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This page was generated on 2022-06-24 12:06:14 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 palomino3


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? 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 1046/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lumi 2.48.0  (landing page)
Lei Huang
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/lumi
git_branch: RELEASE_3_15
git_last_commit: 1f988ff
git_last_commit_date: 2022-04-26 10:59:08 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: lumi
Version: 2.48.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:lumi.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings lumi_2.48.0.tar.gz
StartedAt: 2022-06-24 02:13:36 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 02:22:11 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 515.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: lumi.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:lumi.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings lumi_2.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/lumi.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (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 '2.48.0'
* 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 ... 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    65.89   4.21   70.10
getChipInfo         4.74   0.61   43.28
getNuIDMappingInfo  0.89   0.06    5.22
* checking PDF version of manual ... OK
* DONE

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



Installation output

lumi.Rcheck/00install.out

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


* installing to library 'F:/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
** 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-class1.160.081.25
MAplot-methods3.790.083.86
addAnnotationInfo0.050.000.05
addControlData2lumi000
addNuID2lumi000
adjColorBias.quantile1.590.001.59
adjColorBias.ssn0.440.020.45
bgAdjust0.060.000.06
bgAdjustMethylation0.220.000.22
boxplot-MethyLumiM-methods0.580.010.60
boxplot-methods0.090.000.09
boxplotColorBias0.160.000.16
density-methods0.060.000.06
detectOutlier0.060.030.09
detectionCall0.140.020.16
estimateBeta0.140.000.14
estimateIntensity1.190.011.20
estimateLumiCV0.120.020.14
estimateM0.610.000.61
estimateMethylationBG0.110.020.13
example.lumi0.060.000.06
example.lumiMethy0.050.000.05
example.methyTitration0.160.000.16
gammaFitEM3.890.754.64
getChipInfo 4.74 0.6143.28
getControlData000
getControlProbe0.010.000.02
getControlType000
getNuIDMappingInfo0.890.065.22
hist-methods0.110.000.11
id2seq000
inverseVST0.430.000.42
is.nuID000
lumiB0.100.000.11
lumiExpresso0.330.000.33
lumiMethyB0.070.000.06
lumiMethyC1.170.011.19
lumiMethyN0.060.000.06
lumiMethyStatus65.89 4.2170.10
lumiN0.480.010.50
lumiQ0.250.030.28
lumiR000
lumiR.batch000
lumiT0.300.020.31
methylationCall3.390.363.75
normalizeMethylation.quantile0.160.000.16
normalizeMethylation.ssn0.120.010.14
nuID2EntrezID0.690.040.72
nuID2IlluminaID3.410.033.43
nuID2RefSeqID0.700.030.75
nuID2probeID3.530.003.54
nuID2targetID3.640.003.64
pairs-methods0.860.010.88
plot-methods1.720.031.75
plotCDF0.100.040.13
plotColorBias1D0.170.010.19
plotColorBias2D0.190.000.19
plotControlData000
plotDensity0.110.000.11
plotGammaFit4.070.084.16
plotHousekeepingGene000
plotSampleRelation0.410.050.45
plotStringencyGene000
plotVST0.360.000.36
probeID2nuID3.620.013.64
produceGEOPlatformFile000
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile000
seq2id000
targetID2nuID3.250.033.28
vst0.160.000.16