Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:10 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
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 1956/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sesame 1.27.1 (landing page) Wanding Zhou
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | 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: 2025-08-08 21:35:57 -0400 (Fri, 08 Aug 2025) |
EndedAt: 2025-08-08 21:40:35 -0400 (Fri, 08 Aug 2025) |
EllapsedTime: 277.5 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 (2025-06-14 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 13.7.1 * 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 13.989 0.539 14.570 inferSex 9.464 0.450 9.943 sesameQC_calcStats 7.944 0.707 8.658 sesameQC_plotHeatSNPs 7.864 0.769 8.643 imputeBetas 7.005 0.594 7.623 inferSpecies 6.746 0.293 7.047 ELBAR 5.607 1.102 6.747 sesameQC_plotBar 5.910 0.180 6.111 diffRefSet 5.767 0.183 5.953 getRefSet 5.111 0.136 5.263 * 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 (2025-06-14 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 8.342 0.444 8.788
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0 | 0 | 0 | |
DML | 2.631 | 0.346 | 3.002 | |
DMLpredict | 0.398 | 0.035 | 0.441 | |
DMR | 2.987 | 0.092 | 3.083 | |
ELBAR | 5.607 | 1.102 | 6.747 | |
MValueToBetaValue | 0 | 0 | 0 | |
SigDF | 0.089 | 0.015 | 0.105 | |
addMask | 0.020 | 0.001 | 0.021 | |
betasCollapseToPfx | 0.004 | 0.000 | 0.004 | |
bisConversionControl | 2.231 | 0.066 | 2.301 | |
calcEffectSize | 0.367 | 0.031 | 0.397 | |
checkLevels | 1.550 | 0.074 | 1.629 | |
cnSegmentation | 0.079 | 0.013 | 0.093 | |
compareMouseStrainReference | 3.695 | 0.147 | 3.870 | |
compareMouseTissueReference | 0 | 0 | 0 | |
compareReference | 4.297 | 0.129 | 4.443 | |
controls | 0.734 | 0.060 | 0.797 | |
createUCSCtrack | 2.201 | 0.106 | 2.339 | |
deIdentify | 1.969 | 0.090 | 2.111 | |
detectionPnegEcdf | 0.400 | 0.009 | 0.413 | |
diffRefSet | 5.767 | 0.183 | 5.953 | |
dmContrasts | 0.690 | 0.058 | 0.751 | |
dyeBiasCorr | 0.981 | 0.100 | 1.083 | |
dyeBiasCorrMostBalanced | 3.279 | 0.089 | 3.397 | |
dyeBiasL | 0.792 | 0.053 | 0.846 | |
dyeBiasNL | 2.013 | 0.189 | 2.209 | |
estimateLeukocyte | 2.640 | 0.174 | 2.823 | |
formatVCF | 0.779 | 0.092 | 0.880 | |
getAFTypeIbySumAlleles | 0.574 | 0.059 | 0.634 | |
getAFs | 0.325 | 0.052 | 0.377 | |
getBetas | 0.293 | 0.040 | 0.334 | |
getMask | 2.559 | 0.207 | 2.777 | |
getRefSet | 5.111 | 0.136 | 5.263 | |
imputeBetas | 7.005 | 0.594 | 7.623 | |
imputeBetasByGenomicNeighbors | 13.989 | 0.539 | 14.570 | |
imputeBetasMatrixByMean | 0.000 | 0.000 | 0.001 | |
inferEthnicity | 0 | 0 | 0 | |
inferInfiniumIChannel | 0.132 | 0.151 | 0.292 | |
inferSex | 9.464 | 0.450 | 9.943 | |
inferSpecies | 6.746 | 0.293 | 7.047 | |
inferStrain | 3.614 | 0.253 | 3.891 | |
