Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJK[L]MNOPQRSTUVWXYZ

This page was generated on 2022-06-24 12:04:58 -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 nebbiolo1


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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings lumi_2.48.0.tar.gz
StartedAt: 2022-06-23 20:34:11 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 20:40:53 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 401.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: lumi.Rcheck
Warnings: 3

Command output

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


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/lumi.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘2.48.0’
* 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 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 38.243  0.624  38.873
MAplot-methods   5.745  0.211   5.957
* checking PDF version of manual ... OK
* DONE

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



Installation output

lumi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL lumi
###
##############################################################################
##############################################################################


* installing to library ‘/home/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-class0.9670.0961.063
MAplot-methods5.7450.2115.957
addAnnotationInfo0.0500.0010.050
addControlData2lumi0.0000.0000.001
addNuID2lumi0.0000.0000.001
adjColorBias.quantile0.6740.0230.697
adjColorBias.ssn1.4230.0641.488
bgAdjust0.0710.0030.075
bgAdjustMethylation0.1230.0150.140
boxplot-MethyLumiM-methods0.4130.0120.425
boxplot-methods0.0770.0070.085
boxplotColorBias0.1210.0200.141
density-methods0.0860.0000.086
detectOutlier0.0860.0000.086
detectionCall0.1420.0000.142
estimateBeta0.1430.0040.146
estimateIntensity0.1510.0200.171
estimateLumiCV0.0990.0040.103
estimateM0.3890.0040.393
estimateMethylationBG0.1100.0040.114
example.lumi0.0780.0030.081
example.lumiMethy0.0530.0000.053
example.methyTitration0.1740.0070.181
gammaFitEM1.8740.0271.902
getChipInfo3.6450.3274.074
getControlData0.0010.0000.001
getControlProbe0.0000.0000.001
getControlType0.0010.0000.000
getNuIDMappingInfo0.8260.0400.886
hist-methods0.1160.0000.117
id2seq0.0010.0000.001
inverseVST0.4550.0280.483
is.nuID0.0010.0000.000
lumiB0.0930.0000.093
lumiExpresso0.2230.0120.234
lumiMethyB0.0630.0000.064
lumiMethyC1.0950.0121.107
lumiMethyN0.0830.0040.087
lumiMethyStatus38.243 0.62438.873
lumiN0.4830.0240.506
lumiQ0.2650.0000.264
lumiR0.0000.0000.001
lumiR.batch000
lumiT0.3480.0080.356
methylationCall2.0960.0082.105
normalizeMethylation.quantile0.1610.0000.161
normalizeMethylation.ssn0.1170.0080.125
nuID2EntrezID0.8450.0080.853
nuID2IlluminaID3.5920.0163.608
nuID2RefSeqID1.0290.0161.044
nuID2probeID3.1250.0083.133
nuID2targetID3.1410.0163.157
pairs-methods0.8180.0160.833
plot-methods1.8690.0321.902
plotCDF0.1420.0080.149
plotColorBias1D0.2410.0120.254
plotColorBias2D0.1570.0030.159
plotControlData0.0010.0000.001
plotDensity0.1220.0000.122
plotGammaFit3.1680.0043.173
plotHousekeepingGene0.0010.0000.001
plotSampleRelation0.4560.0200.476
plotStringencyGene0.0010.0000.000
plotVST0.3140.0000.315
probeID2nuID3.1630.0363.201
produceGEOPlatformFile0.0010.0000.001
produceGEOSubmissionFile0.0010.0000.001
produceMethylationGEOSubmissionFile0.0010.0000.001
seq2id0.0010.0000.001
targetID2nuID4.7370.1324.869
vst0.1720.0040.176