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This page was generated on 2022-01-21 11:07:53 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for lumi on riesling1


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 1017/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lumi 2.47.0  (landing page)
Lei Huang
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/lumi
git_branch: master
git_last_commit: 2336503
git_last_commit_date: 2021-10-26 11:50:43 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'Biobase' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: lumi
Version: 2.47.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:lumi.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings lumi_2.47.0.tar.gz
StartedAt: 2022-01-20 19:15:54 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 19:21:59 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 364.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: lumi.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:lumi.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings lumi_2.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/lumi.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'lumi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lumi' version '2.47.0'
* 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 whether package 'lumi' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.6Mb
* 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 'bigmemoryExtras' 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 (user + system) or elapsed time > 5s
                 user system elapsed
lumiMethyStatus 47.04   8.71   55.75
getChipInfo      4.19   0.26    5.77
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/lumi.Rcheck/00check.log'
for details.



Installation output

lumi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL lumi
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'lumi'
    finding HTML links ... done
    IlluminaID2nuID                         html  
    LumiBatch-class                         html  
    MAplot-methods                          html  
    addAnnotationInfo                       html  
    addControlData2lumi                     html  
    addControlData2methyLumiM               html  
    addNuID2lumi                            html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-lumi/00new/lumi/help/addNuId2lumi.html
    adjColorBias.quantile                   html  
    adjColorBias.ssn                        html  
    asBigMatrix-methods                     html  
    beta2m                                  html  
    bgAdjust                                html  
    bgAdjustMethylation                     html  
    boxplot-MethyLumiM-methods              html  
    finding level-2 HTML links ... done

    boxplot-methods                         html  
    boxplotColorBias                        html  
    colorBiasSummary                        html  
    density-methods                         html  
    detectOutlier                           html  
    detectionCall                           html  
    estimateBeta                            html  
    estimateIntensity                       html  
    estimateLumiCV                          html  
    estimateM                               html  
    estimateMethylationBG                   html  
    example.lumi                            html  
    example.lumiMethy                       html  
    example.methyTitration                  html  
    gammaFitEM                              html  
    getChipInfo                             html  
    getChrInfo                              html  
    getControlData                          html  
    getControlProbe                         html  
    getControlType                          html  
    getNuIDMappingInfo                      html  
    hist-methods                            html  
    id2seq                                  html  
    importMethyIDAT                         html  
    inverseVST                              html  
    is.nuID                                 html  
    lumi.package                            html  
    lumiB                                   html  
    lumiExpresso                            html  
    lumiMethyB                              html  
    lumiMethyC                              html  
    lumiMethyN                              html  
    lumiMethyR                              html  
    lumiMethyStatus                         html  
    lumiN                                   html  
    lumiQ                                   html  
    lumiR                                   html  
    lumiR.batch                             html  
    lumiT                                   html  
    m2beta                                  html  
    methylationCall                         html  
    monoSmu                                 html  
    monoSpline                              html  
    normalizeMethylation.quantile           html  
    normalizeMethylation.ssn                html  
    nuID2EntrezID                           html  
    nuID2IlluminaID                         html  
    nuID2RefSeqID                           html  
    nuID2probeID                            html  
    nuID2targetID                           html  
    pairs-methods                           html  
    plot-methods                            html  
    plotCDF                                 html  
    plotColorBias1D                         html  
    plotColorBias2D                         html  
    plotControlData                         html  
    plotDensity                             html  
    plotGammaFit                            html  
    plotHousekeepingGene                    html  
    plotSampleRelation                      html  
    plotStringencyGene                      html  
    plotVST                                 html  
    probeID2nuID                            html  
    produceGEOPlatformFile                  html  
    produceGEOSampleInfoTemplate            html  
    produceGEOSubmissionFile                html  
    produceMethylationGEOSubmissionFile     html  
    rankinvariant                           html  
    rsn                                     html  
    seq2id                                  html  
    smoothQuantileNormalization             html  
    ssn                                     html  
    targetID2nuID                           html  
    vst                                     html  
** 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)
Making 'packages.html' ... done

Tests output


Example timings

lumi.Rcheck/lumi-Ex.timings

nameusersystemelapsed
LumiBatch-class0.830.040.86
MAplot-methods3.430.013.45
addAnnotationInfo0.030.030.07
addControlData2lumi000
addNuID2lumi000
adjColorBias.quantile1.630.021.64
adjColorBias.ssn0.310.030.34
bgAdjust0.050.010.06
bgAdjustMethylation0.120.000.13
boxplot-MethyLumiM-methods0.440.000.43
boxplot-methods0.050.020.07
boxplotColorBias0.090.020.11
density-methods0.060.000.06
detectOutlier0.070.000.06
detectionCall0.110.010.13
estimateBeta0.110.000.11
estimateIntensity0.130.000.13
estimateLumiCV0.070.000.07
estimateM0.460.000.46
estimateMethylationBG0.090.020.11
example.lumi0.050.010.06
example.lumiMethy0.040.000.05
example.methyTitration0.160.020.17
gammaFitEM2.340.002.34
getChipInfo4.190.265.77
getControlData000
getControlProbe000
getControlType0.000.020.01
getNuIDMappingInfo0.600.110.77
hist-methods0.070.010.09
id2seq000
inverseVST0.30.00.3
is.nuID000
lumiB0.060.000.06
lumiExpresso0.210.020.22
lumiMethyB0.040.010.06
lumiMethyC0.860.060.92
lumiMethyN0.100.000.09
lumiMethyStatus47.04 8.7155.75
lumiN0.270.040.32
lumiQ0.220.050.26
lumiR000
lumiR.batch000
lumiT0.280.000.28
methylationCall2.330.392.72
normalizeMethylation.quantile0.130.000.12
normalizeMethylation.ssn0.190.050.24
nuID2EntrezID0.590.010.61
nuID2IlluminaID3.080.043.11
nuID2RefSeqID0.600.010.61
nuID2probeID2.810.022.83
nuID2targetID2.550.002.55
pairs-methods0.810.030.84
plot-methods1.310.081.39
plotCDF0.090.010.11
plotColorBias1D0.160.000.16
plotColorBias2D0.130.000.12
plotControlData000
plotDensity0.070.020.10
plotGammaFit2.470.232.70
plotHousekeepingGene000
plotSampleRelation0.320.020.33
plotStringencyGene000
plotVST0.230.010.25
probeID2nuID2.330.022.34
produceGEOPlatformFile000
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile000
seq2id000
targetID2nuID2.350.002.34
vst0.170.000.17