Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 1898/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sesame 1.23.6 (landing page) Wanding Zhou
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
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: 1.23.6 |
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_1.23.6.tar.gz |
StartedAt: 2024-06-10 09:58:52 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 10:29:19 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 1827.2 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_1.23.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-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 Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.23.6’ * 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 73.294 4.330 83.506 imputeBetasByGenomicNeighbors 62.327 1.588 71.951 inferSex 38.345 1.220 43.061 sesameQC_calcStats 36.948 1.973 42.620 KYCG_plotMeta 36.327 1.116 40.590 sesameQC_plotHeatSNPs 32.085 1.977 37.663 KYCG_plotEnrichAll 32.089 1.442 41.372 compareMouseStrainReference 32.177 0.913 36.571 imputeBetas 29.700 1.737 35.822 compareReference 29.335 0.771 33.112 KYCG_annoProbes 25.009 1.311 29.449 ELBAR 23.523 2.746 28.983 diffRefSet 24.932 0.879 28.634 matchDesign 22.534 1.110 25.584 inferSpecies 21.270 1.002 24.522 KYCG_plotMetaEnrichment 19.689 0.701 22.759 sesameQC_plotBar 19.715 0.565 25.754 getRefSet 19.495 0.675 22.965 testEnrichmentSEA 18.401 1.225 21.612 DML 17.247 1.754 21.505 visualizeGene 17.382 0.734 21.436 DMR 17.288 0.443 19.774 KYCG_buildGeneDBs 17.075 0.646 19.980 sdf_read_table 16.723 0.718 19.384 sesameQC_plotBetaByDesign 15.261 1.204 16.946 deidentify 14.890 0.457 17.106 inferStrain 13.861 0.858 16.471 inferTissue 12.868 1.396 15.630 estimateLeukocyte 12.317 0.631 14.841 reIdentify 12.623 0.325 13.894 getMask 11.614 0.750 14.213 dbStats 10.645 0.917 13.021 KYCG_plotSetEnrichment 10.388 0.533 12.405 createUCSCtrack 10.328 0.442 11.932 probeSuccessRate 9.622 0.768 11.768 openSesame 9.605 0.705 11.118 testEnrichment 9.218 0.995 11.174 dyeBiasCorrMostBalanced 9.787 0.365 11.413 dyeBiasNL 8.707 0.534 10.091 totalIntensities 7.892 0.584 9.599 bisConversionControl 7.627 0.278 8.734 prepSesame 7.199 0.459 8.607 scrubSoft 5.346 1.267 7.171 sesameQC_rankStats 5.917 0.579 8.434 noMasked 6.038 0.303 7.215 sdf_write_table 5.753 0.326 6.734 KYCG_plotWaterfall 5.605 0.235 6.423 parseGEOsignalMU 5.247 0.527 6.327 mapToMammal40 5.149 0.544 6.325 updateSigDF 5.233 0.399 6.509 print.DMLSummary 4.500 1.097 6.186 KYCG_getDBs 4.951 0.366 5.942 summaryExtractTest 4.444 0.869 5.957 meanIntensity 4.693 0.608 6.110 detectionPnegEcdf 5.101 0.189 5.826 dyeBiasCorr 4.888 0.298 5.848 sesame-package 4.555 0.593 5.733 checkLevels 4.653 0.315 5.432 KYCG_plotPointRange 4.466 0.235 5.276 qualityMask 4.150 0.540 5.547 formatVCF 3.796 0.364 5.204 * 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-x86_64/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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 38.200 2.939 46.623
