Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-09 21:31 -0500 (Sat, 09 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1938/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sesame 1.24.0 (landing page) Wanding Zhou
| teran2 | Linux (Ubuntu 24.04.1 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 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.24.0 |
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_1.24.0.tar.gz |
StartedAt: 2024-11-09 13:14:07 -0500 (Sat, 09 Nov 2024) |
EndedAt: 2024-11-09 13:22:47 -0500 (Sat, 09 Nov 2024) |
EllapsedTime: 520.1 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_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.24.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 testEnrichmentGene 14.101 0.685 14.798 imputeBetasByGenomicNeighbors 12.199 0.438 12.640 inferSex 8.047 0.400 8.447 sesameQC_calcStats 7.716 0.639 8.357 KYCG_plotMeta 6.800 0.240 7.041 sesameQC_plotHeatSNPs 6.159 0.573 6.733 imputeBetas 5.829 0.336 6.168 KYCG_plotEnrichAll 5.798 0.284 6.088 sesameQC_plotBar 5.729 0.145 5.878 ELBAR 4.646 0.802 5.452 inferSpecies 5.051 0.192 5.248 * 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/4.4-arm64/Resources/library’ * installing *source* package ‘sesame’ ... ** 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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 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 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, 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 7.093 0.379 7.498
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0 | 0 | 0 | |
DML | 2.485 | 0.226 | 2.713 | |
DMLpredict | 0.334 | 0.025 | 0.359 | |
DMR | 2.145 | 0.056 | 2.201 | |
ELBAR | 4.646 | 0.802 | 5.452 | |
KYCG_annoProbes | 4.630 | 0.166 | 4.797 | |
KYCG_buildGeneDBs | 4.323 | 0.096 | 4.419 | |
KYCG_getDBs | 0.783 | 0.043 | 0.826 | |
KYCG_listDBGroups | 0.105 | 0.001 | 0.106 | |
KYCG_loadDBs | 0.000 | 0.000 | 0.001 | |
KYCG_plotBar | 0.057 | 0.001 | 0.057 | |
KYCG_plotDot | 0.081 | 0.000 | 0.081 | |
KYCG_plotEnrichAll | 5.798 | 0.284 | 6.088 | |
KYCG_plotLollipop | 0.046 | 0.002 | 0.048 | |
KYCG_plotManhattan | 0.626 | 0.029 | 0.654 | |
KYCG_plotMeta | 6.800 | 0.240 | 7.041 | |
KYCG_plotMetaEnrichment | 3.729 | 0.129 | 3.858 | |
KYCG_plotPointRange | 0.591 | 0.092 | 0.684 | |
KYCG_plotSetEnrichment | 1.795 | 0.180 | 1.975 | |
KYCG_plotVolcano | 0.043 | 0.005 | 0.048 | |
KYCG_plotWaterfall | 0.681 | 0.081 | 0.763 | |
MValueToBetaValue | 0.001 | 0.000 | 0.000 | |
SigDF | 0.072 | 0.009 | 0.082 | |
addMask | 0.015 | 0.001 | 0.015 | |
aggregateTestEnrichments | 0.518 | 0.070 | 0.589 | |
betasCollapseToPfx | 0.004 | 0.000 | 0.004 | |
bisConversionControl | 2.154 | 0.050 | 2.203 | |
calcEffectSize | 0.345 | 0.026 | 0.371 | |
checkLevels | 1.129 | 0.075 | 1.206 | |
cnSegmentation | 0.074 | 0.016 | 0.092 | |
compareMouseStrainReference | 3.448 | 0.170 | 3.621 | |
compareMouseTissueReference | 0 | 0 | 0 | |
compareReference | 3.566 | 0.144 | 3.712 | |
controls | 0.584 | 0.062 | 0.645 | |
createUCSCtrack | 1.713 | 0.146 | 1.859 | |
dbStats | 1.831 | 0.157 | 1.992 | |
deidentify | 1.676 | 0.128 | 1.808 | |
detectionPnegEcdf | 0.903 | 0.036 | 0.939 | |
diffRefSet | 4.667 | 0.296 | 4.966 | |
dmContrasts | 0.584 | 0.043 | 0.627 | |
dyeBiasCorr | 0.792 | 0.061 | 0.852 | |
dyeBiasCorrMostBalanced | 2.733 | 0.054 | 2.787 | |
dyeBiasL | 0.899 | 0.022 | 0.921 | |
dyeBiasNL | 2.158 | 0.202 | 2.359 | |
estimateLeukocyte | 2.220 | 0.094 | 2.315 | |
formatVCF | 0.654 | 0.041 | 0.696 | |
