Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-08-30 12:08 -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 kjohnson3

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sesame.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sesame_1.27.1.tar.gz
StartedAt: 2025-08-29 21:41:33 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 21:46:09 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 276.5 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sesame.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sesame_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/sesame.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* 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 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 14.373  0.628  15.028
sesameQC_calcStats             8.687  0.677   9.449
inferSex                       8.335  0.493   8.836
sesameQC_plotHeatSNPs          7.912  0.741   8.661
imputeBetas                    7.125  0.509   7.674
sesameQC_plotBar               7.034  0.233   7.440
ELBAR                          5.600  1.119   6.776
inferSpecies                   5.648  0.337   6.008
diffRefSet                     5.689  0.202   5.933
getRefSet                      5.305  0.148   5.463
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 
  7.975   0.481   8.467 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0000.0000.001
DML2.6260.3142.974
DMLpredict0.4120.0300.443
DMR3.0210.0873.108
ELBAR5.6001.1196.776
MValueToBetaValue000
SigDF0.1150.0210.143
addMask0.0180.0010.021
betasCollapseToPfx0.0040.0000.005
bisConversionControl2.0850.1022.216
calcEffectSize0.3960.0350.431
checkLevels1.6280.0651.704
cnSegmentation0.0820.0170.099
compareMouseStrainReference3.6680.1593.851
compareMouseTissueReference000
compareReference4.0090.1584.183
controls0.7290.0900.840
createUCSCtrack2.2410.1542.407
deIdentify1.9280.0742.022
detectionPnegEcdf0.3810.0080.389
diffRefSet5.6890.2025.933
dmContrasts0.7050.0440.754
dyeBiasCorr1.0020.0881.095
dyeBiasCorrMostBalanced3.2710.1333.434
dyeBiasL1.3240.0461.370
dyeBiasNL2.0050.1672.201
estimateLeukocyte2.6550.1482.807
formatVCF0.7650.0680.840
getAFTypeIbySumAlleles0.5690.0500.620
getAFs0.3830.0430.426
getBetas0.2740.0400.314
getMask2.2280.1322.372
getRefSet5.3050.1485.463
imputeBetas7.1250.5097.674
imputeBetasByGenomicNeighbors14.373 0.62815.028
imputeBetasMatrixByMean000
inferEthnicity0.0010.0000.000
inferInfiniumIChannel0.1390.1500.303
inferSex8.3350.4938.836
inferSpecies5.6480.3376.008
inferStrain2.7310.2913.041
inferTissue2.2210.2992.528
initFileSet0.3750.0910.475
listAvailableMasks0.3860.0800.467
mLiftOver0.0010.0000.000
mapFileSet0.0150.0010.017
mapToMammal400.8700.1451.030
matchDesign4.2520.2664.532
meanIntensity0.9360.0771.014
medianTotalIntensity0.2740.0550.330
noMasked1.3170.1121.430
noob0.8680.1491.019
openSesame1.7390.2331.986
openSesameToFile0.5820.0670.651
pOOBAH0.4980.0210.523
palgen0.0150.0030.018
parseGEOsignalMU1.2390.1301.372
predictAge0.9820.0401.041
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.1770.0010.179
prefixMaskButC0.0450.0010.046
prefixMaskButCG0.0160.0010.017
prepSesame1.3490.1741.528
prepSesameList0.0010.0000.001
print.DMLSummary1.0930.1591.258
print.fileSet0.3830.0790.463
probeID_designType000
probeSuccessRate1.9650.1852.160
qualityMask0.6440.0870.732
reIdentify1.9420.0772.058
readFileSet0.0260.0030.029
readIDATpair0.0440.0040.048
recommendedMaskNames000
resetMask0.1080.0190.126
scrub1.0050.1811.186
scrubSoft1.3570.2641.622
sdfPlatform0.0790.0120.092
sdf_read_table3.3390.2123.587
sdf_write_table0.9290.0470.981
searchIDATprefixes0.0010.0010.002
sesame-package0.9340.0941.034
sesameAnno_attachManifest0.0000.0010.000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV000
sesameQC_calcStats8.6870.6779.449
sesameQC_getStats0.8940.0380.954
sesameQC_plotBar7.0340.2337.440
sesameQC_plotBetaByDesign3.8260.6384.503
sesameQC_plotHeatSNPs7.9120.7418.661
sesameQC_plotIntensVsBetas0.7480.1150.871
sesameQC_plotRedGrnQQ0.4440.0780.523
sesameQC_rankStats1.1880.1371.330
sesameQCtoDF0.9020.0430.946
sesame_checkVersion0.0010.0010.001
sesamize000
setMask0.0260.0010.028
signalMU0.2640.0350.301
sliceFileSet0.0160.0010.016
summaryExtractTest1.1390.1561.301
totalIntensities0.8610.0930.957
updateSigDF1.0940.2031.303
visualizeGene3.7580.1863.968
visualizeProbes0.4110.0380.448
visualizeRegion0.1110.0120.123
visualizeSegments0.7330.0590.791