Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:07:52 -0400 (Thu, 12 Apr 2018).
Package 763/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
lumi 2.30.0 Pan Du
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | ![]() |
Package: lumi |
Version: 2.30.0 |
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.30.0.tar.gz |
StartedAt: 2018-04-12 00:40:47 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 00:47:19 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 392.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: lumi.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/lumi.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-pc-linux-gnu (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 ‘2.30.0’ * 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 Package unavailable to check Rd xrefs: ‘hdrcde’ 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 or elapsed time > 5s user system elapsed lumiMethyStatus 62.792 0.008 62.841 plotGammaFit 5.700 0.000 5.702 getChipInfo 4.940 0.092 5.233 * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs See ‘/home/biocbuild/bbs-3.6-bioc/meat/lumi.Rcheck/00check.log’ for details.
lumi.Rcheck/00install.out
* installing *source* package ‘lumi’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (lumi)
lumi.Rcheck/lumi-Ex.timings
name | user | system | elapsed | |
LumiBatch-class | 1.584 | 0.012 | 1.596 | |
MAplot-methods | 4.592 | 0.020 | 4.614 | |
addAnnotationInfo | 0.056 | 0.000 | 0.054 | |
addControlData2lumi | 0 | 0 | 0 | |
addNuID2lumi | 0 | 0 | 0 | |
adjColorBias.quantile | 0.972 | 0.004 | 0.976 | |
adjColorBias.ssn | 0.440 | 0.012 | 0.454 | |
bgAdjust | 0.076 | 0.000 | 0.074 | |
bgAdjustMethylation | 0.66 | 0.00 | 0.66 | |
boxplot-MethyLumiM-methods | 0.500 | 0.000 | 0.498 | |
boxplot-methods | 0.588 | 0.004 | 0.590 | |
boxplotColorBias | 0.120 | 0.004 | 0.124 | |
density-methods | 0.088 | 0.000 | 0.089 | |
detectOutlier | 0.084 | 0.000 | 0.083 | |
detectionCall | 0.168 | 0.008 | 0.173 | |
estimateBeta | 0.148 | 0.000 | 0.149 | |
estimateIntensity | 0.192 | 0.000 | 0.190 | |
estimateLumiCV | 0.096 | 0.000 | 0.097 | |
estimateM | 0.980 | 0.008 | 0.992 | |
estimateMethylationBG | 0.128 | 0.000 | 0.131 | |
example.lumi | 0.072 | 0.000 | 0.074 | |
example.lumiMethy | 0.052 | 0.004 | 0.056 | |
example.methyTitration | 0.172 | 0.000 | 0.173 | |
gammaFitEM | 4.364 | 0.000 | 4.367 | |
getChipInfo | 4.940 | 0.092 | 5.233 | |
getControlData | 0.000 | 0.000 | 0.002 | |
getControlProbe | 0.004 | 0.000 | 0.001 | |
getControlType | 0.000 | 0.000 | 0.001 | |
getNuIDMappingInfo | 1.576 | 0.004 | 1.584 | |
hist-methods | 0.12 | 0.00 | 0.12 | |
id2seq | 0.004 | 0.000 | 0.001 | |
inverseVST | 0.604 | 0.016 | 0.623 | |
is.nuID | 0 | 0 | 0 | |
lumiB | 0.124 | 0.000 | 0.122 | |
lumiExpresso | 0.532 | 0.000 | 0.545 | |
lumiMethyB | 0.084 | 0.000 | 0.085 | |
lumiMethyC | 1.916 | 0.008 | 1.927 | |
lumiMethyN | 0.096 | 0.000 | 0.098 | |
lumiMethyStatus | 62.792 | 0.008 | 62.841 | |
lumiN | 0.504 | 0.008 | 0.517 | |
lumiQ | 0.280 | 0.004 | 0.287 | |
lumiR | 0 | 0 | 0 | |
lumiR.batch | 0 | 0 | 0 | |
lumiT | 0.844 | 0.004 | 0.850 | |
methylationCall | 3.400 | 0.000 | 3.399 | |
normalizeMethylation.quantile | 0.18 | 0.00 | 0.18 | |
normalizeMethylation.ssn | 0.688 | 0.004 | 0.691 | |
nuID2EntrezID | 1.044 | 0.000 | 1.046 | |
nuID2IlluminaID | 4.292 | 0.016 | 4.311 | |
nuID2RefSeqID | 1.164 | 0.004 | 1.171 | |
nuID2probeID | 3.292 | 0.016 | 3.308 | |
nuID2targetID | 3.808 | 0.000 | 3.807 | |
pairs-methods | 0.960 | 0.008 | 0.969 | |
plot-methods | 1.868 | 0.024 | 1.896 | |
plotCDF | 0.144 | 0.004 | 0.150 | |
plotColorBias1D | 0.264 | 0.000 | 0.263 | |
plotColorBias2D | 0.192 | 0.000 | 0.194 | |
plotControlData | 0.004 | 0.000 | 0.001 | |
plotDensity | 0.116 | 0.004 | 0.121 | |
plotGammaFit | 5.700 | 0.000 | 5.702 | |
plotHousekeepingGene | 0.000 | 0.000 | 0.001 | |
plotSampleRelation | 0.600 | 0.020 | 0.621 | |
plotStringencyGene | 0.004 | 0.000 | 0.001 | |
plotVST | 0.288 | 0.008 | 0.297 | |
probeID2nuID | 3.012 | 0.012 | 3.026 | |
produceGEOPlatformFile | 0 | 0 | 0 | |
produceGEOSubmissionFile | 0 | 0 | 0 | |
produceMethylationGEOSubmissionFile | 0.000 | 0.000 | 0.001 | |
seq2id | 0.000 | 0.000 | 0.001 | |
targetID2nuID | 3.340 | 0.000 | 3.346 | |
vst | 0.300 | 0.004 | 0.304 | |