getAFTypeIbySumAlleles | 0.482 | 0.069 | 0.553 | |
getAFs | 0.336 | 0.033 | 0.368 | |
getBetas | 0.241 | 0.022 | 0.263 | |
getMask | 1.943 | 0.167 | 2.113 | |
getRefSet | 4.284 | 0.143 | 4.428 | |
imputeBetas | 5.829 | 0.336 | 6.168 | |
imputeBetasByGenomicNeighbors | 12.199 | 0.438 | 12.640 | |
imputeBetasMatrixByMean | 0.001 | 0.000 | 0.000 | |
inferEthnicity | 0 | 0 | 0 | |
inferInfiniumIChannel | 0.132 | 0.133 | 0.267 | |
inferSex | 8.047 | 0.400 | 8.447 | |
inferSpecies | 5.051 | 0.192 | 5.248 | |
inferStrain | 2.430 | 0.192 | 2.622 | |
inferTissue | 2.146 | 0.250 | 2.396 | |
initFileSet | 0.329 | 0.034 | 0.365 | |
listAvailableMasks | 0.363 | 0.053 | 0.417 | |
mLiftOver | 0.000 | 0.001 | 0.000 | |
mapFileSet | 0.016 | 0.001 | 0.017 | |
mapToMammal40 | 0.749 | 0.097 | 0.848 | |
matchDesign | 4.385 | 0.243 | 4.630 | |
meanIntensity | 0.838 | 0.050 | 0.888 | |
medianTotalIntensity | 0.258 | 0.042 | 0.299 | |
noMasked | 1.262 | 0.109 | 1.370 | |
noob | 0.783 | 0.129 | 0.912 | |
openSesame | 1.632 | 0.155 | 1.791 | |
openSesameToFile | 0.524 | 0.035 | 0.558 | |
pOOBAH | 0.490 | 0.014 | 0.505 | |
palgen | 0.015 | 0.002 | 0.017 | |
parseGEOsignalMU | 1.209 | 0.073 | 1.281 | |
predictAge | 0.879 | 0.027 | 0.907 | |
predictAgeHorvath353 | 0 | 0 | 0 | |
predictAgeSkinBlood | 0 | 0 | 0 | |
predictMouseAgeInMonth | 0 | 0 | 0 | |
prefixMask | 0.234 | 0.001 | 0.236 | |
prefixMaskButC | 0.063 | 0.001 | 0.064 | |
prefixMaskButCG | 0.025 | 0.000 | 0.026 | |
prepSesame | 1.235 | 0.140 | 1.374 | |
prepSesameList | 0 | 0 | 0 | |
print.DMLSummary | 1.110 | 0.152 | 1.261 | |
print.fileSet | 0.332 | 0.039 | 0.371 | |
probeID_designType | 0 | 0 | 0 | |
probeSuccessRate | 1.684 | 0.110 | 1.795 | |
qualityMask | 0.605 | 0.072 | 0.678 | |
reIdentify | 1.315 | 0.049 | 1.365 | |
readFileSet | 0.027 | 0.002 | 0.028 | |
readIDATpair | 0.048 | 0.002 | 0.051 | |
recommendedMaskNames | 0 | 0 | 0 | |
resetMask | 0.112 | 0.011 | 0.124 | |
scrub | 0.814 | 0.071 | 0.885 | |
scrubSoft | 1.222 | 0.261 | 1.484 | |
sdfPlatform | 0.065 | 0.009 | 0.074 | |
sdf_read_table | 3.055 | 0.137 | 3.194 | |
sdf_write_table | 0.891 | 0.028 | 0.920 | |
searchIDATprefixes | 0.002 | 0.001 | 0.002 | |
sesame-package | 0.566 | 0.033 | 0.599 | |
sesameAnno_attachManifest | 0 | 0 | 0 | |
sesameAnno_buildAddressFile | 0 | 0 | 0 | |
sesameAnno_buildManifestGRanges | 0 | 0 | 0 | |
sesameAnno_download | 0 | 0 | 0 | |
sesameAnno_readManifestTSV | 0 | 0 | 0 | |
sesameQC_calcStats | 7.716 | 0.639 | 8.357 | |
sesameQC_getStats | 0.826 | 0.019 | 0.846 | |
sesameQC_plotBar | 5.729 | 0.145 | 5.878 | |
sesameQC_plotBetaByDesign | 3.861 | 0.464 | 4.325 | |
sesameQC_plotHeatSNPs | 6.159 | 0.573 | 6.733 | |
sesameQC_plotIntensVsBetas | 0.623 | 0.072 | 0.707 | |
sesameQC_plotRedGrnQQ | 0.513 | 0.055 | 0.570 | |
sesameQC_rankStats | 1.043 | 0.221 | 1.266 | |
sesameQCtoDF | 0.787 | 0.064 | 0.850 | |
sesame_checkVersion | 0.001 | 0.000 | 0.001 | |
sesamize | 0 | 0 | 0 | |
setMask | 0.019 | 0.004 | 0.023 | |
signalMU | 0.200 | 0.043 | 0.243 | |
sliceFileSet | 0.014 | 0.001 | 0.015 | |
summaryExtractTest | 0.913 | 0.077 | 0.991 | |
testEnrichment | 1.411 | 0.171 | 1.583 | |
testEnrichmentGene | 14.101 | 0.685 | 14.798 | |
testEnrichmentSEA | 4.287 | 0.226 | 4.514 | |
totalIntensities | 0.967 | 0.070 | 1.038 | |
updateSigDF | 0.851 | 0.106 | 0.957 | |
visualizeGene | 3.682 | 0.135 | 3.819 | |
visualizeProbes | 0.274 | 0.005 | 0.278 | |
visualizeRegion | 0.212 | 0.006 | 0.218 | |
visualizeSegments | 0.991 | 0.076 | 1.067 | |