210.0241.348
checkLevels3.9190.0243.953
cnSegmentation0.3320.0160.348
compareMouseStrainReference17.447 0.08817.588
compareMouseTissueReference000
compareReference14.590 0.18314.813
controls2.2560.0722.335
createUCSCtrack6.2200.1166.355
deIdentify8.7060.1318.870
detectionPnegEcdf1.0830.0161.103
diffRefSet15.892 0.22716.166
dmContrasts2.1040.0362.145
dyeBiasCorr3.2480.0443.300
dyeBiasCorrMostBalanced7.3390.0727.431
dyeBiasL3.7160.0603.784
dyeBiasNL7.1140.0797.217
estimateLeukocyte7.6860.1407.857
formatVCF2.4010.1002.508
getAFTypeIbySumAlleles2.0720.0552.136
getAFs1.2790.0121.295
getBetas1.2580.0161.278
getMask7.1740.1407.342
getRefSet13.267 0.08813.388
imputeBetas24.821 0.33825.359
imputeBetasByGenomicNeighbors43.364 0.53844.039
imputeBetasMatrixByMean0.0020.0000.001
inferEthnicity0.0010.0000.001
inferInfiniumIChannel0.3000.0920.392
inferSex26.350 0.27126.700
inferSpecies18.864 0.59919.513
inferStrain9.0320.3959.451
inferTissue8.1350.0998.261
initFileSet1.3230.0441.370
listAvailableMasks1.4490.0401.492
mLiftOver0.0010.0000.000
mapFileSet0.040.000.04
mapToMammal403.2230.0683.302
matchDesign16.021 0.09916.164
meanIntensity2.9980.0803.085
medianTotalIntensity1.0720.0281.102
noMasked3.9050.0483.961
noob2.7250.0402.770
openSesame6.1060.1076.261
openSesameToFile1.8310.0161.858
pOOBAH1.4250.0001.427
palgen0.0460.0000.049
parseGEOsignalMU3.1610.0403.217
predictAge2.4920.0602.559
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.4700.0000.471
prefixMaskButC0.1330.0000.134
prefixMaskButCG0.0550.0000.056
prepSesame4.4630.0684.547
prepSesameList0.0020.0000.001
print.DMLSummary3.1050.1233.238
print.fileSet1.3980.0241.427
probeID_designType000
probeSuccessRate5.7710.0795.867
qualityMask3.1230.0603.192
reIdentify6.0090.1126.137
readFileSet0.0540.0040.058
readIDATpair0.1260.0000.127
recommendedMaskNames000
resetMask0.5360.0190.557
scrub2.8670.0322.905
scrubSoft4.3610.0284.400
sdfPlatform0.3780.0240.403
sdf_read_table8.3600.1408.521
sdf_write_table2.3020.0722.439
searchIDATprefixes0.0060.0000.009
sesame-package2.8030.0632.879
sesameAnno_attachManifest000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV000
sesameQC_calcStats23.103 0.12723.338
sesameQC_getStats2.1490.0322.187
sesameQC_plotBar13.369 0.25113.677
sesameQC_plotBetaByDesign12.837 0.07112.958
sesameQC_plotHeatSNPs21.852 0.18322.106
sesameQC_plotIntensVsBetas2.8190.0282.855
sesameQC_plotRedGrnQQ1.7880.0391.831
sesameQC_rankStats4.0190.0804.112
sesameQCtoDF2.1770.0082.190
sesame_checkVersion0.0050.0000.005
sesamize000
setMask0.1220.0000.123
signalMU0.9570.0360.996
sliceFileSet0.040.000.04
summaryExtractTest3.1090.1713.291
totalIntensities2.7540.0762.837
updateSigDF3.5750.1283.722
visualizeGene9.6320.1519.818
visualizeProbes1.6950.0081.708
visualizeRegion0.4610.0000.462
visualizeSegments1.7020.0161.723