Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:03:15 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 1952/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sesame 1.22.1 (landing page) Wanding Zhou
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 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: 1.22.1 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings sesame_1.22.1.tar.gz |
StartedAt: 2024-05-31 08:11:24 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 08:33:22 -0400 (Fri, 31 May 2024) |
EllapsedTime: 1318.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sesame.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings sesame_1.22.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.22.1’ * 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 testEnrichmentGene 102.525 7.593 113.479 imputeBetasByGenomicNeighbors 32.758 1.520 34.751 KYCG_plotMeta 23.297 1.659 25.439 KYCG_plotEnrichAll 21.090 2.296 24.542 inferSex 21.605 1.123 23.043 imputeBetas 18.710 1.572 20.796 sesameQC_calcStats 18.680 1.188 20.025 inferSpecies 16.250 2.016 18.805 ELBAR 16.629 1.072 17.877 KYCG_annoProbes 15.435 1.408 17.379 sesameQC_plotHeatSNPs 16.288 0.528 16.974 diffRefSet 13.392 1.308 15.016 compareMouseStrainReference 11.693 1.065 13.116 matchDesign 11.497 0.907 12.562 compareReference 11.199 1.179 12.694 getRefSet 11.511 0.784 12.651 KYCG_buildGeneDBs 11.168 0.896 12.382 KYCG_plotMetaEnrichment 10.688 1.036 12.200 sesameQC_plotBar 10.816 0.400 11.671 testEnrichmentSEA 9.908 0.969 11.390 visualizeGene 8.889 0.844 10.242 DMR 8.865 0.588 9.811 sesameQC_plotBetaByDesign 9.053 0.352 9.405 sdf_read_table 8.629 0.524 9.491 estimateLeukocyte 7.915 0.804 9.037 inferStrain 7.301 0.651 8.267 inferTissue 6.897 0.952 8.179 dbStats 6.893 0.800 8.072 getMask 6.516 0.708 7.857 DML 6.692 0.381 7.438 dyeBiasNL 6.058 0.544 6.760 updateSigDF 5.780 0.808 6.907 createUCSCtrack 6.080 0.420 6.815 deidentify 5.809 0.528 6.705 dyeBiasCorrMostBalanced 5.892 0.408 6.652 testEnrichment 5.273 0.799 6.546 KYCG_plotSetEnrichment 5.298 0.471 6.092 probeSuccessRate 5.040 0.439 5.985 openSesame 4.837 0.395 5.600 bisConversionControl 4.384 0.376 5.120 * 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-3.19-bioc/R/bin/R CMD INSTALL sesame ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 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 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 19.388 0.963 20.656
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0 | 0 | 0 | |
DML | 6.692 | 0.381 | 7.438 | |
DMLpredict | 1.408 | 0.107 | 1.672 | |
DMR | 8.865 | 0.588 | 9.811 | |
ELBAR | 16.629 | 1.072 | 17.877 | |
KYCG_annoProbes | 15.435 | 1.408 | 17.379 | |
