Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-27 12:33 -0400 (Fri, 27 Sep 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" | 4451 |
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4417 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4456 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4489 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4436 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4435 |
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 1916/2262 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sesame 1.23.9 (landing page) Wanding Zhou
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 22.04.3 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: 1.23.9 |
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_1.23.9.tar.gz |
StartedAt: 2024-09-27 00:23:16 -0400 (Fri, 27 Sep 2024) |
EndedAt: 2024-09-27 00:28:38 -0400 (Fri, 27 Sep 2024) |
EllapsedTime: 322.6 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_1.23.9.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 ‘1.23.9’ * 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 testEnrichmentGene 16.113 1.078 17.253 imputeBetasByGenomicNeighbors 13.028 0.502 13.549 sesameQC_calcStats 8.027 0.715 8.746 inferSex 8.134 0.546 8.683 KYCG_plotMeta 7.715 0.381 8.116 sesameQC_plotHeatSNPs 6.936 0.701 7.652 imputeBetas 6.512 0.507 7.027 KYCG_plotEnrichAll 6.445 0.473 6.947 ELBAR 5.586 0.935 6.540 sesameQC_plotBar 6.079 0.179 6.267 inferSpecies 5.723 0.283 6.028 diffRefSet 5.404 0.233 5.654 * 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, 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 7.483 0.462 7.950
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0 | 0 | 0 | |
DML | 2.859 | 0.268 | 3.135 | |
DMLpredict | 0.388 | 0.029 | 0.417 | |
DMR | 2.295 | 0.088 | 2.392 | |
ELBAR | 5.586 | 0.935 | 6.540 | |
KYCG_annoProbes | 4.741 | 0.214 | 4.974 | |
KYCG_buildGeneDBs | 4.610 | 0.117 | 4.730 | |
KYCG_getDBs | 0.902 | 0.073 | 0.978 | |
KYCG_listDBGroups | 0.01 | 0.00 | 0.01 | |
KYCG_loadDBs | 0 | 0 | 0 | |
KYCG_plotBar | 0.064 | 0.006 | 0.070 | |
KYCG_plotDot | 0.229 | 0.009 | 0.239 | |
KYCG_plotEnrichAll | 6.445 | 0.473 | 6.947 | |
KYCG_plotLollipop | 0.048 | 0.006 | 0.053 | |
KYCG_plotManhattan | 0.605 | 0.034 | 0.640 | |
KYCG_plotMeta | 7.715 | 0.381 | 8.116 | |
KYCG_plotMetaEnrichment | 4.252 | 0.168 | 4.421 | |
KYCG_plotPointRange | 0.696 | 0.058 | 0.755 | |
KYCG_plotSetEnrichment | 1.861 | 0.176 | 2.041 | |
KYCG_plotVolcano | 0.045 | 0.000 | 0.046 | |
KYCG_plotWaterfall | 0.723 | 0.099 | 0.825 | |
MValueToBetaValue | 0 | 0 | 0 | |
SigDF | 0.082 | 0.012 | 0.093 | |
addMask | 0.017 | 0.002 | 0.019 | |
aggregateTestEnrichments | 0.550 | 0.073 | 0.622 | |
betasCollapseToPfx | 0.004 | 0.000 | 0.004 | |
bisConversionControl | 2.310 | 0.062 | 2.374 | |
calcEffectSize | 0.474 | 0.054 | 0.531 | |
checkLevels | 1.104 | 0.118 | 1.224 | |
cnSegmentation | 0.081 | 0.018 | 0.099 | |
compareMouseStrainReference | 3.710 | 0.159 | 3.875 | |
compareMouseTissueReference | 0 | 0 | 0 | |
compareReference | 3.723 | 0.177 | 3.904 | |
controls | 0.708 | 0.117 | 0.827 | |
createUCSCtrack | 2.124 | 0.250 | 2.379 | |
dbStats | 2.620 | 0.261 | 2.886 | |
deidentify | 1.733 | 0.175 | 1.916 | |
detectionPnegEcdf | 1.013 | 0.050 | 1.064 | |
diffRefSet | 5.404 | 0.233 | 5.654 | |
dmContrasts | 0.668 | 0.085 | 0.754 | |
dyeBiasCorr | 0.881 | 0.133 | 1.015 | |
dyeBiasCorrMostBalanced | 2.763 | 0.067 | 2.831 | |
dyeBiasL | 0.882 | 0.035 | 0.916 | |
