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This page was generated on 2022-01-17 13:07:53 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 machv2


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 1020/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lumi 2.46.0  (landing page)
Lei Huang
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/lumi
git_branch: RELEASE_3_14
git_last_commit: a68932c
git_last_commit_date: 2021-10-26 11:50:43 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 2.46.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:lumi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings lumi_2.46.0.tar.gz
StartedAt: 2022-01-16 14:36:21 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 14:46:45 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 624.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: lumi.Rcheck
Warnings: 3

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:lumi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings lumi_2.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/lumi.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.46.0’
* 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 ‘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 66.227 12.111  78.406
plotGammaFit     5.078  0.854   5.987
MAplot-methods   5.820  0.099   5.949
getChipInfo      5.319  0.293   5.733
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/lumi.Rcheck/00check.log’
for details.



Installation output

lumi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL lumi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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-class1.7040.1381.844
MAplot-methods5.8200.0995.949
addAnnotationInfo0.0730.0030.076
addControlData2lumi000
addNuID2lumi0.0000.0000.001
adjColorBias.quantile0.9250.0791.009
adjColorBias.ssn0.5050.0340.541
bgAdjust0.1140.0030.117
bgAdjustMethylation0.2040.0190.223
boxplot-MethyLumiM-methods0.6580.0130.671
boxplot-methods0.1160.0040.120
boxplotColorBias0.1930.0130.208
density-methods0.1310.0040.135
detectOutlier0.1270.0060.134
detectionCall0.1920.0060.198
estimateBeta0.2500.0080.299
estimateIntensity0.3000.0090.310
estimateLumiCV1.0790.0111.091
estimateM0.6540.0100.665
estimateMethylationBG0.1700.0040.175
example.lumi0.1050.0040.109
example.lumiMethy0.0840.0040.088
example.methyTitration0.2430.0060.249
gammaFitEM3.5840.6624.249
getChipInfo5.3190.2935.733
getControlData0.0010.0010.002
getControlProbe0.0020.0010.002
getControlType0.0010.0010.002
getNuIDMappingInfo1.4610.0671.530
hist-methods0.1530.0060.159
id2seq0.0020.0000.002
inverseVST0.6290.0130.643
is.nuID0.0000.0000.001
lumiB0.1130.0020.115
lumiExpresso0.2860.0070.293
lumiMethyB0.0800.0030.082
lumiMethyC1.3400.0761.418
lumiMethyN0.1260.0030.130
lumiMethyStatus66.22712.11178.406
lumiN0.5890.0670.657
lumiQ0.3570.0150.372
lumiR000
lumiR.batch0.0000.0000.001
lumiT0.3750.0160.393
methylationCall3.8280.8954.727
normalizeMethylation.quantile0.2330.0250.258
normalizeMethylation.ssn0.2010.0030.204
nuID2EntrezID1.3550.0261.382
nuID2IlluminaID4.6940.0294.725
nuID2RefSeqID1.7760.0681.844
nuID2probeID4.4720.0554.536
nuID2targetID4.4540.0224.477
pairs-methods1.1950.0901.287
plot-methods2.3520.0382.416
plotCDF0.1800.0080.188
plotColorBias1D0.2710.0070.279
plotColorBias2D0.2490.0060.255
plotControlData0.0010.0000.002
plotDensity0.1620.0030.165
plotGammaFit5.0780.8545.987
plotHousekeepingGene0.0020.0000.002
plotSampleRelation1.0080.1131.124
plotStringencyGene0.0010.0000.002
plotVST0.3760.0170.395
probeID2nuID4.5700.0314.610
produceGEOPlatformFile0.0000.0000.001
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile000
seq2id0.0000.0000.001
targetID2nuID4.6440.0234.671
vst0.2580.0070.265