Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-22 12:06 -0400 (Mon, 22 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4814 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
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 1968/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sesame 1.27.1 (landing page) Wanding Zhou
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | 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: 1.27.1 |
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: 2025-09-21 21:49:21 -0400 (Sun, 21 Sep 2025) |
EndedAt: 2025-09-21 21:54:18 -0400 (Sun, 21 Sep 2025) |
EllapsedTime: 296.8 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_1.27.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/sesame.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * 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 14.775 0.516 15.602 inferSex 9.863 0.435 10.659 sesameQC_calcStats 8.420 0.794 9.692 sesameQC_plotHeatSNPs 7.453 0.842 8.504 imputeBetas 7.414 0.602 8.530 ELBAR 5.841 1.233 7.301 inferSpecies 6.720 0.295 7.243 sesameQC_plotBar 6.494 0.177 6.854 diffRefSet 6.306 0.263 6.710 getRefSet 5.534 0.181 5.929 sesameQC_plotBetaByDesign 4.466 0.611 5.182 * 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 ‘1.27.1’ ** 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)
sesame.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "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 8.431 0.495 9.338
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0 | 0 | 0 | |
DML | 2.937 | 0.291 | 3.296 | |
DMLpredict | 0.403 | 0.035 | 0.452 | |
DMR | 3.064 | 0.093 | 3.346 | |
ELBAR | 5.841 | 1.233 | 7.301 | |
MValueToBetaValue | 0 | 0 | 0 | |
SigDF | 0.086 | 0.016 | 0.109 | |
addMask | 0.017 | 0.000 | 0.018 | |
betasCollapseToPfx | 0.004 | 0.000 | 0.004 | |
bisConversionControl | 2.180 | 0.063 | 2.322 | |
calcEffectSize | 0.370 | 0.032 | 0.423 | |
checkLevels | 1.608 | 0.082 | 1.733 | |
cnSegmentation | 0.081 | 0.013 | 0.095 | |
compareMouseStrainReference | 3.623 | 0.127 | 3.782 | |
compareMouseTissueReference | 0.000 | 0.001 | 0.000 | |
compareReference | 4.164 | 0.203 | 4.429 | |
controls | 0.783 | 0.078 | 0.907 | |
createUCSCtrack | 2.341 | 0.117 | 2.569 | |
deIdentify | 2.013 | 0.074 | 2.190 | |
detectionPnegEcdf | 0.398 | 0.014 | 0.416 | |
diffRefSet | 6.306 | 0.263 | 6.710 | |
dmContrasts | 0.707 | 0.057 | 0.817 | |
dyeBiasCorr | 1.034 | 0.148 | 1.234 | |
dyeBiasCorrMostBalanced | 3.296 | 0.089 | 3.493 | |
dyeBiasL | 0.981 | 0.067 | 1.075 | |
dyeBiasNL | 2.526 | 0.210 | 2.880 | |
estimateLeukocyte | 2.716 | 0.157 | 2.971 | |
formatVCF | 0.771 | 0.071 | 0.882 | |
getAFTypeIbySumAlleles | 0.574 | 0.084 | 0.760 | |
getAFs | 0.417 | 0.070 | 0.524 | |
getBetas | 0.270 | 0.049 | 0.330 | |
getMask | 2.217 | 0.130 | 2.442 | |
getRefSet | 5.534 | 0.181 | 5.929 | |
imputeBetas | 7.414 | 0.602 | 8.530 | |
imputeBetasByGenomicNeighbors | 14.775 | 0.516 | 15.602 | |
imputeBetasMatrixByMean | 0.001 | 0.000 | 0.001 | |
inferEthnicity | 0.000 | 0.000 | 0.001 | |
