Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:13 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 |
To the developers/maintainers of the lumi package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/lumi.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1065/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
lumi 2.50.0 (landing page) Lei Huang
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: lumi |
Version: 2.50.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:lumi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings lumi_2.50.0.tar.gz |
StartedAt: 2023-04-10 20:57:05 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 21:03:48 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 403.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: lumi.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:lumi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings lumi_2.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/lumi.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘lumi/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘lumi’ version ‘2.50.0’ * 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 ‘lumi’ can be installed ... OK * checking installed package size ... OK * checking package 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 ... WARNING '::' or ':::' imports not declared from: ‘IRanges’ ‘bigmemoryExtras’ * 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 ... WARNING Unknown package ‘bigmemoryExtras’ in Rd xrefs Missing link or links in documentation object 'lumiN.Rd': ‘[vsn]{vsn}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘IlluminaAnnotation.R’, ‘IlluminaAnnotation.pdf’, ‘lumi.R’, ‘lumi.pdf’, ‘lumi_VST_evaluation.R’, ‘lumi_VST_evaluation.pdf’, ‘methylationAnalysis.R’, ‘methylationAnalysis.pdf’ Package has no Sweave vignette sources and no VignetteBuilder field. * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed lumiMethyStatus 40.165 11.846 52.311 * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs See ‘/Users/biocbuild/bbs-3.16-bioc/meat/lumi.Rcheck/00check.log’ for details.
lumi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL lumi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘lumi’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** testing if installed package can be loaded from final location No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** testing if installed package keeps a record of temporary installation path * DONE (lumi)
lumi.Rcheck/lumi-Ex.timings
name | user | system | elapsed | |
LumiBatch-class | 0.968 | 0.075 | 1.054 | |
MAplot-methods | 4.600 | 0.057 | 4.670 | |
addAnnotationInfo | 0.038 | 0.003 | 0.040 | |
addControlData2lumi | 0.000 | 0.001 | 0.000 | |
addNuID2lumi | 0 | 0 | 0 | |
adjColorBias.quantile | 0.559 | 0.100 | 0.662 | |
adjColorBias.ssn | 1.172 | 0.032 | 1.206 | |
bgAdjust | 0.067 | 0.003 | 0.069 | |
bgAdjustMethylation | 0.113 | 0.008 | 0.122 | |
boxplot-MethyLumiM-methods | 0.375 | 0.017 | 0.394 | |
boxplot-methods | 0.070 | 0.003 | 0.074 | |
boxplotColorBias | 0.094 | 0.008 | 0.103 | |
density-methods | 0.071 | 0.003 | 0.074 | |
detectOutlier | 0.084 | 0.015 | 0.100 | |
detectionCall | 0.117 | 0.004 | 0.122 | |
estimateBeta | 0.130 | 0.005 | 0.137 | |
estimateIntensity | 0.135 | 0.004 | 0.139 | |
estimateLumiCV | 0.086 | 0.004 | 0.090 | |
estimateM | 0.326 | 0.020 | 0.346 | |
estimateMethylationBG | 0.087 | 0.004 | 0.090 | |
example.lumi | 0.056 | 0.002 | 0.058 | |
example.lumiMethy | 0.038 | 0.003 | 0.041 | |
example.methyTitration | 0.138 | 0.004 | 0.141 | |
gammaFitEM | 2.090 | 0.658 | 2.765 | |
getChipInfo | 3.908 | 0.212 | 4.173 | |
getControlData | 0.000 | 0.001 | 0.001 | |
getControlProbe | 0.001 | 0.000 | 0.001 | |
getControlType | 0.001 | 0.000 | 0.001 | |
getNuIDMappingInfo | 0.863 | 0.054 | 0.919 | |
hist-methods | 0.109 | 0.004 | 0.113 | |
id2seq | 0.000 | 0.000 | 0.001 | |
inverseVST | 0.449 | 0.017 | 0.468 | |
is.nuID | 0 | 0 | 0 | |
lumiB | 0.083 | 0.001 | 0.086 | |
lumiExpresso | 0.257 | 0.022 | 0.279 | |
lumiMethyB | 0.052 | 0.002 | 0.055 | |
lumiMethyC | 0.800 | 0.092 | 0.897 | |
lumiMethyN | 0.062 | 0.003 | 0.065 | |
lumiMethyStatus | 40.165 | 11.846 | 52.311 | |
lumiN | 0.342 | 0.027 | 0.370 | |
lumiQ | 0.234 | 0.010 | 0.245 | |
lumiR | 0 | 0 | 0 | |
lumiR.batch | 0 | 0 | 0 | |
lumiT | 0.272 | 0.011 | 0.285 | |
methylationCall | 2.152 | 0.630 | 2.798 | |
normalizeMethylation.quantile | 0.157 | 0.038 | 0.196 | |
normalizeMethylation.ssn | 0.098 | 0.002 | 0.100 | |
nuID2EntrezID | 0.664 | 0.021 | 0.686 | |
nuID2IlluminaID | 3.512 | 0.056 | 3.575 | |
nuID2RefSeqID | 1.080 | 0.048 | 1.132 | |
nuID2probeID | 3.183 | 0.027 | 3.215 | |
nuID2targetID | 3.296 | 0.057 | 3.362 | |
pairs-methods | 0.681 | 0.075 | 0.759 | |
plot-methods | 1.667 | 0.061 | 1.737 | |
plotCDF | 0.110 | 0.004 | 0.115 | |
plotColorBias1D | 0.166 | 0.005 | 0.172 | |
plotColorBias2D | 0.204 | 0.023 | 0.227 | |
plotControlData | 0.000 | 0.000 | 0.001 | |
plotDensity | 0.108 | 0.003 | 0.111 | |
plotGammaFit | 4.201 | 0.591 | 4.810 | |
plotHousekeepingGene | 0.000 | 0.000 | 0.002 | |
plotSampleRelation | 0.378 | 0.033 | 0.412 | |
plotStringencyGene | 0.001 | 0.000 | 0.002 | |
plotVST | 0.263 | 0.014 | 0.279 | |
probeID2nuID | 3.152 | 0.046 | 3.205 | |
produceGEOPlatformFile | 0 | 0 | 0 | |
produceGEOSubmissionFile | 0.001 | 0.000 | 0.000 | |
produceMethylationGEOSubmissionFile | 0 | 0 | 0 | |
seq2id | 0.001 | 0.000 | 0.001 | |
targetID2nuID | 3.231 | 0.069 | 3.304 | |
vst | 0.132 | 0.004 | 0.137 | |