dyeBiasNL | 1.962 | 0.120 | 2.085 | |
estimateLeukocyte | 2.830 | 0.140 | 2.976 | |
formatVCF | 0.698 | 0.084 | 0.782 | |
getAFTypeIbySumAlleles | 0.489 | 0.059 | 0.549 | |
getAFs | 0.358 | 0.039 | 0.397 | |
getBetas | 0.249 | 0.038 | 0.290 | |
getMask | 2.070 | 0.210 | 2.295 | |
getRefSet | 4.436 | 0.184 | 4.627 | |
imputeBetas | 6.512 | 0.507 | 7.027 | |
imputeBetasByGenomicNeighbors | 13.028 | 0.502 | 13.549 | |
imputeBetasMatrixByMean | 0.001 | 0.000 | 0.001 | |
inferEthnicity | 0 | 0 | 0 | |
inferInfiniumIChannel | 0.145 | 0.156 | 0.303 | |
inferSex | 8.134 | 0.546 | 8.683 | |
inferSpecies | 5.723 | 0.283 | 6.028 | |
inferStrain | 2.691 | 0.290 | 3.012 | |
inferTissue | 2.101 | 0.351 | 2.463 | |
initFileSet | 0.355 | 0.050 | 0.406 | |
listAvailableMasks | 0.356 | 0.075 | 0.431 | |
mLiftOver | 0.000 | 0.001 | 0.000 | |
mapFileSet | 0.014 | 0.003 | 0.017 | |
mapToMammal40 | 0.824 | 0.170 | 1.004 | |
matchDesign | 4.333 | 0.248 | 4.586 | |
meanIntensity | 0.884 | 0.088 | 0.975 | |
medianTotalIntensity | 0.257 | 0.035 | 0.293 | |
noMasked | 1.215 | 0.136 | 1.352 | |
noob | 0.722 | 0.064 | 0.787 | |
openSesame | 1.719 | 0.230 | 1.957 | |
openSesameToFile | 0.525 | 0.049 | 0.575 | |
pOOBAH | 0.519 | 0.043 | 0.564 | |
palgen | 0.017 | 0.002 | 0.020 | |
parseGEOsignalMU | 1.252 | 0.145 | 1.403 | |
predictAge | 0.879 | 0.027 | 0.907 | |
predictAgeHorvath353 | 0 | 0 | 0 | |
predictAgeSkinBlood | 0 | 0 | 0 | |
predictMouseAgeInMonth | 0 | 0 | 0 | |
prefixMask | 0.200 | 0.001 | 0.202 | |
prefixMaskButC | 0.052 | 0.001 | 0.052 | |
prefixMaskButCG | 0.019 | 0.001 | 0.019 | |
prepSesame | 1.245 | 0.108 | 1.359 | |
prepSesameList | 0.001 | 0.000 | 0.000 | |
print.DMLSummary | 1.315 | 0.144 | 1.459 | |
print.fileSet | 0.364 | 0.071 | 0.435 | |
probeID_designType | 0 | 0 | 0 | |
probeSuccessRate | 1.913 | 0.157 | 2.084 | |
qualityMask | 0.645 | 0.055 | 0.700 | |
reIdentify | 1.480 | 0.080 | 1.561 | |
readFileSet | 0.026 | 0.001 | 0.028 | |
readIDATpair | 0.041 | 0.003 | 0.044 | |
recommendedMaskNames | 0 | 0 | 0 | |
resetMask | 0.103 | 0.016 | 0.120 | |
scrub | 0.871 | 0.108 | 0.979 | |
scrubSoft | 1.287 | 0.359 | 1.647 | |
sdfPlatform | 0.068 | 0.010 | 0.077 | |
sdf_read_table | 3.205 | 0.159 | 3.371 | |
sdf_write_table | 0.913 | 0.038 | 0.955 | |
searchIDATprefixes | 0.001 | 0.001 | 0.003 | |
sesame-package | 0.637 | 0.057 | 0.694 | |
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 | 8.027 | 0.715 | 8.746 | |
sesameQC_getStats | 0.869 | 0.071 | 0.939 | |
sesameQC_plotBar | 6.079 | 0.179 | 6.267 | |
sesameQC_plotBetaByDesign | 4.147 | 0.522 | 4.671 | |
sesameQC_plotHeatSNPs | 6.936 | 0.701 | 7.652 | |
sesameQC_plotIntensVsBetas | 0.617 | 0.089 | 0.709 | |
sesameQC_plotRedGrnQQ | 0.519 | 0.064 | 0.584 | |
sesameQC_rankStats | 1.113 | 0.146 | 1.267 | |
sesameQCtoDF | 0.813 | 0.026 | 0.840 | |
sesame_checkVersion | 0.001 | 0.000 | 0.002 | |
sesamize | 0 | 0 | 0 | |
setMask | 0.022 | 0.004 | 0.026 | |
signalMU | 0.323 | 0.039 | 0.363 | |
sliceFileSet | 0.016 | 0.001 | 0.016 | |
summaryExtractTest | 1.175 | 0.127 | 1.304 | |
testEnrichment | 1.740 | 0.269 | 2.012 | |
testEnrichmentGene | 16.113 | 1.078 | 17.253 | |
testEnrichmentSEA | 3.970 | 0.371 | 4.353 | |
totalIntensities | 1.109 | 0.074 | 1.185 | |
updateSigDF | 1.107 | 0.115 | 1.223 | |
visualizeGene | 3.747 | 0.142 | 3.890 | |
visualizeProbes | 1.231 | 0.022 | 1.253 | |
visualizeRegion | 0.109 | 0.010 | 0.120 | |
visualizeSegments | 0.900 | 0.158 | 1.071 | |