inferTissue | 2.405 | 0.331 | 2.737 | |
initFileSet | 0.369 | 0.095 | 0.464 | |
listAvailableMasks | 0.422 | 0.086 | 0.509 | |
mLiftOver | 0.000 | 0.001 | 0.000 | |
mapFileSet | 0.016 | 0.002 | 0.018 | |
mapToMammal40 | 0.899 | 0.176 | 1.079 | |
matchDesign | 4.382 | 0.325 | 4.737 | |
meanIntensity | 0.901 | 0.108 | 1.010 | |
medianTotalIntensity | 0.268 | 0.051 | 0.319 | |
noMasked | 1.312 | 0.094 | 1.413 | |
noob | 0.903 | 0.151 | 1.081 | |
openSesame | 1.729 | 0.226 | 1.965 | |
openSesameToFile | 0.587 | 0.078 | 0.676 | |
pOOBAH | 0.548 | 0.029 | 0.582 | |
palgen | 0.015 | 0.002 | 0.017 | |
parseGEOsignalMU | 1.270 | 0.137 | 1.411 | |
predictAge | 1.039 | 0.042 | 1.093 | |
predictAgeHorvath353 | 0 | 0 | 0 | |
predictAgeSkinBlood | 0 | 0 | 0 | |
predictMouseAgeInMonth | 0 | 0 | 0 | |
prefixMask | 0.212 | 0.003 | 0.215 | |
prefixMaskButC | 0.052 | 0.001 | 0.053 | |
prefixMaskButCG | 0.021 | 0.001 | 0.022 | |
prepSesame | 1.371 | 0.151 | 1.541 | |
prepSesameList | 0.000 | 0.000 | 0.001 | |
print.DMLSummary | 1.107 | 0.155 | 1.283 | |
print.fileSet | 0.381 | 0.047 | 0.474 | |
probeID_designType | 0 | 0 | 0 | |
probeSuccessRate | 2.000 | 0.200 | 2.208 | |
qualityMask | 0.665 | 0.131 | 0.798 | |
reIdentify | 1.711 | 0.171 | 1.888 | |
readFileSet | 0.026 | 0.001 | 0.029 | |
readIDATpair | 0.039 | 0.006 | 0.044 | |
recommendedMaskNames | 0 | 0 | 0 | |
resetMask | 0.103 | 0.016 | 0.127 | |
scrub | 0.933 | 0.121 | 1.054 | |
scrubSoft | 1.353 | 0.235 | 1.590 | |
sdfPlatform | 0.085 | 0.015 | 0.099 | |
sdf_read_table | 3.743 | 0.248 | 4.027 | |
sdf_write_table | 0.922 | 0.043 | 0.970 | |
searchIDATprefixes | 0.001 | 0.000 | 0.003 | |
sesame-package | 0.942 | 0.071 | 1.015 | |
sesameAnno_attachManifest | 0 | 0 | 0 | |
sesameAnno_buildAddressFile | 0 | 0 | 0 | |
sesameAnno_buildManifestGRanges | 0 | 0 | 0 | |
sesameAnno_download | 0 | 0 | 0 | |
sesameAnno_readManifestTSV | 0.001 | 0.000 | 0.000 | |
sesameQC_calcStats | 7.944 | 0.707 | 8.658 | |
sesameQC_getStats | 0.799 | 0.042 | 0.840 | |
sesameQC_plotBar | 5.910 | 0.180 | 6.111 | |
sesameQC_plotBetaByDesign | 3.628 | 0.673 | 4.327 | |
sesameQC_plotHeatSNPs | 7.864 | 0.769 | 8.643 | |
sesameQC_plotIntensVsBetas | 0.628 | 0.124 | 0.756 | |
sesameQC_plotRedGrnQQ | 0.446 | 0.061 | 0.512 | |
sesameQC_rankStats | 1.713 | 0.261 | 1.989 | |
sesameQCtoDF | 0.783 | 0.029 | 0.815 | |
sesame_checkVersion | 0.001 | 0.001 | 0.001 | |
sesamize | 0 | 0 | 0 | |
setMask | 0.021 | 0.001 | 0.022 | |
signalMU | 0.252 | 0.040 | 0.292 | |
sliceFileSet | 0.015 | 0.001 | 0.018 | |
summaryExtractTest | 1.081 | 0.117 | 1.207 | |
totalIntensities | 0.851 | 0.120 | 0.971 | |
updateSigDF | 1.063 | 0.165 | 1.232 | |
visualizeGene | 3.597 | 0.206 | 3.814 | |
visualizeProbes | 0.393 | 0.008 | 0.400 | |
visualizeRegion | 0.120 | 0.005 | 0.125 | |
visualizeSegments | 0.839 | 0.112 | 0.960 | |