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This page was generated on 2021-10-15 15:05:44 -0400 (Fri, 15 Oct 2021).

CHECK results for lumi on nebbiolo1

To the developers/maintainers of the lumi package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/lumi.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1008/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lumi 2.44.0  (landing page)
Lei Huang
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/lumi
git_branch: RELEASE_3_13
git_last_commit: 9783629
git_last_commit_date: 2021-05-19 11:38:35 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: lumi
Version: 2.44.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings lumi_2.44.0.tar.gz
StartedAt: 2021-10-14 10:24:22 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:30:35 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 373.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: lumi.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings lumi_2.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/lumi.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.44.0’
* 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
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 (user + system) or elapsed time > 5s
                  user system elapsed
lumiMethyStatus 37.658  1.428  39.089
MAplot-methods   5.897  0.088   5.985
getChipInfo      5.086  0.312   5.522
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/lumi.Rcheck/00check.log’
for details.



Installation output

lumi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL lumi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘lumi’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** testing if installed package can be loaded from final location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** testing if installed package keeps a record of temporary installation path
* DONE (lumi)

Tests output


Example timings

lumi.Rcheck/lumi-Ex.timings

nameusersystemelapsed
LumiBatch-class1.0390.0881.127
MAplot-methods5.8970.0885.985
addAnnotationInfo0.0480.0040.051
addControlData2lumi0.0010.0000.000
addNuID2lumi000
adjColorBias.quantile0.6550.0200.676
adjColorBias.ssn0.3540.0000.355
bgAdjust0.0670.0040.072
bgAdjustMethylation0.1210.0120.134
boxplot-MethyLumiM-methods0.4100.0320.443
boxplot-methods0.0750.0040.079
boxplotColorBias0.1170.0000.117
density-methods0.0700.0070.078
detectOutlier0.0810.0000.082
detectionCall0.1400.0000.139
estimateBeta0.1400.0040.144
estimateIntensity0.1590.0000.158
estimateLumiCV0.0920.0000.092
estimateM0.3930.0000.393
estimateMethylationBG1.3620.0121.374
example.lumi0.0680.0040.073
example.lumiMethy0.0500.0000.051
example.methyTitration0.1820.0160.198
gammaFitEM1.8990.0281.927
getChipInfo5.0860.3125.522
getControlData0.0000.0000.001
getControlProbe0.0000.0010.001
getControlType0.0000.0010.001
getNuIDMappingInfo0.7630.0590.848
hist-methods0.1090.0000.109
id2seq0.0010.0000.001
inverseVST0.3460.0000.346
is.nuID0.0000.0000.001
lumiB0.0840.0000.084
lumiExpresso0.2900.0160.306
lumiMethyB0.0570.0000.057
lumiMethyC0.9200.0120.933
lumiMethyN0.0920.0000.091
lumiMethyStatus37.658 1.42839.089
lumiN0.3850.0120.397
lumiQ0.2390.0080.248
lumiR0.0000.0000.001
lumiR.batch000
lumiT0.3170.0160.333
methylationCall2.0750.0042.079
normalizeMethylation.quantile0.1570.0000.158
normalizeMethylation.ssn0.1120.0160.128
nuID2EntrezID0.7020.0240.725
nuID2IlluminaID3.3080.0843.391
nuID2RefSeqID2.1050.0082.112
nuID2probeID3.1550.0063.160
nuID2targetID3.0440.0003.044
pairs-methods0.7620.0040.766
plot-methods1.8020.0161.818
plotCDF0.1400.0040.143
plotColorBias1D0.2110.0040.215
plotColorBias2D0.1810.0000.181
plotControlData0.0010.0000.001
plotDensity0.1020.0080.110
plotGammaFit3.1290.0203.151
plotHousekeepingGene0.0010.0000.001
plotSampleRelation0.3820.0120.394
plotStringencyGene0.0010.0000.001
plotVST0.2900.0160.306
probeID2nuID3.2180.0083.226
produceGEOPlatformFile000
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile000
seq2id0.0010.0000.001
targetID2nuID4.2080.0004.209
vst0.1640.0000.164