Pan Du
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/lumi |
| Branch: RELEASE_3_6 |
| Last Commit: de64da0 |
| Last Changed Date: 2017-10-30 12:39:19 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
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 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.30.0.tar.gz
###
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* 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 | |