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This page was generated on 2022-01-26 13:05:34 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 nebbiolo2


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: 2022-01-25 01:55:07 -0500 (Tue, 25 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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings lumi_2.46.0.tar.gz
StartedAt: 2022-01-25 08:16:23 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 08:22:20 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 356.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: lumi.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings lumi_2.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/lumi.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘2.46.0’
* 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 38.093  0.112  38.207
MAplot-methods   5.217  0.068   5.285
* checking PDF version of manual ... OK
* DONE

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



Installation output

lumi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL lumi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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-class0.9380.0641.002
MAplot-methods5.2170.0685.285
addAnnotationInfo0.0490.0000.049
addControlData2lumi000
addNuID2lumi000
adjColorBias.quantile0.6480.0120.660
adjColorBias.ssn0.3640.0000.364
bgAdjust0.0710.0000.071
bgAdjustMethylation0.1300.0030.134
boxplot-MethyLumiM-methods0.4120.0120.424
boxplot-methods0.0790.0000.079
boxplotColorBias0.1180.0000.118
density-methods0.0780.0160.094
detectOutlier0.0710.0080.079
detectionCall0.1230.0120.134
estimateBeta0.1380.0000.138
estimateIntensity0.1540.0000.154
estimateLumiCV0.0820.0040.086
estimateM1.3510.0161.367
estimateMethylationBG0.1030.0000.103
example.lumi0.0730.0000.072
example.lumiMethy0.0490.0000.050
example.methyTitration0.1640.0040.168
gammaFitEM1.7730.0401.813
getChipInfo3.5010.1403.647
getControlData0.0010.0000.001
getControlProbe0.0000.0000.001
getControlType0.0000.0000.001
getNuIDMappingInfo0.6860.0160.702
hist-methods0.1260.0000.127
id2seq0.0010.0000.000
inverseVST0.5230.0040.527
is.nuID000
lumiB0.0910.0040.094
lumiExpresso0.2470.0040.250
lumiMethyB0.0660.0000.066
lumiMethyC0.8600.0080.869
lumiMethyN0.1120.0000.111
lumiMethyStatus38.093 0.11238.207
lumiN0.3770.0000.377
lumiQ0.2510.0040.255
lumiR000
lumiR.batch000
lumiT0.3350.0040.339
methylationCall1.9360.0041.940
normalizeMethylation.quantile0.150.000.15
normalizeMethylation.ssn0.1180.0000.118
nuID2EntrezID0.7070.0080.715
nuID2IlluminaID3.2000.0083.208
nuID2RefSeqID0.9240.0000.924
nuID2probeID3.0460.0043.050
nuID2targetID2.9320.0002.933
pairs-methods0.7000.0040.703
plot-methods1.6770.0081.684
plotCDF0.1320.0000.131
plotColorBias1D0.2160.0000.215
plotColorBias2D0.1380.0040.142
plotControlData0.0010.0000.000
plotDensity0.1010.0040.105
plotGammaFit2.6280.0002.628
plotHousekeepingGene0.0000.0000.001
plotSampleRelation0.3930.0000.393
plotStringencyGene0.0010.0000.000
plotVST0.3620.0120.375
probeID2nuID2.9790.0162.995
produceGEOPlatformFile000
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile000
seq2id0.0010.0000.000
targetID2nuID3.0250.0003.025
vst0.2110.0040.215