Pan Du
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/lumi |
| Branch: master |
| Last Commit: fe6ee8a |
| Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:25:15 -0400 (Tue, 09 Apr 2019).
| Package 878/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| lumi 2.35.0 Pan Du
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: lumi |
| Version: 2.35.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings lumi_2.35.0.tar.gz |
| StartedAt: 2019-04-09 01:37:54 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:45:15 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 441.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: lumi.Rcheck |
| Warnings: 3 |
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### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings lumi_2.35.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/lumi.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘2.35.0’
* 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 47.096 0.028 47.170
MAplot-methods 5.878 0.008 5.951
getChipInfo 5.600 0.200 5.956
nuID2targetID 5.125 0.004 5.130
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/lumi.Rcheck/00check.log’
for details.
lumi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL lumi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘lumi’ ... ** using staged installation ** 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 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 (lumi)
lumi.Rcheck/lumi-Ex.timings
| name | user | system | elapsed | |
| LumiBatch-class | 1.549 | 0.040 | 1.600 | |
| MAplot-methods | 5.878 | 0.008 | 5.951 | |
| addAnnotationInfo | 0.083 | 0.000 | 0.084 | |
| addControlData2lumi | 0 | 0 | 0 | |
| addNuID2lumi | 0 | 0 | 0 | |
| adjColorBias.quantile | 1.839 | 0.012 | 1.865 | |
| adjColorBias.ssn | 0.463 | 0.012 | 0.480 | |
| bgAdjust | 0.102 | 0.000 | 0.103 | |
| bgAdjustMethylation | 0.192 | 0.004 | 0.196 | |
| boxplot-MethyLumiM-methods | 0.642 | 0.000 | 0.642 | |
| boxplot-methods | 0.123 | 0.000 | 0.123 | |
| boxplotColorBias | 0.184 | 0.000 | 0.184 | |
| density-methods | 0.12 | 0.00 | 0.12 | |
| detectOutlier | 0.109 | 0.004 | 0.113 | |
| detectionCall | 0.206 | 0.000 | 0.206 | |
| estimateBeta | 0.198 | 0.000 | 0.198 | |
| estimateIntensity | 0.252 | 0.000 | 0.252 | |
| estimateLumiCV | 0.134 | 0.004 | 0.138 | |
| estimateM | 0.605 | 0.000 | 0.605 | |
| estimateMethylationBG | 0.178 | 0.000 | 0.178 | |
| example.lumi | 0.106 | 0.004 | 0.109 | |
| example.lumiMethy | 0.085 | 0.000 | 0.086 | |
| example.methyTitration | 0.274 | 0.007 | 0.280 | |
| gammaFitEM | 3.256 | 0.008 | 3.278 | |
| getChipInfo | 5.600 | 0.200 | 5.956 | |
| getControlData | 0.002 | 0.000 | 0.001 | |
| getControlProbe | 0.002 | 0.000 | 0.001 | |
| getControlType | 0.001 | 0.000 | 0.001 | |
| getNuIDMappingInfo | 2.493 | 0.020 | 2.577 | |
| hist-methods | 0.155 | 0.000 | 0.157 | |
| id2seq | 0.001 | 0.000 | 0.001 | |
| inverseVST | 0.496 | 0.000 | 0.507 | |
| is.nuID | 0.001 | 0.000 | 0.001 | |
| lumiB | 0.131 | 0.000 | 0.131 | |
| lumiExpresso | 0.338 | 0.012 | 0.354 | |
| lumiMethyB | 0.078 | 0.004 | 0.083 | |
| lumiMethyC | 1.202 | 0.004 | 1.206 | |
| lumiMethyN | 0.120 | 0.000 | 0.122 | |
| lumiMethyStatus | 47.096 | 0.028 | 47.170 | |
| lumiN | 0.523 | 0.008 | 0.531 | |
| lumiQ | 0.369 | 0.000 | 0.369 | |
| lumiR | 0 | 0 | 0 | |
| lumiR.batch | 0 | 0 | 0 | |
| lumiT | 0.490 | 0.008 | 0.499 | |
| methylationCall | 2.505 | 0.004 | 2.509 | |
| normalizeMethylation.quantile | 0.130 | 0.004 | 0.135 | |
| normalizeMethylation.ssn | 0.134 | 0.000 | 0.135 | |
| nuID2EntrezID | 0.628 | 0.012 | 0.640 | |
| nuID2IlluminaID | 3.917 | 0.008 | 3.926 | |
| nuID2RefSeqID | 0.798 | 0.000 | 0.798 | |
| nuID2probeID | 4.008 | 0.004 | 4.011 | |
| nuID2targetID | 5.125 | 0.004 | 5.130 | |
| pairs-methods | 0.762 | 0.008 | 0.769 | |
| plot-methods | 1.861 | 0.008 | 1.869 | |
| plotCDF | 0.135 | 0.000 | 0.136 | |
| plotColorBias1D | 0.177 | 0.000 | 0.178 | |
| plotColorBias2D | 0.163 | 0.004 | 0.166 | |
| plotControlData | 0.001 | 0.000 | 0.001 | |
| plotDensity | 0.100 | 0.008 | 0.107 | |
| plotGammaFit | 2.878 | 0.000 | 2.879 | |
| plotHousekeepingGene | 0.001 | 0.000 | 0.001 | |
| plotSampleRelation | 0.652 | 0.000 | 0.655 | |
| plotStringencyGene | 0.001 | 0.000 | 0.001 | |
| plotVST | 0.430 | 0.012 | 0.446 | |
| probeID2nuID | 3.780 | 0.004 | 3.785 | |
| produceGEOPlatformFile | 0 | 0 | 0 | |
| produceGEOSubmissionFile | 0.000 | 0.000 | 0.001 | |
| produceMethylationGEOSubmissionFile | 0 | 0 | 0 | |
| seq2id | 0 | 0 | 0 | |
| targetID2nuID | 3.253 | 0.008 | 3.261 | |
| vst | 0.229 | 0.000 | 0.230 | |