Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:59:35 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE sesame PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1638/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
sesame 1.6.0 Wanding Zhou
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK |
Package: sesame |
Version: 1.6.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sesame.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sesame_1.6.0.tar.gz |
StartedAt: 2020-10-17 05:16:07 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 05:32:46 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 998.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sesame.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sesame.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sesame_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/sesame.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.6.0’ * 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 R 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 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 cnSegmentation 72.039 3.013 75.164 RGChannelSetToSigSets 35.137 2.116 40.060 as.data.frame.sesameQC 18.548 0.534 19.102 diffRefSet 17.523 0.260 17.818 dyeBiasCorrMostBalanced 16.287 0.224 16.528 DMR 13.541 0.265 13.815 SigSetToRatioSet 11.271 0.188 11.473 sesameQC 10.564 0.357 11.003 SigSetsToRGChannelSet 10.271 0.231 10.516 print.sesameQC 10.079 0.400 10.502 DML 9.023 0.777 9.808 SNPcheck 8.293 0.188 8.501 topLoci 6.557 1.246 7.853 topSegments 5.919 0.528 6.464 getBetas 5.717 0.015 5.736 getSegment 5.561 0.168 5.778 openSesame 5.468 0.207 5.709 detectionPoobEcdf 5.146 0.049 5.200 noobsb 4.938 0.110 5.051 estimateLeukocyte 4.852 0.148 5.034 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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/Versions/Current/Resources/bin/R CMD INSTALL sesame ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) 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: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, 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, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: AnnotationHub Loading required package: BiocFileCache Loading required package: dbplyr Loading sesameData. > > test_check("sesame") ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 19 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ] > > proc.time() user system elapsed 109.504 8.735 111.067
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0.000 | 0.001 | 0.000 | |
DML | 9.023 | 0.777 | 9.808 | |
DMR | 13.541 | 0.265 | 13.815 | |
IG-methods | 4.327 | 0.147 | 4.478 | |
IG-replace-methods | 0.002 | 0.001 | 0.003 | |
II-methods | 0.001 | 0.001 | 0.002 | |
II-replace-methods | 0.007 | 0.004 | 0.011 | |
IR-methods | 0.001 | 0.001 | 0.001 | |
IR-replace-methods | 0.002 | 0.001 | 0.003 | |
MValueToBetaValue | 0.001 | 0.000 | 0.001 | |
RGChannelSetToSigSets | 35.137 | 2.116 | 40.060 | |
SNPcheck | 8.293 | 0.188 | 8.501 | |
SigSet-class | 0.005 | 0.002 | 0.007 | |
SigSetList-methods | 3.090 | 0.073 | 3.170 | |
SigSetList | 0.599 | 0.015 | 0.615 | |
SigSetListFromIDATs | 0.226 | 0.004 | 0.230 | |
