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 11:48:17 -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: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings lumi_2.34.0.tar.gz |
| StartedAt: 2019-04-16 01:03:09 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:16:31 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 802.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: lumi.Rcheck |
| Warnings: 3 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings lumi_2.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/lumi.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.34.0’
* 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
Unknown package ‘hdrcde’ in Rd xrefs
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 60.124 0.056 60.255
getChipInfo 5.208 0.088 5.442
MAplot-methods 5.060 0.008 5.082
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs
See
‘/home/biocbuild/bbs-3.8-bioc/meat/lumi.Rcheck/00check.log’
for details.
lumi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL lumi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-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 | 1.784 | 0.080 | 1.873 | |
| MAplot-methods | 5.060 | 0.008 | 5.082 | |
| addAnnotationInfo | 0.120 | 0.004 | 0.135 | |
| addControlData2lumi | 0 | 0 | 0 | |
| addNuID2lumi | 0 | 0 | 0 | |
| adjColorBias.quantile | 1.508 | 0.012 | 1.522 | |
| adjColorBias.ssn | 0.424 | 0.008 | 0.436 | |
| bgAdjust | 0.116 | 0.004 | 0.122 | |
| bgAdjustMethylation | 1.024 | 0.000 | 1.026 | |
| boxplot-MethyLumiM-methods | 0.700 | 0.008 | 0.713 | |
| boxplot-methods | 0.140 | 0.000 | 0.141 | |
| boxplotColorBias | 0.18 | 0.02 | 0.20 | |
| density-methods | 0.088 | 0.004 | 0.092 | |
| detectOutlier | 0.088 | 0.000 | 0.086 | |
| detectionCall | 0.144 | 0.000 | 0.146 | |
| estimateBeta | 0.156 | 0.000 | 0.153 | |
| estimateIntensity | 0.184 | 0.000 | 0.186 | |
| estimateLumiCV | 0.092 | 0.000 | 0.091 | |
| estimateM | 0.408 | 0.000 | 0.407 | |
| estimateMethylationBG | 0.156 | 0.004 | 0.159 | |
| example.lumi | 0.072 | 0.004 | 0.074 | |
| example.lumiMethy | 0.06 | 0.00 | 0.06 | |
| example.methyTitration | 0.188 | 0.012 | 0.213 | |
| gammaFitEM | 2.604 | 0.004 | 2.618 | |
| getChipInfo | 5.208 | 0.088 | 5.442 | |
| getControlData | 0.000 | 0.000 | 0.001 | |
| getControlProbe | 0 | 0 | 0 | |
| getControlType | 0.004 | 0.000 | 0.001 | |
| getNuIDMappingInfo | 1.000 | 0.016 | 1.018 | |
| hist-methods | 0.112 | 0.008 | 0.118 | |
| id2seq | 0.000 | 0.000 | 0.001 | |
| inverseVST | 0.496 | 0.004 | 0.507 | |
| is.nuID | 0.000 | 0.000 | 0.001 | |
| lumiB | 0.132 | 0.000 | 0.134 | |
| lumiExpresso | 0.544 | 0.008 | 0.564 | |
| lumiMethyB | 0.084 | 0.000 | 0.083 | |
| lumiMethyC | 1.364 | 0.008 | 1.376 | |
| lumiMethyN | 0.112 | 0.004 | 0.120 | |
| lumiMethyStatus | 60.124 | 0.056 | 60.255 | |
| lumiN | 0.372 | 0.000 | 0.378 | |
| lumiQ | 0.236 | 0.004 | 0.243 | |
| lumiR | 0 | 0 | 0 | |
| lumiR.batch | 0 | 0 | 0 | |
| lumiT | 0.324 | 0.012 | 0.336 | |
| methylationCall | 4.732 | 0.004 | 4.740 | |
| normalizeMethylation.quantile | 0.200 | 0.004 | 0.204 | |
| normalizeMethylation.ssn | 0.188 | 0.000 | 0.188 | |
| nuID2EntrezID | 0.928 | 0.000 | 0.930 | |
| nuID2IlluminaID | 4.024 | 0.012 | 4.041 | |
| nuID2RefSeqID | 1.184 | 0.004 | 1.192 | |
| nuID2probeID | 4.648 | 0.000 | 4.657 | |
| nuID2targetID | 3.780 | 0.000 | 3.786 | |
| pairs-methods | 0.840 | 0.012 | 0.850 | |
| plot-methods | 2.548 | 0.032 | 2.581 | |
| plotCDF | 0.152 | 0.000 | 0.153 | |
| plotColorBias1D | 0.292 | 0.012 | 0.302 | |
| plotColorBias2D | 0.176 | 0.004 | 0.182 | |
| plotControlData | 0.000 | 0.000 | 0.001 | |
| plotDensity | 0.108 | 0.004 | 0.111 | |
| plotGammaFit | 3.880 | 0.000 | 3.883 | |
| plotHousekeepingGene | 0.000 | 0.000 | 0.002 | |
| plotSampleRelation | 1.976 | 0.000 | 1.975 | |
| plotStringencyGene | 0.000 | 0.000 | 0.001 | |
| plotVST | 0.452 | 0.020 | 0.470 | |
| probeID2nuID | 4.088 | 0.004 | 4.098 | |
| produceGEOPlatformFile | 0 | 0 | 0 | |
| produceGEOSubmissionFile | 0 | 0 | 0 | |
| produceMethylationGEOSubmissionFile | 0 | 0 | 0 | |
| seq2id | 0 | 0 | 0 | |
| targetID2nuID | 4.972 | 0.004 | 4.978 | |
| vst | 0.380 | 0.004 | 0.384 | |