KYCG_buildGeneDBs | 11.168 | 0.896 | 12.382 | |
KYCG_getDBs | 3.159 | 0.428 | 3.908 | |
KYCG_listDBGroups | 0.037 | 0.000 | 0.037 | |
KYCG_loadDBs | 0 | 0 | 0 | |
KYCG_plotBar | 0.208 | 0.020 | 0.228 | |
KYCG_plotDot | 0.647 | 0.072 | 0.719 | |
KYCG_plotEnrichAll | 21.090 | 2.296 | 24.542 | |
KYCG_plotLollipop | 0.159 | 0.012 | 0.170 | |
KYCG_plotManhattan | 1.310 | 0.192 | 1.503 | |
KYCG_plotMeta | 23.297 | 1.659 | 25.439 | |
KYCG_plotMetaEnrichment | 10.688 | 1.036 | 12.200 | |
KYCG_plotPointRange | 2.223 | 0.168 | 2.590 | |
KYCG_plotSetEnrichment | 5.298 | 0.471 | 6.092 | |
KYCG_plotVolcano | 0.138 | 0.012 | 0.150 | |
KYCG_plotWaterfall | 2.642 | 0.261 | 3.074 | |
MValueToBetaValue | 0 | 0 | 0 | |
SigDF | 0.366 | 0.057 | 0.579 | |
addMask | 0.080 | 0.008 | 0.088 | |
aggregateTestEnrichments | 1.885 | 0.228 | 2.114 | |
betasCollapseToPfx | 0.017 | 0.000 | 0.016 | |
bisConversionControl | 4.384 | 0.376 | 5.120 | |
calcEffectSize | 1.327 | 0.156 | 1.640 | |
checkLevels | 3.363 | 0.632 | 4.155 | |
cnSegmentation | 0.373 | 0.068 | 0.601 | |
compareMouseStrainReference | 11.693 | 1.065 | 13.116 | |
compareMouseTissueReference | 0.000 | 0.000 | 0.001 | |
compareReference | 11.199 | 1.179 | 12.694 | |
controls | 2.247 | 0.228 | 2.789 | |
createUCSCtrack | 6.080 | 0.420 | 6.815 | |
dataFrame2sesameQC | 1.251 | 0.115 | 1.526 | |
dbStats | 6.893 | 0.800 | 8.072 | |
deidentify | 5.809 | 0.528 | 6.705 | |
detectionPnegEcdf | 2.936 | 0.207 | 3.316 | |
diffRefSet | 13.392 | 1.308 | 15.016 | |
dmContrasts | 2.254 | 0.376 | 2.789 | |
dyeBiasCorr | 2.956 | 0.278 | 3.547 | |
dyeBiasCorrMostBalanced | 5.892 | 0.408 | 6.652 | |
dyeBiasL | 2.835 | 0.572 | 3.565 | |
dyeBiasNL | 6.058 | 0.544 | 6.760 | |
estimateLeukocyte | 7.915 | 0.804 | 9.037 | |
formatVCF | 2.329 | 0.288 | 2.947 | |
getAFTypeIbySumAlleles | 1.841 | 0.247 | 2.455 | |
getAFs | 1.207 | 0.152 | 1.515 | |
getBetas | 0.901 | 0.100 | 1.158 | |
getMask | 6.516 | 0.708 | 7.857 | |
getRefSet | 11.511 | 0.784 | 12.651 | |
imputeBetas | 18.710 | 1.572 | 20.796 | |
imputeBetasByGenomicNeighbors | 32.758 | 1.520 | 34.751 | |
imputeBetasMatrixByMean | 0.001 | 0.000 | 0.002 | |
inferEthnicity | 0.001 | 0.000 | 0.001 | |
inferInfiniumIChannel | 0.348 | 0.564 | 0.912 | |
inferSex | 21.605 | 1.123 | 23.043 | |
inferSpecies | 16.250 | 2.016 | 18.805 | |
inferStrain | 7.301 | 0.651 | 8.267 | |
inferTissue | 6.897 | 0.952 | 8.179 | |
initFileSet | 1.214 | 0.128 | 1.500 | |
listAvailableMasks | 1.364 | 0.144 | 1.685 | |
mLiftOver | 0.001 | 0.000 | 0.001 | |
mapFileSet | 0.035 | 0.000 | 0.035 | |
mapToMammal40 | 2.722 | 0.301 | 3.338 | |
matchDesign | 11.497 | 0.907 | 12.562 | |
meanIntensity | 2.688 | 0.278 | 3.280 | |
