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

This page was generated on 2025-08-12 12:10 -0400 (Tue, 12 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 1956/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.27.1  (landing page)
Wanding Zhou
Snapshot Date: 2025-08-11 13:45 -0400 (Mon, 11 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 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 lconway

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: 2025-08-12 00:11:07 -0400 (Tue, 12 Aug 2025)
EndedAt: 2025-08-12 00:24:12 -0400 (Tue, 12 Aug 2025)
EllapsedTime: 784.4 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 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 37.817  1.518  39.569
inferSex                      25.122  1.340  26.581
sesameQC_calcStats            22.806  1.803  24.796
sesameQC_plotHeatSNPs         19.336  1.558  21.077
imputeBetas                   19.033  1.577  20.751
ELBAR                         16.663  3.179  20.102
diffRefSet                    16.671  0.657  17.493
inferSpecies                  15.303  0.740  16.153
sesameQC_plotBar              14.299  0.497  14.927
sesameQC_plotBetaByDesign     11.900  1.768  13.842
compareMouseStrainReference   13.058  0.404  13.565
getRefSet                     12.855  0.442  13.377
compareReference              12.409  0.565  13.128
matchDesign                   11.563  0.817  12.490
DML                            9.243  1.298  10.654
visualizeGene                  9.499  0.683  10.304
sdf_read_table                 9.381  0.461   9.938
DMR                            9.211  0.282   9.578
estimateLeukocyte              8.641  0.600   9.317
inferTissue                    7.464  1.589   9.146
inferStrain                    7.928  0.644   8.638
getMask                        6.777  0.645   7.488
dyeBiasCorrMostBalanced        7.080  0.328   7.460
dyeBiasNL                      6.297  0.516   6.858
deIdentify                     6.276  0.302   6.636
createUCSCtrack                6.182  0.343   6.591
probeSuccessRate               5.644  0.459   6.146
openSesame                     5.404  0.654   6.133
reIdentify                     5.194  0.188   5.415
bisConversionControl           4.943  0.269   5.260
* 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-x86_64/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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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 
 22.614   1.990  24.762 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML 9.243 1.29810.654
DMLpredict1.3750.1241.520
DMR9.2110.2829.578
ELBAR16.663 3.17920.102
MValueToBetaValue0.0010.0010.002
SigDF0.2910.0750.374
addMask0.0870.0010.088
betasCollapseToPfx0.0120.0010.012
bisConversionControl4.9430.2695.260
calcEffectSize1.2920.1661.487
checkLevels3.9600.2664.268
cnSegmentation0.2950.0570.356
compareMouseStrainReference13.058 0.40413.565
compareMouseTissueReference000
compareReference12.409 0.56513.128
controls2.2620.2402.524
createUCSCtrack6.1820.3436.591
deIdentify6.2760.3026.636
detectionPnegEcdf1.2990.0191.325
diffRefSet16.671 0.65717.493
dmContrasts2.0060.1962.221
dyeBiasCorr3.0730.2403.349
dyeBiasCorrMostBalanced7.0800.3287.460
dyeBiasL2.4350.1482.602
dyeBiasNL6.2970.5166.858
estimateLeukocyte8.6410.6009.317
formatVCF2.3090.2612.591
getAFTypeIbySumAlleles1.8560.1882.081
getAFs0.9210.0490.975
getBetas0.8930.1471.045
getMask6.7770.6457.488
getRefSet12.855 0.44213.377
imputeBetas19.033 1.57720.751
imputeBetasByGenomicNeighbors37.817 1.51839.569
imputeBetasMatrixByMean0.0010.0000.001
inferEthnicity0.0010.0000.001
inferInfiniumIChannel0.3950.4430.842
inferSex25.122 1.34026.581
inferSpecies15.303 0.74016.153
inferStrain7.9280.6448.638
inferTissue7.4641.5899.146
initFileSet1.2730.3271.636
listAvailableMasks1.3840.1781.588
mLiftOver0.0000.0010.001
mapFileSet0.0400.0030.042
mapToMammal403.3770.4843.925
matchDesign11.563 0.81712.490
meanIntensity2.7730.2323.031
medianTotalIntensity0.8750.0640.950
noMasked3.9190.2084.163
noob2.4330.6343.112
openSesame5.4040.6546.133
openSesameToFile1.7100.2591.984
pOOBAH1.4330.0111.456
palgen0.0440.0130.061
parseGEOsignalMU3.0780.1483.248
predictAge2.4770.1202.619
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.6480.0020.652
prefixMaskButC0.1950.0010.196
prefixMaskButCG0.0710.0010.071
prepSesame4.0270.3974.457
prepSesameList0.0010.0000.002
print.DMLSummary3.0711.0624.193
print.fileSet1.2780.2281.515
probeID_designType0.0000.0010.001
probeSuccessRate5.6440.4596.146
qualityMask2.1180.4612.636
reIdentify5.1940.1885.415
readFileSet0.0650.0040.070
readIDATpair0.1510.0030.157
recommendedMaskNames0.0010.0000.000
resetMask0.4030.0470.454
scrub2.3000.0162.323
scrubSoft3.4421.1784.664
sdfPlatform0.3160.0830.404
sdf_read_table9.3810.4619.938
sdf_write_table2.7650.1943.007
searchIDATprefixes0.0040.0030.008
sesame-package2.6770.4713.176
sesameAnno_attachManifest0.0000.0000.001
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges0.0010.0010.001
sesameAnno_download000
sesameAnno_readManifestTSV000
sesameQC_calcStats22.806 1.80324.796
sesameQC_getStats2.2960.0172.330
sesameQC_plotBar14.299 0.49714.927
sesameQC_plotBetaByDesign11.900 1.76813.842
sesameQC_plotHeatSNPs19.336 1.55821.077
sesameQC_plotIntensVsBetas2.2100.3802.608
sesameQC_plotRedGrnQQ1.2040.1601.433
sesameQC_rankStats3.7080.3994.149
sesameQCtoDF2.4510.1052.567
sesame_checkVersion0.0030.0010.004
sesamize000
setMask0.1060.0000.107
signalMU1.0520.1241.184
sliceFileSet0.0330.0030.036
summaryExtractTest2.9460.9763.995
totalIntensities2.5970.3262.968
updateSigDF3.4050.4323.902
visualizeGene 9.499 0.68310.304
visualizeProbes1.3240.0311.359
visualizeRegion0.3620.0070.373
visualizeSegments1.8120.4702.319