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This page was generated on 2023-04-12 11:05:08 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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? 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 1065/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lumi 2.50.0  (landing page)
Lei Huang
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/lumi
git_branch: RELEASE_3_16
git_last_commit: 8711b77
git_last_commit_date: 2022-11-01 10:42:41 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: lumi
Version: 2.50.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings lumi_2.50.0.tar.gz
StartedAt: 2023-04-10 21:38:30 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 21:45:39 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 428.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: lumi.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings lumi_2.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/lumi.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘lumi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lumi’ version ‘2.50.0’
* 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 loading without being on the library search path ... 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 39.261  0.780  40.043
MAplot-methods   5.583  0.167   5.751
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/lumi.Rcheck/00check.log’
for details.



Installation output

lumi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL lumi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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-class0.9780.1201.098
MAplot-methods5.5830.1675.751
addAnnotationInfo0.050.000.05
addControlData2lumi0.0010.0010.001
addNuID2lumi000
adjColorBias.quantile0.6260.0190.647
adjColorBias.ssn1.3960.1321.528
bgAdjust0.0720.0000.071
bgAdjustMethylation0.1180.0160.133
boxplot-MethyLumiM-methods0.4510.0000.450
boxplot-methods0.0840.0000.084
boxplotColorBias0.1000.0040.105
density-methods0.0820.0000.082
detectOutlier0.0940.0000.094
detectionCall0.1340.0000.133
estimateBeta0.1510.0120.163
estimateIntensity0.1640.0120.177
estimateLumiCV0.0880.0040.091
estimateM0.3900.0120.402
estimateMethylationBG0.1070.0000.106
example.lumi0.0670.0000.066
example.lumiMethy0.0480.0000.048
example.methyTitration0.1670.0000.168
gammaFitEM2.0280.0042.033
getChipInfo3.5110.1333.651
getControlData0.0010.0000.001
getControlProbe000
getControlType000
getNuIDMappingInfo0.7080.0240.732
hist-methods0.1110.0080.119
id2seq0.0010.0000.001
inverseVST0.4240.0120.436
is.nuID0.0010.0000.000
lumiB0.0940.0000.094
lumiExpresso0.2940.0160.309
lumiMethyB0.0590.0000.059
lumiMethyC0.8940.0040.897
lumiMethyN0.0930.0000.093
lumiMethyStatus39.261 0.78040.043
lumiN0.4140.0040.418
lumiQ0.2480.0040.251
lumiR000
lumiR.batch000
lumiT0.3270.0160.342
methylationCall2.1680.0042.173
normalizeMethylation.quantile0.1620.0000.163
normalizeMethylation.ssn0.1200.0000.121
nuID2EntrezID0.7660.0040.770
nuID2IlluminaID3.1530.0163.169
nuID2RefSeqID1.0660.0241.091
nuID2probeID3.1130.0003.114
nuID2targetID3.1800.0163.196
pairs-methods0.7260.0160.743
plot-methods1.8020.0121.814
plotCDF0.1320.0120.145
plotColorBias1D0.2790.0200.299
plotColorBias2D0.1530.0000.154
plotControlData0.0010.0000.000
plotDensity0.1070.0040.111
plotGammaFit2.9700.0082.977
plotHousekeepingGene0.0010.0000.001
plotSampleRelation1.7500.1441.894
plotStringencyGene0.0010.0000.001
plotVST0.2810.0120.295
probeID2nuID2.9920.0113.004
produceGEOPlatformFile000
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile000
seq2id0.0000.0000.001
targetID2nuID2.9750.0042.979
vst0.2080.0120.219