medianTotalIntensity | 0.871 | 0.077 | 1.106 | |
noMasked | 3.301 | 0.295 | 3.912 | |
noob | 2.078 | 0.196 | 2.274 | |
openSesame | 4.837 | 0.395 | 5.600 | |
openSesameToFile | 1.37 | 0.06 | 1.43 | |
pOOBAH | 1.148 | 0.072 | 1.219 | |
palgen | 0.040 | 0.008 | 0.048 | |
parseGEOsignalMU | 3.066 | 0.184 | 3.447 | |
predictAge | 2.270 | 0.100 | 2.527 | |
predictAgeHorvath353 | 0.001 | 0.000 | 0.000 | |
predictAgeSkinBlood | 0 | 0 | 0 | |
predictMouseAgeInMonth | 0 | 0 | 0 | |
prefixMask | 0.390 | 0.004 | 0.393 | |
prefixMaskButC | 0.099 | 0.004 | 0.102 | |
prefixMaskButCG | 0.036 | 0.000 | 0.037 | |
prepSesame | 3.608 | 0.307 | 4.074 | |
prepSesameList | 0.001 | 0.001 | 0.001 | |
print.DMLSummary | 2.876 | 0.559 | 3.749 | |
print.fileSet | 1.265 | 0.096 | 1.518 | |
probeID_designType | 0 | 0 | 0 | |
probeSuccessRate | 5.040 | 0.439 | 5.985 | |
qualityMask | 2.222 | 0.252 | 2.789 | |
reIdentify | 4.007 | 0.396 | 4.562 | |
readFileSet | 0.047 | 0.008 | 0.054 | |
readIDATpair | 0.118 | 0.000 | 0.118 | |
recommendedMaskNames | 0.000 | 0.000 | 0.001 | |
resetMask | 0.390 | 0.076 | 0.623 | |
scrub | 2.195 | 0.276 | 2.472 | |
scrubSoft | 3.093 | 0.224 | 3.316 | |
sdfPlatform | 0.369 | 0.051 | 0.577 | |
sdf_read_table | 8.629 | 0.524 | 9.491 | |
sdf_write_table | 2.722 | 0.120 | 3.047 | |
searchIDATprefixes | 0.006 | 0.000 | 0.007 | |
sesame-package | 2.633 | 0.307 | 3.097 | |
sesameAnno_buildAddressFile | 0 | 0 | 0 | |
sesameAnno_buildManifestGRanges | 0.001 | 0.000 | 0.000 | |
sesameAnno_download | 0 | 0 | 0 | |
sesameAnno_get | 0.000 | 0.001 | 0.001 | |
sesameAnno_readManifestTSV | 0.000 | 0.001 | 0.000 | |
sesameData_getAnno | 0 | 0 | 0 | |
sesameQC_calcStats | 18.680 | 1.188 | 20.025 | |
sesameQC_getStats | 1.512 | 0.068 | 1.581 | |
sesameQC_plotBar | 10.816 | 0.400 | 11.671 | |
sesameQC_plotBetaByDesign | 9.053 | 0.352 | 9.405 | |
sesameQC_plotHeatSNPs | 16.288 | 0.528 | 16.974 | |
sesameQC_plotIntensVsBetas | 2.059 | 0.103 | 2.320 | |
sesameQC_plotRedGrnQQ | 2.146 | 0.081 | 2.382 | |
sesameQC_rankStats | 3.805 | 0.156 | 4.278 | |
sesame_checkVersion | 0.003 | 0.004 | 0.007 | |
sesamize | 0.000 | 0.000 | 0.001 | |
setMask | 0.166 | 0.002 | 0.167 | |
signalMU | 1.059 | 0.084 | 1.342 | |
sliceFileSet | 0.039 | 0.000 | 0.038 | |
summaryExtractTest | 2.784 | 0.561 | 3.660 | |
testEnrichment | 5.273 | 0.799 | 6.546 | |
testEnrichmentGene | 102.525 | 7.593 | 113.479 | |
testEnrichmentSEA | 9.908 | 0.969 | 11.390 | |
totalIntensities | 3.705 | 0.427 | 4.445 | |
updateSigDF | 5.780 | 0.808 | 6.907 | |
visualizeGene | 8.889 | 0.844 | 10.242 | |
visualizeProbes | 1.219 | 0.140 | 1.358 | |
visualizeRegion | 0.319 | 0.024 | 0.342 | |
visualizeSegments | 1.854 | 0.540 | 2.553 | |