inferInfiniumIChannel | 0.140 | 0.206 | 0.382 | |
inferSex | 9.863 | 0.435 | 10.659 | |
inferSpecies | 6.720 | 0.295 | 7.243 | |
inferStrain | 2.866 | 0.225 | 3.179 | |
inferTissue | 2.438 | 0.280 | 2.793 | |
initFileSet | 0.383 | 0.090 | 0.472 | |
listAvailableMasks | 0.385 | 0.056 | 0.442 | |
mLiftOver | 0 | 0 | 0 | |
mapFileSet | 0.016 | 0.001 | 0.017 | |
mapToMammal40 | 0.801 | 0.095 | 0.897 | |
matchDesign | 4.527 | 0.263 | 4.808 | |
meanIntensity | 0.920 | 0.093 | 1.032 | |
medianTotalIntensity | 0.263 | 0.038 | 0.316 | |
noMasked | 1.365 | 0.120 | 1.533 | |
noob | 0.812 | 0.091 | 0.909 | |
openSesame | 1.797 | 0.218 | 2.066 | |
openSesameToFile | 0.589 | 0.065 | 0.681 | |
pOOBAH | 0.496 | 0.021 | 0.524 | |
palgen | 0.020 | 0.003 | 0.025 | |
parseGEOsignalMU | 1.252 | 0.099 | 1.380 | |
predictAge | 1.094 | 0.063 | 1.195 | |
predictAgeHorvath353 | 0 | 0 | 0 | |
predictAgeSkinBlood | 0 | 0 | 0 | |
predictMouseAgeInMonth | 0 | 0 | 0 | |
prefixMask | 0.217 | 0.002 | 0.226 | |
prefixMaskButC | 0.054 | 0.001 | 0.058 | |
prefixMaskButCG | 0.022 | 0.001 | 0.024 | |
prepSesame | 1.377 | 0.128 | 1.552 | |
prepSesameList | 0.001 | 0.000 | 0.001 | |
print.DMLSummary | 1.099 | 0.143 | 1.274 | |
print.fileSet | 0.371 | 0.033 | 0.433 | |
probeID_designType | 0.000 | 0.000 | 0.001 | |
probeSuccessRate | 2.166 | 0.197 | 2.469 | |
qualityMask | 0.697 | 0.072 | 0.776 | |
reIdentify | 2.025 | 0.071 | 2.102 | |
readFileSet | 0.041 | 0.001 | 0.043 | |
readIDATpair | 0.049 | 0.004 | 0.054 | |
recommendedMaskNames | 0 | 0 | 0 | |
resetMask | 0.139 | 0.025 | 0.164 | |
scrub | 0.985 | 0.158 | 1.198 | |
scrubSoft | 1.428 | 0.351 | 1.900 | |
sdfPlatform | 0.093 | 0.011 | 0.124 | |
sdf_read_table | 3.814 | 0.204 | 4.068 | |
sdf_write_table | 1.159 | 0.058 | 1.250 | |
searchIDATprefixes | 0.002 | 0.001 | 0.004 | |
sesame-package | 0.994 | 0.137 | 1.208 | |
sesameAnno_attachManifest | 0 | 0 | 0 | |
sesameAnno_buildAddressFile | 0.000 | 0.000 | 0.001 | |
sesameAnno_buildManifestGRanges | 0 | 0 | 0 | |
sesameAnno_download | 0.000 | 0.001 | 0.000 | |
sesameAnno_readManifestTSV | 0 | 0 | 0 | |
sesameQC_calcStats | 8.420 | 0.794 | 9.692 | |
sesameQC_getStats | 0.823 | 0.019 | 0.859 | |
sesameQC_plotBar | 6.494 | 0.177 | 6.854 | |
sesameQC_plotBetaByDesign | 4.466 | 0.611 | 5.182 | |
sesameQC_plotHeatSNPs | 7.453 | 0.842 | 8.504 | |
sesameQC_plotIntensVsBetas | 0.657 | 0.121 | 0.803 | |
sesameQC_plotRedGrnQQ | 0.456 | 0.074 | 0.547 | |
sesameQC_rankStats | 1.184 | 0.190 | 1.385 | |
sesameQCtoDF | 0.915 | 0.035 | 0.974 | |
sesame_checkVersion | 0.002 | 0.000 | 0.002 | |
sesamize | 0.000 | 0.000 | 0.001 | |
setMask | 0.024 | 0.003 | 0.026 | |
signalMU | 0.268 | 0.030 | 0.316 | |
sliceFileSet | 0.016 | 0.001 | 0.017 | |
summaryExtractTest | 1.222 | 0.151 | 1.409 | |
totalIntensities | 0.884 | 0.109 | 1.013 | |
updateSigDF | 1.055 | 0.153 | 1.230 | |
visualizeGene | 3.818 | 0.206 | 4.202 | |
visualizeProbes | 0.394 | 0.012 | 0.422 | |
visualizeRegion | 0.110 | 0.009 | 0.119 | |
visualizeSegments | 0.868 | 0.071 | 0.942 | |