Pan Du
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/lumi |
| Branch: RELEASE_3_8 |
| Last Commit: ff60f7d |
| Last Changed Date: 2018-10-30 11:41:43 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:54:35 -0400 (Tue, 16 Apr 2019).
| Package 854/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| lumi 2.34.0 Pan Du
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: lumi |
| Version: 2.34.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:lumi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings lumi_2.34.0.tar.gz |
| StartedAt: 2019-04-16 00:56:04 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:03:46 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 461.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: lumi.Rcheck |
| Warnings: 3 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:lumi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings lumi_2.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/lumi.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.34.0’
* 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 63.519 4.211 68.683
getChipInfo 4.955 0.263 5.272
nuID2IlluminaID 5.111 0.106 5.373
methylationCall 4.793 0.311 5.230
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs
See
‘/Users/biocbuild/bbs-3.8-bioc/meat/lumi.Rcheck/00check.log’
for details.
lumi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL lumi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘lumi’ ... ** R ** data ** 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 * DONE (lumi)
lumi.Rcheck/lumi-Ex.timings
| name | user | system | elapsed | |
| LumiBatch-class | 1.690 | 0.136 | 1.862 | |
| MAplot-methods | 4.355 | 0.078 | 4.458 | |
| addAnnotationInfo | 0.062 | 0.005 | 0.070 | |
| addControlData2lumi | 0 | 0 | 0 | |
| addNuID2lumi | 0.000 | 0.000 | 0.001 | |
| adjColorBias.quantile | 1.641 | 0.089 | 1.750 | |
| adjColorBias.ssn | 0.491 | 0.019 | 0.515 | |
| bgAdjust | 0.112 | 0.006 | 0.120 | |
| bgAdjustMethylation | 0.209 | 0.010 | 0.222 | |
| boxplot-MethyLumiM-methods | 0.574 | 0.022 | 0.602 | |
| boxplot-methods | 0.101 | 0.005 | 0.117 | |
| boxplotColorBias | 0.172 | 0.023 | 0.196 | |
| density-methods | 0.133 | 0.010 | 0.147 | |
| detectOutlier | 0.101 | 0.007 | 0.111 | |
| detectionCall | 0.145 | 0.009 | 0.157 | |
| estimateBeta | 0.932 | 0.013 | 0.952 | |
| estimateIntensity | 0.224 | 0.011 | 0.236 | |
| estimateLumiCV | 0.132 | 0.007 | 0.139 | |
| estimateM | 0.606 | 0.023 | 0.631 | |
| estimateMethylationBG | 0.181 | 0.013 | 0.194 | |
| example.lumi | 0.098 | 0.005 | 0.104 | |
| example.lumiMethy | 0.077 | 0.002 | 0.081 | |
| example.methyTitration | 0.221 | 0.010 | 0.233 | |
| gammaFitEM | 3.228 | 0.306 | 3.561 | |
| getChipInfo | 4.955 | 0.263 | 5.272 | |
| getControlData | 0.002 | 0.000 | 0.003 | |
| getControlProbe | 0.002 | 0.001 | 0.001 | |
| getControlType | 0.001 | 0.000 | 0.001 | |
| getNuIDMappingInfo | 1.365 | 0.064 | 1.450 | |
| hist-methods | 0.124 | 0.006 | 0.130 | |
| id2seq | 0.001 | 0.000 | 0.001 | |
| inverseVST | 0.427 | 0.011 | 0.440 | |
| is.nuID | 0.001 | 0.000 | 0.000 | |
| lumiB | 0.104 | 0.005 | 0.108 | |
| lumiExpresso | 0.298 | 0.014 | 0.313 | |
| lumiMethyB | 0.068 | 0.005 | 0.073 | |
| lumiMethyC | 1.198 | 0.034 | 1.238 | |
| lumiMethyN | 0.094 | 0.003 | 0.099 | |
| lumiMethyStatus | 63.519 | 4.211 | 68.683 | |
| lumiN | 0.544 | 0.025 | 0.573 | |
| lumiQ | 0.371 | 0.019 | 0.443 | |
| lumiR | 0 | 0 | 0 | |
| lumiR.batch | 0 | 0 | 0 | |
| lumiT | 0.323 | 0.014 | 0.345 | |
| methylationCall | 4.793 | 0.311 | 5.230 | |
| normalizeMethylation.quantile | 0.215 | 0.013 | 0.228 | |
| normalizeMethylation.ssn | 0.227 | 0.009 | 0.243 | |
| nuID2EntrezID | 1.409 | 0.035 | 1.559 | |
| nuID2IlluminaID | 5.111 | 0.106 | 5.373 | |
| nuID2RefSeqID | 1.611 | 0.038 | 1.684 | |
| nuID2probeID | 4.112 | 0.072 | 4.219 | |
| nuID2targetID | 3.510 | 0.057 | 3.588 | |
| pairs-methods | 0.762 | 0.050 | 0.822 | |
| plot-methods | 2.369 | 0.036 | 2.426 | |
| plotCDF | 0.125 | 0.008 | 0.132 | |
| plotColorBias1D | 0.268 | 0.008 | 0.277 | |
| plotColorBias2D | 0.250 | 0.006 | 0.258 | |
| plotControlData | 0.002 | 0.000 | 0.002 | |
| plotDensity | 0.122 | 0.006 | 0.129 | |
| plotGammaFit | 4.558 | 0.199 | 4.785 | |
| plotHousekeepingGene | 0.001 | 0.000 | 0.001 | |
| plotSampleRelation | 1.766 | 0.016 | 1.796 | |
| plotStringencyGene | 0.001 | 0.000 | 0.002 | |
| plotVST | 0.354 | 0.016 | 0.372 | |
| probeID2nuID | 3.973 | 0.060 | 4.078 | |
| produceGEOPlatformFile | 0.000 | 0.000 | 0.001 | |
| produceGEOSubmissionFile | 0.001 | 0.001 | 0.000 | |
| produceMethylationGEOSubmissionFile | 0.001 | 0.000 | 0.000 | |
| seq2id | 0 | 0 | 0 | |
| targetID2nuID | 4.086 | 0.074 | 4.201 | |
| vst | 0.261 | 0.011 | 0.271 | |