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0.000 | 0.001 | 0.001 | |
DML | 17.247 | 1.754 | 21.505 | |
DMLpredict | 2.510 | 0.176 | 2.998 | |
DMR | 17.288 | 0.443 | 19.774 | |
ELBAR | 23.523 | 2.746 | 28.983 | |
KYCG_annoProbes | 25.009 | 1.311 | 29.449 | |
KYCG_buildGeneDBs | 17.075 | 0.646 | 19.980 | |
KYCG_getDBs | 4.951 | 0.366 | 5.942 | |
KYCG_listDBGroups | 0.060 | 0.005 | 0.074 | |
KYCG_loadDBs | 0.001 | 0.001 | 0.002 | |
KYCG_plotBar | 0.410 | 0.035 | 0.487 | |
KYCG_plotDot | 1.298 | 0.060 | 1.492 | |
KYCG_plotEnrichAll | 32.089 | 1.442 | 41.372 | |
KYCG_plotLollipop | 0.399 | 0.010 | 0.457 | |
KYCG_plotManhattan | 1.667 | 0.287 | 2.195 | |
KYCG_plotMeta | 36.327 | 1.116 | 40.590 | |
KYCG_plotMetaEnrichment | 19.689 | 0.701 | 22.759 | |
KYCG_plotPointRange | 4.466 | 0.235 | 5.276 | |
KYCG_plotSetEnrichment | 10.388 | 0.533 | 12.405 | |
KYCG_plotVolcano | 0.341 | 0.004 | 0.368 | |
KYCG_plotWaterfall | 5.605 | 0.235 | 6.423 | |
MValueToBetaValue | 0 | 0 | 0 | |
SigDF | 0.587 | 0.070 | 0.776 | |
addMask | 0.163 | 0.001 | 0.175 | |
aggregateTestEnrichments | 3.911 | 0.165 | 4.446 | |
betasCollapseToPfx | 0.029 | 0.001 | 0.030 | |
bisConversionControl | 7.627 | 0.278 | 8.734 | |
calcEffectSize | 2.818 | 0.174 | 3.340 | |
checkLevels | 4.653 | 0.315 | 5.432 | |
cnSegmentation | 0.591 | 0.102 | 0.871 | |
compareMouseStrainReference | 32.177 | 0.913 | 36.571 | |
compareMouseTissueReference | 0.000 | 0.001 | 0.001 | |
compareReference | 29.335 | 0.771 | 33.112 | |
controls | 3.803 | 0.306 | 4.606 | |
createUCSCtrack | 10.328 | 0.442 | 11.932 | |
dbStats | 10.645 | 0.917 | 13.021 | |
deidentify | 14.890 | 0.457 | 17.106 | |
detectionPnegEcdf | 5.101 | 0.189 | 5.826 | |
diffRefSet | 24.932 | 0.879 | 28.634 | |
dmContrasts | 3.311 | 0.247 | 4.099 | |
dyeBiasCorr | 4.888 | 0.298 | 5.848 | |
dyeBiasCorrMostBalanced | 9.787 | 0.365 | 11.413 | |
dyeBiasL | 4.157 | 0.216 | 4.793 | |
dyeBiasNL | 8.707 | 0.534 | 10.091 | |
estimateLeukocyte | 12.317 | 0.631 | 14.841 | |
formatVCF | 3.796 | 0.364 | 5.204 | |
getAFTypeIbySumAlleles | 3.080 | 0.292 | 3.987 | |
getAFs | 1.895 | 0.155 | 2.369 | |
getBetas | 1.478 | 0.141 | 1.950 | |
getMask | 11.614 | 0.750 | 14.213 | |
getRefSet | 19.495 | 0.675 | 22.965 | |
imputeBetas | 29.700 | 1.737 | 35.822 | |
imputeBetasByGenomicNeighbors | 62.327 | 1.588 | 71.951 | |
imputeBetasMatrixByMean | 0.002 | 0.001 | 0.005 | |
inferEthnicity | 0.001 | 0.000 | 0.001 | |
inferInfiniumIChannel | 0.901 | 1.427 | 2.567 | |
inferSex | 38.345 | 1.220 | 43.061 | |
inferSpecies | 21.270 | 1.002 | 24.522 | |
inferStrain | 13.861 | 0.858 | 16.471 | |
inferTissue | 12.868 | 1.396 | 15.630 | |
initFileSet | 2.409 | 0.321 | 3.022 | |
listAvailableMasks | 2.497 | 0.245 | 3.011 | |
mLiftOver | 0.001 | 0.003 | 0.004 | |
mapFileSet | 0.061 | 0.005 | 0.076 | |
