Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-19 12:03 -0400 (Fri, 19 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" | 4808 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4541 |
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 1967/2330 | 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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings sesame_1.27.1.tar.gz |
StartedAt: 2025-09-19 05:03:38 -0400 (Fri, 19 Sep 2025) |
EndedAt: 2025-09-19 05:22:03 -0400 (Fri, 19 Sep 2025) |
EllapsedTime: 1105.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sesame.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings sesame_1.27.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/sesame.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * 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 loading without being on the library search path ... 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 40.435 1.449 41.896 imputeBetas 24.815 0.646 25.477 inferSex 21.036 1.543 22.581 sesameQC_calcStats 19.111 0.300 19.419 ELBAR 18.498 0.298 18.874 sesameQC_plotHeatSNPs 17.757 0.454 18.212 diffRefSet 17.402 0.321 17.783 inferSpecies 15.382 1.311 16.694 getRefSet 14.786 0.250 15.050 compareReference 12.203 0.227 12.470 compareMouseStrainReference 12.177 0.199 12.478 sesameQC_plotBar 11.257 0.173 11.431 matchDesign 11.108 0.307 11.420 DMR 10.602 0.338 10.942 estimateLeukocyte 10.121 0.183 10.305 getMask 9.978 0.173 10.216 sesameQC_plotBetaByDesign 9.891 0.086 9.980 DML 8.794 0.364 9.328 dyeBiasNL 8.382 0.077 8.460 visualizeGene 8.239 0.137 8.377 dyeBiasCorrMostBalanced 7.572 0.095 7.668 sdf_read_table 7.303 0.125 7.428 inferStrain 6.667 0.485 7.160 createUCSCtrack 7.021 0.065 7.087 inferTissue 6.714 0.338 7.056 deIdentify 5.968 0.076 6.047 probeSuccessRate 5.052 0.120 5.176 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
sesame.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL sesame ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-08-23 r88802) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 18.257 0.967 19.215
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0.001 | 0.000 | 0.001 | |
DML | 8.794 | 0.364 | 9.328 | |
DMLpredict | 1.412 | 0.034 | 1.446 | |
DMR | 10.602 | 0.338 | 10.942 | |
ELBAR | 18.498 | 0.298 | 18.874 | |
MValueToBetaValue | 0 | 0 | 0 | |
SigDF | 0.297 | 0.016 | 0.313 | |
addMask | 0.165 | 0.007 | 0.172 | |
betasCollapseToPfx | 0.013 | 0.000 | 0.013 | |
bisConversionControl | 4.859 | 0.104 | 4.976 | |
calcEffectSize | 1.448 | 0.058 | 1.506 | |
checkLevels | 3.502 | 0.144 | 3.646 | |
cnSegmentation | 0.337 | 0.011 | 0.348 | |
compareMouseStrainReference | 12.177 | 0.199 | 12.478 | |
compareMouseTissueReference | 0 | 0 | 0 | |
compareReference | 12.203 | 0.227 | 12.470 | |
controls | 2.306 | 0.056 | 2.363 | |
createUCSCtrack | 7.021 | 0.065 | 7.087 | |
deIdentify | 5.968 | 0.076 | 6.047 | |
detectionPnegEcdf | 1.153 | 0.014 | 1.205 | |
diffRefSet | 17.402 | 0.321 | 17.783 | |
dmContrasts | 2.426 | 0.041 | 2.469 | |
dyeBiasCorr | 3.281 | 0.083 | 3.365 | |
dyeBiasCorrMostBalanced | 7.572 | 0.095 | 7.668 | |
dyeBiasL | 2.869 | 0.089 | 2.966 | |
dyeBiasNL | 8.382 | 0.077 | 8.460 | |
estimateLeukocyte | 10.121 | 0.183 | 10.305 | |
formatVCF | 3.601 | 0.072 | 3.685 | |
getAFTypeIbySumAlleles | 2.768 | 0.068 | 2.837 | |
getAFs | 2.006 | 0.081 | 2.088 | |
