Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 1974/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sesame 1.26.0 (landing page) Wanding Zhou
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: sesame |
Version: 1.26.0 |
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_1.26.0.tar.gz |
StartedAt: 2025-10-15 12:20:05 -0400 (Wed, 15 Oct 2025) |
EndedAt: 2025-10-15 12:34:44 -0400 (Wed, 15 Oct 2025) |
EllapsedTime: 879.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sesame.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-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 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.26.0’ * 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 45.469 1.723 47.679 inferSex 29.137 1.577 31.186 sesameQC_calcStats 24.571 3.000 28.096 imputeBetas 23.317 2.089 25.722 sesameQC_plotHeatSNPs 21.977 1.975 24.295 inferSpecies 19.934 1.020 21.179 diffRefSet 20.173 0.707 21.570 sesameQC_plotBar 19.844 0.410 20.435 ELBAR 15.476 3.325 19.073 getRefSet 17.632 0.476 18.326 sesameQC_plotBetaByDesign 13.273 1.705 15.155 matchDesign 13.317 0.782 14.475 visualizeGene 12.630 0.665 13.465 compareReference 12.646 0.464 13.319 compareMouseStrainReference 12.243 0.405 12.743 sdf_read_table 11.097 0.474 11.808 dyeBiasCorrMostBalanced 10.878 0.373 11.747 estimateLeukocyte 10.297 0.462 10.848 DML 9.540 0.920 10.547 DMR 9.887 0.255 10.157 inferStrain 8.971 0.771 9.896 inferTissue 7.665 0.950 8.734 getMask 7.777 0.511 8.414 createUCSCtrack 7.838 0.401 8.319 probeSuccessRate 7.244 0.784 8.129 bisConversionControl 7.368 0.213 7.704 dyeBiasNL 6.291 0.530 6.897 openSesame 5.730 0.713 6.536 deidentify 6.116 0.239 6.428 prepSesame 5.514 0.776 6.365 * 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
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 ‘1.26.0’ ** 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)
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 25.434 1.752 27.661
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0.000 | 0.001 | 0.000 | |
DML | 9.540 | 0.920 | 10.547 | |
DMLpredict | 1.429 | 0.113 | 1.548 | |
DMR | 9.887 | 0.255 | 10.157 | |
ELBAR | 15.476 | 3.325 | 19.073 | |
MValueToBetaValue | 0 | 0 | 0 | |
SigDF | 0.249 | 0.044 | 0.306 | |
addMask | 0.076 | 0.005 | 0.084 | |
betasCollapseToPfx | 0.013 | 0.000 | 0.013 | |
bisConversionControl | 7.368 | 0.213 | 7.704 | |
calcEffectSize | 1.443 | 0.116 | 1.569 | |
checkLevels | 4.063 | 0.198 | 4.294 | |
cnSegmentation | 0.286 | 0.063 | 0.350 | |
compareMouseStrainReference | 12.243 | 0.405 | 12.743 | |
compareMouseTissueReference | 0 | 0 | 0 | |
compareReference | 12.646 | 0.464 | 13.319 | |
controls | 2.592 | 0.223 | 2.881 | |
createUCSCtrack | 7.838 | 0.401 | 8.319 | |
deidentify | 6.116 | 0.239 | 6.428 | |
detectionPnegEcdf | 1.661 | 0.080 | 1.759 | |
diffRefSet | 20.173 | 0.707 | 21.570 | |
dmContrasts | 2.307 | 0.144 | 2.475 | |
dyeBiasCorr | 3.261 | 0.364 | 3.736 | |
dyeBiasCorrMostBalanced | 10.878 | 0.373 | 11.747 | |
dyeBiasL | 2.625 | 0.261 | 2.942 | |
dyeBiasNL | 6.291 | 0.530 | 6.897 | |
estimateLeukocyte | 10.297 | 0.462 | 10.848 | |
formatVCF | 2.605 | 0.236 | 2.888 | |
getAFTypeIbySumAlleles | 1.981 | 0.253 | 2.260 | |
getAFs | 1.005 | 0.186 | 1.202 | |
getBetas | 0.899 | 0.188 | 1.099 | |
getMask | 7.777 | 0.511 | 8.414 | |