mapToMammal40 | 5.149 | 0.544 | 6.325 | |
matchDesign | 22.534 | 1.110 | 25.584 | |
meanIntensity | 4.693 | 0.608 | 6.110 | |
medianTotalIntensity | 1.340 | 0.118 | 1.663 | |
noMasked | 6.038 | 0.303 | 7.215 | |
noob | 3.612 | 0.748 | 4.768 | |
openSesame | 9.605 | 0.705 | 11.118 | |
openSesameToFile | 2.906 | 0.037 | 3.160 | |
pOOBAH | 2.241 | 0.024 | 2.495 | |
palgen | 0.074 | 0.013 | 0.100 | |
parseGEOsignalMU | 5.247 | 0.527 | 6.327 | |
predictAge | 4.097 | 0.176 | 4.716 | |
predictAgeHorvath353 | 0.001 | 0.000 | 0.000 | |
predictAgeSkinBlood | 0.000 | 0.000 | 0.001 | |
predictMouseAgeInMonth | 0.000 | 0.001 | 0.000 | |
prefixMask | 1.285 | 0.009 | 1.623 | |
prefixMaskButC | 0.362 | 0.003 | 0.419 | |
prefixMaskButCG | 0.150 | 0.001 | 0.155 | |
prepSesame | 7.199 | 0.459 | 8.607 | |
prepSesameList | 0.003 | 0.002 | 0.005 | |
print.DMLSummary | 4.500 | 1.097 | 6.186 | |
print.fileSet | 2.304 | 0.323 | 2.920 | |
probeID_designType | 0.000 | 0.001 | 0.002 | |
probeSuccessRate | 9.622 | 0.768 | 11.768 | |
qualityMask | 4.150 | 0.540 | 5.547 | |
reIdentify | 12.623 | 0.325 | 13.894 | |
readFileSet | 0.095 | 0.011 | 0.115 | |
readIDATpair | 0.244 | 0.003 | 0.266 | |
recommendedMaskNames | 0.000 | 0.001 | 0.001 | |
resetMask | 0.767 | 0.088 | 0.984 | |
scrub | 3.676 | 0.046 | 4.051 | |
scrubSoft | 5.346 | 1.267 | 7.171 | |
sdfPlatform | 0.613 | 0.110 | 0.845 | |
sdf_read_table | 16.723 | 0.718 | 19.384 | |
sdf_write_table | 5.753 | 0.326 | 6.734 | |
searchIDATprefixes | 0.007 | 0.005 | 0.012 | |
sesame-package | 4.555 | 0.593 | 5.733 | |
sesameAnno_buildAddressFile | 0.000 | 0.000 | 0.001 | |
sesameAnno_buildManifestGRanges | 0.000 | 0.001 | 0.001 | |
sesameAnno_download | 0.000 | 0.001 | 0.001 | |
sesameAnno_get | 0.001 | 0.000 | 0.002 | |
sesameAnno_readManifestTSV | 0.000 | 0.001 | 0.001 | |
sesameData_getAnno | 0.000 | 0.000 | 0.001 | |
sesameQC_calcStats | 36.948 | 1.973 | 42.620 | |
sesameQC_getStats | 3.768 | 0.425 | 4.597 | |
sesameQC_plotBar | 19.715 | 0.565 | 25.754 | |
sesameQC_plotBetaByDesign | 15.261 | 1.204 | 16.946 | |
sesameQC_plotHeatSNPs | 32.085 | 1.977 | 37.663 | |
sesameQC_plotIntensVsBetas | 3.351 | 0.412 | 4.208 | |
sesameQC_plotRedGrnQQ | 2.047 | 0.243 | 2.476 | |
sesameQC_rankStats | 5.917 | 0.579 | 8.434 | |
sesameQCtoDF | 3.436 | 0.017 | 3.565 | |
sesame_checkVersion | 0.006 | 0.002 | 0.007 | |
sesamize | 0.000 | 0.000 | 0.001 | |
setMask | 0.170 | 0.001 | 0.178 | |
signalMU | 1.644 | 0.262 | 2.039 | |
sliceFileSet | 0.060 | 0.008 | 0.072 | |
summaryExtractTest | 4.444 | 0.869 | 5.957 | |
testEnrichment | 9.218 | 0.995 | 11.174 | |
testEnrichmentGene | 73.294 | 4.330 | 83.506 | |
testEnrichmentSEA | 18.401 | 1.225 | 21.612 | |
totalIntensities | 7.892 | 0.584 | 9.599 | |
updateSigDF | 5.233 | 0.399 | 6.509 | |
visualizeGene | 17.382 | 0.734 | 21.436 | |
visualizeProbes | 2.414 | 0.012 | 2.728 | |
visualizeRegion | 4.307 | 0.069 | 4.908 | |
visualizeSegments | 2.435 | 0.739 | 4.005 | |