getBetas | 1.444 | 0.046 | 1.490 | |
getMask | 9.978 | 0.173 | 10.216 | |
getRefSet | 14.786 | 0.250 | 15.050 | |
imputeBetas | 24.815 | 0.646 | 25.477 | |
imputeBetasByGenomicNeighbors | 40.435 | 1.449 | 41.896 | |
imputeBetasMatrixByMean | 0.001 | 0.001 | 0.001 | |
inferEthnicity | 0.001 | 0.000 | 0.001 | |
inferInfiniumIChannel | 0.230 | 0.103 | 0.333 | |
inferSex | 21.036 | 1.543 | 22.581 | |
inferSpecies | 15.382 | 1.311 | 16.694 | |
inferStrain | 6.667 | 0.485 | 7.160 | |
inferTissue | 6.714 | 0.338 | 7.056 | |
initFileSet | 1.174 | 0.033 | 1.207 | |
listAvailableMasks | 1.249 | 0.038 | 1.288 | |
mLiftOver | 0 | 0 | 0 | |
mapFileSet | 0.033 | 0.001 | 0.033 | |
mapToMammal40 | 2.501 | 0.120 | 2.621 | |
matchDesign | 11.108 | 0.307 | 11.420 | |
meanIntensity | 2.496 | 0.128 | 2.625 | |
medianTotalIntensity | 0.765 | 0.097 | 0.863 | |
noMasked | 3.489 | 0.085 | 3.575 | |
noob | 1.804 | 0.115 | 1.920 | |
openSesame | 4.824 | 0.109 | 4.941 | |
openSesameToFile | 1.349 | 0.034 | 1.384 | |
pOOBAH | 1.249 | 0.004 | 1.253 | |
palgen | 0.033 | 0.007 | 0.040 | |
parseGEOsignalMU | 2.849 | 0.071 | 2.920 | |
predictAge | 2.429 | 0.076 | 2.505 | |
predictAgeHorvath353 | 0 | 0 | 0 | |
predictAgeSkinBlood | 0 | 0 | 0 | |
predictMouseAgeInMonth | 0 | 0 | 0 | |
prefixMask | 0.407 | 0.002 | 0.410 | |
prefixMaskButC | 0.114 | 0.000 | 0.115 | |
prefixMaskButCG | 0.046 | 0.000 | 0.046 | |
prepSesame | 3.417 | 0.138 | 3.556 | |
prepSesameList | 0.001 | 0.001 | 0.001 | |
print.DMLSummary | 2.924 | 0.204 | 3.127 | |
print.fileSet | 1.228 | 0.031 | 1.261 | |
probeID_designType | 0.001 | 0.000 | 0.001 | |
probeSuccessRate | 5.052 | 0.120 | 5.176 | |
qualityMask | 1.727 | 0.054 | 1.781 | |
reIdentify | 4.218 | 0.042 | 4.261 | |
readFileSet | 0.051 | 0.001 | 0.052 | |
readIDATpair | 0.114 | 0.001 | 0.114 | |
recommendedMaskNames | 0.001 | 0.000 | 0.000 | |
resetMask | 0.373 | 0.017 | 0.390 | |
scrub | 2.187 | 0.201 | 2.388 | |
scrubSoft | 3.087 | 0.055 | 3.143 | |
sdfPlatform | 0.284 | 0.017 | 0.301 | |
sdf_read_table | 7.303 | 0.125 | 7.428 | |
sdf_write_table | 1.668 | 0.070 | 1.866 | |
searchIDATprefixes | 0.003 | 0.001 | 0.005 | |
sesame-package | 2.228 | 0.109 | 2.338 | |
sesameAnno_attachManifest | 0 | 0 | 0 | |
sesameAnno_buildAddressFile | 0 | 0 | 0 | |
sesameAnno_buildManifestGRanges | 0 | 0 | 0 | |
sesameAnno_download | 0 | 0 | 0 | |
sesameAnno_readManifestTSV | 0.000 | 0.001 | 0.000 | |
sesameQC_calcStats | 19.111 | 0.300 | 19.419 | |
sesameQC_getStats | 1.781 | 0.019 | 1.801 | |
sesameQC_plotBar | 11.257 | 0.173 | 11.431 | |
sesameQC_plotBetaByDesign | 9.891 | 0.086 | 9.980 | |
sesameQC_plotHeatSNPs | 17.757 | 0.454 | 18.212 | |
sesameQC_plotIntensVsBetas | 1.777 | 0.029 | 1.805 | |
sesameQC_plotRedGrnQQ | 1.583 | 0.042 | 1.625 | |
sesameQC_rankStats | 2.944 | 0.088 | 3.032 | |
sesameQCtoDF | 1.571 | 0.022 | 1.592 | |
sesame_checkVersion | 0.002 | 0.001 | 0.003 | |
sesamize | 0 | 0 | 0 | |
setMask | 0.088 | 0.002 | 0.090 | |
signalMU | 0.895 | 0.017 | 0.912 | |
sliceFileSet | 0.035 | 0.000 | 0.034 | |
summaryExtractTest | 2.549 | 0.051 | 2.599 | |
totalIntensities | 2.405 | 0.061 | 2.465 | |
updateSigDF | 3.075 | 0.091 | 3.166 | |
visualizeGene | 8.239 | 0.137 | 8.377 | |
visualizeProbes | 1.077 | 0.003 | 1.081 | |
visualizeRegion | 0.327 | 0.000 | 0.328 | |
visualizeSegments | 1.666 | 0.013 | 1.679 | |