getRefSet | 17.632 | 0.476 | 18.326 | |
imputeBetas | 23.317 | 2.089 | 25.722 | |
imputeBetasByGenomicNeighbors | 45.469 | 1.723 | 47.679 | |
imputeBetasMatrixByMean | 0.001 | 0.000 | 0.002 | |
inferEthnicity | 0.000 | 0.000 | 0.001 | |
inferInfiniumIChannel | 0.399 | 0.379 | 0.817 | |
inferSex | 29.137 | 1.577 | 31.186 | |
inferSpecies | 19.934 | 1.020 | 21.179 | |
inferStrain | 8.971 | 0.771 | 9.896 | |
inferTissue | 7.665 | 0.950 | 8.734 | |
initFileSet | 1.356 | 0.236 | 1.614 | |
listAvailableMasks | 1.579 | 0.205 | 1.804 | |
mLiftOver | 0.000 | 0.002 | 0.001 | |
mapFileSet | 0.048 | 0.005 | 0.054 | |
mapToMammal40 | 4.194 | 0.561 | 4.826 | |
matchDesign | 13.317 | 0.782 | 14.475 | |
meanIntensity | 2.976 | 0.306 | 3.427 | |
medianTotalIntensity | 0.914 | 0.119 | 1.057 | |
noMasked | 4.583 | 0.237 | 4.855 | |
noob | 2.718 | 0.391 | 3.132 | |
openSesame | 5.730 | 0.713 | 6.536 | |
openSesameToFile | 1.793 | 0.359 | 2.189 | |
pOOBAH | 1.583 | 0.115 | 1.714 | |
palgen | 0.051 | 0.008 | 0.063 | |
parseGEOsignalMU | 4.163 | 0.443 | 4.668 | |
predictAge | 3.304 | 0.122 | 3.448 | |
predictAgeHorvath353 | 0 | 0 | 0 | |
predictAgeSkinBlood | 0 | 0 | 0 | |
predictMouseAgeInMonth | 0 | 0 | 0 | |
prefixMask | 0.634 | 0.010 | 0.654 | |
prefixMaskButC | 0.172 | 0.004 | 0.179 | |
prefixMaskButCG | 0.068 | 0.002 | 0.070 | |
prepSesame | 5.514 | 0.776 | 6.365 | |
prepSesameList | 0.002 | 0.000 | 0.003 | |
print.DMLSummary | 3.405 | 0.395 | 3.861 | |
print.fileSet | 1.351 | 0.206 | 1.602 | |
probeID_designType | 0 | 0 | 0 | |
probeSuccessRate | 7.244 | 0.784 | 8.129 | |
qualityMask | 2.622 | 0.273 | 2.930 | |
reIdentify | 4.748 | 0.137 | 4.924 | |
readFileSet | 0.082 | 0.005 | 0.087 | |
readIDATpair | 0.144 | 0.006 | 0.152 | |
recommendedMaskNames | 0.000 | 0.000 | 0.001 | |
resetMask | 0.370 | 0.058 | 0.431 | |
scrub | 2.814 | 0.274 | 3.105 | |
scrubSoft | 4.117 | 0.782 | 4.937 | |
sdfPlatform | 0.304 | 0.046 | 0.351 | |
sdf_read_table | 11.097 | 0.474 | 11.808 | |
sdf_write_table | 2.955 | 0.135 | 3.135 | |
searchIDATprefixes | 0.003 | 0.002 | 0.006 | |
sesame-package | 3.334 | 0.342 | 3.720 | |
sesameAnno_attachManifest | 0.000 | 0.000 | 0.001 | |
sesameAnno_buildAddressFile | 0.000 | 0.000 | 0.001 | |
sesameAnno_buildManifestGRanges | 0 | 0 | 0 | |
sesameAnno_download | 0.001 | 0.000 | 0.000 | |
sesameAnno_readManifestTSV | 0 | 0 | 0 | |
sesameQC_calcStats | 24.571 | 3.000 | 28.096 | |
sesameQC_getStats | 2.460 | 0.062 | 2.539 | |
sesameQC_plotBar | 19.844 | 0.410 | 20.435 | |
sesameQC_plotBetaByDesign | 13.273 | 1.705 | 15.155 | |
sesameQC_plotHeatSNPs | 21.977 | 1.975 | 24.295 | |
sesameQC_plotIntensVsBetas | 1.975 | 0.200 | 2.191 | |
sesameQC_plotRedGrnQQ | 1.657 | 0.131 | 1.798 | |
sesameQC_rankStats | 3.828 | 0.283 | 4.151 | |
sesameQCtoDF | 2.708 | 0.038 | 2.777 | |
sesame_checkVersion | 0.005 | 0.002 | 0.007 | |
sesamize | 0.001 | 0.001 | 0.000 | |
setMask | 0.074 | 0.002 | 0.076 | |
signalMU | 1.047 | 0.065 | 1.121 | |
sliceFileSet | 0.050 | 0.003 | 0.053 | |
summaryExtractTest | 3.913 | 0.504 | 4.475 | |
totalIntensities | 2.988 | 0.299 | 3.311 | |
updateSigDF | 4.201 | 0.457 | 4.789 | |
visualizeGene | 12.630 | 0.665 | 13.465 | |
visualizeProbes | 1.253 | 0.058 | 1.333 | |
visualizeRegion | 0.378 | 0.023 | 0.408 | |
visualizeSegments | 2.413 | 0.250 | 2.704 | |