Pan Du
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/lumi |
| Branch: RELEASE_3_7 |
| Last Commit: 051198b |
| Last Changed Date: 2018-04-30 10:35:06 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:21:54 -0400 (Wed, 17 Oct 2018).
| Package 806/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| lumi 2.32.0 Pan Du
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: lumi |
| Version: 2.32.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings lumi_2.32.0.tar.gz |
| StartedAt: 2018-10-16 01:34:02 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 01:39:39 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 337.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: lumi.Rcheck |
| Warnings: 3 |
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### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings lumi_2.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/lumi.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘2.32.0’
* 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 41.956 0.016 41.994
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/lumi.Rcheck/00check.log’
for details.
lumi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL lumi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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 | 1.028 | 0.060 | 1.091 | |
| MAplot-methods | 3.988 | 0.012 | 4.004 | |
| addAnnotationInfo | 0.06 | 0.00 | 0.07 | |
| addControlData2lumi | 0 | 0 | 0 | |
| addNuID2lumi | 0.000 | 0.000 | 0.001 | |
| adjColorBias.quantile | 1.392 | 0.000 | 1.393 | |
| adjColorBias.ssn | 0.396 | 0.000 | 0.395 | |
| bgAdjust | 0.076 | 0.000 | 0.076 | |
| bgAdjustMethylation | 0.148 | 0.004 | 0.153 | |
| boxplot-MethyLumiM-methods | 0.636 | 0.012 | 0.652 | |
| boxplot-methods | 0.136 | 0.000 | 0.138 | |
| boxplotColorBias | 0.176 | 0.000 | 0.175 | |
| density-methods | 0.792 | 0.004 | 0.798 | |
| detectOutlier | 0.080 | 0.004 | 0.085 | |
| detectionCall | 0.148 | 0.000 | 0.147 | |
| estimateBeta | 0.152 | 0.000 | 0.151 | |
| estimateIntensity | 0.164 | 0.000 | 0.165 | |
| estimateLumiCV | 0.092 | 0.000 | 0.095 | |
| estimateM | 0.416 | 0.004 | 0.421 | |
| estimateMethylationBG | 0.128 | 0.000 | 0.127 | |
| example.lumi | 0.080 | 0.000 | 0.079 | |
| example.lumiMethy | 0.056 | 0.000 | 0.058 | |
| example.methyTitration | 0.172 | 0.004 | 0.179 | |
| gammaFitEM | 3.296 | 0.000 | 3.315 | |
| getChipInfo | 3.512 | 0.072 | 3.758 | |
| getControlData | 0.004 | 0.000 | 0.001 | |
| getControlProbe | 0.000 | 0.000 | 0.001 | |
| getControlType | 0.000 | 0.000 | 0.001 | |
| getNuIDMappingInfo | 0.768 | 0.024 | 0.793 | |
| hist-methods | 0.112 | 0.000 | 0.111 | |
| id2seq | 0.000 | 0.000 | 0.001 | |
| inverseVST | 0.400 | 0.008 | 0.412 | |
| is.nuID | 0.000 | 0.000 | 0.001 | |
| lumiB | 0.084 | 0.004 | 0.091 | |
| lumiExpresso | 0.368 | 0.004 | 0.380 | |
| lumiMethyB | 0.056 | 0.000 | 0.055 | |
| lumiMethyC | 0.840 | 0.008 | 0.847 | |
| lumiMethyN | 0.084 | 0.004 | 0.096 | |
| lumiMethyStatus | 41.956 | 0.016 | 41.994 | |
| lumiN | 0.336 | 0.016 | 0.359 | |
| lumiQ | 0.252 | 0.004 | 0.254 | |
| lumiR | 0 | 0 | 0 | |
| lumiR.batch | 0.004 | 0.000 | 0.001 | |
| lumiT | 0.296 | 0.000 | 0.299 | |
| methylationCall | 2.328 | 0.000 | 2.326 | |
| normalizeMethylation.quantile | 0.156 | 0.000 | 0.156 | |
| normalizeMethylation.ssn | 0.156 | 0.000 | 0.156 | |
| nuID2EntrezID | 0.692 | 0.000 | 0.690 | |
| nuID2IlluminaID | 3.736 | 0.008 | 3.744 | |
| nuID2RefSeqID | 0.780 | 0.004 | 0.785 | |
| nuID2probeID | 3.100 | 0.004 | 3.108 | |
| nuID2targetID | 3.228 | 0.004 | 3.233 | |
| pairs-methods | 0.764 | 0.012 | 0.776 | |
| plot-methods | 1.968 | 0.008 | 1.974 | |
| plotCDF | 0.144 | 0.000 | 0.143 | |
| plotColorBias1D | 0.188 | 0.000 | 0.189 | |
| plotColorBias2D | 0.180 | 0.000 | 0.177 | |
| plotControlData | 0.000 | 0.000 | 0.001 | |
| plotDensity | 0.116 | 0.004 | 0.117 | |
| plotGammaFit | 3.204 | 0.004 | 3.212 | |
| plotHousekeepingGene | 0.000 | 0.000 | 0.001 | |
| plotSampleRelation | 1.104 | 0.000 | 1.102 | |
| plotStringencyGene | 0.000 | 0.000 | 0.001 | |
| plotVST | 0.304 | 0.004 | 0.307 | |
| probeID2nuID | 3.176 | 0.008 | 3.183 | |
| produceGEOPlatformFile | 0 | 0 | 0 | |
| produceGEOSubmissionFile | 0.000 | 0.000 | 0.001 | |
| produceMethylationGEOSubmissionFile | 0 | 0 | 0 | |
| seq2id | 0.000 | 0.000 | 0.001 | |
| targetID2nuID | 3.168 | 0.000 | 3.169 | |
| vst | 0.232 | 0.000 | 0.230 | |