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This page was generated on 2021-10-15 15:06:40 -0400 (Fri, 15 Oct 2021).

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 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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:lumi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings lumi_2.44.0.tar.gz
StartedAt: 2021-10-14 20:34:31 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 20:43:18 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 527.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: lumi.Rcheck
Warnings: 3

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:lumi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings lumi_2.44.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/lumi.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.44.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 55.273 10.223  65.588
MAplot-methods   5.214  0.063   5.282
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/lumi.Rcheck/00check.log’
for details.



Installation output

lumi.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/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-class1.5760.1041.681
MAplot-methods5.2140.0635.282
addAnnotationInfo0.0570.0020.059
addControlData2lumi000
addNuID2lumi000
adjColorBias.quantile0.7230.0730.796
adjColorBias.ssn0.4380.0360.475
bgAdjust0.1150.0020.116
bgAdjustMethylation0.2090.0170.225
boxplot-MethyLumiM-methods0.6460.0200.667
boxplot-methods0.0930.0030.096
boxplotColorBias0.1820.0230.206
density-methods0.1090.0040.114
detectOutlier0.1250.0030.129
detectionCall0.1680.0050.174
estimateBeta0.2200.0060.226
estimateIntensity0.2620.0040.267
estimateLumiCV0.1190.0030.121
estimateM0.5920.0140.607
estimateMethylationBG0.9380.0080.946
example.lumi0.0900.0030.093
example.lumiMethy0.0550.0030.058
example.methyTitration0.2300.0050.235
gammaFitEM3.0660.6543.728
getChipInfo4.4300.2934.791
getControlData0.0010.0000.001
getControlProbe0.0000.0000.002
getControlType0.0010.0010.001
getNuIDMappingInfo1.1960.0621.265
hist-methods0.1330.0060.141
id2seq0.0010.0010.001
inverseVST0.5340.0160.550
is.nuID0.0010.0000.001
lumiB0.0910.0030.096
lumiExpresso0.2070.0060.215
lumiMethyB0.0630.0030.065
lumiMethyC1.0100.0861.105
lumiMethyN0.0990.0050.104
lumiMethyStatus55.27310.22365.588
lumiN0.4770.0160.493
lumiQ0.3540.0150.369
lumiR0.0000.0010.001
lumiR.batch0.0000.0010.001
lumiT0.3540.0230.378
methylationCall4.2040.6394.849
normalizeMethylation.quantile0.1950.0040.199
normalizeMethylation.ssn0.1980.0580.257
nuID2EntrezID1.2570.0291.287
nuID2IlluminaID4.1980.0324.231
nuID2RefSeqID1.4070.0271.435
nuID2probeID4.6810.0214.708
nuID2targetID3.8890.0163.907
pairs-methods0.9710.0661.037
plot-methods2.0510.0452.106
plotCDF0.1310.0070.139
plotColorBias1D0.2820.0160.300
plotColorBias2D0.2110.0050.216
plotControlData0.0010.0000.002
plotDensity0.1530.0030.157
plotGammaFit4.0550.6874.746
plotHousekeepingGene0.0010.0000.001
plotSampleRelation0.9760.0361.014
plotStringencyGene0.0010.0000.002
plotVST0.3700.0150.388
probeID2nuID3.8790.0233.910
produceGEOPlatformFile0.0000.0010.000
produceGEOSubmissionFile0.0000.0000.001
produceMethylationGEOSubmissionFile0.0010.0010.000
seq2id0.0010.0000.000
targetID2nuID3.9460.0274.020
vst0.2520.0070.260