SigSetListFromPath | 0.634 | 0.020 | 0.654 | |
SigSetToRatioSet | 11.271 | 0.188 | 11.473 | |
SigSetsToRGChannelSet | 10.271 | 0.231 | 10.516 | |
as.data.frame.sesameQC | 18.548 | 0.534 | 19.102 | |
bisConversionControl | 2.986 | 0.178 | 3.170 | |
buildControlMatrix450k | 2.787 | 0.061 | 2.851 | |
cnSegmentation | 72.039 | 3.013 | 75.164 | |
ctl-methods | 0.002 | 0.001 | 0.003 | |
ctl-replace-methods | 0.001 | 0.001 | 0.001 | |
detectionPfixedNorm | 2.623 | 0.062 | 2.686 | |
detectionPnegEcdf | 4.484 | 0.048 | 4.539 | |
detectionPnegNorm | 3.045 | 0.062 | 3.108 | |
detectionPnegNormGS | 2.860 | 0.028 | 2.891 | |
detectionPnegNormTotal | 3.264 | 0.227 | 3.493 | |
detectionPoobEcdf | 5.146 | 0.049 | 5.200 | |
detectionZero | 2.648 | 0.027 | 2.677 | |
diffRefSet | 17.523 | 0.260 | 17.818 | |
dyeBiasCorr | 0.197 | 0.001 | 0.199 | |
dyeBiasCorrMostBalanced | 16.287 | 0.224 | 16.528 | |
dyeBiasCorrTypeINorm | 2.049 | 0.097 | 2.147 | |
estimateLeukocyte | 4.852 | 0.148 | 5.034 | |
getAFTypeIbySumAlleles | 0.063 | 0.000 | 0.064 | |
getBetas | 5.717 | 0.015 | 5.736 | |
getNormCtls | 0.222 | 0.006 | 0.227 | |
getProbesByGene | 3.386 | 0.056 | 3.455 | |
getProbesByRegion | 0.104 | 0.001 | 0.105 | |
getProbesByTSS | 0.355 | 0.006 | 0.362 | |
getRefSet | 3.687 | 0.093 | 3.786 | |
getSegment | 5.561 | 0.168 | 5.778 | |
getSexInfo | 3.889 | 0.078 | 3.971 | |
inferEthnicity | 2.668 | 0.083 | 2.754 | |
inferSex | 1.351 | 0.007 | 1.358 | |
inferSexKaryotypes | 2.310 | 0.133 | 2.447 | |
inferTypeIChannel | 0.058 | 0.001 | 0.058 | |
initFileSet | 0.064 | 0.004 | 0.069 | |
makeExampleSeSAMeDataSet | 2.641 | 0.012 | 2.666 | |
makeExampleTinyEPICDataSet | 0.010 | 0.001 | 0.011 | |
mapFileSet | 0.072 | 0.004 | 0.077 | |
meanIntensity | 2.752 | 0.112 | 2.866 | |
noob | 0.013 | 0.001 | 0.013 | |
noobsb | 4.938 | 0.110 | 5.051 | |
oobG-methods | 0.001 | 0.000 | 0.001 | |
oobG-replace-methods | 0.002 | 0.000 | 0.002 | |
oobR-methods | 0 | 0 | 0 | |
oobR-replace-methods | 0.001 | 0.000 | 0.002 | |
openSesame | 5.468 | 0.207 | 5.709 | |
openSesameToFile | 3.073 | 0.088 | 3.184 | |
parseGEOSignalABFile | 1.416 | 0.766 | 1.334 | |
predictAgeHorvath353 | 0.183 | 0.053 | 0.237 | |
predictAgePheno | 0.208 | 0.011 | 0.219 | |
predictAgeSkinBlood | 0.206 | 0.008 | 0.214 | |
print.fileSet | 0.053 | 0.004 | 0.057 | |
print.sesameQC | 10.079 | 0.400 | 10.502 | |
probeNames-methods | 0.051 | 0.001 | 0.052 | |
pval-methods | 0.001 | 0.000 | 0.002 | |
pval-replace-methods | 0.002 | 0.001 | 0.004 | |
readFileSet | 0.109 | 0.005 | 0.114 | |
readIDATpair | 0.329 | 0.026 | 0.357 | |
searchIDATprefixes | 0.006 | 0.003 | 0.011 | |
sesame-package | 1.295 | 0.117 | 1.418 | |
sesameQC | 10.564 | 0.357 | 11.003 | |
show-methods | 0.002 | 0.002 | 0.004 | |
sliceFileSet | 0.074 | 0.006 | 0.082 | |
subsetSignal | 0.188 | 0.006 | 0.194 | |
topLoci | 6.557 | 1.246 | 7.853 | |
topSegments | 5.919 | 0.528 | 6.464 | |
totalIntensities | 2.790 | 0.081 | 2.874 | |
totalIntensityZscore | 2.497 | 0.009 | 2.507 | |
visualizeGene | 1.172 | 0.020 | 1.194 | |
visualizeProbes | 1.638 | 0.041 | 1.680 | |
visualizeRegion | 0.711 | 0.009 | 0.720 | |
visualizeSegments | 1.115 | 0.096 | 1.214 | |